Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

*EC 1.1.1.49 glucose-6-phosphate dehydrogenase (NADP+) (17 September 2015)
*EC 1.1.1.276 serine 3-dehydrogenase (NADP+) (17 September 2015)
*EC 1.1.1.363 glucose-6-phosphate dehydrogenase [NAD(P)+] (17 September 2015)
*EC 1.1.1.381 3-hydroxy acid dehydrogenase (17 September 2015)
EC 1.1.1.387 L-serine 3-dehydrogenase (NAD+) (17 September 2015)
EC 1.1.1.388 glucose-6-phosphate dehydrogenase (NAD+) (17 September 2015)
EC 1.1.3.48 3-deoxy-α-D-manno-octulosonate 8-oxidase (17 September 2015)
EC 1.2.1.93 formate dehydrogenase (NAD+, ferredoxin) (17 September 2015)
EC 1.2.1.94 farnesal dehydrogenase (17 September 2015)
EC 1.2.1.95 L-2-aminoadipate reductase (17 September 2015)
EC 1.3.1.35 transferred now EC 1.14.19.22 (17 September 2015)
*EC 1.3.1.43 arogenate dehydrogenase (17 September 2015)
EC 1.3.1.63 transferred now EC 1.21.1.2 (17 September 2015)
EC 1.3.7.11 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase (17 September 2015)
EC 1.3.99.34 transferred now EC 1.3.7.11 (17 September 2015)
EC 1.3.99.37 1-hydroxy-2-isopentenylcarotenoid 3,4-desaturase (17 September 2015)
EC 1.4.99.1 transferred now EC 1.4.99.6 (17 September 2015)
EC 1.4.99.6 D-arginine dehydrogenase (17 September 2015)
EC 1.5.1.50 dihydromonapterin reductase (17 September 2015)
EC 1.6.1.4 NAD(P)+ transhydrogenase (ferredoxin) (17 September 2015)
*EC 1.8.1.2 assimilatory sulfite reductase (NADPH) (17 September 2015)
*EC 1.8.7.1 assimilatory sulfite reductase (ferredoxin) (17 September 2015)
EC 1.8.99.1 deleted now covered by EC 1.8.1.2 and EC 1.8.7.1 (17 September 2015)
EC 1.8.99.5 dissimilatory sulfite reductase (17 September 2015)
*EC 1.11.1.12 phospholipid-hydroperoxide glutathione peroxidase (17 September 2015)
*EC 1.13.11.18 persulfide dioxygenase (17 September 2015)
EC 1.14.12.23 nitroarene dioxygenase (17 September 2015)
EC 1.14.13.26 transferred now EC 1.14.18.4 (17 September 2015)
EC 1.14.13.169 transferred now EC 1.14.18.5 (17 September 2015)
EC 1.14.13.204 long-chain acyl-CoA ω-monooxygenase (17 September 2015)
EC 1.14.13.205 long-chain fatty acid ω-monooxygenase (17 September 2015)
EC 1.14.18.4 phosphatidylcholine 12-monooxygenase (17 September 2015)
EC 1.14.18.5 sphingolipid C4-monooxygenase (17 September 2015)
EC 1.14.18.6 4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase (17 September 2015)
EC 1.14.18.7 dihydroceramide fatty acyl 2-hydroxylase (17 September 2015)
*EC 1.14.19.2 stearoyl-[acyl-carrier-protein] 9-desaturase (17 September 2015)
*EC 1.14.19.3 acyl-CoA 6-desaturase (17 September 2015)
*EC 1.14.19.5 acyl-CoA 11-(Z)-desaturase (17 September 2015)
EC 1.14.19.11 palmitoyl-[acyl-carrier-protein] 4-desaturase (17 September 2015)
EC 1.14.19.12 acyl-lipid ω-(9-4) desaturase (17 September 2015)
EC 1.14.19.13 acyl-CoA 15-desaturase (17 September 2015)
EC 1.14.19.14 linoleoyl-lipid Δ9 conjugase (17 September 2015)
EC 1.14.19.15 (11Z)-hexadec-11-enoyl-CoA conjugase (17 September 2015)
EC 1.14.19.16 linoleoyl-lipid Δ12 conjugase (11E,13Z-forming) (17 September 2015)
EC 1.14.19.17 sphingolipid 4-desaturase (17 September 2015)
EC 1.14.19.18 sphingolipid 8-(E)-desaturase (17 September 2015)
EC 1.14.19.19 sphingolipid 10-desaturase (17 September 2015)
EC 1.14.19.20 Δ7-sterol 5(6)-desaturase (17 September 2015)
EC 1.14.19.21 cholesterol 7-desaturase (17 September 2015)
EC 1.14.19.22 acyl-lipid ω-6 desaturase (cytochrome b5) (17 September 2015)
EC 1.14.19.23 acyl-lipid (n+3)-(Z)-desaturase (ferredoxin) (17 September 2015)
EC 1.14.19.24 acyl-CoA 11-(E)-desaturase (17 September 2015)
EC 1.14.19.25 acyl-lipid ω-3 desaturase (cytochrome b5) (17 September 2015)
EC 1.14.19.26 acyl-[acyl-carrier-protein] 6-desaturase (17 September 2015)
EC 1.14.19.27 sn-2 palmitoyl-lipid 9-desaturase (17 September 2015)
EC 1.14.19.28 sn-1 stearoyl-lipid 9-desaturase (17 September 2015)
EC 1.14.19.29 sphingolipid 8-(E/Z)-desaturase (17 September 2015)
EC 1.14.19.30 acyl-lipid (8-3)-desaturase (17 September 2015)
EC 1.14.19.31 acyl-lipid (7-3)-desaturase (17 September 2015)
EC 1.14.19.32 palmitoyl-CoA 14-(E/Z)-desaturase (17 September 2015)
EC 1.14.19.33 Δ12 acyl-lipid conjugase (11E,13E-forming) (17 September 2015)
EC 1.14.19.34 acyl-lipid (9+3)-(E)-desaturase (17 September 2015)
EC 1.14.19.35 sn-2 acyl-lipid ω-3 desaturase (ferredoxin) (17 September 2015)
EC 1.14.19.36 sn-1 acyl-lipid ω-3 desaturase (ferredoxin) (17 September 2015)
EC 1.14.21.6 transferred now EC 1.14.19.20 (17 September 2015)
EC 1.14.99.31 transferred now EC 1.14.19.24 (17 September 2015)
EC 1.14.99.32 transferred now EC 1.14.19.5 (17 September 2015)
EC 1.14.99.50 γ-glutamyl hercynylcysteine S-oxide synthase (17 September 2015)
EC 1.14.99.51 hercynylcysteine S-oxide synthase (17 September 2015)
EC 1.14.99.52 L-cysteinyl-L-histidinylsulfoxide synthase (17 September 2015)
EC 1.18.1.8 ferredoxin-NAD+ oxidoreductase (Na+-transporting) (17 September 2015)
EC 1.21.1.1 iodotyrosine deiodinase (17 September 2015)
EC 1.21.1.2 2,4-dichlorobenzoyl-CoA reductase (17 September 2015)
EC 1.21.99.3 thyroxine 5-deiodinase (17 September 2015)
EC 1.22.1.1 transferred now EC 1.21.1.1 (17 September 2015)
EC 1.97.1.11 transferred now EC 1.21.99.3 (17 September 2015)
EC 2.1.1.316 mitomycin 6-O-methyltransferase (17 September 2015)
EC 2.1.1.317 sphingolipid C9-methyltransferase (17 September 2015)
EC 2.1.1.318 [trehalose-6-phosphate synthase]-L-cysteine S-methyltransferase (17 September 2015)
*EC 2.3.1.82 aminoglycoside 6'-N-acetyltransferase (17 September 2015)
EC 2.3.1.119 deleted now covered by EC 2.3.1.199, EC 1.1.1.330 and EC 4.2.1.134 (17 September 2015)
*EC 2.3.1.169 CO-methylating acetyl-CoA synthase (17 September 2015)
EC 2.3.1.247 3-keto-5-aminohexanoate cleavage enzyme (17 September 2015)
EC 2.3.1.248 spermidine disinapoyl transferase (17 September 2015)
EC 2.3.1.249 spermidine dicoumaroyl transferase (17 September 2015)
EC 2.3.1.250 [Wnt protein] O-palmitoleoyl transferase (17 September 2015)
EC 2.3.2.23 E2 ubiquitin-conjugating enzyme (17 September 2015)
EC 2.3.2.24 (E3-independent) E2 ubiquitin-conjugating enzyme (17 September 2015)
EC 2.3.2.25 N-terminal E2 ubiquitin-conjugating enzyme (17 September 2015)
EC 2.3.2.26 HECT-type E3 ubiquitin transferase (17 September 2015)
EC 2.3.2.27 RING-type E3 ubiquitin transferase (17 September 2015)
EC 2.3.2.28 L-allo-isoleucyltransferase (17 September 2015)
*EC 2.4.1.33 mannuronan synthase (17 September 2015)
*EC 2.4.1.147 acetylgalactosaminyl-O-glycosyl-glycoprotein β-1,3-N-acetylglucosaminyltransferase (17 September 2015)
*EC 2.4.1.153 UDP-N-acetylglucosamine—dolichyl-phosphate N-acetylglucosaminyltransferase (17 September 2015)
*EC 2.4.1.159 flavonol-3-O-glucoside L-rhamnosyltransferase (17 September 2015)
*EC 2.4.1.184 galactolipid galactosyltransferase (17 September 2015)
*EC 2.4.1.213 glucosylglycerol-phosphate synthase (17 September 2015)
*EC 2.4.2.37 NAD+—dinitrogen-reductase ADP-D-ribosyltransferase (17 September 2015)
EC 2.6.1.108 (5-formylfuran-3-yl)methyl phosphate transaminase (17 September 2015)
EC 2.6.1.109 8-amino-3,8-dideoxy-α-D-manno-octulosonate transaminase (17 September 2015)
EC 2.7.1.189 autoinducer-2 kinase (17 September 2015)
EC 2.7.4.30 lipid A phosphoethanolamine transferase (17 September 2015)
EC 2.7.7.88 GDP polyribonucleotidyltransferase (17 September 2015)
EC 2.7.7.89 [glutamate—ammonia ligase]-adenylyl-L-tyrosine phosphorylase (17 September 2015)
EC 2.7.8.42 Kdo2-lipid A phosphoethanolamine 7''-transferase (17 September 2015)
EC 2.8.1.13 tRNA-uridine 2-sulfurtransferase (17 September 2015)
EC 2.8.1.14 tRNA-5-taurinomethyluridine 2-sulfurtransferase (17 September 2015)
EC 2.8.3.23 caffeate CoA-transferase (17 September 2015)
*EC 2.8.4.3 tRNA-2-methylthio-N6-dimethylallyladenosine synthase (17 September 2015)
*EC 2.8.4.5 tRNA (N6-L-threonylcarbamoyladenosine37-C2)-methylthiotransferase (17 September 2015)
*EC 3.1.1.59 juvenile-hormone esterase (17 September 2015)
*EC 3.1.1.97 methylated diphthine methylhydrolase (17 September 2015)
EC 3.1.1.98 [Wnt protein] O-palmitoleoyl-L-serine hydrolase (17 September 2015)
*EC 3.1.3.69 glucosylglycerol 3-phosphatase (17 September 2015)
EC 3.1.4.15 transferred (17 September 2015)
EC 3.4.24.88 desampylase (17 September 2015)
EC 3.4.24.89 Pro-Pro endopeptidase (17 September 2015)
EC 4.1.1.101 malolactic enzyme (17 September 2015)
*EC 4.2.1.42 galactarate dehydratase (17 September 2015)
EC 4.2.1.156 L-talarate dehydratase (17 September 2015)
EC 4.2.1.157 (R)-2-hydroxyisocaproyl-CoA dehydratase (17 September 2015)
EC 4.2.1.158 galactarate dehydratase (D-threo-forming) (17 September 2015)
EC 5.1.1.21 isoleucine 2-epimerase (17 September 2015)
EC 5.1.3.33 2-epi-5-epi-valiolone epimerase (17 September 2015)
EC 5.1.3.34 monoglucosyldiacylglycerol epimerase (17 September 2015)
EC 5.1.3.35 2-epi-5-epi-valiolone 7-phosphate 2-epimerase (17 September 2015)
EC 5.1.99.7 dihydroneopterin triphosphate 2'-epimerase (17 September 2015)
EC 5.3.3.19 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase (17 September 2015)
EC 5.4.1.4 D-galactarolactone isomerase (17 September 2015)
EC 5.4.99.63 ethylmalonyl-CoA mutase (17 September 2015)
EC 5.5.1.27 D-galactarolactone cycloisomerase (17 September 2015)
EC 6.2.1.45 E1 ubiquitin-activating enzyme (17 September 2015)
EC 6.2.1.46 L-allo-isoleucine:holo-[CmaA peptidyl-carrier protein] ligase (17 September 2015)
EC 6.3.2.19 deleted now covered by EC 6.2.1.45, EC 2.3.2.23 and EC 2.3.2.27 (17 September 2015)
EC 6.3.2.21 deleted now covered by EC 6.2.1.45 and EC 2.3.2.27 (17 September 2015)
EC 6.3.2.28 transferred now EC 6.3.2.49 (17 September 2015)
EC 6.3.2.48 L-arginine-specific L-amino acid ligase (17 September 2015)
EC 6.3.2.49 L-alanine-L-anticapsin ligase (17 September 2015)

*EC 1.1.1.49

Accepted name: glucose-6-phosphate dehydrogenase (NADP+)

Reaction: D-glucose 6-phosphate + NADP+ = 6-phospho-D-glucono-1,5-lactone + NADPH + H+

For diagram of reaction click here.

Other name(s): NADP-glucose-6-phosphate dehydrogenase; Zwischenferment; D-glucose 6-phosphate dehydrogenase; glucose 6-phosphate dehydrogenase (NADP); NADP-dependent glucose 6-phosphate dehydrogenase; 6-phosphoglucose dehydrogenase; Entner-Doudoroff enzyme; glucose-6-phosphate 1-dehydrogenase; G6PDH; GPD; glucose-6-phosphate dehydrogenase

Systematic name: D-glucose-6-phosphate:NADP+ 1-oxidoreductase

Comments: The enzyme catalyses a step of the pentose phosphate pathway. The enzyme is specific for NADP+. cf. EC 1.1.1.363, glucose-6-phosphate dehydrogenase [NAD(P)+] and EC 1.1.1.388, glucose-6-phosphate dehydrogenase (NAD+).

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9001-40-5

References:

1. Engel, H.J., Domschke, W., Alberti, M. and Domagk, G.F. Protein structure and enzymatic activity. II. Purification and properties of a crystalline glucose-6-phosphate dehydrogenase from Candida utilis. Biochim. Biophys. Acta 191 (1969) 509-516. [PMID: 5363983]

2. Glaser, L. and Brown, D.H. Purification and properties of D-glucose-6-phosphate dehydrogenase. J. Biol. Chem. 216 (1955) 67-79. [PMID: 13252007]

3. Julian, G.R., Wolfe, R.G. and Reithel, F.J. The enzymes of mammary gland. II. The preparation of glucose 6-phosphate dehydrogenase. J. Biol. Chem. 236 (1961) 754-758. [PMID: 13790996]

4. Noltmann, E.A., Gubler, C.J. and Kuby, S.A. Glucose 6-phosphate dehydrogenase (Zwischenferment). I. Isolation of the crystalline enzyme from yeast. J. Biol. Chem. 236 (1961) 1225-1230. [PMID: 13729473]

5. Miclet, E., Stoven, V., Michels, P.A., Opperdoes, F.R., Lallemand, J.-Y. and Duffieux, F. NMR spectroscopic analysis of the first two steps of the pentose-phosphate pathway elucidates the role of 6-phosphogluconolactonase. J. Biol. Chem. 276 (2001) 34840-34846. [PMID: 11457850]

6. Olavarria, K., Valdes, D. and Cabrera, R. The cofactor preference of glucose-6-phosphate dehydrogenase from Escherichia coli - modeling the physiological production of reduced cofactors. FEBS J. 279 (2012) 2296-2309. [PMID: 22519976]

7. Hansen, T., Schlichting, B. and Schonheit, P. Glucose-6-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima: expression of the g6pd gene and characterization of an extremely thermophilic enzyme. FEMS Microbiol. Lett. 216 (2002) 249-253. [PMID: 12435510]

8. Ibraheem, O., Adewale, I.O. and Afolayan, A. Purification and properties of glucose 6-phosphate dehydrogenase from Aspergillus aculeatus. J. Biochem. Mol. Biol. 38 (2005) 584-590. [PMID: 16202239]

9. Iyer, R.B., Wang, J. and Bachas, L.G. Cloning, expression, and characterization of the gsdA gene encoding thermophilic glucose-6-phosphate dehydrogenase from Aquifex aeolicus. Extremophiles 6 (2002) 283-289. [PMID: 12215813]

10. Cho, S.W. and Joshi, J.G. Characterization of glucose-6-phosphate dehydrogenase isozymes from human and pig brain. Neuroscience 38 (1990) 819-828. [PMID: 2270145]

[EC 1.1.1.49 created 1961, modified 2013, modified 2015]

*EC 1.1.1.276

Accepted name: serine 3-dehydrogenase (NADP+)

Reaction: L-serine + NADP+ = 2-aminoacetaldehyde + CO2 + NADPH + H+ (overall reaction)
(1a) L-serine + NADP+ = 2-aminomalonate semialdehyde + NADPH + H+
(1b) 2-aminomalonate semialdehyde = 2-aminoacetaldehyde + CO2 (spontaneous)

Other name(s): serine 3-dehydrogenase

Systematic name: L-serine:NADP+ 3-oxidoreductase

Comments: NAD+ cannot replace NADP+ [cf. EC 1.1.1.387, serine 3-dehydrogenase (NAD+)].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9038-55-5

References:

1. Fujisawa, H., Nagata, S., Chowdhury, E.K., Matsumoto, M. and Misono, H. Cloning and sequencing of the serine dehydrogenase gene from Agrobacterium tumefaciens. Biosci. Biotechnol. Biochem. 66 (2002) 1137-1139. [PMID: 12092831]

2. Chowdhury, E.K., Higuchi, K., Nagata, S. and Misono, H. A novel NADP+ dependent serine dehydrogenase from Agrobacterium tumefaciens. Biosci. Biotechnol. Biochem. 61 (1997) 152-157. [PMID: 9028042]

[EC 1.1.1.276 created 2003, modified 2015]

*EC 1.1.1.363

Accepted name: glucose-6-phosphate dehydrogenase [NAD(P)+]

Reaction: D-glucose 6-phosphate + NAD(P)+ = 6-phospho-D-glucono-1,5-lactone + NAD(P)H + H+

Other name(s): G6PDH; G6PD; Glc6PD

Systematic name: D-glucose-6-phosphate:NAD(P)+ 1-oxidoreductase

Comments: The enzyme catalyses a step of the pentose phosphate pathway. The enzyme from the Gram-positive bacterium Leuconostoc mesenteroides prefers NADP+ while the enzyme from the Gram-negative bacterium Gluconacetobacter xylinus prefers NAD+. cf. EC 1.1.1.49, glucose-6-phosphate dehydrogenase (NADP+) and EC 1.1.1.388, glucose-6-phosphate dehydrogenase (NAD+).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Olive, C., Geroch, M.E. and Levy, H.R. Glucose 6-phosphate dehydrogenase from Leuconostoc mesenteroides. Kinetic studies. J. Biol. Chem. 246 (1971) 2047-2057. [PMID: 4396688]

2. Lee, W.T. and Levy, H.R. Lysine-21 of Leuconostoc mesenteroides glucose 6-phosphate dehydrogenase participates in substrate binding through charge-charge interaction. Protein Sci. 1 (1992) 329-334. [PMID: 1304341]

3. Cosgrove, M.S., Naylor, C., Paludan, S., Adams, M.J. and Levy, H.R. On the mechanism of the reaction catalyzed by glucose 6-phosphate dehydrogenase. Biochemistry 37 (1998) 2759-2767. [PMID: 9485426]

4. Ragunathan, S. and Levy, H.R. Purification and characterization of the NAD-preferring glucose 6-phosphate dehydrogenase from Acetobacter hansenii (Acetobacter xylinum). Arch. Biochem. Biophys. 310 (1994) 360-366. [PMID: 8179320]

[EC 1.1.1.363 created 2013, modified 2015]

*EC 1.1.1.381

Accepted name: 3-hydroxy acid dehydrogenase

Reaction: L-allo-threonine + NADP+ = aminoacetone + CO2 + NADPH + H+ (overall reaction)
(1a) L-allo-threonine + NADP+ = L-2-amino-3-oxobutanoate + NADPH + H+
(1b) L-2-amino-3-oxobutanoate = aminoacetone + CO2 (spontaneous)

Glossary: L-allo-threonine = (2S,3S)-2-amino-3-hydroxybutanoic acid
aminoacetone = 1-aminopropan-2-one
L-2-amino-3-oxobutanoate = (2S)-2-amino-3-oxobutanoate

Other name(s): ydfG (gene name); YMR226c (gene name)

Systematic name: L-allo-threonine:NADP+ 3-oxidoreductase

Comments: The enzyme, purified from the bacterium Escherichia coli and the yeast Saccharomyces cerevisiae, shows activity with a range of 3- and 4-carbon 3-hydroxy acids. The highest activity is seen with L-allo-threonine and D-threonine. The enzyme from Escherichia coli also shows high activity with L-serine, D-serine, (S)-3-hydroxy-2-methylpropanoate and (R)-3-hydroxy-2-methylpropanoate. The enzyme has no activity with NAD+ or L-threonine (cf. EC 1.1.1.103, L-threonine 3-dehydrogenase).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Fujisawa, H., Nagata, S. and Misono, H. Characterization of short-chain dehydrogenase/reductase homologues of Escherichia coli (YdfG) and Saccharomyces cerevisiae (YMR226C). Biochim. Biophys. Acta 1645 (2003) 89-94. [PMID: 12535615]

[EC 1.1.1.381 created 2014, modified 2015]

EC 1.1.1.387

Accepted name: L-serine 3-dehydrogenase (NAD+)

Reaction: L-serine + NAD+ = 2-aminoacetaldehyde + CO2 + NADH + H+ (overall reaction)
(1a) L-serine + NAD+ = 2-aminomalonate semialdehyde + NADH + H+
(1b) 2-aminomalonate semialdehyde = 2-aminoacetaldehyde + CO2 (spontaneous)

Other name(s): NAD+-dependent L-serine dehydrogenase

Systematic name: L-serine:NAD+ 3-oxidoreductase

Comments: The enzyme, purified from the bacterium Pseudomonas aeruginosa, also shows activity with L-threonine (cf. EC 1.1.1.103, L-threonine 3-dehydrogenase). The enzyme has only very low activity with NADP+ [cf. EC 1.1.1.276, serine 3-dehydrogenase (NADP+)].

References:

1. Tchigvintsev, A., Singer, A., Brown, G., Flick, R., Evdokimova, E., Tan, K., Gonzalez, C.F., Savchenko, A. and Yakunin, A.F. Biochemical and structural studies of uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed NAD+-dependent L-serine dehydrogenase. J. Biol. Chem. 287 (2012) 1874-1883. [PMID: 22128181]

[EC 1.1.1.387 created 2015]

EC 1.1.1.388

Accepted name: glucose-6-phosphate dehydrogenase (NAD+)

Reaction: D-glucose 6-phosphate + NAD+ = 6-phospho-D-glucono-1,5-lactone + NADH + H+

Other name(s): Glc6PDH; azf (gene name); archaeal zwischenferment

Systematic name: D-glucose-6-phosphate:NAD+ 1-oxidoreductase

Comments: The enzyme catalyses a step of the pentose phosphate pathway. The enzyme from the archaeon Haloferax volcanii is specific for NAD+. cf. EC 1.1.1.363, glucose-6-phosphate dehydrogenase [NAD(P)+] and EC 1.1.1.49, glucose-6-phosphate dehydrogenase (NADP+).

References:

1. Pickl, A. and Schonheit, P. The oxidative pentose phosphate pathway in the haloarchaeon Haloferax volcanii involves a novel type of glucose-6-phosphate dehydrogenase--The archaeal Zwischenferment. FEBS Lett. 589 (2015) 1105-1111. [PMID: 25836736]

[EC 1.1.1.388 created 2015]

EC 1.1.3.48

Accepted name: 3-deoxy-α-D-manno-octulosonate 8-oxidase

Reaction: 3-deoxy-α-D-manno-octulopyranosonate + O2 = 3,8-dideoxy-8-oxo-α-D-manno-octulosonate + H2O2

Glossary: 3-deoxy-α-D-manno-octulosonate = Kdo
3,8-dideoxy-8-oxo-α-D-manno-octulosonate = (2R,4R,5R,6S)-2,4,5-trihydroxy-6-[(1S)-1-hydroxy-2-oxoethyl]oxane-2-carboxylate

Other name(s): kdnB (gene name)

Systematic name: 3-deoxy-α-D-manno-octulopyranosonate:oxygen 8-oxidoreductase

Comments: The enzyme, characterized from the bacterium Shewanella oneidensis, is involved in the formation of 8-amino-3,8-dideoxy-α-D-manno-octulosonate, an aminated form of Kdo found in lipopolysaccharides of members of the Shewanella genus. cf. EC 2.6.1.109, 8-amino-3,8-dideoxy-α-D-manno-octulosonate transaminase.

References:

1. Gattis, S.G., Chung, H.S., Trent, M.S. and Raetz, C.R. The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis. J. Biol. Chem. 288 (2013) 9216-9225. [PMID: 23413030]

[EC 1.1.3.48 created 2015]

EC 1.2.1.93

Accepted name: formate dehydrogenase (NAD+, ferredoxin)

Reaction: 2 formate + NAD+ + 2 oxidized ferredoxin [iron-sulfur] cluster = 2 CO2 + NADH + H+ + 2 reduced ferredoxin [iron-sulfur] cluster

Other name(s): electron-bifurcating formate dehydrogenase

Systematic name: formate:NAD+, ferredoxin oxidoreductase

Comments: The enzyme complex, isolated from the bacterium Gottschalkia acidurici, couples the reduction of NAD+ and the reduction of ferredoxin with formate via flavin-based electron bifurcation.

References:

1. Wang, S., Huang, H., Kahnt, J. and Thauer, R.K. Clostridium acidurici electron-bifurcating formate dehydrogenase. Appl. Environ. Microbiol. 79 (2013) 6176-6179. [PMID: 23872566]

[EC 1.2.1.93 created 2015]

EC 1.2.1.94

Accepted name: farnesal dehydrogenase

Reaction: (2E,6E)-farnesal + NAD+ + H2O = (2E,6E)-farnesoate + NADH + 2 H+

For diagram of reaction click here.

Glossary: farnesal = 3,7,11-trimethyldodeca-2,6,10-trienal
farnesoate = 3,7,11-trimethyldodeca-2,6,10-trienoate

Other name(s): AaALDH3

Systematic name: farnesal:NAD+ oxidoreductase

Comments: Invoved in juvenile hormone production in insects. The enzyme was described from the corpora allata of Drosophila melanogaster (fruit fly), Manduca sexta (tobacco hornworm) and Aedes aegypti (dengue mosquito).

References:

1. Madhavan, K., Conscience-Egli, M., Sieber, F. and Ursprung, H. Farnesol metabolism in Drosophila melanogaster: ontogeny and tissue distribution of octanol dehydrogenase and aldehyde oxidase. J Insect Physiol 19 (1973) 235-241. [PMID: 4631837]

2. Baker, F.C., Mauchamp, B., Tsai, L.W. and Schooley, D.A. Farnesol and farnesal dehydrogenase(s) in corpora allata of the tobacco hornworm moth, Manduca sexta. J. Lipid Res. 24 (1983) 1586-1594. [PMID: 6366103]

3. Rivera-Perez, C., Nouzova, M., Clifton, M.E., Garcia, E.M., LeBlanc, E. and Noriega, F.G. Aldehyde dehydrogenase 3 converts farnesal into farnesoic acid in the corpora allata of mosquitoes. Insect Biochem. Mol. Biol. 43 (2013) 675-682. [PMID: 23639754]

[EC 1.2.1.94 created 2015]

EC 1.2.1.95

Accepted name: L-2-aminoadipate reductase

Reaction: (S)-2-amino-6-oxohexanoate + NADP+ + AMP + diphosphate = L-2-aminoadipate + NADPH + H+ + ATP (overall reaction)
(1a) L-2-aminoadipyl-[LYS2 peptidyl-carrier-protein] + AMP + diphosphate = L-2-aminoadipate + holo-[LYS2 peptidyl-carrier-protein] + ATP
(1b) (S)-2-amino-6-oxohexanoate + holo-[LYS2 peptidyl-carrier-protein] + NADP+ = L-2-aminoadipyl-[LYS2 peptidyl-carrier-protein] + NADPH + H+

Glossary: L-2-aminoadipate = (2S)-2-aminohexanedioate

Other name(s): LYS2; α-aminoadipate reductase

Systematic name: (S)-2-amino-6-oxohexanoate:NADP+ oxidoreductase (ATP-forming)

Comments: This enzyme, characterized from the yeast Saccharomyces cerevisiae, catalyses the reduction of L-2-aminoadipate to (S)-2-amino-6-oxohexanoate during L-lysine biosynthesis. An adenylation domain activates the substrate at the expense of ATP hydrolysis, and forms L-2-aminoadipate adenylate, which is attached to a peptidyl-carrier protein (PCP) domain. Binding of NADPH results in reductive cleavage of the acyl-S-enzyme intermediate, releasing (S)-2-amino-6-oxohexanoate. Different from EC 1.2.1.31, L-aminoadipate-semialdehyde dehydrogenase, which catalyses a similar transformation in the opposite direction without ATP hydrolysis.

References:

1. Ehmann, D.E., Gehring, A.M. and Walsh, C.T. Lysine biosynthesis in Saccharomyces cerevisiae: mechanism of α-aminoadipate reductase (Lys2) involves posttranslational phosphopantetheinylation by Lys5. Biochemistry 38 (1999) 6171-6177. [PMID: 10320345]

[EC 1.2.1.95 created 2015]

[EC 1.3.1.35 Transferred entry: phosphatidylcholine desaturase. Now EC 1.14.19.22, microsomal oleoyl-lipid 12-desaturase (EC 1.3.1.35 created 1984, deleted 2015)]

*EC 1.3.1.43

Accepted name: arogenate dehydrogenase

Reaction: L-arogenate + NAD+ = L-tyrosine + NADH + CO2

For diagram of reaction click here.

Glossary: L-arogenate = 1-[(2S)-2-amino-2-carboxyethyl]-4-hydroxycyclohexa-2,5-diene-1-carboxylate

Other name(s): arogenic dehydrogenase (ambiguous); cyclohexadienyl dehydrogenase; pretyrosine dehydrogenase (ambiguous); L-arogenate:NAD+ oxidoreductase; arogenate dehydrogenase (NAD+)

Systematic name: L-arogenate:NAD+ oxidoreductase (decarboxylating)

Comments: Arogenate dehydrogenases may utilize NAD+ (EC 1.3.1.43), NADP+ (EC 1.3.1.78), or both (EC 1.3.1.79). NAD+-specific enzymes have been reported from some bacteria [2] and plants [3]. Some enzymes also possess the activity of EC 1.3.1.12, prephenate dehydrogenase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 64295-75-6

References:

1. Stenmark, S.L., Pierson, D.L., Jensen, R.A. and Glover, G.I. Blue-green bacteria synthesise L-tyrosine by the pretyrosine pathway. Nature 247 (1974) 290-292. [PMID: 4206476]

2. Byng, G.S., Whitaker, R.J., Gherna, R.L. and Jensen, R.A. Variable enzymological patterning in tyrosine biosynthesis as a means of determining natural relatedness among the Pseudomonadaceae. J. Bacteriol. 144 (1980) 247-257. [PMID: 7419490]

3. Byng, G., Whitaker, R., Flick, C. and Jensen, R.A. Enzymology of L-tyrosine biosynthesis in corn (Zea mays). Phytochemistry 20 (1981) 1289-1292.

4. Mayer, E., Waldner-Sander, S., Keller, B., Keller, E. and Lingens, F. Purification of arogenate dehydrogenase from Phenylobacterium immobile. FEBS Lett. 179 (1985) 208-212. [PMID: 3967752]

5. Lingens, F., Keller, E. and Keller, B. Arogenate dehydrogenase from Phenylobacterium immobile. Methods Enzymol. 142 (1987) 513-518.

6. Zamir, L.O., Tiberio, R., Devor, K.A., Sauriol, F., Ahmad, S. and Jensen, R.A. Structure of D-prephenyllactate. A carboxycyclohexadienyl metabolite from Neurospora crassa. J. Biol. Chem. 263 (1988) 17284-17290. [PMID: 2972718]

[EC 1.3.1.43 created 1989, modified 2003, modified 2005, modified 2015]

[EC 1.3.1.63 Transferred entry: 2,4-dichlorobenzoyl-CoA reductase. Now EC 1.21.1.2, 2,4-dichlorobenzoyl-CoA reductase (EC 1.3.1.63 created 2000, modified 2011, deleted 2015)]

EC 1.3.7.11

Accepted name: 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase

Reaction: a 2,3-bis-(O-phytanyl)-sn-glycero-phospholipid + 16 oxidized ferredoxin [iron-sulfur] cluster = a 2,3-bis-(O-geranylgeranyl)-sn-glycero-phospholipid + 16 reduced ferredoxin [iron-sulfur] cluster + 16 H+

For diagram of reaction click here.

Other name(s): AF0464 (gene name); 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor)

Systematic name: 2,3-bis-(O-phytanyl)-sn-glycero-phospholipid:ferredoxin oxidoreductase

Comments: A flavoprotein (FAD). The enzyme is involved in the biosynthesis of archaeal membrane lipids. It catalyses the reduction of all 8 double bonds in 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipids and all 4 double bonds in 3-O-geranylgeranyl-sn-glycerol phospholipids with comparable activity. Unlike EC 1.3.1.101, 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H], this enzyme shows no activity with NADPH, and requires a dedicated ferredoxin [4].

References:

1. Murakami, M., Shibuya, K., Nakayama, T., Nishino, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase involved in the biosynthesis of archaeal membrane lipids in the hyperthermophilic archaeon Archaeoglobus fulgidus. FEBS J. 274 (2007) 805-814. [PMID: 17288560]

2. Sato, S., Murakami, M., Yoshimura, T. and Hemmi, H. Specific partial reduction of geranylgeranyl diphosphate by an enzyme from the thermoacidophilic archaeon Sulfolobus acidocaldarius yields a reactive prenyl donor, not a dead-end product. J. Bacteriol. 190 (2008) 3923-3929. [PMID: 18375567]

3. Sasaki, D., Fujihashi, M., Iwata, Y., Murakami, M., Yoshimura, T., Hemmi, H. and Miki, K. Structure and mutation analysis of archaeal geranylgeranyl reductase. J. Mol. Biol. 409 (2011) 543-557. [PMID: 21515284]

4. Isobe, K., Ogawa, T., Hirose, K., Yokoi, T., Yoshimura, T. and Hemmi, H. Geranylgeranyl reductase and ferredoxin from Methanosarcina acetivorans are required for the synthesis of fully reduced archaeal membrane lipid in Escherichia coli cells. J. Bacteriol. 196 (2014) 417-423. [PMID: 24214941]

[EC 1.3.7.11 created 2013 as EC 1.3.99.34, transferred 2015 to EC 1.3.7.11]

[EC 1.3.99.34 Transferred entry: 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor). Now classified as EC 1.3.7.11, 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase. (EC 1.3.99.34 created 2013, deleted 2015)]

EC 1.3.99.37

Accepted name: 1-hydroxy-2-isopentenylcarotenoid 3,4-desaturase

Reaction: (1) dihydroisopentenyldehydrorhodopin + acceptor = isopentenyldehydrorhodopin + reduced acceptor
(2) dihydrobisanhydrobacterioruberin + acceptor = bisanhydrobacterioruberin + reduced acceptor

For diagram of reaction click here.

Glossary: bisanhydrobacterioruberin = (2S,2S')-2,2'-bis(3-methylbut-2-en-1-yl)-3,4-didehydro-1,1',2,2'-tetrahydro-ψ,ψ-carotene-1,1'-diol
dihydrobisanhydrobacterioruberin = (2S,2S')-2,2'-bis(3-methylbut-2-en-1-yl)-3,3',4,4'-tetradehydro-1,1',2,2'-tetrahydro-ψ,ψ-carotene-1,1'-diol
dihydroisopentenyldehydrorhodopin = (2S)-2-(3-methylbut-2-en-1-yl)-3,4-didehydro-1,2-dihydro-ψ,ψ-caroten-1-ol
isopentenyldehydrorhodopin = (2S)-2-(3-methylbut-2-en-1-yl)-1,2-dihydro-ψ,ψ-caroten-1-ol

Other name(s): crtD (gene name)

Systematic name: dihydroisopentenyldehydrorhodopin:acceptor 3,4-oxidoreductase

Comments: The enzyme, isolated from the archaeon Haloarcula japonica, is involved in the biosynthesis of the C50 carotenoid bacterioruberin. In this pathway it catalyses the desaturation of the C-3,4 double bond in dihydroisopentenyldehydrorhodopin and the desaturation of the C-3',4' double bond in dihydrobisanhydrobacterioruberin.

References:

1. Yang, Y., Yatsunami, R., Ando, A., Miyoko, N., Fukui, T., Takaichi, S. and Nakamura, S. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. J. Bacteriol. 197 (2015) 1614-1623. [PMID: 25712483]

[EC 1.3.99.37 created 2015]

[EC 1.4.99.1 Transferred entry: D-amino-acid dehydrogenase. Now listed as EC 1.4.99.6, D-arginine dehydrogenase (EC 1.4.99.1 created 1972, deleted 2015)]

EC 1.4.99.6

Accepted name: D-arginine dehydrogenase

Reaction: D-arginine + acceptor + H2O = 5-guanidino-2-oxopentanoate + NH3 + reduced acceptor (overall reaction)
(1a) D-arginine + acceptor = iminoarginine + reduced acceptor
(1b) iminoarginine + H2O = 5-guanidino-2-oxopentanoate + NH3 (spontaneous)

Glossary: 5-guanidino-2-oxopentanoate = 2-ketoarginine
iminoarginine = 5-carbamimidamido-2-iminopentanoate

Other name(s): D-amino-acid:(acceptor) oxidoreductase (deaminating); D-amino-acid dehydrogenase; D-amino-acid:acceptor oxidoreductase (deaminating)

Systematic name: D-arginine:acceptor oxidoreductase (deaminating)

Comments: Contains a non-covalent FAD cofactor. The enzyme, which has been isolated from the bacterium Pseudomonas aeruginosa PAO1, is a catabolic enzyme that is part of a two-enzyme complex involved in the racemization of D and L-arginine. The enzyme has a broad substrate range and can act on most D-amino acids with the exception of D-glutamate and D-aspartate. However, activity is maximal with D-arginine and D-lysine. Not active on glycine.

References:

1. Tsukada, K. D-Amino acid dehydrogenases of Pseudomonas fluorescens. J. Biol. Chem. 241 (1966) 4522-4528. [PMID: 5925166]

2. Li, C. and Lu, C.D. Arginine racemization by coupled catabolic and anabolic dehydrogenases. Proc. Natl. Acad. Sci. USA 106 (2009) 906-911. [PMID: 19139398]

3. Fu, G., Yuan, H., Li, C., Lu, C.D., Gadda, G. and Weber, I.T. Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase. Biochemistry 49 (2010) 8535-8545. [PMID: 20809650]

4. Yuan, H., Fu, G., Brooks, P.T., Weber, I. and Gadda, G. Steady-state kinetic mechanism and reductive half-reaction of D-arginine dehydrogenase from Pseudomonas aeruginosa. Biochemistry 49 (2010) 9542-9550. [PMID: 20932054]

5. Fu, G., Yuan, H., Wang, S., Gadda, G. and Weber, I.T. Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase. Biochemistry 50 (2011) 6292-6294. [PMID: 21707047]

6. Yuan, H., Xin, Y., Hamelberg, D. and Gadda, G. Insights on the mechanism of amine oxidation catalyzed by D-arginine dehydrogenase through pH and kinetic isotope effects. J. Am. Chem. Soc. 133 (2011) 18957-18965. [PMID: 21999550]

[EC 1.4.99.6 created 1972 as EC 1.4.99.1, transferred 2015 to EC 1.4.99.6]

EC 1.5.1.50

Accepted name: dihydromonapterin reductase

Reaction: 5,6,7,8-tetrahydromonapterin + NADP+ = 7,8-dihydromonapterin + NADPH + H+

Glossary: 7,8-dihydromonapterin = 2-amino-6-[(1S,2S)-1,2,3-trihydroxypropyl]-7,8-dihydropteridin-4(3H)-one

Other name(s): FolM; H2-MPt reductase

Systematic name: 5,6,7,8-tetrahydromonapterin:NADP+ oxidoreductase

Comments: The enzyme, found in many Gram negative bacteria, also slowly reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate (cf. EC 1.5.1.3, dihydrofolate reductase). The enzyme has no activity with NADH.

References:

1. Pribat, A., Blaby, I.K., Lara-Nunez, A., Gregory, J.F., 3rd, de Crecy-Lagard, V. and Hanson, A.D. FolX and FolM are essential for tetrahydromonapterin synthesis in Escherichia coli and Pseudomonas aeruginosa. J. Bacteriol. 192 (2010) 475-482. [PMID: 19897652]

[EC 1.5.1.50 created 2015]

EC 1.6.1.4

Accepted name: NAD(P)+ transhydrogenase (ferredoxin)

Reaction: NADH + H+ + 2 NADP+ + 2 reduced ferredoxin [iron-sulfur] cluster = NAD+ + 2 NADPH + 2 oxidized ferredoxin [iron-sulfur] cluster

Other name(s): NADH-dependent reduced ferredoxin:NADP+ oxidoreductase

Systematic name: NADH:NADP+, ferredoxin oxidoreductase

Comments: The iron-sulfur flavoprotein complex, isolated from the bacterium Clostridium kluyveri, couples the exergonic reduction of NADP+ with reduced ferredoxin and the endergonic reduction of NADP+ with NADH.

References:

1. Wang, S., Huang, H., Moll, J. and Thauer, R.K. NADP+ reduction with reduced ferredoxin and NADP+ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridium kluyveri. J. Bacteriol. 192 (2010) 5115-5123. [PMID: 20675474]

[EC 1.6.1.4 created 2015]

*EC 1.8.1.2

Accepted name: assimilatory sulfite reductase (NADPH)

Reaction: hydrogen sulfide + 3 NADP+ + 3 H2O = sulfite + 3 NADPH + 3 H+

Other name(s): sulfite reductase (NADPH); sulfite (reduced nicotinamide adenine dinucleotide phosphate) reductase; NADPH-sulfite reductase; NADPH-dependent sulfite reductase; H2S-NADP oxidoreductase; sulfite reductase (NADPH2); MET5 (gene name); MET10 (gene name); cysI (gene name); cysJ (gene name)

Systematic name: hydrogen-sulfide:NADP+ oxidoreductase

Comments: Contains siroheme, [4Fe-4S] cluster, FAD and FMN. The enzyme, which catalyses the six-electron reduction of sulfite to sulfide, is involved in sulfate assimilation in bacteria and yeast. Different from EC 1.8.99.5, dissimilatory sulfite reductase, which is involved in prokaryotic sulfur-based energy metabolism. cf. EC 1.9.7.1, assimilatory sulfite reductase (ferredoxin).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9029-35-0

References:

1. Hilz, H., Kittler, M. and Knape, G. Die Reduktion von Sulfate in der Hefe. Biochem. Z. 332 (1959) 151-166. [PMID: 14401842]

2. Yoshimoto, A. and Sato, R. Studies on yeast sulfite reductase. I. Purification and characterization. Biochim. Biophys. Acta 153 (1968) 555-575. [PMID: 4384979]

3. Siegel, L.M., Murphy, M.J. and Kamin, H. Reduced nicotinamide adenine dinucleotide phosphate-sulfite reductase of enterobacteria. I. The Escherichia coli hemoflavoprotein: molecular parameters and prosthetic groups. J. Biol. Chem. 248 (1973) 251-264. [PMID: 4144254]

4. Kobayashi, K. and Yoshimoto, A. Studies on yeast sulfite reductase. IV. Structure and steady-state kinetics. Biochim. Biophys. Acta 705 (1982) 348-356. [PMID: 6751400]

5. Siegel, L.M., Rueger, D.C., Barber, M.J., Krueger, R.J., Orme-Johnson, N.R. and Orme-Johnson, W.H. Escherichia coli sulfite reductase hemoprotein subunit. Prosthetic groups, catalytic parameters, and ligand complexes. J. Biol. Chem. 257 (1982) 6343-6350. [PMID: 6281269]

6. Coves, J., Zeghouf, M., Macherel, D., Guigliarelli, B., Asso, M. and Fontecave, M. Flavin mononucleotide-binding domain of the flavoprotein component of the sulfite reductase from Escherichia coli. Biochemistry 36 (1997) 5921-5928. [PMID: 9153434]

7. Crane, B.R., Siegel, L.M. and Getzoff, E.D. Structures of the siroheme- and Fe4S4-containing active center of sulfite reductase in different states of oxidation: heme activation via reduction-gated exogenous ligand exchange. Biochemistry 36 (1997) 12101-12119. [PMID: 9315848]

[EC 1.8.1.2 created 1961, modified 2015]

*EC 1.8.7.1

Accepted name: assimilatory sulfite reductase (ferredoxin)

Reaction: hydrogen sulfide + 6 oxidized ferredoxin [iron-sulfur] cluster + 3 H2O = sulfite + 6 reduced ferredoxin [iron-sulfur] cluster + 6 H+

Other name(s): ferredoxin-sulfite reductase; SIR (gene name); sulfite reductase (ferredoxin)

Systematic name: hydrogen-sulfide:ferredoxin oxidoreductase

Comments: An iron protein. The enzyme participates in sulfate assimilation. While it is usually found in cyanobacteria, plants and algae, it has also been reported in bacteria [4]. Different from EC 1.8.99.5, dissimilatory sulfite reductase, which is involved in prokaryotic sulfur-based energy metabolism. cf. EC 1.8.1.2, assimilatory sulfite reductase (NADPH).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37256-50-1

References:

1. Schmidt, A. and Trebst, A. The mechanism of photosynthetic sulfate reduction by isolated chloroplasts. Biochim. Biophys. Acta 180 (1969) 529-535. [PMID: 4390248]

2. Gisselmann, G., Klausmeier, P. and Schwenn, J.D. The ferredoxin:sulphite reductase gene from Synechococcus PCC7942. Biochim. Biophys. Acta 1144 (1993) 102-106. [PMID: 8347657]

3. Bork, C., Schwenn, J.D. and Hell, R. Isolation and characterization of a gene for assimilatory sulfite reductase from Arabidopsis thaliana. Gene 212 (1998) 147-153. [PMID: 9661674]

4. Neumann, S., Wynen, A., Truper, H.G. and Dahl, C. Characterization of the cys gene locus from Allochromatium vinosum indicates an unusual sulfate assimilation pathway. Mol. Biol. Rep. 27 (2000) 27-33. [PMID: 10939523]

[EC 1.8.7.1 created 1972, modified 2015]

[EC 1.8.99.1 Deleted entry: sulfite reductase. Now covered by EC 1.8.1.2, assimilatory sulfite reductase (NADPH) and EC 1.8.7.1, assimilatory sulfite reductase (ferredoxin). (EC 1.8.99.1 created 1972, deleted 2015)]

EC 1.8.99.5

Accepted name: dissimilatory sulfite reductase

Reaction: (1) hydrogen sulfide + a [DsrC protein]-disulfide + 2 acceptor + 3 H2O = sulfite + a [DsrC protein]-dithiol + 2 reduced acceptor + 2 H+ (overall reaction)
(1a) hydrogen sulfide + a [DsrC protein]-disulfide = a [DsrC protein]-S-sulfanyl-L-cysteine
(1b) a [DsrC protein]-S-sulfanyl-L-cysteine + 2 acceptor + 3 H2O = sulfite + a [DsrC protein]-dithiol + 2 reduced acceptor + 2 H+
(2) a [DsrC protein]-S-sulfanyl-L-cysteine + 3 acceptor + 3 H2O = sulfite + a [DsrC protein]-disulfide + 3 reduced acceptor + 2 H+ (overall reaction)
(2a) a [DsrC protein]-S-sulfanyl-L-cysteine + 3 acceptor + 3 H2O = a [DsrC]-S-sulfo-L-cysteine + 3 reduced acceptor + H+
(2b) a [DsrC]-S-sulfo-L-cysteine = sulfite + a [DsrC protein]-disulfide

Other name(s): siroheme sulfite reductase; hydrogen-sulfide:(acceptor) oxidoreductase (ambiguous); DsrAB

Systematic name: hydrogen-sulfide:[DsrC sulfur-carrier protein],acceptor oxidoreductase

Comments: Contain siroheme. The enzyme is essential in prokaryotic sulfur-based energy metabolism, including sulfate/sulfite reducing organisms, sulfur-oxidizing bacteria, and organosulfonate reducers. In sulfur reducers it catalyses the reduction of sulfite to sulfide (reaction 1 in the right to left direction), while in sulfur oxidizers it catalyses the opposite reaction (reaction 2 in the left to right direction) [1]. The reaction involves the small protein DsrC, which is present in all the organisms that contain dissimilatory sulfite reductase. During the process an intramolecular disulfide bond is formed between two L-cysteine residues of DsrC. This disulfide can be reduced by a number of proteins including DsrK and TcmB [5]. This enzyme is different from EC 1.8.1.2, assimilatory sulfite reductase (NADPH), and EC 1.8.7.1, assimilatory sulfite reductase (ferredoxin), which are involved in sulfate assimilation.

References:

1. Schedel, M., Vanselow, M. and Trueper, H. G. Siroheme sulfite reductase from Chromatium vinosum. Purification and investigation of some of its molecular and catalytic properties. Arch. Microbiol. 121 (1979) 29-36.

2. Seki, Y., Sogawa, N. and Ishimoto, M. Siroheme as an active catalyst in sulfite reduction. J. Biochem. 90 (1981) 1487-1492. [PMID: 7338517]

3. Pott, A.S. and Dahl, C. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Microbiology 144 (1998) 1881-1894. [PMID: 9695921]

4. Oliveira, T.F., Vonrhein, C., Matias, P.M., Venceslau, S.S., Pereira, I.A. and Archer, M. The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration. J. Biol. Chem. 283 (2008) 34141-34149. [PMID: 18829451]

5. Venceslau, S.S., Stockdreher, Y., Dahl, C. and Pereira, I.A. The "bacterial heterodisulfide" DsrC is a key protein in dissimilatory sulfur metabolism. Biochim. Biophys. Acta 1837 (2014) 1148-1164. [PMID: 24662917]

[EC 1.8.99.5 created 1972]

*EC 1.11.1.12

Accepted name: phospholipid-hydroperoxide glutathione peroxidase

Reaction: 2 glutathione + a hydroperoxy-fatty-acyl-[lipid] = glutathione disulfide + a hydroxy-fatty-acyl-[lipid] + H2O

Other name(s): peroxidation-inhibiting protein; PHGPX; peroxidation-inhibiting protein:peroxidase,glutathione (phospholipid hydroperoxide-reducing); phospholipid hydroperoxide glutathione peroxidase; hydroperoxide glutathione peroxidase

Systematic name: glutathione:lipid-hydroperoxide oxidoreductase

Comments: A protein containing a selenocysteine residue. The products of action of EC 1.13.11.12 lipoxygenase on phospholipids can act as acceptors; H2O2 can also act, but much more slowly (cf. EC 1.11.1.9 glutathione peroxidase).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 97089-70-8

References:

1. Ursini, F., Maiorino, M. and Gregolin, C. The selenoenzyme phospholipid hydroperoxide glutathione peroxidase. Biochim. Biophys. Acta 839 (1985) 62-70. [PMID: 3978121]

2. Schnurr, K., Belkner, J., Ursini, F., Schewe, T. and Kuhn, H. The selenoenzyme phospholipid hydroperoxide glutathione peroxidase controls the activity of the 15-lipoxygenase with complex substrates and preserves the specificity of the oxygenation products. J. Biol. Chem. 271 (1996) 4653-4658. [PMID: 8617728]

[EC 1.11.1.12 created 1989, modified 2015]

*EC 1.13.11.18

Accepted name: persulfide dioxygenase

Reaction: S-sulfanylglutathione + O2 + H2O = glutathione + sulfite + 2 H+ (overall reaction)
(1a) S-sulfanylglutathione + O2 = S-sulfinatoglutathione + H+
(1b) S-sulfinatoglutathione + H2O = glutathione + sulfite + H+ (spontaneous)

Other name(s): sulfur oxygenase (incorrect); sulfur:oxygen oxidoreductase (incorrect); sulfur dioxygenase (incorrect)

Systematic name: S-sulfanylglutathione:oxygen oxidoreductase

Comments: An iron protein. Perthiols, formed spontaneously by interactions between thiols and elemental sulfur or sulfide, are the only acceptable substrate to the enzyme. The sulfite that is formed by the enzyme can be further converted into sulfate, thiosulfate or S-sulfoglutathione (GSSO3-) non-enzymically [2].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-58-9

References:

1. Suzuki, I. and Silver, M. The initial product and properties of the sulfur-oxidizing enzyme of thiobacilli. Biochim. Biophys. Acta 122 (1966) 22-33. [PMID: 5968172]

2. Rohwerder, T. and Sand, W. The sulfane sulfur of persulfides is the actual substrate of the sulfur-oxidizing enzymes from Acidithiobacillus and Acidiphilium spp. Microbiology 149 (2003) 1699-1710. [PMID: 12855721]

3. Liu, H., Xin, Y. and Xun, L. Distribution, diversity, and activities of sulfur dioxygenases in heterotrophic bacteria. Appl. Environ. Microbiol. 80 (2014) 1799-1806. [PMID: 24389926]

4. Holdorf, M.M., Owen, H.A., Lieber, S.R., Yuan, L., Adams, N., Dabney-Smith, C. and Makaroff, C.A. Arabidopsis ETHE1 encodes a sulfur dioxygenase that is essential for embryo and endosperm development. Plant Physiol. 160 (2012) 226-236. [PMID: 22786886]

5. Pettinati, I., Brem, J., McDonough, M.A. and Schofield, C.J. Crystal structure of human persulfide dioxygenase: structural basis of ethylmalonic encephalopathy. Hum. Mol. Genet. 24 (2015) 2458-2469. [PMID: 25596185]

[EC 1.13.11.18 created 1972, modified 2015]

EC 1.14.12.23

Accepted name: nitroarene dioxygenase

Reaction: nitrobenzene + NADH + O2 = catechol + nitrite + NAD+

Other name(s): cnbA (gene name)

Systematic name: nitrobenzene,NADH:oxygen oxidoreductase (1,2-hydroxylating, denitrifying)

Comments: This enzyme is a member of the naphthalene family of bacterial Rieske non-heme iron dioxygenases. It comprises a multicomponent system, containing a Rieske [2Fe-2S] ferredoxin, an NADH-dependent flavoprotein reductase (EC 1.18.1.3, ferredoxin—NAD+ reductase), and an α3β3 oxygenase. The enzyme forms of a cis-dihydroxylated product that spontaneously rearranges to form a catechol with accompanying release of nitrite. It can typically act on many different nitroaromatic compounds, including chlorinated species. Enzymes found in different strains may have different substrate preferences. Requires Fe2+.

References:

1. Parales, J.V., Parales, R.E., Resnick, S.M. and Gibson, D.T. Enzyme specificity of 2-nitrotoluene 2,3-dioxygenase from Pseudomonas sp. strain JS42 is determined by the C-terminal region of the α subunit of the oxygenase component. J. Bacteriol. 180 (1998) 1194-1199. [PMID: 9495758]

2. Lessner, D.J., Johnson, G.R., Parales, R.E., Spain, J.C. and Gibson, D.T. Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765. Appl. Environ. Microbiol. 68 (2002) 634-641. [PMID: 11823201]

3. Liu, H., Wang, S.J., Zhang, J.J., Dai, H., Tang, H. and Zhou, N.Y. Patchwork assembly of nag-like nitroarene dioxygenase genes and the 3-chlorocatechol degradation cluster for evolution of the 2-chloronitrobenzene catabolism pathway in Pseudomonas stutzeri ZWLR2-1. Appl. Environ. Microbiol. 77 (2011) 4547-4552. [PMID: 21602392]

4. Singh, D., Kumari, A., Ramaswamy, S. and Ramanathan, G. Expression, purification and substrate specificities of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2. Biochem. Biophys. Res. Commun. 445 (2014) 36-42. [PMID: 24491551]

[EC 1.14.12.23 created 2015]

[EC 1.14.13.26 Transferred entry: phosphatidylcholine 12-monooxygenase. Now classified as EC 1.14.18.4, phosphatidylcholine 12-monooxygenase. (EC 1.14.13.26 created 1984, deleted 2015)]

[EC 1.14.13.169 Transferred entry: sphinganine C4-monooxygenase. Now EC 1.14.18.5, sphingolipid C4-monooxygenase (EC 1.14.13.169 created 2012, deleted 2015)]

EC 1.14.13.204

Accepted name: long-chain acyl-CoA ω-monooxygenase

Reaction: (1) oleoyl-CoA + NADPH + H+ + O2 = 18-hydroxyoleoyl-CoA + NADP+ + H2O
(2) linoleoyl-CoA + NADPH + H+ + O2 = 18-hydroxylinoleoyl-CoA + NADP+ + H2O

Other name(s): long-chain acyl-CoA ω-hydroxylase; CYP86A22 (gene name); CYP52M1 (gene name)

Systematic name: long-chain acyl-CoA,NADPH:O2 oxidoreductase (ω-hydroxylating)

Comments: The enzymes from solanaceous plants are involved in the biosynthesis of stigmatic estolide, a lipid-based polyester that forms a major component of the exudate.

References:

1. Han, J., Clement, J.M., Li, J., King, A., Ng, S. and Jaworski, J.G. The cytochrome P450 CYP86A22 is a fatty acyl-CoA ω-hydroxylase essential for estolide synthesis in the stigma of Petunia hybrida. J. Biol. Chem. 285 (2010) 3986-3996. [PMID: 19940120]

[EC 1.14.13.204 created 2015]

EC 1.14.13.205

Accepted name: long-chain fatty acid ω-monooxygenase

Reaction: a long-chain fatty acid + NADPH + H+ + O2 = an ω-hydroxy-long-chain fatty acid + NADP+ + H2O

Other name(s): CYP704B1 (gene name); CYP52M1 (gene name); CYP4A (gene name); CYP86A (gene name)

Systematic name: long-chain fatty acid,NADPH:O2 oxidoreductase (ω-hydroxylating)

Comments: The plant enzyme CYP704B1, which is involved in the synthesis of sporopollenin, a complex polymer found at the outer layer of spores and pollen, acts on palmitate (18:0), stearate (18:0) and oleate (18:1). The plant enzyme CYP86A1 also acts on laurate (12:0). The enzyme from the yeast Starmerella bombicola (CYP52M1) acts on C16 to C20 saturated and unsaturated fatty acids and can also hydroxylate the (ω-1) position. The mammalian enzyme CYP4A acts on laurate (12:0), myristate (14:0), palmitate (16:0), oleate (18:1), and arachidonate (20:4).

References:

1. Benveniste, I., Tijet, N., Adas, F., Philipps, G., Salaun, J.P. and Durst, F. CYP86A1 from Arabidopsis thaliana encodes a cytochrome P450-dependent fatty acid ω-hydroxylase. Biochem. Biophys. Res. Commun. 243 (1998) 688-693. [PMID: 9500987]

2. Hoch, U., Zhang, Z., Kroetz, D.L. and Ortiz de Montellano, P.R. Structural determination of the substrate specificities and regioselectivities of the rat and human fatty acid ω-hydroxylases. Arch. Biochem. Biophys. 373 (2000) 63-71. [PMID: 10620324]

3. Dobritsa, A.A., Shrestha, J., Morant, M., Pinot, F., Matsuno, M., Swanson, R., Møller, B.L. and Preuss, D. CYP704B1 is a long-chain fatty acid ω-hydroxylase essential for sporopollenin synthesis in pollen of Arabidopsis. Plant Physiol. 151 (2009) 574-589. [PMID: 19700560]

4. Huang, F.C., Peter, A. and Schwab, W. Expression and characterization of CYP52 genes involved in the biosynthesis of sophorolipid and alkane metabolism from Starmerella bombicola. Appl. Environ. Microbiol. 80 (2014) 766-776. [PMID: 24242247]

[EC 1.14.13.205 created 2015]

EC 1.14.18.4

Accepted name: phosphatidylcholine 12-monooxygenase

Reaction: a 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine + 2 ferrocytochrome b5 + O2 + 2 H+ = a 1-acyl-2-[(12R)-12-hydroxyoleoyl]-sn-glycero-3-phosphocholine + 2 ferricytochrome b5 + H2O

Glossary: ricinoleic acid = (9Z,12R)-12-hydroxyoctadec-9-enoic acid

Other name(s): ricinoleic acid synthase; oleate Δ12-hydroxylase; oleate Δ12-monooxygenase

Systematic name: 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine,ferrocytochrome-b5:oxygen oxidoreductase (12-hydroxylating)

Comments: The enzyme, characterized from the plant Ricinus communis (castor bean), is involved in production of the 12-hydroxylated fatty acid ricinoleate. The enzyme, which shares sequence similarity with fatty-acyl desaturases, requires a cytochrome b5 as the electron donor.

References:

1. Galliard, T. and Stumpf, P.K. Fat metabolism in higher plants. 30. Enzymatic synthesis of ricinoleic acid by a microsomal preparation from developing Ricinus communis seeds. J. Biol. Chem. 241 (1966) 5806-5812. [PMID: 4289003]

2. Moreau, R.A. and Stumpf, P.K. Recent studies of the enzymic-synthesis of ricinoleic acid by developing castor beans. Plant Physiol. 67 (1981) 672-676. [PMID: 16661734]

3. Smith, M.A., Jonsson, L., Stymne, S. and Stobart, K. Evidence for cytochrome b5 as an electron donor in ricinoleic acid biosynthesis in microsomal preparations from developing castor bean (Ricinus communis L.). Biochem. J. 287 (1992) 141-144. [PMID: 1417766]

4. Lin, J.T., McKeon, T.A., Goodrich-Tanrikulu, M. and Stafford, A.E. Characterization of oleoyl-12-hydroxylase in castor microsomes using the putative substrate, 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine. Lipids 31 (1996) 571-577. [PMID: 8784737]

5. Broun, P. and Somerville, C. Accumulation of ricinoleic, lesquerolic, and densipolic acids in seeds of transgenic Arabidopsis plants that express a fatty acyl hydroxylase cDNA from castor bean. Plant Physiol. 113 (1997) 933-942. [PMID: 9085577]

[EC 1.14.18.4 created 1984 as EC 1.14.13.26, transferred 2015 to EC 1.14.18.4]

EC 1.14.18.5

Accepted name: sphingolipid C4-monooxygenase

Reaction: a dihydroceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4R)-4-hydroxysphinganine ceramide + 2 ferricytochrome b5 + H2O

Other name(s): sphinganine C4-monooxygenase; sphingolipid C4-hydroxylase; SUR2 (gene name); SBH1 (gene name); SBH2 (gene name); DEGS2 (gene name)

Systematic name: dihydroceramide,ferrocytochrome b5:oxygen oxidoreductase (C4-hydroxylating)

Comments: The enzyme, which belongs to the familiy of endoplasmic reticular cytochrome b5-dependent enzymes, is involved in the biosynthesis of sphingolipids in eukaryotes. Some enzymes are bifunctional and also catalyse EC 1.14.19.17, sphingolipid 4-desaturase [4].

References:

1. Haak, D., Gable, K., Beeler, T. and Dunn, T. Hydroxylation of Saccharomyces cerevisiae ceramides requires Sur2p and Scs7p. J. Biol. Chem. 272 (1997) 29704-29710. [PMID: 9368039]

2. Grilley, M.M., Stock, S.D., Dickson, R.C., Lester, R.L. and Takemoto, J.Y. Syringomycin action gene SYR2 is essential for sphingolipid 4-hydroxylation in Saccharomyces cerevisiae. J. Biol. Chem. 273 (1998) 11062-11068. [PMID: 9556590]

3. Sperling, P., Ternes, P., Moll, H., Franke, S., Zähringer, U. and Heinz, E. Functional characterization of sphingolipid C4-hydroxylase genes from Arabidopsis thaliana. FEBS Lett. 494 (2001) 90-94. [PMID: 11297741]

4. Ternes, P., Franke, S., Zähringer, U., Sperling, P. and Heinz, E. Identification and characterization of a sphingolipid Δ4-desaturase family. J. Biol. Chem. 277 (2002) 25512-25518. [PMID: 11937514]

5. Mizutani, Y., Kihara, A. and Igarashi, Y. Identification of the human sphingolipid C4-hydroxylase, hDES2, and its up-regulation during keratinocyte differentiation. FEBS Lett. 563 (2004) 93-97. [PMID: 15063729]

[EC 1.14.18.5 created 2012 as EC 1.14.13.169, transferred 2015 to EC 1.14.18.5]

EC 1.14.18.6

Accepted name: 4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase

Reaction: a phytoceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (2'R)-2'-hydroxyphytoceramide + 2 ferricytochrome b5 + H2O

Glossary: a phytoceramide = a (4R)-4-hydroxysphinganine ceramide = an N-acyl-4-hydroxysphinganine

Other name(s): FA2H (gene name); SCS7 (gene name)

Systematic name: (4R)-4-hydroxysphinganine ceramide,ferrocytochrome-b5:oxygen oxidoreductase (fatty acyl 2-hydroxylating)

Comments: The enzyme, characterized from yeast and mammals, catalyses the hydroxylation of carbon 2 of long- or very-long-chain fatty acids attached to (4R)-4-hydroxysphinganine during de novo ceramide synthesis. The enzymes from yeast and from mammals contain an N-terminal cytochrome b5 domain that acts as the direct electron donor to the desaturase active site. The newly introduced 2-hydroxyl group has R-configuration. cf. EC 1.14.18.7, dihydroceramide fatty acyl 2-hydroxylase.

References:

1. Mitchell, A.G. and Martin, C.E. Fah1p, a Saccharomyces cerevisiae cytochrome b5 fusion protein, and its Arabidopsis thaliana homolog that lacks the cytochrome b5 domain both function in the α-hydroxylation of sphingolipid-associated very long chain fatty acids. J. Biol. Chem. 272 (1997) 28281-28288. [PMID: 9353282]

2. Dunn, T.M., Haak, D., Monaghan, E. and Beeler, T.J. Synthesis of monohydroxylated inositolphosphorylceramide (IPC-C) in Saccharomyces cerevisiae requires Scs7p, a protein with both a cytochrome b5-like domain and a hydroxylase/desaturase domain. Yeast 14 (1998) 311-321. [PMID: 9559540]

3. Alderson, N.L., Rembiesa, B.M., Walla, M.D., Bielawska, A., Bielawski, J. and Hama, H. The human FA2H gene encodes a fatty acid 2-hydroxylase. J. Biol. Chem. 279 (2004) 48562-48568. [PMID: 15337768]

4. Eckhardt, M., Yaghootfam, A., Fewou, S.N., Zoller, I. and Gieselmann, V. A mammalian fatty acid hydroxylase responsible for the formation of α-hydroxylated galactosylceramide in myelin. Biochem. J. 388 (2005) 245-254. [PMID: 15658937]

5. Guo, L., Zhang, X., Zhou, D., Okunade, A.L. and Su, X. Stereospecificity of fatty acid 2-hydroxylase and differential functions of 2-hydroxy fatty acid enantiomers. J. Lipid Res. 53 (2012) 1327-1335. [PMID: 22517924]

[EC 1.14.18.6 created 2015]

EC 1.14.18.7

Accepted name: dihydroceramide fatty acyl 2-hydroxylase

Reaction: a dihydroceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (2'R)-2'-hydroxydihydroceramide + 2 ferricytochrome b5 + H2O

Glossary: a dihydroceramide = an N-acylsphinganine

Other name(s): FAH1 (gene name); FAH2 (gene name); plant sphingolipid fatty acid 2-hydroxylase

Systematic name: dihydroceramide,ferrocytochrome-b5:oxygen oxidoreductase (fatty acyl 2-hydroxylating)

Comments: The enzyme, characterized from plants, catalyses the hydroxylation of carbon 2 of long- or very-long-chain fatty acids attached to sphinganine during de novo ceramide synthesis. The enzyme requires an external cytochrome b5 as the electron donor. The newly introduced 2-hydroxyl group has R-configuration. cf. EC 1.14.18.6, 4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase.

References:

1. Nagano, M., Ihara-Ohori, Y., Imai, H., Inada, N., Fujimoto, M., Tsutsumi, N., Uchimiya, H. and Kawai-Yamada, M. Functional association of cell death suppressor, Arabidopsis Bax inhibitor-1, with fatty acid 2-hydroxylation through cytochrome b5. Plant J. 58 (2009) 122-134. [PMID: 19054355]

2. Nagano, M., Takahara, K., Fujimoto, M., Tsutsumi, N., Uchimiya, H. and Kawai-Yamada, M. Arabidopsis sphingolipid fatty acid 2-hydroxylases (AtFAH1 and AtFAH2) are functionally differentiated in fatty acid 2-hydroxylation and stress responses. Plant Physiol. 159 (2012) 1138-1148. [PMID: 22635113]

3. Nagano, M., Uchimiya, H. and Kawai-Yamada, M. Plant sphingolipid fatty acid 2-hydroxylases have unique characters unlike their animal and fungus counterparts. Plant Signal Behav 7 (2012) 1388-1392. [PMID: 22918503]

[EC 1.14.18.7 created 2015]

*EC 1.14.19.2

Accepted name: stearoyl-[acyl-carrier-protein] 9-desaturase

Reaction: stearoyl-[acyl-carrier protein] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = oleoyl-[acyl-carrier protein] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O

Other name(s): stearyl acyl carrier protein desaturase; stearyl-ACP desaturase; acyl-[acyl-carrier-protein] desaturase; acyl-[acyl-carrier protein],hydrogen-donor:oxygen oxidoreductase

Systematic name: stearoyl-[acyl-carrier protein],reduced ferredoxin:oxygen oxidoreductase (9,10 cis-dehydrogenating)

Comments: The enzyme is found in the lumen of plastids, where de novo biosynthesis of fatty acids occurs, and acts on freshly synthesized saturated fatty acids that are still linked to acyl-carrier protein. The enzyme determines the position of the double bond by its distance from the carboxylic acid end of the fatty acid. It also acts on palmitoyl-[acyl-carrier-protein] [4,5].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37256-86-3

References:

1. Jaworski, J.G. and Stumpf, P.K. Fat metabolism in higher plants. Properties of a soluble stearyl-acyl carrier protein desaturase from maturing Carthamus tinctorius. Arch. Biochem. Biophys. 162 (1974) 158-165. [PMID: 4831331]

2. Nagai, J. and Bloch, K. Enzymatic desaturation of stearyl acyl carrier protein. J. Biol. Chem. 243 (1968) 4626-4633. [PMID: 4300868]

3. Shanklin, J. and Somerville, C. Stearoyl-acyl-carrier-protein desaturase from higher plants is structurally unrelated to the animal and fungal homologs. Proc. Natl. Acad. Sci. USA 88 (1991) 2510-2514. [PMID: 2006187]

4. Cahoon, E.B., Lindqvist, Y., Schneider, G. and Shanklin, J. Redesign of soluble fatty acid desaturases from plants for altered substrate specificity and double bond position. Proc. Natl. Acad. Sci. USA 94 (1997) 4872-4877. [PMID: 9144157]

5. Cao, Y., Xian, M., Yang, J., Xu, X., Liu, W. and Li, L. Heterologous expression of stearoyl-acyl carrier protein desaturase (S-ACP-DES) from Arabidopsis thaliana in Escherichia coli. Protein Expr. Purif. 69 (2010) 209-214. [PMID: 19716420]

[EC 1.14.19.2 created 1972 as EC 1.14.99.6, modified 2000, transferred 2000 to EC 1.14.19.2, modified 2015]

*EC 1.14.19.3

Accepted name: acyl-CoA 6-desaturase

Reaction: (1) linoleoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = γ-linolenoyl-CoA + 2 ferricytochrome b5+ 2 H2O
(2) α-linolenoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = stearidonoyl-CoA + 2 ferricytochrome b5+ 2 H2O

Other name(s): Δ6-desaturase; Δ6-fatty acyl-CoA desaturase; Δ6-acyl CoA desaturase; fatty acid Δ6-desaturase; fatty acid 6-desaturase; linoleate desaturase; linoleic desaturase; linoleic acid desaturase; linoleoyl CoA desaturase; linoleoyl-coenzyme A desaturase; long-chain fatty acid Δ6-desaturase; linoleoyl-CoA,hydrogen-donor:oxygen oxidoreductase; linoleoyl-CoA desaturase; FADS2 (gene name)

Systematic name: acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (6,7 cis-dehydrogenating)

Comments: An iron protein. The enzyme introduces a cis double bond at carbon 6 of acyl-CoAs. It is a front-end desaturase, introducing the new double bond between a pre-existing double bond and the carboxyl-end of the fatty acid. The human enzyme has a broad substrate range. It also acts on palmitoyl-CoA, generating sapienoyl-CoA [4], and on (9Z,12Z,15Z,18Z,21Z)-tetracosa-9,12,15,18,21-pentaenoyl-CoA, converting it to (6Z,9Z,12Z,15Z,18Z,21Z)-tetracosa-6,9,12,15,18,21-hexaenoyl-CoA as part of a pathway that produces docosahexaenoate [3]. The enzyme contains a cytochrome b5 domain that is assumed to act in vivo as the electron donor to the active site of the desaturase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9082-66-0

References:

1. Okayasu, T., Nagao, M., Ishibashi, T. and Imai, Y. Purification and partial characterization of linoleoyl-CoA desaturase from rat liver microsomes. Arch. Biochem. Biophys. 206 (1981) 21-28. [PMID: 7212717]

2. Cho, H.P., Nakamura, M.T. and Clarke, S.D. Cloning, expression, and nutritional regulation of the mammalian Δ-6 desaturase. J. Biol. Chem. 274 (1999) 471-477. [PMID: 9867867]

3. Sprecher, H. Metabolism of highly unsaturated n-3 and n-6 fatty acids. Biochim. Biophys. Acta 1486 (2000) 219-231. [PMID: 10903473]

4. Ge, L., Gordon, J.S., Hsuan, C., Stenn, K. and Prouty, S.M. Identification of the Δ-6 desaturase of human sebaceous glands: expression and enzyme activity. J. Invest. Dermatol. 120 (2003) 707-714. [PMID: 12713571]

5. Domergue, F., Abbadi, A., Zähringer, U., Moreau, H. and Heinz, E. In vivo characterization of the first acyl-CoA Δ6-desaturase from a member of the plant kingdom, the microalga Ostreococcus tauri. Biochem. J. 389 (2005) 483-490. [PMID: 15769252]

[EC 1.14.19.3 created 1986 as EC 1.14.99.25, transferred 2000 to EC 1.14.19.3, modified 2015]

*EC 1.14.19.5

Accepted name: acyl-CoA 11-(Z)-desaturase

Reaction: an acyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = an (11Z)-enoyl-CoA + 2 ferricytochrome b5 + 2 H2O

Other name(s): Δ11 desaturase; fatty acid Δ11-desaturase; TpDESN; Cro-PG; Δ11 fatty acid desaturase; Z/E11-desaturase; Δ11-palmitoyl-CoA desaturase; acyl-CoA,hydrogen donor:oxygen Δ11-oxidoreductase; Δ11-fatty-acid desaturase

Systematic name: acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (11,12 cis-dehydrogenating)

Comments: The enzyme introduces a cis double bond at position C-11 of saturated fatty acyl-CoAs. In moths the enzyme participates in the biosynthesis of their sex pheromones. The enzyme from the marine microalga Thalassiosira pseudonana is specific for palmitoyl-CoA (16:0) [4], that from the leafroller moth Choristoneura rosaceana desaturates myristoyl-CoA (14:0) [5], while that from the moth Spodoptera littoralis accepts both substrates [1]. The enzyme contains three histidine boxes that are conserved in all desaturases [2]. It is membrane-bound, and contains a cytochrome b5-like domain at the N-terminus that serves as the electron donor for the active site of the desaturase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Martinez, T., Fabrias, G. and Camps, F. Sex pheromone biosynthetic pathway in Spodoptera littoralis and its activation by a neurohormone. J. Biol. Chem. 265 (1990) 1381-1387. [PMID: 2295634]

2. Rodriguez, F., Hallahan, D.L., Pickett, J.A. and Camps, F. Characterization of the Δ11-palmitoyl-CoA-desaturase from Spodoptera littoralis (Lepidoptera:Noctuidae). Insect Biochem. Mol. Biol. 22 (1992) 143-148.

3. Navarro, I., Font, I., Fabrias, G. and Camps, F. Stereospecificity of the (E)- and (Z)-11 myristoyl desaturases in the biosynthesis of Spodoptera littoralis sex pheromone. J. Am. Chem. Soc. 119 (1997) 11335-11336.

4. Tonon, T., Harvey, D., Qing, R., Li, Y., Larson, T.R. and Graham, I.A. Identification of a fatty acid Δ11-desaturase from the microalga Thalassiosira pseudonana. FEBS Lett. 563 (2004) 28-34. [PMID: 15063718]

5. Hao, G., O'Connor, M., Liu, W. and Roelofs, W.L. Characterization of Z/E11- and Z9-desaturases from the obliquebanded leafroller moth, Choristoneura rosaceana. J. Insect Sci. 2:26 (2002) 1-7. [PMID: 15455060]

[EC 1.14.19.5 created 2008 (EC 1.14.99.32 created 2000, incorporated 2015), modified 2015]

EC 1.14.19.11

Accepted name: palmitoyl-[acyl-carrier-protein] 4-desaturase

Reaction: palmitoyl-[acyl-carrier protein] + reduced acceptor + O2 = (4Z)-hexadec-4-enoyl-[acyl-carrier protein] + acceptor + 2 H2O

Other name(s): Δ4-palmitoyl-[acyl carrier protein] desaturase

Systematic name: palmitoyl-[acyl-carrier protein],reduced acceptor:oxygen oxidoreductase (4,5 cis-dehydrogenating)

Comments: The enzyme, characterized from the plant Coriandrum sativum (coriander), is involved in biosynthesis of petroselinate [(6Z)-octadec-6-enoate], which is formed by elongation of (4Z)-hexadec-4-enoate.

References:

1. Cahoon, E.B., Shanklin, J. and Ohlrogge, J.B. Expression of a coriander desaturase results in petroselinic acid production in transgenic tobacco. Proc. Natl. Acad. Sci. USA 89 (1992) 11184-11188. [PMID: 1454797]

2. Cahoon, E.B. and Ohlrogge, J.B. Metabolic evidence for the involvement of a Δ4-palmitoyl-acyl carrier protein desaturase in petroselinic acid synthesis in coriander endosperm and transgenic tobacco cells. Plant Physiol. 104 (1994) 827-837. [PMID: 12232129]

[EC 1.14.19.11 created 2015]

EC 1.14.19.12

Accepted name: acyl-lipid ω-(9-4) desaturase

Reaction: (1) linoleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = pinolenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) α-linolenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = coniferonoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O

Glossary: taxoleate = (5Z,9Z)-octadeca-5,9-dienoate
pinolenoate = (5Z,9Z,12Z)-octadeca-5,9,12-trienoate
coniferonate = (5Z,9Z,12Z,15Z)-octadeca-5,9,12,15-tetraenoate

Other name(s): acyl-lipid ω-13 desaturase; acyl-lipid 7-desaturase (ambiguous)

Systematic name: acyl-[glycerolipid],ferrocytochrome b5:oxygen oxidoreductase [ω(9-4),ω(9-5) cis-dehydrogenating]

Comments: The enzyme, characterized from the green alga Chlamydomonas reinhardtii, is a front-end desaturase that introduces a cis double bond in ω9 unsaturated C18 or C20 fatty acids incorporated into lipids, at a position 4 carbon atoms from the existing ω9 bond, towards the carboxy end of the fatty acid (at the ω13 position). When acting on 20:2Δ(11,14) and 20:3Δ(11,14,17) substrates it introduces the new double bond between carbons 7 and 8. The enzyme contains a cytochrome b5 domain that acts as the direct electron donor for the active site of the desaturase.

References:

1. Kajikawa, M., Yamato, K.T., Kohzu, Y., Shoji, S., Matsui, K., Tanaka, Y., Sakai, Y. and Fukuzawa, H. A front-end desaturase from Chlamydomonas reinhardtii produces pinolenic and coniferonic acids by ω13 desaturation in methylotrophic yeast and tobacco. Plant Cell Physiol 47 (2006) 64-73. [PMID: 16267098]

[EC 1.14.19.12 created 2015]

EC 1.14.19.13

Accepted name: acyl-CoA 15-desaturase

Reaction: (9Z,12Z)-hexadeca-9,12-dienoyl-CoA + reduced acceptor + O2 = (9Z,12Z,15Z)-hexadeca-9,12,15-trienoyl-CoA + acceptor + 2 H2O

Other name(s): DES3 (gene name)

Systematic name: acyl-CoA,reduced acceptor:oxygen oxidoreductase (15,16 cis-dehydrogenating)

Comments: The enzyme, characterized from the the plant Sorghum bicolor, is involved in the biosynthesis of sorgoleone, an allelopathic compound produced in root hair cells. The enzyme inserts a cis double bond at carbon 15. When acting on its natural substrate, (9Z,12Z)-hexadeca-9,12-dienoyl-CoA, it produces a product with a terminal double bond.

References:

1. Pan, Z., Rimando, A.M., Baerson, S.R., Fishbein, M. and Duke, S.O. Functional characterization of desaturases involved in the formation of the terminal double bond of an unusual 16:3Δ(9,12,15) fatty acid isolated from Sorghum bicolor root hairs. J. Biol. Chem. 282 (2007) 4326-4335. [PMID: 17178719]

[EC 1.14.19.13 created 2015]

EC 1.14.19.14

Accepted name: linoleoyl-lipid Δ9 conjugase

Reaction: a linoleoyl-[glycerolipid] + reduced acceptor + O2 = an (8E,10E,12Z)-octadeca-8,10,12-trienoyl-[glycerolipid] + acceptor + 2 H2O

Glossary: calendate = (8E,10E,12Z)-octadeca-8,10,12-trienoate

Systematic name: linoleoyl-lipid,reduced acceptor:oxygen 8,11-allylic oxidase (8E,10E-forming)

Comments: The enzyme, characterized from the plant Calendula officinalis, converts a single cis double bond at position 9 of fatty acids incorporated into glycerolipids into two conjugated trans double bonds at positions 8 and 10.

References:

1. Qiu, X., Reed, D.W., Hong, H., MacKenzie, S.L. and Covello, P.S. Identification and analysis of a gene from Calendula officinalis encoding a fatty acid conjugase. Plant Physiol. 125 (2001) 847-855. [PMID: 11161042]

2. Cahoon, E.B., Ripp, K.G., Hall, S.E. and Kinney, A.J. Formation of conjugated Δ810-double bonds by Δ12-oleic-acid desaturase-related enzymes: biosynthetic origin of calendic acid. J. Biol. Chem. 276 (2001) 2637-2643. [PMID: 11067856]

[EC 1.14.19.14 created 2015]

EC 1.14.19.15

Accepted name: (11Z)-hexadec-11-enoyl-CoA conjugase

Reaction: (11Z)-hexadec-11-enoyl-CoA + reduced acceptor + O2 = (10E,12Z)-hexadeca-10,12-dienoyl-CoA + acceptor + 2 H2O

Other name(s): Bmpgdesat1 (gene name)

Systematic name: (11Z)-hexadec-11-enoyl-CoA,reduced acceptor:oxygen 10,13-allylic oxidase (10E,12E-forming)

Comments: The enzyme, characterized from the silk moth Bombyx mori, catalyses a step in the pathway for the biosynthesis of bombykol, a sex pheromone produced by the moth. The enzyme converts a single cis double bond at position 11 of (11Z)-hexadec-11-enoyl-CoA into conjugated 10 trans and 12 cis double bonds. Prior to catalysing this reaction, the enzyme catalyses the introduction of the cis bond in position 11 (cf. EC 1.14.19.5, acyl-CoA 11-desaturase).

References:

1. Moto, K., Suzuki, M.G., Hull, J.J., Kurata, R., Takahashi, S., Yamamoto, M., Okano, K., Imai, K., Ando, T. and Matsumoto, S. Involvement of a bifunctional fatty-acyl desaturase in the biosynthesis of the silkmoth, Bombyx mori, sex pheromone. Proc. Natl. Acad. Sci. USA 101 (2004) 8631-8636. [PMID: 15173596]

[EC 1.14.19.15 created 2015]

EC 1.14.19.16

Accepted name: linoleoyl-lipid Δ12 conjugase (11E,13Z-forming)

Reaction: a linoleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (9Z,11E,13Z)-octadeca-9,11,13-trienoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O

Glossary: punicate = (9Z,11E,13Z)-octadeca-9,11,13-trienoate
linoleate = (9Z,12Z)-octadeca-9,12-dienoate

Other name(s): Fac (gene name)

Systematic name: linoleoyl-lipid,ferrocytochrome-b5:oxygen 11,14 allylic oxidase (11E,13Z-forming)

Comments: The enzyme, characterized from the plants Punica granatum (pomegranate) and Trichosanthes kirilowii (Mongolian snake-gourd), converts a single cis double bond at position 12 of linoleate incorporated into phosphatidylcholine into conjugated 11-trans and 13-cis double bonds. cf. EC 1.14.19.33, Δ12 acyl-lipid conjugase (11E,13E-forming).

References:

1. Hornung, E., Pernstich, C. and Feussner, I. Formation of conjugated Δ11Δ13-double bonds by Δ12-linoleic acid (1,4)-acyl-lipid-desaturase in pomegranate seeds. Eur. J. Biochem. 269 (2002) 4852-4859. [PMID: 12354116]

2. Iwabuchi, M., Kohno-Murase, J. and Imamura, J. Δ12-oleate desaturase-related enzymes associated with formation of conjugated trans-Δ11, cis-Δ13 double bonds. J. Biol. Chem. 278 (2003) 4603-4610. [PMID: 12464604]

[EC 1.14.19.16 created 2015]

EC 1.14.19.17

Accepted name: sphingolipid 4-desaturase

Reaction: a dihydroceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4E)-sphing-4-enine ceramide + 2 ferricytochrome b5 + 2 H2O

Glossary: a dihydroceramide = an N-acylsphinganine

Other name(s): dehydroceramide desaturase

Systematic name: dihydroceramide,ferrocytochrome b5:oxygen oxidoreductase (4,5-dehydrogenating)

Comments: The enzyme, which has been characterized from plants, fungi, and mammals, generates a trans double bond at position 4 of sphinganine bases in sphingolipids [1]. The preferred substrate is dihydroceramide, but the enzyme is also active with dihydroglucosylceramide [2]. Unlike EC 1.14.19.29, sphingolipid 8-desaturase, this enzyme does not contain an integral cytochrome b5 domain [4] and requires an external cytochrome b5 [3]. The product serves as an important signalling molecules in mammals and is required for spermatide differentiation [5].

References:

1. Stoffel, W., Assmann, G. and Bister, K. Metabolism of sphingosine bases. XVII. Stereospecificities in the introduction of the 4t-double bond into sphinganine yielding 4t-sphingenine (sphingosine). Hoppe-Seylers Z. Physiol. Chem. 352 (1971) 1531-1544. [PMID: 5140816]

2. Michel, C., van Echten-Deckert, G., Rother, J., Sandhoff, K., Wang, E. and Merrill, A.H., Jr. Characterization of ceramide synthesis. A dihydroceramide desaturase introduces the 4,5-trans-double bond of sphingosine at the level of dihydroceramide. J. Biol. Chem. 272 (1997) 22432-22437. [PMID: 9312549]

3. Causeret, C., Geeraert, L., Van der Hoeven, G., Mannaerts, G.P. and Van Veldhoven, P.P. Further characterization of rat dihydroceramide desaturase: tissue distribution, subcellular localization, and substrate specificity. Lipids 35 (2000) 1117-1125. [PMID: 11104018]

4. Ternes, P., Franke, S., Zähringer, U., Sperling, P. and Heinz, E. Identification and characterization of a sphingolipid Δ4-desaturase family. J. Biol. Chem. 277 (2002) 25512-25518. [PMID: 11937514]

5. Michaelson, L.V., Zäuner, S., Markham, J.E., Haslam, R.P., Desikan, R., Mugford, S., Albrecht, S., Warnecke, D., Sperling, P., Heinz, E. and Napier, J.A. Functional characterization of a higher plant sphingolipid Δ4-desaturase: defining the role of sphingosine and sphingosine-1-phosphate in Arabidopsis. Plant Physiol. 149 (2009) 487-498. [PMID: 18978071]

[EC 1.14.19.17 created 2015]

EC 1.14.19.18

Accepted name: sphingolipid 8-(E)-desaturase

Reaction: a (4E)-sphing-4-enine ceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4E,8E)-sphing-4,8-dienine ceramide + 2 ferricytochrome b5 + 2 H2O

Other name(s): 8-sphingolipid desaturase (ambiguous); 8 fatty acid desaturase (ambiguous); DELTA8-sphingolipid desaturase (ambiguous)

Systematic name: (4E)-sphing-4-enine ceramide,ferrocytochrome b5:oxygen oxidoreductase (8,9-trans dehydrogenating)

Comments: The enzyme, characterized from the yeasts Kluyveromyces lactis and Candida albicans [1] and from the diatom Thalassiosira pseudonana [2], introduces a trans double bond at the 8-position of sphingoid bases in sphingolipids. The enzyme determines the position of the double bond by its distance from the alcohol end of the sphingoid base, and contains a cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase [3]. The homologous enzymes from higher plants, EC 1.14.19.29, sphingolipid 8-(E/Z)-desaturase, act on phytosphinganine (4-hydroxysphinganine) and produces a mixture of trans and cis isomers.

References:

1. Takakuwa, N., Kinoshita, M., Oda, Y. and Ohnishi, M. Isolation and characterization of the genes encoding Δ8-sphingolipid desaturase from Saccharomyces kluyveri and Kluyveromyces lactis. Curr. Microbiol. 45 (2002) 459-461. [PMID: 12402089]

2. Tonon, T., Sayanova, O., Michaelson, L.V., Qing, R., Harvey, D., Larson, T.R., Li, Y., Napier, J.A. and Graham, I.A. Fatty acid desaturases from the microalga Thalassiosira pseudonana. FEBS J. 272 (2005) 3401-3412. [PMID: 15978045]

3. Oura, T. and Kajiwara, S. Disruption of the sphingolipid Δ8-desaturase gene causes a delay in morphological changes in Candida albicans. Microbiology 154 (2008) 3795-3803. [PMID: 19047747]

[EC 1.14.19.18 created 2015]

EC 1.14.19.19

Accepted name: sphingolipid 10-desaturase

Reaction: a (4E,8E)-sphinga-4,8-dienine ceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4E,8E,10E)-sphinga-4,8,10-trienine ceramide + 2 ferricytochrome b5 + 2 H2O

Other name(s): desA (gene name)

Systematic name: a (4E,8E)-sphinga-4,8-dienine ceramide,ferrocytochrome b5:oxygen oxidoreductase (10,11 trans-dehydrogenating)

Comments: The enzyme, characterized from the marine diatom Thalassiosira pseudonana, produces an all-trans product. Similar triunsaturated sphingoid bases are found in some marine invertebrates. The enzyme determines the position of the double bond by its distance from the alcohol end of the sphingoid base, and contains a cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase.

References:

1. Michaelson, L.V., Markham, J.E., Zäuner, S., Matsumoto, M., Chen, M., Cahoon, E.B. and Napier, J.A. Identification of a cytochrome b5-fusion desaturase responsible for the synthesis of triunsaturated sphingolipid long chain bases in the marine diatom Thalassiosira pseudonana. Phytochemistry 90 (2013) 50-55. [PMID: 23510654]

[EC 1.14.19.19 created 2015]

EC 1.14.19.20

Accepted name: Δ7-sterol 5(6)-desaturase

Reaction: a Δ7-sterol + 2 ferrocytochrome b5 + O2 + 2 H+ = a Δ5,7-sterol + 2 ferricytochrome b5 + 2 H2O

For diagram of reaction click here.

Other name(s): lathosterol oxidase; Δ7-sterol Δ5-dehydrogenase; Δ7-sterol 5-desaturase; Δ7-sterol-C5(6)-desaturase; 5-DES; SC5DL (gene name); ERG3 (gene name)

Systematic name: Δ7-sterol,ferrocytochrome b5:oxygen oxidoreductase 5,6-dehydrogenating

Comments: This enzyme, found in eukaryotic organisms, catalyses the introduction of a double bond between the C5 and C6 carbons of the B ring of Δ7-sterols, to yield the corresponding Δ5,7-sterols. The enzymes from yeast, plants and vertebrates act on avenasterol, episterol, and lathosterol, respectively. The enzyme is located at the endoplasmic reticulum and is membrane bound.

References:

1. Dempsey, M.E., Seaton, J.D., Schroepfer, G.J. and Trockman, R.W. The intermediary role of Δ5,7-cholestadien-3β-ol in cholesterol biosynthesis. J. Biol. Chem. 239 (1964) 1381-1387. [PMID: 14189869]

2. Honjo, K., Ishibashi, T. and Imai, Y. Partial purification and characterization of lathosterol 5-desaturase from rat liver microsomes. J. Biochem. 97 (1985) 955-959. [PMID: 4019441]

3. Arthington, B.A., Bennett, L.G., Skatrud, P.L., Guynn, C.J., Barbuch, R.J., Ulbright, C.E. and Bard, M. Cloning, disruption and sequence of the gene encoding yeast C-5 sterol desaturase. Gene 102 (1991) 39-44. [PMID: 1864507]

4. Taton, M. and Rahier, A. Plant sterol biosynthesis: identification and characterization of higher plant Δ7-sterol C5(6)-desaturase. Arch. Biochem. Biophys. 325 (1996) 279-288. [PMID: 8561508]

5. Nishino, H., Nakaya, J., Nishi, S., Kurosawa, T. and Ishibashi, T. Temperature-induced differential kinetic properties between an initial burst and the following steady state in membrane-bound enzymes: studies on lathosterol 5-desaturase. Arch. Biochem. Biophys. 339 (1997) 298-304. [PMID: 9056262]

6. Taton, M., Husselstein, T., Benveniste, P. and Rahier, A. Role of highly conserved residues in the reaction catalyzed by recombinant Δ7-sterol-C5(6)-desaturase studied by site-directed mutagenesis. Biochemistry 39 (2000) 701-711. [PMID: 10651635]

7. Poklepovich, T.J., Rinaldi, M.A., Tomazic, M.L., Favale, N.O., Turkewitz, A.P., Nudel, C.B. and Nusblat, A.D. The cytochrome b5 dependent C-5(6) sterol desaturase DES5A from the endoplasmic reticulum of Tetrahymena thermophila complements ergosterol biosynthesis mutants in Saccharomyces cerevisiae. Steroids 77 (2012) 1313-1320. [PMID: 22982564]

[EC 1.14.19.20 created 1972 as EC 1.3.3.2, transferred 2005 to EC 1.14.21.6, transferred 2015 to EC 1.14.19.20]

EC 1.14.19.21

Accepted name: cholesterol 7-desaturase

Reaction: cholesterol + O2 + NAD(P)H + H+ = cholesta-5,7-dien-3β-ol + NAD(P)+ + 2 H2O

Other name(s): nvd (gene name); daf-36 (gene name)

Systematic name: cholesterol,NAD(P)H:oxygen oxidoreductase (7,8 dehydrogenating)

Comments: The enzyme, characterized from several organisms including the worm Caenorhabditis elegans, the fly Drosophila melanogaster, and the ciliate Tetrahymena thermophila, is a Rieske oxygenase. In insects it participates in the the biosythesis of ecdysteroid hormones. The electrons are transferred from NAD(P)H via an electron transfer chain likely to include ferredoxin reductase and ferredoxin. The enzyme differs from regular desaturases, such as EC 1.14.19.20, 7-sterol 5(6)-desaturase, which are cytochrome b5-dependent and contain the three His-boxes that are typical to most desaturases.

References:

1. Yoshiyama-Yanagawa, T., Enya, S., Shimada-Niwa, Y., Yaguchi, S., Haramoto, Y., Matsuya, T., Shiomi, K., Sasakura, Y., Takahashi, S., Asashima, M., Kataoka, H. and Niwa, R. The conserved Rieske oxygenase DAF-36/Neverland is a novel cholesterol-metabolizing enzyme. J. Biol. Chem. 286 (2011) 25756-25762. [PMID: 21632547]

2. Wollam, J., Magomedova, L., Magner, D.B., Shen, Y., Rottiers, V., Motola, D.L., Mangelsdorf, D.J., Cummins, C.L. and Antebi, A. The Rieske oxygenase DAF-36 functions as a cholesterol 7-desaturase in steroidogenic pathways governing longevity. Aging Cell 10 (2011) 879-884. [PMID: 21749634]

3. Najle, S.R., Nusblat, A.D., Nudel, C.B. and Uttaro, A.D. The sterol-C7 desaturase from the ciliate Tetrahymena thermophila is a Rieske oxygenase, which is highly conserved in animals. Mol Biol Evol 30 (2013) 1630-1643. [PMID: 23603937]

4. Barry, S.M. and Challis, G.L. Mechanism and catalytic diversity of Rieske non-heme iron-dependent oxygenases. ACS Catal. 3 (2013) 2362-2370. [PMID: 24244885]

[EC 1.14.19.21 created 2015]

EC 1.14.19.22

Accepted name: acyl-lipid ω-6 desaturase (cytochrome b5)

Reaction: an oleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a linoleoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O

Other name(s): oleate desaturase (ambiguous); linoleate synthase (ambiguous); oleoyl-CoA desaturase (incorrect); oleoylphosphatidylcholine desaturase (ambiguous); phosphatidylcholine desaturase (ambiguous); n-6 desaturase (ambiguous); FAD2 (gene name)

Systematic name: 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine,ferrocytochrome-b5:oxygen oxidoreductase (12,13 cis-dehydrogenating)

Comments: This microsomal enzyme introduces a cis double bond in fatty acids attached to lipid molecules at a location 6 carbons away from the methyl end of the fatty acid. The distance from the carboxylic acid end of the molecule does not affect the location of the new double bond. The most common substrates are oleoyl groups attached to either the sn-1 or sn-2 position of the glycerol backbone in phosphatidylcholine. cf. EC 1.14.19.23, acyl-lipid ω-6 desaturase (ferredoxin).

References:

1. Pugh, E.L. and Kates, M. Characterization of a membrane-bound phospholipid desaturase system of Candida lipolytica. Biochim. Biophys. Acta 380 (1975) 442-453. [PMID: 166662]

2. Slack, C.R., Roughan, P.G. and Browse, J. Evidence for an oleoyl phosphatidylcholine desaturase in microsomal preparations from cotyledons of safflower (Carthamus tinctorius) seed. Biochem. J. 179 (1979) 649-656. [PMID: 475773]

3. Stymne, S. and Appelqvist, L.-A. The biosynthesis of linoleate from oleoyl-CoA via oleoyl-phosphatidylcholine in microsomes of developing safflower seeds. Eur. J. Biochem. 90 (1978) 223-229. [PMID: 710426]

4. Smith, M.A., Cross, A.R., Jones, O.T., Griffiths, W.T., Stymne, S. and Stobart, K. Electron-transport components of the 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine Δ12-desaturase (Δ12-desaturase) in microsomal preparations from developing safflower (Carthamus tinctorius L.) cotyledons. Biochem. J. 272 (1990) 23-29. [PMID: 2264826]

5. Kearns, E.V., Hugly, S. and Somerville, C.R. The role of cytochrome b5 in Δ12 desaturation of oleic acid by microsomes of safflower (Carthamus tinctorius L.). Arch. Biochem. Biophys. 284 (1991) 431-436. [PMID: 1989527]

6. Miquel, M. and Browse, J. Arabidopsis mutants deficient in polyunsaturated fatty acid synthesis. Biochemical and genetic characterization of a plant oleoyl-phosphatidylcholine desaturase. J. Biol. Chem. 267 (1992) 1502-1509. [PMID: 1730697]

[EC 1.14.19.22 created 1984 as EC 1.3.1.35, transferred 2015 to EC 1.14.19.22]

EC 1.14.19.23

Accepted name: acyl-lipid (n+3)-(Z)-desaturase (ferredoxin)

Reaction: an oleoyl-[glycerolipid] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = a linoleoyl-[glycerolipid] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O

Other name(s): acyl-lipid ω6-desaturase (ferredoxin); oleate desaturase (ambiguous); linoleate synthase (ambiguous); oleoyl-CoA desaturase (ambiguous); oleoylphosphatidylcholine desaturase (ambiguous); phosphatidylcholine desaturase (ambiguous); FAD6 (gene name)

Systematic name: oleoyl-[glycerolipid],ferredoxin:oxygen oxidoreductase (12,13 cis-dehydrogenating)

Comments: This plastidial enzyme is able to insert a cis double bond in monounsaturated fatty acids incorporated into glycerolipids. The enzyme introduces the new bond at a position 3 carbons away from the existing double bond, towards the methyl end of the fatty acid. The native substrates are oleoyl (18:1 Δ9) and (Z)-hexadec-7-enoyl (16:1 Δ7) groups attached to either position of the glycerol backbone in glycerolipids, resulting in the introduction of the second double bond at positions 12 and 10, respectively This prompted the suggestion that this is an ω6 desaturase. However, when acting on palmitoleoyl groups(16:1 Δ9), the enzyme introduces the second double bond at position 12 (ω4), indicating it is an (n+3) desaturase [3]. cf. EC 1.14.19.34, acyl-lipid (9+3)-(E)-desaturase.

References:

1. Schmidt, H. and Heinz, E. Desaturation of oleoyl groups in envelope membranes from spinach chloroplasts. Proc. Natl. Acad. Sci. USA 87 (1990) 9477-9480. [PMID: 11607123]

2. Schmidt, H. and Heinz, E. Involvement of ferredoxin in desaturation of lipid-bound oleate in chloroplasts. Plant Physiol. 94 (1990) 214-220. [PMID: 16667689]

3. Hitz, W.D., Carlson, T.J., Booth, J.R., Jr., Kinney, A.J., Stecca, K.L. and Yadav, N.S. Cloning of a higher-plant plastid ω-6 fatty acid desaturase cDNA and its expression in a cyanobacterium. Plant Physiol. 105 (1994) 635-641. [PMID: 8066133]

4. Falcone, D.L., Gibson, S., Lemieux, B. and Somerville, C. Identification of a gene that complements an Arabidopsis mutant deficient in chloroplast ω 6 desaturase activity. Plant Physiol. 106 (1994) 1453-1459. [PMID: 7846158]

5. Schmidt, H., Dresselhaus, T., Buck, F. and Heinz, E. Purification and PCR-based cDNA cloning of a plastidial n-6 desaturase. Plant Mol. Biol. 26 (1994) 631-642. [PMID: 7948918]

[EC 1.14.19.23 created 2015]

EC 1.14.19.24

Accepted name: acyl-CoA 11-(E)-desaturase

Reaction: an acyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = an (11E)-enoyl-CoA + 2 ferricytochrome b5 + 2 H2O

Systematic name: acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (11,12 trans-dehydrogenating)

Comments: Involved in sex pheromone synthesis in the Lepidoptera (moths). The enzyme from the moth Spodoptera littoralis prefers 13:0 and 14:0 substrates. The product is formed by the stereospecific removal of the pro-R H at C-11 and the pro-S H at C-12. cf. EC 1.14.19.5, acyl-CoA 11-(Z)-desaturase.

References:

1. Foster, S. P. and Roelofs, W. L. Biosynthesis of a monoene and a conjugated diene sex pheromone component of the lightbrown apple moth by 11 desaturation. Experientia 46 (1990) 269-273.

2. Martinez, T., Fabrias, G. and Camps, F. Sex pheromone biosynthetic pathway in Spodoptera littoralis and its activation by a neurohormone. J. Biol. Chem. 265 (1990) 1381-1387. [PMID: 2295634]

3. Navarro, I., Font, I., Fabrias, G. and Camps, F. Stereospecificity of the (E)- and (Z)-11 myristoyl desaturases in the biosynthesis of Spodoptera littoralis sex pheromone. J. Am. Chem. Soc. 119 (1997) 11335-11336.

4. Pinilla, A., Camps, F. and Fabrias, G. Cryptoregiochemistry of the Δ11-myristoyl-CoA desaturase involved in the biosynthesis of Spodoptera littoralis sex pheromone. Biochemistry 38 (1999) 15272-15277. [PMID: 10563812]

[EC 1.14.19.24 created 2000 as EC 1.14.99.31, transferred 2015 to EC 1.14.19.24]

EC 1.14.19.25

Accepted name: acyl-lipid ω-3 desaturase (cytochrome b5)

Reaction: a linoleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = an α-linolenoyl-[glycerolipid] + ferricytochrome b5 + 2 H2O

Glossary: linoleoyl-[glycerolipid] = (9Z,12Z)-octadeca-9,12-dienoyl-[glycerolipid]
α-linolenoyl-[glycerolipid] = (9Z,12Z,15Z)-octadeca-9,12,15-trienoyl-[glycerolipid]

Other name(s): FAD3

Systematic name: (9Z,12Z)-octadeca-9,12-dienoyl-[glycerolipid],ferrocytochrome b5:oxygen oxidoreductase (15,16 cis-dehydrogenating)

Comments: This microsomal enzyme introduces a cis double bond three carbons away from the methyl end of a fatty acid incorporated into a glycerolipid. The distance from the carboxylic acid end of the molecule does not have an effect. The plant enzyme acts on carbon 15 of linoleoyl groups incorporated into both the sn-1 and sn-2 positions of the glycerol backbone of phosphatidylcholine and other phospholipids, converting them into α-linolenoyl groups. The enzyme from the fungus Mortierella alpina acts on γ-linolenoyl and arachidonoyl groups, converting them into stearidonoyl and icosapentaenoyl groups, respectively [3]. cf. EC 1.14.19.35, acyl-lipid ω-3 desaturase (ferredoxin).

References:

1. Browse, J., McConn, M., James, D., Jr. and Miquel, M. Mutants of Arabidopsis deficient in the synthesis of α-linolenate. Biochemical and genetic characterization of the endoplasmic reticulum linoleoyl desaturase. J. Biol. Chem. 268 (1993) 16345-16351. [PMID: 8102138]

2. Arondel, V., Lemieux, B., Hwang, I., Gibson, S., Goodman, H.M. and Somerville, C.R. Map-based cloning of a gene controlling ω-3 fatty acid desaturation in Arabidopsis. Science 258 (1992) 1353-1355. [PMID: 1455229]

3. Sakuradani, E., Abe, T., Iguchi, K. and Shimizu, S. A novel fungal ω3-desaturase with wide substrate specificity from arachidonic acid-producing Mortierella alpina 1S-4. Appl. Microbiol. Biotechnol. 66 (2005) 648-654. [PMID: 15538555]

[EC 1.14.19.25 created 2015]

EC 1.14.19.26

Accepted name: acyl-[acyl-carrier-protein] 6-desaturase

Reaction: palmitoyl-[acyl-carrier protein] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = (6Z)-hexadec-6-enoyl-[acyl-carrier protein] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O

Glossary: (6Z)-hexadec-6-enoyl-[acyl-carrier protein] = Δ6-hexadecenoyl-[acyl-carrier protein] = sapienoyl-[acyl-carrier-protein]
an [acyl-carrier protein] = ACP = [acp]

Other name(s): DELTA6 palmitoyl-ACP desaturase; DELTA6 16:0-ACP desaturase

Systematic name: palmitoyl-[acyl-carrier protein],reduced ferredoxin:oxygen oxidoreductase (6,7 cis-dehydrogenating)

Comments: The enzyme, characterized from the endosperm of the plant Thunbergia alata (black-eyed Susan vine), introduces a cis double bond at carbon 6 of several saturated acyl-[acp]s. It is most active with palmitoyl-[acp] (16:0), but can also act on myristoyl-[acp] (14:0) and stearoyl-[acp] (18:0). The position of the double bond is determined by its distance from the carboxyl end of the fatty acid.

References:

1. Cahoon, E.B., Cranmer, A.M., Shanklin, J. and Ohlrogge, J.B. Δ6 Hexadecenoic acid is synthesized by the activity of a soluble Δ6 palmitoyl-acyl carrier protein desaturase in Thunbergia alata endosperm. J. Biol. Chem. 269 (1994) 27519-27526. [PMID: 7961667]

2. Cahoon, E.B., Lindqvist, Y., Schneider, G. and Shanklin, J. Redesign of soluble fatty acid desaturases from plants for altered substrate specificity and double bond position. Proc. Natl. Acad. Sci. USA 94 (1997) 4872-4877. [PMID: 9144157]

[EC 1.14.19.26 created 2015]

EC 1.14.19.27

Accepted name: sn-2 palmitoyl-lipid 9-desaturase

Reaction: a 1-acyl-2-palmitoyl-[glycerolipid] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = a 1-acyl-2-palmitoleoyl-[glycerolipid] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O

Other name(s): DesC2

Systematic name: 1-acyl-2-palmitoyl-[glycerolipid],ferredoxin:oxygen oxidoreductase (9,10 cis-dehydrogenating)

Comments: The enzyme, characterized from the cyanobacterium Nostoc sp. 36, introduces a cis double bond at carbon 9 of palmitoyl groups (16:0) attached to the sn-2 position of glycerolipids.

References:

1. Chintalapati, S., Prakash, J.S., Gupta, P., Ohtani, S., Suzuki, I., Sakamoto, T., Murata, N. and Shivaji, S. A novel Δ9 acyl-lipid desaturase, DesC2, from cyanobacteria acts on fatty acids esterified to the sn-2 position of glycerolipids. Biochem. J. 398 (2006) 207-214. [PMID: 16689682]

[EC 1.14.19.27 created 2015]

EC 1.14.19.28

Accepted name: sn-1 stearoyl-lipid 9-desaturase

Reaction: a 1-stearoyl-2-acyl-[glycerolipid] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = a 1-oleoyl-2-acyl-[glycerolipid] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O

Other name(s): desC (gene name)

Systematic name: 1-stearoyl-2-acyl-[glycerolipid],ferredoxin:oxygen oxidoreductase (9,10 cis-dehydrogenating)

Comments: The enzyme, characterized from cyanobacteria, introduces a cis double bond at carbon 9 of stearoyl groups (18:0) attached to the sn-1 position of glycerolipids. The enzyme is nonspecific with respect to the polar head group of the glycerolipid.

References:

1. Wada, H., Schmidt, H., Heinz, E. and Murata, N. In vitro ferredoxin-dependent desaturation of fatty acids in cyanobacterial thylakoid membranes. J. Bacteriol. 175 (1993) 544-547. [PMID: 8419301]

2. Higashi, S. and Murata, N. An in vivo study of substrate specificities of acyl-lipid desaturases and acyltransferases in lipid synthesis in Synechocystis PCC6803. Plant Physiol. 102 (1993) 1275-1278. [PMID: 12231903]

3. Sakamoto, T., Wada, H., Nishida, I., Ohmori, M. and Murata, N. Δ9 Acyl-lipid desaturases of cyanobacteria. Molecular cloning and substrate specificities in terms of fatty acids, sn-positions, and polar head groups. J. Biol. Chem. 269 (1994) 25576-25580. [PMID: 7929259]

[EC 1.14.19.28 created 2015]

EC 1.14.19.29

Accepted name: sphingolipid 8-(E/Z)-desaturase

Reaction: (1) a (4R)-4-hydroxysphinganine ceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4R,8E)-4-hydroxysphing-8-enine ceramide + 2 ferricytochrome b5 + 2 H2O
(2) a (4R)-4-hydroxysphinganine ceramide + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4R,8Z)-4-hydroxysphing-8-enine ceramide + 2 ferricytochrome b5 + 2 H2O

Glossary: a (4R)-4-hydroxysphinganine-ceramide = a phytoceramide
(4R)-4-hydroxysphinganine = phytosphinganine

Other name(s): 8-sphingolipid desaturase (ambiguous); 8 fatty acid desaturase (ambiguous); DELTA8-sphingolipid desaturase (ambiguous)

Systematic name: (4R)-4-hydroxysphinganine ceramide,ferrocytochrome b5:oxygen oxidoreductase (8,9 cis/trans-dehydrogenating)

Comments: The enzymes from higher plants convert sphinganine, 4E-sphing-4-enine and phytosphinganine into E/Z-mixtures of Δ8-desaturated products displaying different proportions of geometrical isomers depending on plant species. The nature of the actual desaturase substrate has not yet been studied experimentally. The enzymes contain an N-terminal cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase [1]. The homologous enzymes from some yeasts and diatoms, EC 1.14.19.18, sphingolipid 8-(E)-desaturase, act on sphing-4-enine ceramides and produce only the trans isomer.

References:

1. Sperling, P., Zähringer, U. and Heinz, E. A sphingolipid desaturase from higher plants. Identification of a new cytochrome b5 fusion protein. J. Biol. Chem. 273 (1998) 28590-28596. [PMID: 9786850]

2. Sperling, P., Blume, A., Zähringer, U., and Heinz, E. Further characterization of Δ8-sphingolipid desaturases from higher plants. Biochem Soc Trans. 28 (2000) 638-641.

3. Sperling, P., Libisch, B., Zähringer, U., Napier, J.A. and Heinz, E. Functional identification of a Δ8-sphingolipid desaturase from Borago officinalis. Arch. Biochem. Biophys. 388 (2001) 293-298. [PMID: 11368168]

4. Beckmann, C., Rattke, J., Oldham, N.J., Sperling, P., Heinz, E. and Boland, W. Characterization of a Δ8-sphingolipid desaturase from higher plants: a stereochemical and mechanistic study on the origin of E,Z isomers. Angew. Chem. Int. Ed. Engl. 41 (2002) 2298-2300. [PMID: 12203571]

5. Ryan, P.R., Liu, Q., Sperling, P., Dong, B., Franke, S. and Delhaize, E. A higher plant Δ8 sphingolipid desaturase with a preference for (Z)-isomer formation confers aluminum tolerance to yeast and plants. Plant Physiol. 144 (2007) 1968-1977. [PMID: 17600137]

6. Oura, T. and Kajiwara, S. Disruption of the sphingolipid Δ8-desaturase gene causes a delay in morphological changes in Candida albicans. Microbiology 154 (2008) 3795-3803. [PMID: 19047747]

7. Chen, M., Markham, J.E. and Cahoon, E.B. Sphingolipid Δ8 unsaturation is important for glucosylceramide biosynthesis and low-temperature performance in Arabidopsis. Plant J. 69 (2012) 769-781. [PMID: 22023480]

[EC 1.14.19.29 created 2015]

EC 1.14.19.30

Accepted name: acyl-lipid (8-3)-desaturase

Reaction: (1) an (8Z,11Z,14Z)-icosa-8,11,14-trienoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (5Z,8Z,11Z,14Z)-icosatetra-5,8,11,14-tetraenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) an (8Z,11Z,14Z,17Z)-icosa-8,11,14,17-tetraenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O

Glossary: (8Z,11Z,14Z)-icosa-8,11,14-trienoate = di-homo-γ-linolenate
(5Z,8Z,11Z,14Z)-icosa-8,11,14-trienoate = arachidonate

Other name(s): acyl-lipid 5-desaturase; Δ5-fatty-acid desaturase; DES5 (gene name); D5des (gene name); FADS1

Systematic name: Δ8 acyl-lipid,ferrocytochrome b5:oxygen oxidoreductase (5,6 cis-dehydrogenating)

Comments: The enzyme, which has been characterized from multiple organisms including the moss Physcomitrella patens, the marine microalga Rebecca salina, and the filamentous fungus Mortierella alpina, introduces a cis double bond at the 5-position in 20-carbon polyunsaturated fatty acids incorporated in a glycerolipid that contain a Δ8 double bond. The enzyme contains a cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase, and does not require an external cytochrome.

References:

1. Michaelson, L.V., Lazarus, C.M., Griffiths, G., Napier, J.A. and Stobart, A.K. Isolation of a Δ5-fatty acid desaturase gene from Mortierella alpina. J. Biol. Chem. 273 (1998) 19055-19059. [PMID: 9668087]

2. Kaewsuwan, S., Cahoon, E.B., Perroud, P.F., Wiwat, C., Panvisavas, N., Quatrano, R.S., Cove, D.J. and Bunyapraphatsara, N. Identification and functional characterization of the moss Physcomitrella patens Δ5-desaturase gene involved in arachidonic and eicosapentaenoic acid biosynthesis. J. Biol. Chem. 281 (2006) 21988-21997. [PMID: 16728405]

3. Zhou, X.R., Robert, S.S., Petrie, J.R., Frampton, D.M., Mansour, M.P., Blackburn, S.I., Nichols, P.D., Green, A.G. and Singh, S.P. Isolation and characterization of genes from the marine microalga Pavlova salina encoding three front-end desaturases involved in docosahexaenoic acid biosynthesis. Phytochemistry 68 (2007) 785-796. [PMID: 17291553]

[EC 1.14.19.30 created 2015]

EC 1.14.19.31

Accepted name: acyl-lipid (7-3)-desaturase

Reaction: (1) a (7Z,10Z,13Z,16Z,19Z)-docosa-7,10,13,16,19-pentaenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) a (7Z,10Z,13Z,16Z)-docosa-7,10,13,16-tetraenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O

Glossary: (7Z,10Z,13Z,16Z)-docosa-7,10,13,16-tetraenoate = adrenate

Other name(s): D4Des (gene name); des1 (gene name); CrΔ4FAD (gene name); acyl-lipid 4-desaturase

Systematic name: Δ7 acyl-lipid,ferrocytochrome b5:oxygen oxidoreductase (4,5 cis-dehydrogenating)

Comments: The enzymes from several algae introduce a cis double bond at the 4-position in 22-carbon polyunsaturated fatty acids that contain a Δ7 double bond. The enzyme from the fresh water alga Chlamydomonas reinhardtii acts on the 16 carbon fatty acid (7Z,10Z,13Z)-hexadeca-7,10,13-trienoate [5]. The enzyme contains an N-terminal cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase, and does not require an external cytochrome.

References:

1. Qiu, X., Hong, H. and MacKenzie, S.L. Identification of a Δ4 fatty acid desaturase from Thraustochytrium sp. involved in the biosynthesis of docosahexanoic acid by heterologous expression in Saccharomyces cerevisiae and Brassica juncea. J. Biol. Chem. 276 (2001) 31561-31566. [PMID: 11397798]

2. Tonon, T., Harvey, D., Larson, T.R. and Graham, I.A. Identification of a very long chain polyunsaturated fatty acid Δ4-desaturase from the microalga Pavlova lutheri. FEBS Lett. 553 (2003) 440-444. [PMID: 14572666]

3. Meyer, A., Cirpus, P., Ott, C., Schlecker, R., Zähringer, U. and Heinz, E. Biosynthesis of docosahexaenoic acid in Euglena gracilis: biochemical and molecular evidence for the involvement of a Δ4-fatty acyl group desaturase. Biochemistry 42 (2003) 9779-9788. [PMID: 12911321]

4. Zhou, X.R., Robert, S.S., Petrie, J.R., Frampton, D.M., Mansour, M.P., Blackburn, S.I., Nichols, P.D., Green, A.G. and Singh, S.P. Isolation and characterization of genes from the marine microalga Pavlova salina encoding three front-end desaturases involved in docosahexaenoic acid biosynthesis. Phytochemistry 68 (2007) 785-796. [PMID: 17291553]

5. Zäuner, S., Jochum, W., Bigorowski, T. and Benning, C. A cytochrome b5-containing plastid-located fatty acid desaturase from Chlamydomonas reinhardtii. Eukaryot Cell 11 (2012) 856-863. [PMID: 22562471]

[EC 1.14.19.31 created 2015]

EC 1.14.19.32

Accepted name: palmitoyl-CoA 14-(E/Z)-desaturase

Reaction: (1) palmitoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = (14E)-hexadec-14-enoyl-CoA + 2 ferricytochrome b5 + 2 H2O
(2) palmitoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = (14Z)-hexadec-14-enoyl-CoA + 2 ferricytochrome b5 + 2 H2O

Systematic name: palmitoyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (14,15 cis/trans-dehydrogenating)

Comments: The enzyme, found in the moth Ostrinia furnacalis (Asian corn borer), produces a mixture of (E)- and (Z)- isomers. The products are subsequently truncated by partial β-oxidation to a blend of 12(E/Z)-tetradec-12-enoyl-CoA, which are converted to the species-specific sex pheromones (E)- and (Z)-tetradec-12-enoyl acetates.

References:

1. Roelofs, W.L., Liu, W., Hao, G., Jiao, H., Rooney, A.P. and Linn, C.E., Jr. Evolution of moth sex pheromones via ancestral genes. Proc. Natl. Acad. Sci. USA 99 (2002) 13621-13626. [PMID: 12237399]

2. Xue, B., Rooney, A.P., Kajikawa, M., Okada, N. and Roelofs, W.L. Novel sex pheromone desaturases in the genomes of corn borers generated through gene duplication and retroposon fusion. Proc. Natl. Acad. Sci. USA 104 (2007) 4467-4472. [PMID: 17360547]

3. Sakai, R., Fukuzawa, M., Nakano, R., Tatsuki, S. and Ishikawa, Y. Alternative suppression of transcription from two desaturase genes is the key for species-specific sex pheromone biosynthesis in two Ostrinia moths. Insect Biochem. Mol. Biol. 39 (2009) 62-67. [PMID: 18992816]

[EC 1.14.19.32 created 2015]

EC 1.14.19.33

Accepted name: Δ12 acyl-lipid conjugase (11E,13E-forming)

Reaction: (1) a linoleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = an α-eleostearoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) a γ-linolenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = an α-parinaroyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O

Glossary: α-eleostearate = (9Z,11E,13E)-octadeca-9,11,13-trienoate
α-parinarate = (9Z,11E,13E,15Z)-octadeca-9,11,13,15-tetraenoate
γ-linolenic acid = (6Z,9Z,12Z)-octadeca-6,9,12-trienoic acid
linoleic acid = (9Z,12Z)-octadeca-9,12-dienoic acid

Other name(s): fatty acid Δ12-conjugase (ambiguous); FADX (gene name)

Systematic name: Δ12 acyl-lipid,ferrocytochrome-b5:oxygen 11,14 allylic oxidase (11E,13E-forming)

Comments: The enzyme, characterized from the plants Impatiens balsamina, Momordica charantia (bitter gourd) and Vernicia fordii (tung tree), converts a single cis double bond at carbon 12 to two conjugated trans bonds at positions 11 and 13. The enzyme from Vernicia fordii can also act as a 12(E) desaturase when acting on the monounsaturated fatty acids oleate and palmitoleate. cf. EC 1.14.19.16, linoleoyl-lipid Δ12 conjugase (11E,13Z-forming).

References:

1. Cahoon, E.B., Carlson, T.J., Ripp, K.G., Schweiger, B.J., Cook, G.A., Hall, S.E. and Kinney, A.J. Biosynthetic origin of conjugated double bonds: production of fatty acid components of high-value drying oils in transgenic soybean embryos. Proc. Natl. Acad. Sci. USA 96 (1999) 12935-12940. [PMID: 10536026]

2. Dyer, J.M., Chapital, D.C., Kuan, J.C., Mullen, R.T., Turner, C., McKeon, T.A. and Pepperman, A.B. Molecular analysis of a bifunctional fatty acid conjugase/desaturase from tung. Implications for the evolution of plant fatty acid diversity. Plant Physiol. 130 (2002) 2027-2038. [PMID: 12481086]

[EC 1.14.19.33 created 2015]

EC 1.14.19.34

Accepted name: acyl-lipid (9+3)-(E)-desaturase

Reaction: (1) an oleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (9Z,12E)-octadeca-9,12-dienoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) a palmitoleoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (9Z,12E)-hexadeca-9,12-dienoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O

Other name(s): acyl-lipid 12-(E)-desaturase; DsFAD2-1; FADX

Systematic name: Δ9 acyl-lipid,ferrocytochrome b5:oxygen oxidoreductase (12,13 trans-dehydrogenating)

Comments: The enzymes from the plants Dimorphotheca sinuata (African daisy) and Vernicia fordii (tung oil tree) insert a trans double bond in position C-12 of oleate and palmitoleate incorporated into glycerolipids. The enzyme introduces the new double bond at a position three carbons away from an existing double bond at position 9, towards the methyl end of the fatty acid. The enzyme from tung oil tree also possesses the activity of EC 1.14.19.33, Δ12 acyl-lipid conjugase.

References:

1. Dyer, J.M., Chapital, D.C., Kuan, J.C., Mullen, R.T., Turner, C., McKeon, T.A. and Pepperman, A.B. Molecular analysis of a bifunctional fatty acid conjugase/desaturase from tung. Implications for the evolution of plant fatty acid diversity. Plant Physiol. 130 (2002) 2027-2038. [PMID: 12481086]

2. Cahoon, E.B. and Kinney, A.J. Dimorphecolic acid is synthesized by the coordinate activities of two divergent Δ12-oleic acid desaturases. J. Biol. Chem. 279 (2004) 12495-12502. [PMID: 14718523]

[EC 1.14.19.34 created 2015]

EC 1.14.19.35

Accepted name: sn-2 acyl-lipid ω-3 desaturase (ferredoxin)

Reaction: (1) a (7Z,10Z)-hexadeca-7,10-dienoyl-[glycerolipid] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = a (7Z,10Z,13Z)-hexadeca-7,10,13-trienoyl-[glycerolipid] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
(2) a linoleoyl-[glycerolipid] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = an α-linolenoyl-[glycerolipid] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O

Glossary: (9Z,12Z)-octadeca-9,12-dienoyl-[glycerolipid] = linoleoyl-[glycerolipid]
(9Z,12Z,15Z)-octadeca-9,12,15-trienoyl-[glycerolipid] = α-linolenoyl-[glycerolipid]

Other name(s): FAD7; FAD8

Systematic name: (7Z,10Z)-hexadeca-7,10-dienoyl-[glycerolipid],ferredoxin:oxygen oxidoreductase (13,14 cis-dehydrogenating)

Comments: This plastidial enzyme desaturates 16:2 fatty acids attached to the sn-2 position of glycerolipids to 16:3 fatty acids, and converts18:2 to 18:3 in both the sn-1 and sn-2 positions. It acts on all 16:2- or 18:2-containing chloroplast membrane lipids, including phosphatidylglycerol, monogalactosyldiacylglycerol, digalactosyldiaclyglycerol, and sulfoquinovosyldiacylglycerol. The enzyme introduces a cis double bond at a location 3 carbons away from the methyl end of the fatty acid. The distance from the carboxylic acid end of the molecule does not affect the location of the new double bond. cf. EC 1.14.19.25, acyl-lipid ω-3 desaturase (cytochrome b5) and EC 1.14.19.36, sn-1 acyl-lipid ω-3 desaturase (ferredoxin).

References:

1. Iba, K., Gibson, S., Nishiuchi, T., Fuse, T., Nishimura, M., Arondel, V., Hugly, S. and Somerville, C. A gene encoding a chloroplast ω-3 fatty acid desaturase complements alterations in fatty acid desaturation and chloroplast copy number of the fad7 mutant of Arabidopsis thaliana. J. Biol. Chem. 268 (1993) 24099-24105. [PMID: 8226956]

2. McConn, M., Hugly, S., Browse, J. and Somerville, C. A mutation at the fad8 locus of Arabidopsis identifies a second chloroplast ω-3 desaturase. Plant Physiol. 106 (1994) 1609-1614. [PMID: 12232435]

3. Venegas-Caleron, M., Muro-Pastor, A.M., Garces, R. and Martinez-Force, E. Functional characterization of a plastidial ω-3 desaturase from sunflower (Helianthus annuus) in cyanobacteria. Plant Physiol. Biochem. 44 (2006) 517-525. [PMID: 17064923]

[EC 1.14.19.35 created 2015]

EC 1.14.19.36

Accepted name: sn-1 acyl-lipid ω-3 desaturase (ferredoxin)

Reaction: (1) a 1-γ-linolenoyl-2-acyl-[glycerolipid] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = a 1-stearidonoyl-2-acyl-[glycerolipid] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
(2) a 1-linoleoyl-2-acyl-[glycerolipid] + 2 reduced ferredoxin [iron-sulfur] cluster + O2 + 2 H+ = a 1-α-linolenoyl-2-acyl-[glycerolipid] + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O

Glossary: stearidonic acid = (6Z,9Z,12Z,15Z)-octadeca-6,9,12,15-tetraenoic acid

Other name(s): desB (gene name)

Systematic name: 1-γ-linolenoyl-2-acyl-[glycerolipid],ferredoxin:oxygen oxidoreductase (15,16 cis-dehydrogenating)

Comments: The enzyme, characterized from cyanobacteria, introduces a cis double bond at carbon 15 of linoleoyl and γ-linolenoyl groups attached to the sn-1 position of glycerolipids. The enzyme is an ω desaturase, and determines the location of the double bond by counting three carbons from the methyl end of the fatty acid. It is nonspecific with respect to the polar head group of the glycerolipid. cf. EC 1.14.19.35, sn-2 acyl-lipid ω-3 desaturase (ferredoxin).

References:

1. Sakamoto, T., Los, D.A., Higashi, S., Wada, H., Nishida, I., Ohmori, M. and Murata, N. Cloning of ω3 desaturase from cyanobacteria and its use in altering the degree of membrane-lipid unsaturation. Plant Mol. Biol. 26 (1994) 249-263. [PMID: 7524725]

[EC 1.14.19.36 created 2015]

[EC 1.14.21.6 Transferred entry: lathosterol oxidase. Now EC 1.14.19.20, Δ7-sterol 5(6)-desaturase (EC 1.14.21.6 created 1972 as EC 1.3.3.2, transferred 2005 to EC 1.14.21.6, deleted 2015)]

[EC 1.14.99.31 Transferred entry: myristoyl-CoA 11-(E) desaturase. Now classified as EC 1.14.19.24, myristoyl-CoA 11-(E) desaturase (EC 1.14.99.31 created 2000, deleted 2015)]

[EC 1.14.99.32 Transferred entry: myristoyl-CoA 11-(Z) desaturase. Now classified as EC 1.14.19.5, acyl-CoA 11-(Z)-desaturase. (EC 1.14.99.32 created 2000, deleted 2015)]

EC 1.14.99.50

Accepted name: γ-glutamyl hercynylcysteine S-oxide synthase

Reaction: hercynine + γ-L-glutamyl-L-cysteine + O2 = γ-L-glutamyl-S-(hercyn-2-yl)-L-cysteine S-oxide + H2O

For diagram of reaction click here.

Glossary: hercynine = Nα,Nα,Nα-trimethyl-L-histidine

Other name(s): EgtB

Systematic name: hercynine,γ-L-glutamyl-L-cysteine:oxygen oxidoreductase [γ-L-glutamyl-S-(hercyn-2-yl)-L-cysteine S-oxide-forming]

Comments: Requires Fe2+ for activity. The enzyme, found in bacteria, is specific for both hercynine and γ-L-glutamyl-L-cysteine. It is part of the biosynthesis pathway of ergothioneine.

References:

1. Seebeck, F.P. In vitro reconstitution of Mycobacterial ergothioneine biosynthesis. J. Am. Chem. Soc. 132 (2010) 6632-6633. [PMID: 20420449]

2. Pluskal, T., Ueno, M. and Yanagida, M. Genetic and metabolomic dissection of the ergothioneine and selenoneine biosynthetic pathway in the fission yeast, S. pombe, and construction of an overproduction system. PLoS One 9 (2014) e97774. [PMID: 24828577]

[EC 1.14.99.50 created 2015]

EC 1.14.99.51

Accepted name: hercynylcysteine S-oxide synthase

Reaction: hercynine + L-cysteine + O2 = S-(hercyn-2-yl)-L-cysteine S-oxide + H2O

For diagram of reaction click here.

Glossary: hercynine = Nα,Nα,Nα-trimethyl-L-histidine

Other name(s): Egt1; Egt-1

Systematic name: hercynine,L-cysteine:oxygen [S-(hercyn-2-yl)-L-cysteine S-oxide-forming]

Comments: Requires Fe2+ for activity. The enzyme, found in fungal species, is part of a fusion protein that also has the the activity of EC 2.1.1.44, L-histidine Nα-methyltransferase. It is part of the biosynthesis pathway of ergothioneine. The enzyme can also use L-selenocysteine to produce hercynylselenocysteine, which can be converted to selenoneine.

References:

1. Pluskal, T., Ueno, M. and Yanagida, M. Genetic and metabolomic dissection of the ergothioneine and selenoneine biosynthetic pathway in the fission yeast, S. pombe, and construction of an overproduction system. PLoS One 9 (2014) e97774. [PMID: 24828577]

[EC 1.14.99.51 created 2015]

EC 1.14.99.52

Accepted name: L-cysteinyl-L-histidinylsulfoxide synthase

Reaction: L-histidine + L-cysteine + O2 = S-(L-histidin-5-yl)-L-cysteine S-oxide + H2O

For diagram of reaction click here.

Glossary: S-(L-histidin-5-yl)-L-cysteine S-oxide = 5-{[(2R)-2-amino-2-carboxyethyl]sulfinyl}-L-histidine

Other name(s): OvoA

Systematic name: L-histidine,L-cysteine:oxygen [S-(L-histidin-5-yl)-L-cysteine S-oxide-forming]

Comments: Requires Fe2+ for activity. The enzyme participates in ovothiol biosynthesis. It also has some activity as EC 1.13.11.20, cysteine dioxygenase, and can perform the reaction of EC 1.14.99.50, γ-glutamyl hercynylcysteine sulfoxide synthase, albeit with low activity [4].

References:

1. Braunshausen, A. and Seebeck, F.P. Identification and characterization of the first ovothiol biosynthetic enzyme. J. Am. Chem. Soc. 133 (2011) 1757-1759. [PMID: 21247153]

2. Song, H., Leninger, M., Lee, N. and Liu, P. Regioselectivity of the oxidative C-S bond formation in ergothioneine and ovothiol biosyntheses. Org. Lett. 15 (2013) 4854-4857. [PMID: 24016264]

3. Mashabela, G.T. and Seebeck, F.P. Substrate specificity of an oxygen dependent sulfoxide synthase in ovothiol biosynthesis. Chem. Commun. (Camb.) 49 (2013) 7714-7716. [PMID: 23877651]

4. Song, H., Her, A.S., Raso, F., Zhen, Z., Huo, Y. and Liu, P. Cysteine oxidation reactions catalyzed by a mononuclear non-heme iron enzyme (OvoA) in ovothiol biosynthesis. Org. Lett. 16 (2014) 2122-2125. [PMID: 24684381]

[EC 1.14.99.52 created 2015]

EC 1.18.1.8

Accepted name: ferredoxin-NAD+ oxidoreductase (Na+-transporting)

Reaction: 2 reduced ferredoxin [iron-sulfur] cluster + NAD+ + H+ + Na+[side 1] = 2 oxidized ferredoxin [iron-sulfur] cluster + NADH + Na+[side 2]

Other name(s): Rnf complex (ambiguous); Na+-translocating ferredoxin:NAD+ oxidoreductase

Systematic name: ferredoxin:NAD+ oxidoreductase (Na+-transporting)

Comments: This iron-sulfur and flavin-containing electron transport complex, isolated from the bacterium Acetobacterium woodii, couples the energy from reduction of NAD+ by ferredoxin to pumping sodium ions out of the cell, generating a gradient across the cytoplasmic membrane.

References:

1. Biegel, E., Schmidt, S. and Muller, V. Genetic, immunological and biochemical evidence for a Rnf complex in the acetogen Acetobacterium woodii. Environ Microbiol 11 (2009) 1438-1443. [PMID: 19222539]

2. Biegel, E. and Muller, V. Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase. Proc. Natl. Acad. Sci. USA 107 (2010) 18138-18142. [PMID: 20921383]

3. Hess, V., Schuchmann, K. and Muller, V. The ferredoxin:NAD+ oxidoreductase (Rnf) from the acetogen Acetobacterium woodii requires Na+ and is reversibly coupled to the membrane potential. J. Biol. Chem. 288 (2013) 31496-31502. [PMID: 24045950]

[EC 1.18.1.8 created 2015]

EC 1.21.1.1

Accepted name: iodotyrosine deiodinase

Reaction: L-tyrosine + 2 NADP+ + 2 iodide = 3,5-diiodo-L-tyrosine + 2 NADPH + 2 H+ (overall reaction)
(1a) L-tyrosine + NADP+ + iodide = 3-iodo-L-tyrosine + NADPH + H+
(1b) 3-iodo-L-tyrosine + NADP+ + iodide = 3,5-diiodo-L-tyrosine + NADPH + H+

Other name(s): iodotyrosine dehalogenase 1; DEHAL1

Systematic name: L-tyrosine,iodide:NADP+ oxidoreductase (iodinating)

Comments: The enzyme activity has only been demonstrated in the direction of 3-deiodination. Present in a transmembrane flavoprotein. Requires FMN.

References:

1. Rosenberg, I.N. Purification of iodotyrosine deiodinase from bovine thyroid. Metabolism 19 (1970) 785-798. [PMID: 4394169]

2. Gnidehou, S., Caillou, B., Talbot, M., Ohayon, R., Kaniewski, J., Noel-Hudson, M.S., Morand, S., Agnangji, D., Sezan, A., Courtin, F., Virion, A. and Dupuy, C. Iodotyrosine dehalogenase 1 (DEHAL1) is a transmembrane protein involved in the recycling of iodide close to the thyroglobulin iodination site. FASEB J. 18 (2004) 1574-1576. [PMID: 15289438]

3. Friedman, J.E., Watson, J.A., Jr., Lam, D.W. and Rokita, S.E. Iodotyrosine deiodinase is the first mammalian member of the NADH oxidase/flavin reductase superfamily. J. Biol. Chem. 281 (2006) 2812-2819. [PMID: 16316988]

4. Thomas, S.R., McTamney, P.M., Adler, J.M., Laronde-Leblanc, N. and Rokita, S.E. Crystal structure of iodotyrosine deiodinase, a novel flavoprotein responsible for iodide salvage in thyroid glands. J. Biol. Chem. 284 (2009) 19659-19667. [PMID: 19436071]

[EC 1.21.1.1 created 2010 as EC 1.22.1.1 transfered 2015 to EC 1.21.1.1]

EC 1.21.1.2

Accepted name: 2,4-dichlorobenzoyl-CoA reductase

Reaction: 4-chlorobenzoyl-CoA + NADP+ + chloride = 2,4-dichlorobenzoyl-CoA + NADPH + H+

Systematic name: 4-chlorobenzoyl-CoA:NADP+ oxidoreductase (halogenating)

Comments: The enzyme, characterized from Corynebacterium strains able to grow on 2,4-dichlorobenzoate, forms part of the 2,4-dichlorobenzoate degradation pathway.

References:

1. Romanov, V. and Hausinger, R.P. NADPH-dependent reductive ortho dehalogenation of 2,4-dichlorobenzoic acid in Corynebacterium sepedonicum KZ-4 and Coryneform bacterium strain NTB-1 via 2,4-dichlorobenzoyl coenzyme A. J. Bacteriol. 178 (1996) 2656-2661. [PMID: 8626335]

[EC 1.21.1.2 created 2000 as EC 1.3.1.63, modified 2011, transferred 2015 to EC 1.21.1.2]

EC 1.21.99.3

Accepted name: thyroxine 5-deiodinase

Reaction: 3,3',5'-triiodo-L-thyronine + iodide + acceptor + H+ = L-thyroxine + reduced acceptor

Other name(s): diiodothyronine 5'-deiodinase (ambiguous); iodothyronine 5-deiodinase; iodothyronine inner ring monodeiodinase; type III iodothyronine deiodinase

Systematic name: 3,3',5'-triiodo-L-thyronine,iodide:acceptor oxidoreductase (iodinating)

Comments: The enzyme activity has only been demonstrated in the direction of 5-deiodination. This removal of the 5-iodine, i.e. from the inner ring, largely inactivates the hormone thyroxine.

References:

1. Chopra, I.J. and Teco, G.N.C. Characteristics of inner ring (3 or 5) monodeiodination of 3,5-diiodothyronine in rat liver: evidence suggesting marked similarities of inner and outer ring deiodinases for iodothyronines. Endocrinology 110 (1982) 89-97. [PMID: 7053997]

2. Körhle, J. Iodothyronine deiodinases. Methods Enzymol. 347 (2002) 125-167. [PMID: 11898402]

[EC 1.21.99.3 created 2003 as EC 1.97.1.11, transferred 2015 to EC 1.21.99.3]

[EC 1.22.1.1 Transferred entry: iodotyrosine deiodinase. Now EC 1.21.1.1, iodotyrosine deiodinase (EC 1.22.1.1 created 2010, deleted 2015)]

[EC 1.97.1.11 Transferred entry: thyroxine 5-deiodinase. Now EC 1.21.99.3 thyroxine 5-deiodinase. (EC 1.97.1.11 created 2003, deleted 2015)]

EC 2.1.1.316

Accepted name: mitomycin 6-O-methyltransferase

Reaction: (1) S-adenosyl-L-methionine + 6-demethylmitomycin A = S-adenosyl-L-homocysteine + mitomycin A
(2) S-adenosyl-L-methionine + 6-demethylmitomycin B = S-adenosyl-L-homocysteine + mitomycin B

Glossary: mitomycin A = [(1aS,8S,8aR,8bS)-5-methyl-6,8a-dimethoxy-4,7-dioxo-1,1a,2,4,7,8,8a,8b-octahydroazirino[2',3':3,4]pyrrolo[1,2-a]indol-8-yl]methyl carbamate
mitomycin B = [(1aS,8S,8aR,8bS)-8a-hydroxy-5-methyl-6-methoxy-4,7-dioxo-1,1a,2,4,7,8,8a,8b-octahydroazirino[2',3':3,4]pyrrolo[1,2-a]indol-8-yl]methyl carbamate

Other name(s): MmcR; mitomycin 7-O-methyltransferase (incorrect); S-adenosyl-L-methionine:7-demethylmitomycin-A 7-O-methyltransferase (incorrect)

Systematic name: S-adenosyl-L-methionine:6-demethylmitomycin-A 6-O-methyltransferase

Comments: The enzyme, characterized from the bacterium Streptomyces lavendulae, is involved in the biosynthesis of the quinone-containing antibiotics mitomycin A and mitomycin B.

References:

1. Gruschow, S., Chang, L.C., Mao, Y. and Sherman, D.H. Hydroxyquinone O-methylation in mitomycin biosynthesis. J. Am. Chem. Soc. 129 (2007) 6470-6476. [PMID: 17461583]

2. Singh, S., Chang, A., Goff, R.D., Bingman, C.A., Gruschow, S., Sherman, D.H., Phillips, G.N., Jr. and Thorson, J.S. Structural characterization of the mitomycin 7-O-methyltransferase. Proteins 79 (2011) 2181-2188. [PMID: 21538548]

[EC 2.1.1.316 created 2015]

EC 2.1.1.317

Accepted name: sphingolipid C9-methyltransferase

Reaction: S-adenosyl-L-methionine + a (4E,8E)-sphinga-4,8-dienine ceramide = S-adenosyl-L-homocysteine + a 9-methyl-(4E,8E)-sphinga-4,8-dienine ceramide

Systematic name: S-adenosyl-L-methionine:(4E,8E)-sphinga-4,8-dienine ceramide C-methyltransferase

Comments: The enzyme, characterized from the fungi Komagataella pastoris and Fusarium graminearum, acts only on ceramides and has no activity with free sphingoid bases or glucosylceramides.

References:

1. Ternes, P., Sperling, P., Albrecht, S., Franke, S., Cregg, J.M., Warnecke, D. and Heinz, E. Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling. J. Biol. Chem. 281 (2006) 5582-5592. [PMID: 16339149]

2. Ramamoorthy, V., Cahoon, E.B., Thokala, M., Kaur, J., Li, J. and Shah, D.M. Sphingolipid C-9 methyltransferases are important for growth and virulence but not for sensitivity to antifungal plant defensins in Fusarium graminearum. Eukaryot Cell 8 (2009) 217-229. [PMID: 19028992]

[EC 2.1.1.317 created 2015]

EC 2.1.1.318

Accepted name: [trehalose-6-phosphate synthase]-L-cysteine S-methyltransferase

Reaction: S-adenosyl-L-methionine + [trehalose-6-phosphate synthase]-L-cysteine = S-adenosyl-L-homocysteine + [trehalose-6-phosphate synthase]-S-methyl-L-cysteine

Systematic name: S-adenosyl-L-methionine:[trehalose-6-phosphate synthase]-L-cysteine S-methyltransferase

Comments: The enzyme, characterized from the yeast Saccharomyces cerevisiae, enhances the activity of EC 2.4.1.15, trehalose-6-phosphate synthase, resulting in elevating the levels of trehalose in the cell and contributing to stationary phase survival. In vitro the enzyme performs S-methylation of L-cysteine residues of various protein substrates.

References:

1. Sengupta, S., Banerjee, S., Lahiri, S., Dutta, T., Dhar, T.K. and Ghosh, A.K. Purification, characterization, sequencing and molecular cloning of a novel cysteine methyltransferase that regulates trehalose-6-phosphate synthase from Saccharomyces cerevisiae. Biochim. Biophys. Acta 1840 (2014) 1861-1871. [PMID: 24412193]

[EC 2.1.1.318 created 2015]

*EC 2.3.1.82

Accepted name: aminoglycoside 6'-N-acetyltransferase

Reaction: acetyl-CoA + kanamycin-B = CoA + N6'-acetylkanamycin-B

Glossary: kanamycin

Other name(s): aminoglycoside N6'-acetyltransferase; aminoglycoside-6'-acetyltransferase; aminoglycoside-6-N-acetyltransferase; kanamycin acetyltransferase

Systematic name: acetyl-CoA:kanamycin-B N6'-acetyltransferase

Comments: The antibiotics kanamycin A, kanamycin B, neomycin, gentamicin C1a, gentamicin C2 and sisomicin are substrates. The antibiotic tobramycin, but not paromomycin, can also act as acceptor. The 6-amino group of the purpurosamine ring is acetylated.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 56467-65-3

References:

1. le Goffic, F. and Martel, A. La résistance aux aminosides provoquée par une isoenzyme la kanamycine acétyltransférase. Biochimie 56 (1974) 893-897. [PMID: 4614862]

2. Benveniste, R. and Davies, J.E. Enzymatic acetylation of aminoglycoside antibiotics by Escherichia coli carrying an R factor. Biochemistry 10 (1971) 1787-1796. [PMID: 4935296]

3. Dowding, J.E. Mechanisms of gentamicin resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 11 (1977) 47-50. [PMID: 836013]

[EC 2.3.1.82 created 1976 as EC 2.3.1.55, transferred 1999 to EC 2.3.1.82, modified 1999, modified 2015]

[EC 2.3.1.119 Deleted entry: icosanoyl-CoA synthase. Now covered by EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase, and EC 1.3.1.193, very-long-chain enoyl-CoA reductase. (EC 2.3.1.119 created 1990, deleted 2015)]

*EC 2.3.1.169

Accepted name: CO-methylating acetyl-CoA synthase

Reaction: acetyl-CoA + a [Co(I) corrinoid Fe-S protein] = CO + CoA + a [methyl-Co(III) corrinoid Fe-S protein]

Systematic name: acetyl-CoA:corrinoid protein O-acetyltransferase

Comments: Contains nickel, copper and iron-sulfur clusters. Involved, together with EC 1.2.7.4, carbon-monoxide dehydrogenase (ferredoxin), in the synthesis of acetyl-CoA from CO2 and H2.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 176591-19-8

References:

1. Ragsdale, S.W. and Wood, H.G. Acetate biosynthesis by acetogenic bacteria. Evidence that carbon monoxide dehydrogenase is the condensing enzyme that catalyzes the final steps of the synthesis. J. Biol. Chem. 260 (1985) 3970-3977. [PMID: 2984190]

2. Doukov, T.I., Iverson, T., Seravalli, J., Ragsdale, S.W. and Drennan, C.L. A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Science 298 (2002) 567-572. [PMID: 12386327]

[EC 2.3.1.169 created 2003, modified 2015]

EC 2.3.1.247

Accepted name: 3-keto-5-aminohexanoate cleavage enzyme

Reaction: (5S)-5-amino-3-oxohexanoate + acetyl-CoA = L-3-aminobutanoyl-CoA + acetoacetate

For diagram of reaction click here.

Glossary: L-3-aminobutyryl-CoA = (3S)-3-aminobutanoyl-CoA

Other name(s): kce (gene name)

Systematic name: (5S)-5-amino-3-oxohexanoate:acetyl-CoA ethylamine transferase

Comments: Requires Zn2+. The enzyme, isolated from the bacteria Fusobacterium nucleatum and Cloacimonas acidaminovorans, is involved in the anaerobic fermentation of lysine.

References:

1. Barker, H.A., Kahn, J.M. and Hedrick, L. Pathway of lysine degradation in Fusobacterium nucleatum. J. Bacteriol. 152 (1982) 201-207. [PMID: 6811551]

2. Kreimeyer, A., Perret, A., Lechaplais, C., Vallenet, D., Medigue, C., Salanoubat, M. and Weissenbach, J. Identification of the last unknown genes in the fermentation pathway of lysine. J. Biol. Chem. 282 (2007) 7191-7197. [PMID: 17166837]

3. Bellinzoni, M., Bastard, K., Perret, A., Zaparucha, A., Perchat, N., Vergne, C., Wagner, T., de Melo-Minardi, R.C., Artiguenave, F., Cohen, G.N., Weissenbach, J., Salanoubat, M. and Alzari, P.M. 3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation. J. Biol. Chem. 286 (2011) 27399-27405. [PMID: 21632536]

[EC 2.3.1.247 created 2015]

EC 2.3.1.248

Accepted name: spermidine disinapoyl transferase

Reaction: 2 sinapoyl-CoA + spermidine = 2 CoA + N1,N8-bis(sinapoyl)-spermidine

Other name(s): SDT

Systematic name: sinapoyl-CoA:spermidine N-(hydroxycinnamoyl)transferase

Comments: The enzyme from the plant Arabidopsis thaliana has no activity with 4-coumaroyl-CoA (cf. EC 2.3.1.249, spermidine dicoumaroyl transferase).

References:

1. Luo, J., Fuell, C., Parr, A., Hill, L., Bailey, P., Elliott, K., Fairhurst, S.A., Martin, C. and Michael, A.J. A novel polyamine acyltransferase responsible for the accumulation of spermidine conjugates in Arabidopsis seed. Plant Cell 21 (2009) 318-333. [PMID: 19168716]

[EC 2.3.1.248 created 2015]

EC 2.3.1.249

Accepted name: spermidine dicoumaroyl transferase

Reaction: 2 4-coumaroyl-CoA + spermidine = 2 CoA + N1,N8-bis(4-coumaroyl)-spermidine

Other name(s): SCT

Systematic name: 4-coumaroyl-CoA:spermidine N-(hydroxycinnamoyl)transferase

Comments: The enzyme from the plant Arabidopsis thaliana has no activity with sinapoyl-CoA (cf. EC 2.3.1.248, spermidine disinapoyl transferase).

References:

1. Luo, J., Fuell, C., Parr, A., Hill, L., Bailey, P., Elliott, K., Fairhurst, S.A., Martin, C. and Michael, A.J. A novel polyamine acyltransferase responsible for the accumulation of spermidine conjugates in Arabidopsis seed. Plant Cell 21 (2009) 318-333. [PMID: 19168716]

[EC 2.3.1.249 created 2015]

EC 2.3.1.250

Accepted name: [Wnt protein] O-palmitoleoyl transferase

Reaction: (9Z)-hexadec-9-enoyl-CoA + [Wnt]-L-serine = CoA + [Wnt]-O-(9Z)-hexadec-9-enoyl-L-serine

Glossary: (9Z)-hexadec-9-enoate = palmitoleoate

Other name(s): porcupine; PORCN (gene name)

Systematic name: (9Z)-hexadec-9-enoyl-CoA:[Wnt]-L-serine O-hexadecenoyltransferase

Comments: The enzyme, found in animals, modifies a specific serine residue in Wnt proteins, e.g. Ser209 in human Wnt3a and Ser224 in chicken WNT1 [2,3]. The enzyme can accept C13 to C16 fatty acids in vitro, but only (9Z)-hexadecenoate modification is observed in vivo [1]. cf. EC 3.1.1.98, [Wnt protein]-O-palmitoleoyl-L-serine hydrolase.

References:

1. Takada, R., Satomi, Y., Kurata, T., Ueno, N., Norioka, S., Kondoh, H., Takao, T. and Takada, S. Monounsaturated fatty acid modification of Wnt protein: its role in Wnt secretion. Dev Cell 11 (2006) 791-801. [PMID: 17141155]

2. Gao, X. and Hannoush, R.N. Single-cell imaging of Wnt palmitoylation by the acyltransferase porcupine. Nat. Chem. Biol. 10 (2014) 61-68. [PMID: 24292069]

3. Miranda, M., Galli, L.M., Enriquez, M., Szabo, L.A., Gao, X., Hannoush, R.N. and Burrus, L.W. Identification of the WNT1 residues required for palmitoylation by Porcupine. FEBS Lett. 588 (2014) 4815-4824. [PMID: 25451226]

[EC 2.3.1.250 created 2015]

EC 2.3.2.23

Accepted name: E2 ubiquitin-conjugating enzyme

Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine

Other name(s): ubiquitin-carrier-protein E2; UBC (ambiguous); ubiquitin-conjugating enzyme E2

Systematic name: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine:[E2 ubiquitin-conjugating enzyme] ubiquitinyl transferase

Comments: The E2 ubiquitin-conjugating enzyme acquires the activated ubquitin from the E1 ubiquitin-activating enzyme (EC 6.2.1.45) and binds it via a transthioesterification reaction to itself. In the human enzyme the catalytic center is located at Cys-87 where ubiquitin is bound via its C-terminal glycine in a thioester linkage.

References:

1. van Wijk, S.J. and Timmers, H.T. The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins. FASEB J. 24 (2010) 981-993. [PMID: 19940261]

2. David, Y., Ziv, T., Admon, A. and Navon, A. The E2 ubiquitin-conjugating enzymes direct polyubiquitination to preferred lysines. J. Biol. Chem. 285 (2010) 8595-8604. [PMID: 20061386]

3. Papaleo, E., Casiraghi, N., Arrigoni, A., Vanoni, M., Coccetti, P. and De Gioia, L. Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade. PLoS One 7 (2012) e40786. [PMID: 22815819]

4. Cook, B.W. and Shaw, G.S. Architecture of the catalytic HPN motif is conserved in all E2 conjugating enzymes. Biochem. J. 445 (2012) 167-174. [PMID: 22563859]

5. Li, D.F., Feng, L., Hou, Y.J. and Liu, W. The expression, purification and crystallization of a ubiquitin-conjugating enzyme E2 from Agrocybe aegerita underscore the impact of His-tag location on recombinant protein properties. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 69 (2013) 153-157. [PMID: 23385757]

[EC 2.3.2.23 created 2015]

EC 2.3.2.24

Accepted name: (E3-independent) E2 ubiquitin-conjugating enzyme

Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N6-monoubiquitinyl-[acceptor protein]-L-lysine (overall reaction)
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
(1b) S-monoubiquitinyl-[(E3-independent) E2 ubiquitin-conjugating E2 enzyme]-L-cysteine + [acceptor protein]-L-lysine = [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-monoubiquitinyl-[acceptor protein]-L-lysine

Other name(s): E2-230K; UBE2O; E3-independent ubiquitin-conjugating enzyme E2

Systematic name: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine:L-lysine ubiquitinyl transferase ([E3 ubiquitin transferase]-independent)

Comments: The enzyme transfers a single ubiquitin directly from an ubiquitinated E1 ubiquitin-activating enzyme to itself, and on to a lysine residue of the acceptor protein without involvement of E3 ubiquitin transferases (cf. EC 2.3.2.26, EC 2.3.2.27). It forms a labile ubiquitin adduct in the presence of E1, ubiquitin, and Mg2+-ATP and catalyses the conjugation of ubiquitin to protein substrates, independently of E3. This transfer has only been observed with small proteins. In vitro a transfer to small acceptors (e.g. L-lysine, N-acetyl-L-lysine methyl ester) has been observed [1].

References:

1. Pickart, C.M. and Rose, I.A. Functional heterogeneity of ubiquitin carrier proteins. J. Biol. Chem. 260 (1985) 1573-1581. [PMID: 2981864]

2. Hoeller, D., Hecker, C.M., Wagner, S., Rogov, V., Dotsch, V. and Dikic, I. E3-independent monoubiquitination of ubiquitin-binding proteins. Mol. Cell 26 (2007) 891-898. [PMID: 17588522]

3. Ramanathan, H.N., Zhang, G. and Ye, Y. Monoubiquitination of EEA1 regulates endosome fusion and trafficking. Cell Biosci 3 (2013) 24. [PMID: 23701900]

[EC 2.3.2.24 created 2015]

EC 2.3.2.25

Accepted name: N-terminal E2 ubiquitin-conjugating enzyme

Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-N-terminal-amino acid = [E1 ubiquitin-activating enzyme]-L-cysteine + N-terminal-ubiquitinyl-[acceptor protein] (overall reaction)
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [N-terminal E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[N-terminal ubiquitin-conjugating enzyme]-L-cysteine
(1b) S-ubiquitinyl-[N-terminal E2 ubiquitin-conjugating E2 enzyme]-L-cysteine + [acceptor protein]-N-terminal-amino acid = [N-terminal E2 ubiquitin-conjugating enzyme]-L-cysteine + N-ubiquitinyl-[acceptor protein]-N-terminal amino acid

Other name(s): Ube2w; N-terminal ubiquitin-conjugating enzyme E2

Systematic name: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine:acceptor protein ubiquitin ligase (peptide bond-forming)

Comments: The enzyme ubiquitinylates the N-terminus of the acceptor protein. It is not reactive towards free lysine.

References:

1. Breitschopf, K., Bengal, E., Ziv, T., Admon, A. and Ciechanover, A. A novel site for ubiquitination: the N-terminal residue, and not internal lysines of MyoD, is essential for conjugation and degradation of the protein. EMBO J. 17 (1998) 5964-5973. [PMID: 9774340]

2. Tatham, M.H., Plechanovova, A., Jaffray, E.G., Salmen, H. and Hay, R.T. Ube2W conjugates ubiquitin to α-amino groups of protein N-termini. Biochem. J. 453 (2013) 137-145. [PMID: 23560854]

3. Scaglione, K.M., Basrur, V., Ashraf, N.S., Konen, J.R., Elenitoba-Johnson, K.S., Todi, S.V. and Paulson, H.L. The ubiquitin-conjugating enzyme (E2) Ube2w ubiquitinates the N terminus of substrates. J. Biol. Chem. 288 (2013) 18784-18788. [PMID: 23696636]

[EC 2.3.2.25 created 2015]

EC 2.3.2.26

Accepted name: HECT-type E3 ubiquitin transferase

Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine (overall reaction)
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
(1b) S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine + [acceptor protein]-L-lysine = [HECT-type E3 ubiquitin transferase]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine

Glossary: HECT protein domain = Homologous to the E6-AP Carboxyl Terminus protein domain

Other name(s): HECT E3 ligase (misleading); ubiquitin transferase HECT-E3

Systematic name: S-ubiquitinyl-[HECT-type E3-ubiquitin transferase]-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming)

Comments: In the first step the enzyme transfers ubiquitin from the E2 ubiquitin-conjugating enzyme (EC 2.3.2.23) to a cysteine residue in its HECT domain (which is located in the C-terminal region), forming a thioester bond. In a subsequent step the enzyme transfers the ubiquitin to an acceptor protein, resulting in the formation of an isopeptide bond between the C-terminal glycine residue of ubiquitin and the ε-amino group of an L-lysine residue of the acceptor protein.

References:

1. Maspero, E., Mari, S., Valentini, E., Musacchio, A., Fish, A., Pasqualato, S. and Polo, S. Structure of the HECT:ubiquitin complex and its role in ubiquitin chain elongation. EMBO Rep. 12 (2011) 342-349. [PMID: 21399620]

2. Metzger, M.B., Hristova, V.A. and Weissman, A.M. HECT and RING finger families of E3 ubiquitin ligases at a glance. J. Cell Sci. 125 (2012) 531-537. [PMID: 22389392]

[EC 2.3.2.26 created 2015]

EC 2.3.2.27

Accepted name: RING-type E3 ubiquitin transferase

Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine

Glossary: RING = Really Interesting New Gene

Other name(s): RING E3 ligase (misleading); ubiquitin transferase RING E3

Systematic name: S-ubiquitinyl-[ubiquitin-conjugating E2 enzyme]-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming; RING-type)

Comments: The RING domain of E3 ubiquitin transferase serves as a mediator bringing the ubiquitin-charged E2 ubiquitin-conjugating enzyme and the acceptor protein together to enable the direct transfer of ubiquitin through the formation of an isopetide bond between the C-terminal glycine residue of ubiquitin an the ε-amino group of an L-lysine residue of the acceptor protein. The RING-E3 domain does not form a catalytic thioester intermediate with ubiquitin (unlike the HECT domain, EC 2.3.2.26). RING-type ubiquitin transferases may occur as single-chain enzymes but also in dimeric forms or in multi-subunit assemblies.

References:

1. Eisele, F. and Wolf, D.H. Degradation of misfolded protein in the cytoplasm is mediated by the ubiquitin ligase Ubr1. FEBS Lett. 582 (2008) 4143-4146. [PMID: 19041308]

2. Metzger, M.B., Hristova, V.A. and Weissman, A.M. HECT and RING finger families of E3 ubiquitin ligases at a glance. J. Cell Sci. 125 (2012) 531-537. [PMID: 22389392]

3. Plechanovova, A., Jaffray, E.G., Tatham, M.H., Naismith, J.H. and Hay, R.T. Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis. Nature 489 (2012) 115-120. [PMID: 22842904]

4. Pruneda, J.N., Littlefield, P.J., Soss, S.E., Nordquist, K.A., Chazin, W.J., Brzovic, P.S. and Klevit, R.E. Structure of an E3:E2~Ub complex reveals an allosteric mechanism shared among RING/U-box ligases. Mol. Cell 47 (2012) 933-942. [PMID: 22885007]

5. Metzger, M.B., Pruneda, J.N., Klevit, R.E. and Weissman, A.M. RING -type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination. Biochim. Biophys. Acta 1843 (2014) 47-60. [PMID: 23747565]

[EC 2.3.2.27 created 2015]

EC 2.3.2.28

Accepted name: L-allo-isoleucyltransferase

Reaction: L-allo-isoleucyl-S-[CmaA peptidyl-carrier protein] + holo-[CmaD peptidyl-carrier protein] = L-allo-isoleucyl-S-[CmaD peptidyl-carrier protein] + holo-[CmaA peptidyl-carrier protein]

Glossary: L-allo-isoleucine = (2S,3R)-2-amino-3-methylpentanoic acid

Other name(s): CmaE

Systematic name: L-allo-isoleucyl-S-[CmaA peptidyl-carrier protein]:holo-[CmaD peptidyl-carrier protein] L-allo-isoleucyltransferase

Comments: The enzyme, characterized from the bacterium Pseudomonas syringae, is involved in the biosynthesis of the toxin coronatine.

References:

1. Vaillancourt, F.H., Yeh, E., Vosburg, D.A., O'Connor, S.E. and Walsh, C.T. Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis. Nature 436 (2005) 1191-1194. [PMID: 16121186]

2. Strieter, E.R., Vaillancourt, F.H. and Walsh, C.T. CmaE: a transferase shuttling aminoacyl groups between carrier protein domains in the coronamic acid biosynthetic pathway. Biochemistry 46 (2007) 7549-7557. [PMID: 17530782]

[EC 2.3.2.28 created 2015]

*EC 2.4.1.33

Accepted name: mannuronan synthase

Reaction: GDP-α-D-mannuronate + [(1→4)-β-D-mannuronosyl]n = GDP + [(1→4)-β-D-mannuronosyl]n+1

Glossary: poly[β-(1,4)-D-mannuronate] = mannuronan

Other name(s): mannuronosyl transferase; alginate synthase (incorrect); alg8 (gene name); alg44 (gene name); GDP-D-mannuronate:alginate D-mannuronyltransferase

Systematic name: GDP-α-D-mannuronate:mannuronan D-mannuronatetransferase

Comments: The enzyme catalyses the polymerization of β-D-mannuronate residues into a mannuronan polymer, an intermediate in the biosynthesis of alginate. It is found in brown algae and in alginate-producing bacterial species from the Pseudomonas and Azotobacter genera.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37257-31-1

References:

1. Lin, T.-Y. and Hassid, W.Z. Pathway of alginic acid synthesis in the marine brown alga, Fucus gardneri Silva. J. Biol. Chem. 241 (1966) 5284-5297. [PMID: 5954796]

2. Remminghorst, U. and Rehm, B.H. In vitro alginate polymerization and the functional role of Alg8 in alginate production by Pseudomonas aeruginosa. Appl. Environ. Microbiol. 72 (2006) 298-305. [PMID: 16391057]

3. Oglesby, L.L., Jain, S. and Ohman, D.E. Membrane topology and roles of Pseudomonas aeruginosa Alg8 and Alg44 in alginate polymerization. Microbiology 154 (2008) 1605-1615. [PMID: 18524915]

[EC 2.4.1.33 created 1972, modified 2015]

*EC 2.4.1.147

Accepted name: acetylgalactosaminyl-O-glycosyl-glycoprotein β-1,3-N-acetylglucosaminyltransferase

Reaction: UDP-N-acetyl-α-D-glucosamine + O3-[N-acetyl-α-D-galactosaminyl]-L-threonyl/L-seryl-[protein] = UDP + O3-[N-acetyl-β-D-glucosaminyl-(1→3)-N-acetyl-α-D-galactosaminyl]-L-threonyl/L-seryl-[protein]

Other name(s): O-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase III; uridine diphosphoacetylglucosamine-mucin β(1→3)-acetylglucosaminyltransferase; mucin core 3 β3-GlcNAc-transferase; Core 3β-GlcNAc-transferase; UDP-N-acetyl-D-glucosamine:O-glycosyl-glycoprotein (N-acetyl-D-glucosamine to N-acetyl-D-galactosaminyl-R) β-1,3-N-acetyl-D-glucosaminyltransferase; UDP-N-acetyl-D-glucosamine:N-acetyl-β-D-galactosaminyl-R 3-β-N-acetyl-D-glucosaminyltransferase (incorrect)

Systematic name: UDP-N-acetyl-α-D-glucosamine:O3-[N-acetyl-α-D-galactosaminyl]-L-threonyl/L-seryl-[protein] 3-β-N-acetyl-D-glucosaminyltransferase

Comments: The product of the enzyme is known as core 3, one of the eight core structures of mucin-type O-glycans. O-Linked glycans are polysaccharides or oligosaccharides that are linked to a protein via the oxygen atom in the side chain of an L-serine or L-threonine residue.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 87927-96-6

References:

1. Brockhausen, I., Rachaman, E.S., Matta, K.L. and Schachter, H. The separation by liquid chromatography (under elevated pressure) of phenyl, benzyl, and O-nitrophenyl glycosides of oligosaccharides. Analysis of substrates and products for four N-acetyl-D-glucosaminyl-transferases involved in mucin synthesis. Carbohydr. Res. 120 (1983) 3-16. [PMID: 6226356]

2. Brockhausen, I., Matta, K.L., Orr, J. and Schachter, H. Mucin synthesis. UDP-GlcNAc:GalNAc-R β 3-N-acetylglucosaminyltransferase and UDP-GlcNAc:GlcNAc β 1-3GalNAc-R (GlcNAc to GalNAc) β 6-N-acetylglucosaminyltransferase from pig and rat colon mucosa. Biochemistry 24 (1985) 1866-1874. [PMID: 3160388]

3. Vavasseur, F., Yang, J.M., Dole, K., Paulsen, H. and Brockhausen, I. Synthesis of O-glycan core 3: characterization of UDP-GlcNAc: GalNAc-R β 3-N-acetyl-glucosaminyltransferase activity from colonic mucosal tissues and lack of the activity in human cancer cell lines. Glycobiology 5 (1995) 351-357. [PMID: 7655172]

[EC 2.4.1.147 created 1984, modified 2015]

*EC 2.4.1.153

Accepted name: UDP-N-acetylglucosamine—dolichyl-phosphate N-acetylglucosaminyltransferase

Reaction: UDP-N-acetyl-α-D-glucosamine + dolichyl phosphate = UDP + dolichyl N-acetyl-α-D-glucosaminyl phosphate

Other name(s): aglK (gene name); dolichyl-phosphate α-N-acetylglucosaminyltransferase; UDP-N-acetyl-D-glucosamine:dolichyl-phosphate α-N-acetyl-D-glucosaminyltransferase

Systematic name: UDP-N-acetyl-α-D-glucosamine:dolichyl-phosphate α-N-acetyl-D-glucosaminyltransferase

Comments: The enzyme, characterized from the methanogenic archaeon Methanococcus voltae, initiates N-linked glycosylation in that organism. The enzyme differs from the eukaryotic enzyme, which leaves one additional phosphate group on the dolichyl product (cf. EC 2.7.8.15, UDP-N-acetylglucosamine—dolichyl-phosphate N-acetylglucosaminephosphotransferase).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 63363-73-5

References:

1. Larkin, A., Chang, M.M., Whitworth, G.E. and Imperiali, B. Biochemical evidence for an alternate pathway in N-linked glycoprotein biosynthesis. Nat. Chem. Biol. 9 (2013) 367-373. [PMID: 23624439]

[EC 2.4.1.153 created 1984, modified 2015]

*EC 2.4.1.159

Accepted name: flavonol-3-O-glucoside L-rhamnosyltransferase

Reaction: UDP-β-L-rhamnose + a flavonol 3-O-β-D-glucoside = UDP + a flavonol 3-O-[α-L-rhamnosyl-(1→6)-β-D-glucoside]

For diagram of reaction click here.

Glossary: UDP-β-L-rhamnose = UDP-6-deoxy-β-L-mannose

Other name(s): uridine diphosphorhamnose-flavonol 3-O-glucoside rhamnosyltransferase; UDP-rhamnose:flavonol 3-O-glucoside rhamnosyltransferase; UDP-L-rhamnose:flavonol-3-O-D-glucoside 6''-O-L-rhamnosyltransferase

Systematic name: UDP-β-L-rhamnose:flavonol-3-O-β-D-glucoside 6''-O-L-rhamnosyltransferase (configuration-inverting)

Comments: A configuration-inverting rhamnosyltransferase that converts flavonol 3-O-glucosides to 3-O-rutinosides. Also acts, more slowly, on rutin, quercetin 3-O-galactoside and flavonol 3-O-rhamnosides.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 83380-89-6

References:

1. Kleinehollenhorst, G., Behrens, H., Pegels, G., Srunk, N. and Wiermann, R. Formation of flavonol 3-O-diglycosides and flavonol 3-O-triglycosides by enzyme extracts from anthers of Tulipa cv apeldoorn - characterization and activity of 3 different O-glycosyltransferases during anther development. Z. Natursforsch. C: Biosci. 37 (1982) 587-599.

2. Jones, P., Messner, B., Nakajima, J., Schaffner, A.R. and Saito, K. UGT73C6 and UGT78D1, glycosyltransferases involved in flavonol glycoside biosynthesis in Arabidopsis thaliana. J. Biol. Chem. 278 (2003) 43910-43918. [PMID: 12900416]

[EC 2.4.1.159 created 1986, modified 2015]

*EC 2.4.1.184

Accepted name: galactolipid galactosyltransferase

Reaction: 2 a 1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol = a 1,2-diacyl-3-O-[β-D-galactosyl-(1→6)-β-D-galactosyl]-sn-glycerol + a 1,2-diacyl-sn-glycerol

For diagram of reaction click here.

Glossary: a 1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol = monogalactosyldiacylglycerol

Other name(s): galactolipid-galactolipid galactosyltransferase; galactolipid:galactolipid galactosyltransferase; interlipid galactosyltransferase; GGGT; DGDG synthase (ambiguous); digalactosyldiacylglycerol synthase (ambiguous); 3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol:mono-3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol β-D-galactosyltransferase; 3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol:3-(β-D-galactosyl)-1,2-diacyl-sn-glycerol β-D-galactosyltransferase; SFR2 (gene name)

Systematic name: 1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol:1,2-diacyl-3-O-(β-D-galactosyl)-sn-glycerol β-D-galactosyltransferase

Comments: The enzyme converts monogalactosyldiacylglycerol to digalactosyldiacylglycerol, trigalactosyldiacylglycerol and tetragalactosyldiacylglycerol. All residues are connected by β linkages. The activity is localized to chloroplast envelope membranes, but it does not contribute to net galactolipid synthesis in plants, which is performed by EC 2.4.1.46, monogalactosyldiacylglycerol synthase, and EC 2.4.1.241, digalactosyldiacylglycerol synthase. Note that the β,β-digalactosyldiacylglycerol formed by this enzyme is different from the more common α,β-digalactosyldiacylglycerol formed by EC 2.4.1.241. The enzyme provides an important mechanism for the stabilization of the chloroplast membranes during freezing and drought stress.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 66676-74-2

References:

1. Dorne, A.-J., Block, M.A., Joyard, J. and Douce, R. The galactolipid-galactolipid galactosyltransferase is located on the outer surface of the outer-membrane of the chloroplast envelope. FEBS Lett. 145 (1982) 30-34.

2. Heemskerk, J.W.M., Wintermans, J.F.G.M., Joyard, J., Block, M.A., Dorne, A.-J. and Douce, R. Localization of galactolipid:galactolipid galactosyltransferase and acyltransferase in outer envelope membrane of spinach chloroplasts. Biochim. Biophys. Acta 877 (1986) 281-289.

3. Heemskerk, J.W.M., Jacobs, F.H.H. and Wintermans, J.F.G.M. UDPgalactose-independent synthesis of monogalactosyldiacylglycerol. An enzymatic activity of the spinach chloroplast envelope. Biochim. Biophys. Acta 961 (1988) 38-47.

4. Kelly, A.A., Froehlich, J.E. and Dörmann, P. Disruption of the two digalactosyldiacylglycerol synthase genes DGD1 and DGD2 in Arabidopsis reveals the existence of an additional enzyme of galactolipid synthesis. Plant Cell 15 (2003) 2694-2706. [PMID: 14600212]

5. Benning, C. and Ohta, H. Three enzyme systems for galactoglycerolipid biosynthesis are coordinately regulated in plants. J. Biol. Chem. 280 (2005) 2397-2400. [PMID: 15590685]

6. Fourrier, N., Bedard, J., Lopez-Juez, E., Barbrook, A., Bowyer, J., Jarvis, P., Warren, G. and Thorlby, G. A role for SENSITIVE TO FREEZING2 in protecting chloroplasts against freeze-induced damage in Arabidopsis. Plant J. 55 (2008) 734-745. [PMID: 18466306]

7. Moellering, E.R., Muthan, B. and Benning, C. Freezing tolerance in plants requires lipid remodeling at the outer chloroplast membrane. Science 330 (2010) 226-228. [PMID: 20798281]

[EC 2.4.1.184 created 1990, modified 2005, modified 2015]

*EC 2.4.1.213

Accepted name: glucosylglycerol-phosphate synthase

Reaction: ADP-α-D-glucose + sn-glycerol 3-phosphate = 2-(α-D-glucopyranosyl)-sn-glycerol 3-phosphate + ADP

Other name(s): ADP-glucose:sn-glycerol-3-phosphate 2-β-D-glucosyltransferase (incorrect)

Systematic name: ADP-α-D-glucose:sn-glycerol-3-phosphate 2-α-D-glucopyranosyltransferase

Comments: Acts with EC 3.1.3.69 (glucosylglycerol phosphatase) to form glucosylglycerol, an osmolyte that endows cyanobacteria with resistance to salt.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 161515-13-5

References:

1. Hagemann, M. and Erdmann, N. Activation and pathway of glucosylglycerol biosynthesis in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology 140 (1994) 1427-1431.

2. Marin, K., Zuther, E., Kerstan, T., Kunert, A. and Hagemann, M. The ggpS gene from Synechocystis sp. strain PCC 6803 encoding glucosylglycerol-phosphate synthase is involved in osmolyte synthesis. J. Bacteriol. 180 (1998) 4843-4849. [PMID: 9733686]

[EC 2.4.1.213 created 2001, modified 2015]

*EC 2.4.2.37

Accepted name: NAD+—dinitrogen-reductase ADP-D-ribosyltransferase

Reaction: NAD+ + [dinitrogen reductase]-L-arginine = nicotinamide + [dinitrogen reductase]-Nω-α-(ADP-D-ribosyl)-L-arginine

Other name(s): NAD-azoferredoxin (ADPribose)transferase; NAD-dinitrogen-reductase ADP-D-ribosyltransferase; draT (gene name)

Systematic name: NAD+:[dinitrogen reductase] (ADP-D-ribosyl)transferase

Comments: The combined action of this enzyme and EC 3.2.2.24, ADP-ribosyl-[dinitrogen reductase] hydrolase, controls the activity level of nitrogenase (EC 1.18.6.1). In the presence of ammonium, the product of nitrogenase, this enzyme covalently links an ADP-ribose moiety to a specific arginine residue of the dinitrogenase reductase component of nitrogenase, blocking its activity.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 117590-45-1

References:

1. Lowery, R.G. and Ludden, P.W. Purification and properties of dinitrogenase reductase ADP-ribosyltransferase from the photosynthetic bacterium Rhodospirillum rubrum. J. Biol. Chem. 263 (1988) 16714-16719. [PMID: 3141411]

2. Fitzmaurice, W.P., Saari, L.L., Lowery, R.G., Ludden, P.W. and Roberts, G.P. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Mol. Gen. Genet. 218 (1989) 340-347. [PMID: 2506427]

3. Moure, V.R., Costa, F.F., Cruz, L.M., Pedrosa, F.O., Souza, E.M., Li, X.D., Winkler, F. and Huergo, L.F. Regulation of nitrogenase by reversible mono-ADP-ribosylation. Curr. Top. Microbiol. Immunol. 384 (2015) 89-106. [PMID: 24934999]

[EC 2.4.2.37 created 1992, modified 2015]

EC 2.6.1.108

Accepted name: (5-formylfuran-3-yl)methyl phosphate transaminase

Reaction: L-alanine + (5-formylfuran-3-yl)methyl phosphate = pyruvate + [5-(aminomethyl)furan-3-yl]methyl phosphate

Other name(s): mfnC (gene name); [5-(hydroxymethyl)furan-3-yl]methyl phosphate transaminase

Systematic name: L-alanine:(5-formylfuran-3-yl)methyl phosphate aminotransferase

Comments: A pyridoxal 5'-phosphate protein. The enzyme, characterized from the archaebacterium Methanocaldococcus jannaschii, participates in the biosynthesis of the cofactor methanofuran. Requires pyridoxal 5'-phosphate.

References:

1. Miller, D., Wang, Y., Xu, H., Harich, K. and White, R.H. Biosynthesis of the 5-(aminomethyl)-3-furanmethanol moiety of methanofuran. Biochemistry 53 (2014) 4635-4647. [PMID: 24977328]

[EC 2.6.1.108 created 2015]

EC 2.6.1.109

Accepted name: 8-amino-3,8-dideoxy-α-D-manno-octulosonate transaminase

Reaction: 8-amino-3,8-dideoxy-α-D-manno-octulosonate + 2-oxoglutarate = 8-dehydro-3-deoxy-α-D-manno-octulosonate + L-glutamate

Glossary: 3-deoxy-α-D-manno-octulosonate = Kdo
8-dehydro-3-deoxy-α-D-manno-octulosonate = (2R,4R,5R,6S)-2,4,5-trihydroxy-6-[(1S)-1-hydroxy-2-oxoethyl]oxane-2-carboxylate

Other name(s): kdnA (gene name)

Systematic name: 8-amino-3,8-dideoxy-α-D-manno-octulosonate:2-oxoglutarate aminotransferase

Comments: The enzyme, characterized from the bacterium Shewanella oneidensis, forms 8-amino-3,8-dideoxy-α-D-manno-octulosonate, an aminated form of Kdo found in lipopolysaccharides of members of the Shewanella genus. cf. EC 1.1.3.48, 3-deoxy-α-D-manno-octulosonate 8-oxidase.

References:

1. Gattis, S.G., Chung, H.S., Trent, M.S. and Raetz, C.R. The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis. J. Biol. Chem. 288 (2013) 9216-9225. [PMID: 23413030]

[EC 2.6.1.109 created 2015]

EC 2.7.1.189

Accepted name: autoinducer-2 kinase

Reaction: ATP + (S)-4,5-dihydroxypentane-2,3-dione = ADP + (S)-4-hydroxypentane-2,3-dione 5-phosphate

Glossary: (S)-4,5-dihydroxypentane-2,3-dione = autoinducer 2 = AI-2

Other name(s): lsrK (gene name)

Systematic name: ATP:(S)-4,5-dihydroxypentane-2,3-dione 5-phosphotransferase

Comments: The enzyme participates in a degradation pathway of the bacterial quorum-sensing autoinducer molecule AI-2.

References:

1. Xavier, K.B., Miller, S.T., Lu, W., Kim, J.H., Rabinowitz, J., Pelczer, I., Semmelhack, M.F. and Bassler, B.L. Phosphorylation and processing of the quorum-sensing molecule autoinducer-2 in enteric bacteria. ACS Chem. Biol. 2 (2007) 128-136. [PMID: 17274596]

2. Roy, V., Fernandes, R., Tsao, C.Y. and Bentley, W.E. Cross species quorum quenching using a native AI-2 processing enzyme. ACS Chem. Biol. 5 (2010) 223-232. [PMID: 20025244]

[EC 2.7.1.189 created 2015]

EC 2.7.4.30

Accepted name: lipid A phosphoethanolamine transferase

Reaction: (1) diacylphosphatidylethanolamine + lipid A = diacylglycerol + lipid A 1-(2-aminoethyl diphosphate)
(2) diacylphosphatidylethanolamine + lipid A = diacylglycerol + lipid A 4'-(2-aminoethyl diphosphate)
(3) diacylphosphatidylethanolamine + lipid A 1-(2-aminoethyl diphosphate) = diacylglycerol + lipid A 1,4'-bis(2-aminoethyl diphosphate)

Glossary: lipid A (Campylobacter jejuni) = 2,3-dideoxy-2,3-bis[(3R)-3-(hexadecanoyloxy)tetradecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A (Escherichia coli) = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid A (Helicobacter pylori) = 2-deoxy-2-[(3R)-3-(octadecanoyloxy)octadecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxyhexadecanoyl]-2-[(3R)-3-hydroxyoctadecanamido]-α-D-glucopyranosyl phosphate
lipid A (Neisseria meningitidis) = 2-deoxy-3-O-[(3R)-3-hydroxydodecanoyl]-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxydodecanoyl]-2-[(3R)-3-(dodecanoyloxy)tetradecanamido]-α-D-glucopyranosyl phosphate
lipid A 1-[(2-aminoethyl) diphosphate] = P1-(2-aminoethyl) P2-(2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl) diphosphate
lipid A 1,4'-bis(2-aminoethyl diphosphate) = P1-(2-aminoethyl) P2-(2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-(2-aminoethyldiphospho)-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl) diphosphate

Other name(s): lipid A PEA transferase; PmrA; LptA

Systematic name: diacylphosphatidylethanolamine:lipid-A phosphoethanolaminetransferase

Comments: The enzyme adds one or two ethanolamine phosphate groups to lipid A giving a diphosphate, sometimes in combination with EC 2.4.2.43 (lipid IVA 4-amino-4-deoxy-L-arabinosyltransferase) giving products with 4-amino-4-deoxy-β-L-arabinose groups at the phosphates of lipid A instead of diphosphoethanolamine groups. It will also act on lipid IVA and Kdo2-lipid A.

References:

1. Tran, A.X., Karbarz, M.J., Wang, X., Raetz, C.R., McGrath, S.C., Cotter, R.J. and Trent, M.S. Periplasmic cleavage and modification of the 1-phosphate group of Helicobacter pylori lipid A. J. Biol. Chem. 279 (2004) 55780-55791. [PMID: 15489235]

2. Herrera, C.M., Hankins, J.V. and Trent, M.S. Activation of PmrA inhibits LpxT-dependent phosphorylation of lipid A promoting resistance to antimicrobial peptides. Mol. Microbiol. 76 (2010) 1444-1460. [PMID: 20384697]

3. Cullen, T.W. and Trent, M.S. A link between the assembly of flagella and lipooligosaccharide of the Gram-negative bacterium Campylobacter jejuni. Proc. Natl. Acad. Sci. USA 107 (2010) 5160-5165. [PMID: 20194750]

4. Anandan, A., Piek, S., Kahler, C.M. and Vrielink, A. Cloning, expression, purification and crystallization of an endotoxin-biosynthesis enzyme from Neisseria meningitidis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 1494-1497. [PMID: 23192031]

5. Wanty, C., Anandan, A., Piek, S., Walshe, J., Ganguly, J., Carlson, R.W., Stubbs, K.A., Kahler, C.M. and Vrielink, A. The structure of the neisserial lipooligosaccharide phosphoethanolamine transferase A (LptA) required for resistance to polymyxin. J. Mol. Biol. 425 (2013) 3389-3402. [PMID: 23810904]

[EC 2.7.4.30 created 2015]

EC 2.7.7.88

Accepted name: GDP polyribonucleotidyltransferase

Reaction: 5'-triphospho-mRNA + GDP = diphosphate + guanosine 5'-triphospho-mRNA

Systematic name: 5'-triphospho-mRNA:GDP 5'-phosphopolyribonucleotidyltransferase [G(5')ppp-mRNA-forming]

Comments: The enzyme from rhabdoviruses transfers 5'-monophosphorylated (p-)mRNA from 5'-triphosphorylated (ppp-)mRNA to GDP to form 5'-capped mRNA (GpppmRNA) in a viral mRNA-start sequence-dependent manner. The (p-)mRNA transfer reaction proceeds through a covalent enzyme-pmRNA intermediate.

References:

1. Ogino, T. and Banerjee, A.K. An unconventional pathway of mRNA cap formation by vesiculoviruses. Virus Res 162 (2011) 100-109. [PMID: 21945214]

2. Ogino, T., Yadav, S.P. and Banerjee, A.K. Histidine-mediated RNA transfer to GDP for unique mRNA capping by vesicular stomatitis virus RNA polymerase. Proc. Natl. Acad. Sci. USA 107 (2010) 3463-3468. [PMID: 20142503]

3. Ogino, T. and Banerjee, A.K. The HR motif in the RNA-dependent RNA polymerase L protein of Chandipura virus is required for unconventional mRNA-capping activity. J. Gen. Virol. 91 (2010) 1311-1314. [PMID: 20107017]

4. Ogino, T. and Banerjee, A.K. Formation of guanosine(5')tetraphospho(5')adenosine cap structure by an unconventional mRNA capping enzyme of vesicular stomatitis virus. J. Virol. 82 (2008) 7729-7734. [PMID: 18495767]

5. Ogino, T. and Banerjee, A.K. Unconventional mechanism of mRNA capping by the RNA-dependent RNA polymerase of vesicular stomatitis virus. Mol. Cell 25 (2007) 85-97. [PMID: 17218273]

[EC 2.7.7.88 created 2015]

EC 2.7.7.89

Accepted name: [glutamate—ammonia ligase]-adenylyl-L-tyrosine phosphorylase

Reaction: [L-glutamate:ammonia ligase (ADP-forming)]-O4-(5'-adenylyl)-L-tyrosine + H2O = adenylate + [L-glutamate:ammonia ligase (ADP-forming)]-L-tyrosine

Other name(s): adenylyl-[glutamine—synthetase]-deadenylase

Systematic name: [L-glutamate:ammonia ligase (ADP-forming)]-O4-(5'-adenylyl)-L-tyrosine adenylyltransferase

Comments: This activity is carried out by a bacterial bifunctional enzyme that also adenylates glutamate-ammonia ligase (EC 2.7.7.42, [glutamate-ammonia-ligase] adenylyltransferase) [3,5]. The two activities are present on separate domains.

References:

1. Anderson, W.B. and Stadtman, E.R. Glutamine synthetase deadenylation: a phosphorolytic reaction yielding ADP as nucleotide product. Biochem. Biophys. Res. Commun. 41 (1970) 704-709. [PMID: 4920873]

2. Anderson, W.B. and Stadtman, E.R. Purification and functional roles of the P I and P II components of Escherichia coli glutamine synthetase deadenylylation system. Arch. Biochem. Biophys. 143 (1971) 428-443. [PMID: 4934180]

3. Jaggi, R., van Heeswijk, W.C., Westerhoff, H.V., Ollis, D.L. and Vasudevan, S.G. The two opposing activities of adenylyl transferase reside in distinct homologous domains, with intramolecular signal transduction. EMBO J. 16 (1997) 5562-5571. [PMID: 9312015]

4. Xu, Y., Wen, D., Clancy, P., Carr, P.D., Ollis, D.L. and Vasudevan, S.G. Expression, purification, crystallization, and preliminary X-ray analysis of the N-terminal domain of Escherichia coli adenylyl transferase. Protein Expr. Purif. 34 (2004) 142-146. [PMID: 14766310]

5. Xu, Y., Zhang, R., Joachimiak, A., Carr, P.D., Huber, T., Vasudevan, S.G. and Ollis, D.L. Structure of the N-terminal domain of Escherichia coli glutamine synthetase adenylyltransferase. Structure 12 (2004) 861-869. [PMID: 15130478]

[EC 2.7.7.89 created 1972 as EC 3.1.4.15, transferred 2015 to EC 2.7.7.89]

EC 2.7.8.42

Accepted name: Kdo2-lipid A phosphoethanolamine 7''-transferase

Reaction: (1) diacylphosphatidylethanolamine + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A = diacyglycerol + 7-O-[2-aminoethoxy(hydroxy)phosphoryl]-α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A
(2) diacylphosphatidylethanolamine + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid IVA = diacyglycerol + 7-O-[2-aminoethoxy(hydroxy)phosphoryl]-α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid IVA

Glossary: lipid A = 2-deoxy-2-[(3R)-3-(tetradecanoyloxy)tetradecanamido]-3-O-[(3R)-3-(dodecanoyloxy)tetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate
lipid IVA = 2-deoxy-2-[(3R)-3-hydroxytetradecanamido]-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phospho-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-[(3R)-3-hydroxytetradecanamido]-α-D-glucopyranosyl phosphate

Other name(s): eptB (gene name)

Systematic name: diacylphosphatidylethanolamine:α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid-A 7''-phosphoethanolaminetransferase

Comments: The enzyme has been characterized from the bacterium Escherichia coli. It is activated by Ca2+ ions and is is silenced by the sRNA MgrR.

References:

1. Kanipes, M.I., Lin, S., Cotter, R.J. and Raetz, C.R. Ca2+-induced phosphoethanolamine transfer to the outer 3-deoxy-D-manno-octulosonic acid moiety of Escherichia coli lipopolysaccharide. A novel membrane enzyme dependent upon phosphatidylethanolamine. J. Biol. Chem. 276 (2001) 1156-1163. [PMID: 11042192]

2. Reynolds, C.M., Kalb, S.R., Cotter, R.J. and Raetz, C.R. A phosphoethanolamine transferase specific for the outer 3-deoxy-D-manno-octulosonic acid residue of Escherichia coli lipopolysaccharide. Identification of the eptB gene and Ca2+ hypersensitivity of an eptB deletion mutant. J. Biol. Chem. 280 (2005) 21202-21211. [PMID: 15795227]

3. Moon, K., Six, D.A., Lee, H.J., Raetz, C.R. and Gottesman, S. Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification. Mol. Microbiol. 89 (2013) 52-64. [PMID: 23659637]

[EC 2.7.8.42 created 2015]

EC 2.8.1.13

Accepted name: tRNA-uridine 2-sulfurtransferase

Reaction: a [protein]-S-sulfanyl-L-cysteine + uridine34 in tRNA + ATP + reduced acceptor = a [protein]-L-cysteine + 2-thiouridine34 in tRNA + AMP + diphosphate + acceptor

Other name(s): mnmA (gene name)

Systematic name: [protein]-S-sulfanyl-L-cysteine:tRNA (uridine34-2-O)-sulfurtransferase

Comments: The enzyme, found in bacteria, catalyses formation of the 2-thiouridine modification in the wobble position of tRNAGln, tRNALys and tRNAGlu.

References:

1. Kambampati, R. and Lauhon, C.T. MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli. Biochemistry 42 (2003) 1109-1117. [PMID: 12549933]

2. Ikeuchi, Y., Shigi, N., Kato, J., Nishimura, A. and Suzuki, T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol. Cell 21 (2006) 97-108. [PMID: 16387657]

[EC 2.8.1.13 created 2015]

EC 2.8.1.14

Accepted name: tRNA-5-taurinomethyluridine 2-sulfurtransferase

Reaction: a [protein]-S-sulfanyl-L-cysteine + 5-taurinomethyluridine34 in tRNA + ATP + reduced acceptor = a [protein]-L-cysteine + 5-taurinomethyl-2-thiouridine34 in tRNA + AMP + diphosphate + acceptor

Other name(s): MTU1 (gene name); SLM3 (gene name); MTO2 (gene name)

Systematic name: [protein]-S-sulfanyl-L-cysteine:tRNA (5-taurinomethyluridine34 2-O)-sulfurtransferase

Comments: The enzyme, found in mitochondria, catalyses formation of 5-taurinomethyl-2-thiouridine in the wobble position of mitochondrial tRNAGln, tRNALys and tRNAGlu.

References:

1. Umeda, N., Suzuki, T., Yukawa, M., Ohya, Y., Shindo, H., Watanabe, K. and Suzuki, T. Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases. J. Biol. Chem. 280 (2005) 1613-1624. [PMID: 15509579]

2. Wang, X., Yan, Q. and Guan, M.X. Deletion of the MTO2 gene related to tRNA modification causes a failure in mitochondrial RNA metabolism in the yeast Saccharomyces cerevisiae. FEBS Lett. 581 (2007) 4228-4234. [PMID: 17706197]

[EC 2.8.1.14 created 2015]

EC 2.8.3.23

Accepted name: caffeate CoA-transferase

Reaction: 3-(3,4-dihydroxyphenyl)propanoyl-CoA + (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate = 3-(3,4-dihydroxyphenyl)propanoate + (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl-CoA

Glossary: 3-(3,4-dihydroxyphenyl)propanoate = hydrocaffeate
(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate = (2E)-3-(3,4-dihydroxyphenyl)acrylate = trans-caffeate

Other name(s): CarA

Systematic name: 3-(3,4-dihydroxyphenyl)propanoyl-CoA:(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate CoA-transferase

Comments: The enzyme, isolated from the bacterium Acetobacterium woodii, catalyses an energy-saving CoA loop for caffeate activation. In addition to caffeate, the enzyme can utilize 4-coumarate or ferulate as CoA acceptor.

References:

1. Hess, V., Gonzalez, J.M., Parthasarathy, A., Buckel, W. and Muller, V. Caffeate respiration in the acetogenic bacterium Acetobacterium woodii: a coenzyme A loop saves energy for caffeate activation. Appl. Environ. Microbiol. 79 (2013) 1942-1947. [PMID: 23315745]

[EC 2.8.3.23 created 2015]

*EC 2.8.4.3

Accepted name: tRNA-2-methylthio-N6-dimethylallyladenosine synthase

Reaction: N6-dimethylallyladenine37 in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = 2-methylthio-N6-dimethylallyladenine37 in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine + electron acceptor (overall reaction)
(1a) N6-dimethylallyladenine37 in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine + reduced electron acceptor = 2-thio-N6-dimethylallyladenine37 in tRNA + (sulfur carrier) + L-methionine + 5'-deoxyadenosine + electron acceptor
(1b) S-adenosyl-L-methionine + 2-thio-N6-dimethylallyladenine37 in tRNA = S-adenosyl-L-homocysteine + 2-methylthio-N6-dimethylallyladenine37 in tRNA

For diagram of reaction click here.

Other name(s): MiaB; 2-methylthio-N-6-isopentenyl adenosine synthase; tRNA-i6A37 methylthiotransferase

Systematic name: tRNA (N6-dimethylallyladenosine37):sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-methylthiotransferase

Comments: This bacterial enzyme binds two [4Fe-4S] clusters as well as the transferred sulfur [3]. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. The sulfur donor is believed to be one of the [4Fe-4S] clusters, which is sacrificed in the process, so that in vitro the reaction is a single turnover. The identity of the electron donor is not known.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Pierrel, F., Bjork, G.R., Fontecave, M. and Atta, M. Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein. J. Biol. Chem. 277 (2002) 13367-13370. [PMID: 11882645]

2. Pierrel, F., Hernandez, H.L., Johnson, M.K., Fontecave, M. and Atta, M. MiaB protein from Thermotoga maritima. Characterization of an extremely thermophilic tRNA-methylthiotransferase. J. Biol. Chem. 278 (2003) 29515-29524. [PMID: 12766153]

3. Pierrel, F., Douki, T., Fontecave, M. and Atta, M. MiaB protein is a bifunctional radical-S-adenosylmethionine enzyme involved in thiolation and methylation of tRNA. J. Biol. Chem. 279 (2004) 47555-47563. [PMID: 15339930]

4. Hernandez, H.L., Pierrel, F., Elleingand, E., Garcia-Serres, R., Huynh, B.H., Johnson, M.K., Fontecave, M. and Atta, M. MiaB, a bifunctional radical-S-adenosylmethionine enzyme involved in the thiolation and methylation of tRNA, contains two essential [4Fe-4S] clusters. Biochemistry 46 (2007) 5140-5147. [PMID: 17407324]

5. Landgraf, B.J., Arcinas, A.J., Lee, K.H. and Booker, S.J. Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. J. Am. Chem. Soc. 135 (2013) 15404-15416. [PMID: 23991893]

[EC 2.8.4.3 created 2014, modified 2015]

*EC 2.8.4.5

Accepted name: tRNA (N6-L-threonylcarbamoyladenosine37-C2)-methylthiotransferase

Reaction: N6-L-threonylcarbamoyladenine37 in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = 2-methylthio-N6-L-threonylcarbamoyladenine37 in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine + electron acceptor (overall reaction)
(1a) N6-L-threonylcarbamoyladenine37 in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine + reduced electron acceptor = 2-thio-N6-L-threonylcarbamoyladenine37 in tRNA + (sulfur carrier) + L-methionine + 5-deoxyadenosine + electron acceptor
(1b) S-adenosyl-L-methionine + 2-thio-N6-L-threonylcarbamoyladenine37 in tRNA = S-adenosyl-L-homocysteine + 2-methylthio-N6-L-threonylcarbamoyladenine37 in tRNA

For diagram of reaction click here.

Glossary: N6-L-threonylcarbamoyladenine37 = t6A37
2-thio-N6-L-threonylcarbamoyladenine37 = ms2t6A37

Other name(s): MtaB; methylthio-threonylcarbamoyl-adenosine transferase B; CDKAL1 (gene name)

Systematic name: tRNA (N6-L-threonylcarbamoyladenosine37):sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-methylthiotransferase

Comments: The enzyme, which is a member of the S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes superfamily, binds two [4Fe-4S] clusters as well as the transferred sulfur. The sulfur donor is believed to be one of the [4Fe-4S] clusters, which is sacrificed in the process, so that in vitro the reaction is a single turnover. The identity of the electron donor is not known.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Arragain, S., Handelman, S.K., Forouhar, F., Wei, F.Y., Tomizawa, K., Hunt, J.F., Douki, T., Fontecave, M., Mulliez, E. and Atta, M. Identification of eukaryotic and prokaryotic methylthiotransferase for biosynthesis of 2-methylthio-N6-threonylcarbamoyladenosine in tRNA. J. Biol. Chem. 285 (2010) 28425-28433. [PMID: 20584901]

[EC 2.8.4.5 created 2014, modified 2015]

*EC 3.1.1.59

Accepted name: juvenile-hormone esterase

Reaction: (1) juvenile hormone I + H2O = juvenile hormone I acid + methanol
(2) juvenile hormone III + H2O = juvenile hormone III acid + methanol

For diagram of reaction click here.

Glossary: juvenile hormone I = methyl (2E,6E,10R,11S)-10,11-epoxy-7-ethyl-3,11-dimethyl-2,6-tridecadienoate
juvenile hormone I acid = (2E,6E,10R,11S)-10,11-epoxy-7-ethyl-3,11-dimethyl-2,6-tridecadienoate
juvenile hormone III = methyl (2E,6E,10R)-10,11-epoxy-3,7,11-trimethyldodeca-2,6-dienoate
juvenile hormone III acid = (2E,6E,10R)-10,11-epoxy-3,7,11-trimethyldodeca-2,6-dienoate

Other name(s): JH-esterase; juvenile hormone analog esterase; juvenile hormone carboxyesterase; methyl-(2E,6E)-(10R,11S)-10,11-epoxy-3,7,11-trimethyltrideca-2,6-dienoate acylhydrolase

Systematic name: methyl-(2E,6E,10R)-10,11-epoxy-3,7,11-trimethyltrideca-2,6-dienoate acylhydrolase

Comments: Demethylates the insect juvenile hormones JH1 and JH3, but does not hydrolyse the analogous ethyl or isopropyl esters.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 50812-15-2

References:

1. de Kort, C.A.D. and Granger, N.A. Regulation of the juvenile hormone titer. Annu. Rev. Entomol. 26 (1981) 1-28.

2. Mitsui, T., Riddiford, L.M. and Bellamy, G. Metabolism of juvenile hormone by the epidermis of the tobacco hornworm (Manduca sexta). Insect Biochem. 9 (1979) 637-643.

[EC 3.1.1.59 created 1989, modified 2015]

*EC 3.1.1.97

Accepted name: methylated diphthine methylhydrolase

Reaction: diphthine methyl ester-[translation elongation factor 2] + H2O = diphthine-[translation elongation factor 2] + methanol

For diagram of reaction click here.

Glossary: diphthine methyl ester = 2-[(3S)-3-carboxy methyl ester-3-(trimethylammonio)propyl]-L-histidine
diphthine = 2-[(3S)-3-carboxy-3-(trimethylammonio)propyl]-L-histidine

Other name(s): Dph7; diphthine methylesterase (incorrect)

Systematic name: diphthine methyl ester acylhydrolase

Comments: The protein is only present in eukaryotes.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Lin, Z., Su, X., Chen, W., Ci, B., Zhang, S. and Lin, H. Dph7 catalyzes a previously unknown demethylation step in diphthamide biosynthesis. J. Am. Chem. Soc. 136 (2014) 6179-6182. [PMID: 24739148]

[EC 3.1.1.97 created 2014, modified 2015]

EC 3.1.1.98

Accepted name: [Wnt protein] O-palmitoleoyl-L-serine hydrolase

Reaction: [Wnt]-O-(9Z)-hexadec-9-enoyl-L-serine + H2O = [Wnt]-L-serine + (9Z)-hexadec-9-enoate

Glossary: (9Z)-hexadec-9-enoate = palmitoleoate

Other name(s): Notum

Systematic name: [Wnt]-O-(9Z)-hexadec-9-enoyl-L-serine acylhydrolase

Comments: The enzyme removes the palmitoleate modification that is introduced to specific L-serine residues in Wnt proteins by EC 2.3.1.250, [Wnt protein]-O-palmitoleoyl transferase.

References:

1. Kakugawa, S., Langton, P.F., Zebisch, M., Howell, S.A., Chang, T.H., Liu, Y., Feizi, T., Bineva, G., O'Reilly, N., Snijders, A.P., Jones, E.Y. and Vincent, J.P. Notum deacylates Wnt proteins to suppress signalling activity. Nature (2015) . [PMID: 25731175]

[EC 3.1.1.98 created 2015]

*EC 3.1.3.69

Accepted name: glucosylglycerol 3-phosphatase

Reaction: 2-O-(α-D-glucosyl)-sn-glycerol-3-phosphate + H2O = 2-O-(α-D-glucopyranosyl)glycerol + phosphate

Other name(s): salt tolerance protein A; StpA; 2-(β-D-glucosyl)-sn-glycerol-3-phosphate phosphohydrolase (incorrect)

Systematic name: 2-O-(α-D-glucopyranosyl)-sn-glycerol-3-phosphate phosphohydrolase

Comments: Acts with EC 2.4.1.213 (glucosylglycerol-phosphate synthase) to form glucosylglycerol, an osmolyte that endows cyanobacteria with resistance to salt.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 161515-14-6

References:

1. Hagemann, M. and Erdmann, N. Activation and pathway of glucosylglycerol biosynthesis in the cyanobacterium Synechocystis sp. PCC 6803. Microbiology 140 (1994) 1427-1431.

2. Hagemann, M., Richter, S., Zuther, E. and Schoor, A. Characterization of a glucosylglycerol-phosphate-accumulating salt-sensitive mutant of the cyanobacterium Synechocystis sp. strain PCC 6803. Arch. Microbiol. 166 (1996) 83-91. [PMID: 8772170]

3. Hagemann, M., Schoor, A., Jeanjean, R., Zuther, E. and Joset, F. The gene stpA from Synechocystis sp. strain PCC 6803 encodes for the glucosylglycerol-phosphate phosphatase involved in cyanobacterial salt adaptation. J. Bacteriol. 179 (1997) 1727-1733. [PMID: 9045835]

[EC 3.1.3.69 created 2001, modified 2015]

[EC 3.1.4.15 Transferred entry: adenylyl-[glutamateammonia ligase] hydrolase. As it has been shown that the enzyme catalyses a transfer of the adenylyl group to phosphate, the enzyme has been transferred to EC 2.7.7.89, adenylyl-[glutamateammonia ligase] phosphorylase (EC 3.1.4.15 created 1972, deleted 2015)]

EC 3.4.24.88

Accepted name: desampylase

Reaction: an N6-[small archaeal modifier protein]-[protein]-L-lysine + H2O = a [protein]-L-lysine + a small archaeal modifier protein

Glossary: SAMP = small archaeal modifier protein

Other name(s): SAMP-protein conjugate cleaving protease; HvJAMM1

Systematic name: N6-[small archaeal modifier protein]-[protein]-L-lysine hydrolase

Comments: The enzyme, characterized from the archaeon Haloferax volcanii, specifically cleaves the ubiquitin-like small modifier proteins SAMP1 and SAMP2 from protein conjugates, hydrolysing the isopeptide bond between a lysine residue of the target protein and the C-terminal glycine of the modifier protein. The enzyme contains Zn2+. cf. EC 3.4.19.12, ubiquitinyl hydrolase 1. In peptidase family M67.

References:

1. Hepowit, N.L., Uthandi, S., Miranda, H.V., Toniutti, M., Prunetti, L., Olivarez, O., De Vera, I.M., Fanucci, G.E., Chen, S. and Maupin-Furlow, J.A. Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates. Mol. Microbiol. 86 (2012) 971-987. [PMID: 22970855]

[EC 3.4.24.88 created 2015]

EC 3.4.24.89

Accepted name: Pro-Pro endopeptidase

Reaction: The enzyme catalyses the hydrolytic cleavage of peptide bonds between two proline residues

Other name(s): metalloprotease CD2830

Comments: This metalloprotease, which is secreted by the bacterium Peptoclostridium difficile, contains zinc.

References:

1. Cafardi, V., Biagini, M., Martinelli, M., Leuzzi, R., Rubino, J.T., Cantini, F., Norais, N., Scarselli, M., Serruto, D. and Unnikrishnan, M. Identification of a novel zinc metalloprotease through a global analysis of Clostridium difficile extracellular proteins. PLoS One 8 (2013) e81306. [PMID: 24303041]

2. Hensbergen, P.J., Klychnikov, O.I., Bakker, D., van Winden, V.J., Ras, N., Kemp, A.C., Cordfunke, R.A., Dragan, I., Deelder, A.M., Kuijper, E.J., Corver, J., Drijfhout, J.W. and van Leeuwen, H.C. A novel secreted metalloprotease (CD2830) from Clostridium difficile cleaves specific proline sequences in LPXTG cell surface proteins. Mol. Cell. Proteomics 13 (2014) 1231-1244. [PMID: 24623589]

[EC 3.4.24.89 created 2015]

EC 4.1.1.101

Accepted name: malolactic enzyme

Reaction: (S)-malate = (S)-lactate + CO2

Other name(s): mleA (gene name); mleS (gene name)

Systematic name: (S)-malate carboxy-lyase

Comments: The enzyme is involved in the malolactic fermentation of wine, which results in a natural decrease in acidity and favorable changes in wine flavors. It has been purified from several lactic acid bacteria, including Leuconostoc mesenteroides [1], Lactobacillus plantarum [2], and Oenococcus oeni [3,4]. The enzyme contains a tightly bound NAD+ cofactor and requires Mn2+.

References:

1. Lonvaud-Funel, A. and de Saad, A.M. Purification and properties of a malolactic Enzyme from a strain of Leuconostoc mesenteroides isolated from grapes. Appl. Environ. Microbiol. 43 (1982) 357-361. [PMID: 16345941]

2. Caspritz, G. and Radler, F. Malolactic enzyme of Lactobacillus plantarum. Purification, properties, and distribution among bacteria. J. Biol. Chem. 258 (1983) 4907-4910. [PMID: 6833282]

3. Naouri, P., Chagnaud, P., Arnaud, A. and Galzy, P. Purification and properties of a malolactic enzyme from Leuconostoc oenos ATCC 23278. J. Basic Microbiol. 30 (1990) 577-585. [PMID: 2097345]

4. Schumann, C., Michlmayr, H., Del Hierro, A.M., Kulbe, K.D., Jiranek, V., Eder, R. and Nguyen, T.H. Malolactic enzyme from Oenococcus oeni: heterologous expression in Escherichia coli and biochemical characterization. Bioengineered 4 (2013) 147-152. [PMID: 23196745]

[EC 4.1.1.101 created 2015]

*EC 4.2.1.42

Accepted name: galactarate dehydratase

Reaction: galactarate = (2R,3S)-2,3-dihydroxy-5-oxohexanedioate + H2O

Glossary: galactarate = (2R,3S,4R,5S)-2,3,4,5-tetrahydroxyhexanedioate
(2R,3S)-2,3-dihydroxy-5-oxohexanedioate = 3-deoxy-L-threo-hex-2-ulosarate

Other name(s): D-galactarate hydro-lyase; D-galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming); talrD (gene name)/galrD (gene name)

Systematic name: galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)

Comments: The enzyme from the bacterium Escherichia coli is specific for galactarate [2], while the enzyme from Salmonella typhimurium also has activity with L-talarate (cf. EC 4.2.1.156, L-talarate dehydratase) [3]. cf. EC 4.2.1.158, galactarate dehydratase (D-threo-forming).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37290-78-1

References:

1. Blumenthal, H.J. and Jepson, T. Galactarate dehydrase. Methods Enzymol. 9 (1966) 665-669.

2. Hubbard, B.K., Koch, M., Palmer, D.R., Babbitt, P.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry 37 (1998) 14369-14375. [PMID: 9772162]

3. Yew, W.S., Fedorov, A.A., Fedorov, E.V., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2. Biochemistry 46 (2007) 9564-9577. [PMID: 17649980]

4. Rakus, J.F., Kalyanaraman, C., Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F.P., Toro, R., Bonanno, J., Bain, K., Sauder, J.M., Burley, S.K., Almo, S.C., Jacobson, M.P. and Gerlt, J.A. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis. Biochemistry 48 (2009) 11546-11558. [PMID: 19883118]

[EC 4.2.1.42 created 1972, modified 2015]

EC 4.2.1.156

Accepted name: L-talarate dehydratase

Reaction: L-altarate = 5-dehydro-4-deoxy-D-glucarate + H2O

Glossary: L-altrarate = L-talarate = (2R,3R,4S,5R)-2,3,4,5-tetrahydroxyhexanedioate

Other name(s): L-talarate hydro-lyase

Systematic name: L-altarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)

Comments: Requires Mg2+. The enzyme, isolated from the bacteria Salmonella typhimurium and Polaromonas sp. JS666, also has activity with galactarate (cf. EC 4.2.1.42, galactarate dehydratase).

References:

1. Yew, W.S., Fedorov, A.A., Fedorov, E.V., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2. Biochemistry 46 (2007) 9564-9577. [PMID: 17649980]

[EC 4.2.1.156 created 2015]

EC 4.2.1.157

Accepted name: (R)-2-hydroxyisocaproyl-CoA dehydratase

Reaction: (R)-2-hydroxy-4-methylpentanoyl-CoA = 4-methylpent-2-enoyl-CoA + H2O

Other name(s): 2-hydroxyisocaproyl-CoA dehydratase; HadBC

Systematic name: (R)-2-hydroxy-4-methylpentanoyl-CoA hydro-lyase

Comments: The enzyme, isolated from the bacterium Peptoclostridium difficile, is involved in the reductive branch of L-leucine fermentation. It catalyses an α/β-dehydration, which depends on the reductive formation of ketyl radicals on the substrate generated by injection of a single electron from the ATP-dependent activator protein HadI.

References:

1. Kim, J., Darley, D. and Buckel, W. 2-Hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium difficile. FEBS J. 272 (2005) 550-561. [PMID: 15654892]

2. Knauer, S.H., Buckel, W. and Dobbek, H. Structural basis for reductive radical formation and electron recycling in (R)-2-hydroxyisocaproyl-CoA dehydratase. J. Am. Chem. Soc. 133 (2011) 4342-4347. [PMID: 21366233]

[EC 4.2.1.157 created 2015]

EC 4.2.1.158

Accepted name: galactarate dehydratase (D-threo-forming)

Reaction: galactarate = (2S,3R)-2,3-dihydroxy-5-oxohexanedioate + H2O

Glossary: galactarate = (2R,3S,4R,5S)-2,3,4,5-tetrahydroxyhexanedioate
(2S,3R)-2,3-dihydroxy-5-oxohexanedioate = 3-deoxy-D-threo-hex-2-ulosarate

Systematic name: galactarate hydro-lyase (3-deoxy-D-threo-hex-2-ulosarate-forming)

Comments: The enzyme has been characterized from the bacterium Oceanobacillus iheyensis. cf. EC 4.2.1.42, galactarate dehydratase.

References:

1. Rakus, J.F., Kalyanaraman, C., Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F.P., Toro, R., Bonanno, J., Bain, K., Sauder, J.M., Burley, S.K., Almo, S.C., Jacobson, M.P. and Gerlt, J.A. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis. Biochemistry 48 (2009) 11546-11558. [PMID: 19883118]

[EC 4.2.1.158 created 2015]

EC 5.1.1.21

Accepted name: isoleucine 2-epimerase

Reaction: L-isoleucine = D-allo-isoleucine

Other name(s): BCAA racemase

Systematic name: isoleucine 2-epimerase

Comments: A pyridoxal phosphate protein. The enzyme, characterized from the bacterium Lactobacillus buchneri, specifically catalyses racemization of nonpolar amino acids at the C-2 position.

References:

1. Mutaguchi, Y., Ohmori, T., Wakamatsu, T., Doi, K. and Ohshima, T. Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species. J. Bacteriol. 195 (2013) 5207-5215. [PMID: 24039265]

[EC 5.1.1.21 created 2015]

EC 5.1.3.33

Accepted name: 2-epi-5-epi-valiolone epimerase

Reaction: 2-epi-5-epi-valiolone = 5-epi-valiolone

Glossary: 2-epi-5-epi-valiolone= (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexanone
5-epi-valiolone = (2R,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexanone

Other name(s): CetB; EVE

Systematic name: 2-epi-5-epi-valiolone 2-epimerase

Comments: The enzyme, characterized from the bacterium Actinomyces sp. Lu 9419, is involved in the biosynthesis of the antitumor agent cetoniacytone A.

References:

1. Wu, X., Flatt, P.M., Xu, H. and Mahmud, T. Biosynthetic gene cluster of cetoniacytone A, an unusual aminocyclitol from the endosymbiotic Bacterium Actinomyces sp. Lu 9419. Chembiochem 10 (2009) 304-314. [PMID: 19101977]

[EC 5.1.3.33 created 2015]

EC 5.1.3.34

Accepted name: monoglucosyldiacylglycerol epimerase

Reaction: a 1,2-diacyl-3-O-(β-D-glucopyranosyl)-sn-glycerol = a 1,2-diacyl-3-O-(β-D-galactopyranosyl)-sn-glycerol

Glossary: a 1,2-diacyl-3-O-(β-D-glucopyranosyl)-sn-glycerol = β-monoglucosyldiacylglycerol = GlcDG
a 1,2-diacyl-3-O-(β-D-galactopyranosyl)-sn-glycerol = β-monogalactosyldiacylglycerol = MGDG

Other name(s): glucolipid epimerase; mgdE (gene name)

Systematic name: 1,2-diacyl-3-O-(β-D-glucopyranosyl)-sn-glycerol 4-epimerase

Comments: The enzyme, characterized from cyanobacteria, is involves in the biosynthesis of galactolipids found in their photosynthetic membranes.

References:

1. Sato, N. and Murata, N. Lipid biosynthesis in the blue-green alga, Anabaena variabilis II. Fatty acids and lipid molecular species. Biochim. Biophys. Acta 710 (1982) 279-289.

2. Awai, K., Ohta, H. and Sato, N. Oxygenic photosynthesis without galactolipids. Proc. Natl. Acad. Sci. USA 111 (2014) 13571-13575. [PMID: 25197079]

[EC 5.1.3.34 created 2015]

EC 5.1.3.35

Accepted name: 2-epi-5-epi-valiolone 7-phosphate 2-epimerase

Reaction: 2-epi-5-epi-valiolone 7-phosphate = 5-epi-valiolone 7-phosphate

Glossary: 2-epi-5-epi-valiolone 7-phosphate = (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(phosphonooxymethyl)cyclohexanone
5-epi-valiolone 7-phosphate = (2R,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(phosphonooxymethyl)cyclohexanone

Other name(s): AcbO

Systematic name: 2-epi-5-epi-valiolone-7-phosphate 2-epimerase

Comments: The enzyme, isolated from the bacterium Actinoplanes sp. SE 50/110, is involved in the biosynthesis of the α-glucosidase inhibitor acarbose.

References:

1. Zhang, C.S., Podeschwa, M., Altenbach, H.J., Piepersberg, W. and Wehmeier, U.F. The acarbose-biosynthetic enzyme AcbO from Actinoplanes sp. SE 50/110 is a 2-epi-5-epi-valiolone-7-phosphate 2-epimerase. FEBS Lett. 540 (2003) 47-52. [PMID: 12681481]

[EC 5.1.3.35 created 2015]

EC 5.1.99.7

Accepted name: dihydroneopterin triphosphate 2'-epimerase

Reaction: 7,8-dihydroneopterin 3'-triphosphate = 7,8-dihydromonapterin 3'-triphosphate

For diagram of reaction click here.

Glossary: 7,8-dihydroneopterin 3'-triphosphate = (2R,3S)-3-(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)-2,3-dihydroxypropyl triphosphate
7,8-dihydromonapterin 3'-triphosphate = (2S,3S)-3-(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)-2,3-dihydroxypropyl triphosphate

Other name(s): D-erythro-7,8-dihydroneopterin triphosphate epimerase; folX (gene name)

Systematic name: 7,8-dihydroneopterin 3'-triphosphate 2'-epimerase

Comments: The enzyme, found in gammaproteobacteria, has almost no activity with 7,8-dihydroneopterin [2].

References:

1. Ahn, C., Byun, J. and Yim, J. Purification, cloning, and functional expression of dihydroneopterin triphosphate 2'-epimerase from Escherichia coli. J. Biol. Chem. 272 (1997) 15323-15328. [PMID: 9182560]

2. Haussmann, C., Rohdich, F., Schmidt, E., Bacher, A. and Richter, G. Biosynthesis of pteridines in Escherichia coli. Structural and mechanistic similarity of dihydroneopterin-triphosphate epimerase and dihydroneopterin aldolase. J. Biol. Chem. 273 (1998) 17418-17424. [PMID: 9651328]

[EC 5.1.99.7 created 2015]

EC 5.3.3.19

Accepted name: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase

Reaction: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate = 3-[(1E,4R)-4-hydroxycyclohex-2-en-1-ylidene]-2-oxopropanoate

Glossary: L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine

Other name(s): BacB

Systematic name: 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase

Comments: The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. The enzyme can interconvert the (E) isomer formed in the reaction into the (Z) isomer [2], although this isomerization is not part of the pathway leading to bacilysin [3].

References:

1. Mahlstedt, S.A. and Walsh, C.T. Investigation of anticapsin biosynthesis reveals a four-enzyme pathway to tetrahydrotyrosine in Bacillus subtilis. Biochemistry 49 (2010) 912-923. [PMID: 20052993]

2. Parker, J.B. and Walsh, C.T. Olefin isomerization regiochemistries during tandem action of BacA and BacB on prephenate in bacilysin biosynthesis. Biochemistry 51 (2012) 3241-3251. [PMID: 22483065]

3. Parker, J.B. and Walsh, C.T. Action and timing of BacC and BacD in the late stages of biosynthesis of the dipeptide antibiotic bacilysin. Biochemistry 52 (2013) 889-901. [PMID: 23317005]

[EC 5.3.3.19 created 2015]

EC 5.4.1.4

Accepted name: D-galactarolactone isomerase

Reaction: D-galactaro-1,5-lactone = D-galactaro-1,4-lactone

Other name(s): GLI

Systematic name: D-galactaro-1,5-lactone isomerase (D-galactaro-1,4-lactone-forming)

Comments: The enzyme, characterized from the bacterium Agrobacterium fabrum strain C58, belongs to the amidohydrolase superfamily. It participates in the degradation of D-galacturonate.

References:

1. Bouvier, J.T., Groninger-Poe, F.P., Vetting, M., Almo, S.C. and Gerlt, J.A. Galactaro δ-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry 53 (2014) 614-616. [PMID: 24450804]

[EC 5.4.1.4 created 2015]

EC 5.4.99.63

Accepted name: ethylmalonyl-CoA mutase

Reaction: (2R)-ethylmalonyl-CoA = (2S)-methylsuccinyl-CoA

Other name(s): Ecm

Systematic name: (2R)-ethylmalonyl-CoA CoA-carbonylmutase

Comments: The enzyme, characterized from the bacterium Rhodobacter sphaeroides, is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Requires coenzyme B12 for activity.

References:

1. Erb, T.J., Retey, J., Fuchs, G. and Alber, B.E. Ethylmalonyl-CoA mutase from Rhodobacter sphaeroides defines a new subclade of coenzyme B12-dependent acyl-CoA mutases. J. Biol. Chem. 283 (2008) 32283-32293. [PMID: 18819910]

[EC 5.4.99.63 created 2015]

EC 5.5.1.27

Accepted name: D-galactarolactone cycloisomerase

Reaction: (1) D-galactaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate
(2) D-glucaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate

Other name(s): GCI

Systematic name: D-galactaro-1,4-lactone lyase (ring-opening)

Comments: The enzyme, characterized from the bacterium Agrobacterium fabrum strain C58, is involved in degradation of D-galacturonate and D-glucuronate. Activity with D-galactaro-1,4-lactone is 4-fold higher than with D-glucaro-1,4-lactone.

References:

1. Andberg, M., Maaheimo, H., Boer, H., Penttila, M., Koivula, A. and Richard, P. Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate. J. Biol. Chem. 287 (2012) 17662-17671. [PMID: 22493433]

2. Bouvier, J.T., Groninger-Poe, F.P., Vetting, M., Almo, S.C. and Gerlt, J.A. Galactaro δ-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry 53 (2014) 614-616. [PMID: 24450804]

[EC 5.5.1.27 created 2015]

EC 6.2.1.45

Accepted name: E1 ubiquitin-activating enzyme

Reaction: ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine

Other name(s): ubiquitin activating enzyme; E1; ubiquitin-activating enzyme E1

Systematic name: ubiquitin:[E1 ubiquitin-activating enzyme] ligase (AMP-forming)

Comments: Catalyses the ATP-dependent activation of ubiquitin through the formation of a thioester bond between the C-terminal glycine of ubiquitin and the sulfhydryl side group of a cysteine residue in the E1 protein. The two-step reaction consists of the ATP-dependent formation of an E1-ubiquitin adenylate intermediate in which the C-terminal glycine of ubiquitin is bound to AMP via an acyl-phosphate linkage, then followed by the conversion to an E1-ubiquitin thioester bond via the cysteine residue on E1 in the second step.

References:

1. Haas, A.L., Warms, J.V., Hershko, A. and Rose, I.A. Ubiquitin-activating enzyme. Mechanism and role in protein-ubiquitin conjugation. J. Biol. Chem. 257 (1982) 2543-2548. [PMID: 6277905]

2. Huzil, J.T., Pannu, R., Ptak, C., Garen, G. and Ellison, M.J. Direct catalysis of lysine 48-linked polyubiquitin chains by the ubiquitin-activating enzyme. J. Biol. Chem. 282 (2007) 37454-37460. [PMID: 17951259]

3. Zheng, M., Liu, J., Yang, Z., Gu, X., Li, F., Lou, T., Ji, C. and Mao, Y. Expression, purification and characterization of human ubiquitin-activating enzyme, UBE1. Mol. Biol. Rep. 37 (2010) 1413-1419. [PMID: 19343538]

4. Carvalho, A.F., Pinto, M.P., Grou, C.P., Vitorino, R., Domingues, P., Yamao, F., Sa-Miranda, C. and Azevedo, J.E. High-yield expression in Escherichia coli and purification of mouse ubiquitin-activating enzyme E1. Mol Biotechnol 51 (2012) 254-261. [PMID: 22012022]

[EC 6.2.1.45 created 2015]

EC 6.2.1.46

Accepted name: L-allo-isoleucine:holo-[CmaA peptidyl-carrier protein] ligase

Reaction: ATP + L-allo-isoleucine + holo-[CmaA peptidyl-carrier protein] = AMP + diphosphate + L-allo-isoleucyl-S-[CmaA peptidyl-carrier protein]

Other name(s): CmaA

Systematic name: L-allo-isoleucine:holo-[CmaA peptidyl-carrier protein] ligase (AMP-forming)

Comments: This two-domain protein from the bacterium Pseudomonas syringae contains an adenylation domain (A domain) and a thiolation domain (T domain). It catalyses the adenylation of L-allo-isoleucine and its attachment to the T domain. The enzyme is involved in the biosynthesis of the toxin coronatine, which mimics the plant hormone jasmonic acid isoleucine. Coronatine promotes opening of the plant stomata allowing bacterial invasion, which is followed by bacterial growth in the apoplast, systemic susceptibility, and disease.

References:

1. Couch, R., O'Connor, S.E., Seidle, H., Walsh, C.T. and Parry, R. Characterization of CmaA, an adenylation-thiolation didomain enzyme involved in the biosynthesis of coronatine. J. Bacteriol. 186 (2004) 35-42. [PMID: 14679222]

[EC 6.2.1.46 created 2015]

[EC 6.3.2.19 Deleted entry: ubiquitinprotein ligase. The ubiquitinylation process is now known to be performed by several enzymes in sequence, starting with EC 6.2.1.45 (ubiquitin-activating enzyme E1) and followed by several transfer reactions, including those of EC 2.3.2.23 (E2 ubiquitin-conjugating enzyme) and EC 2.3.2.27 (RING-type E3 ubiquitin transferase) (EC 6.3.2.19 created 1986, deleted 2015)]

[EC 6.3.2.21 Deleted entry: ubiquitincalmodulin ligase. The reaction is performed by the sequential action of EC 6.2.1.45 (ubiquitin-activating enzyme E1), several ubiquitin transferases and finally by EC 2.3.2.27 [ubiquitin transferase RING E3 (calmodulin-selective)] (EC 6.3.2.21 created 1990, deleted 2015)]

[EC 6.3.2.28 Transferred entry: L-amino-acid α-ligase. Now EC 6.3.2.49, L-alanine-L-anticapsin ligase (EC 6.3.2.28 created 2006, deleted 2015)]

EC 6.3.2.48

Accepted name: L-arginine-specific L-amino acid ligase

Reaction: ATP + L-arginine + an L-amino acid = ADP + phosphate + an L-arginyl-L-amino acid

Other name(s): RizA; L-amino acid ligase RizA

Systematic name: L-arginine:L-amino acid ligase (ADP-forming)

Comments: The enzyme, characterized from the bacterium Bacillus subtilis, requires Mn2+ for activity. It shows strict substrate specificity toward L-arginine as the first (N-terminal) amino acid of the product. The second amino acid could be any standard protein-building amino acid except for L-proline.

References:

1. Kino, K., Kotanaka, Y., Arai, T. and Yagasaki, M. A novel L-amino acid ligase from Bacillus subtilis NBRC3134, a microorganism producing peptide-antibiotic rhizocticin. Biosci. Biotechnol. Biochem. 73 (2009) 901-907. [PMID: 19352016]

[EC 6.3.2.48 created 2015]

EC 6.3.2.49

Accepted name: L-alanine-L-anticapsin ligase

Reaction: ATP + L-alanine + L-anticapsin = ADP + phosphate + bacilysin

Glossary: L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
bacilysin = L-alanyl-3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine

Other name(s): BacD; alanine-anticapsin ligase; L-Ala-L-anticapsin ligase; ywfE (gene name)

Systematic name: L-alanine:L-anticapsin ligase (ADP-forming)

Comments: The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the biosynthesis of the nonribosomally synthesized dipeptide antibiotic bacilysin, composed of L-alanine and L-anticapsin. The enzyme requires Mg2+ or Mn2+ for activity, and has a broad substrate specificity in vitro [1].

References:

1. Tabata, K., Ikeda, H. and Hashimoto, S. ywfE in Bacillus subtilis codes for a novel enzyme, L-amino acid ligase. J. Bacteriol. 187 (2005) 5195-5202. [PMID: 16030213]

2. Tsuda, T., Suzuki, T. and Kojima, S. Crystallization and preliminary X-ray diffraction analysis of Bacillus subtilis YwfE, an L-amino-acid ligase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68 (2012) 203-206. [PMID: 22298000]

3. Shomura, Y., Hinokuchi, E., Ikeda, H., Senoo, A., Takahashi, Y., Saito, J., Komori, H., Shibata, N., Yonetani, Y. and Higuchi, Y. Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis. Protein Sci. 21 (2012) 707-716. [PMID: 22407814]

4. Parker, J.B. and Walsh, C.T. Action and timing of BacC and BacD in the late stages of biosynthesis of the dipeptide antibiotic bacilysin. Biochemistry 52 (2013) 889-901. [PMID: 23317005]

[EC 6.3.2.49 created 2006 as EC 6.3.2.28, trasferred 2015 to EC 6.3.2.49]


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