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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.86 ketol-acid reductoisomerase (NADP+) (28 May 2015)
EC 1.1.1.382 ketol-acid reductoisomerase (NAD+) (28 May 2015)
EC 1.1.1.383 ketol-acid reductoisomerase [NAD(P)+] (28 May 2015)
EC 1.1.1.384 dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose 3-reductase (28 May 2015)
EC 1.1.1.385 dihydroanticapsin dehydrogenase (28 May 2015)
EC 1.1.1.386 ipsdienol dehydrogenase (28 May 2015)
EC 1.2.5.2 aldehyde dehydrogenase (quinone) (28 May 2015)
EC 1.2.98.1 formaldehyde dismutase (28 May 2015)
EC 1.2.99.3 transferred now EC 1.2.5.2 (28 May 2015)
EC 1.2.99.4 transferred now EC 1.2.98.1 (28 May 2015)
EC 1.3.8.12 (2S)-methylsuccinyl-CoA dehydrogenase (28 May 2015)
*EC 1.5.1.1 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (28 May 2015)
*EC 1.5.1.21 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (28 May 2015)
EC 1.5.1.49 1-pyrroline-2-carboxylate reductase [NAD(P)H] (28 May 2015)
EC 1.6.5.11 NADH dehydrogenase (quinone) (28 May 2015)
EC 1.6.99.5 transferred now EC 1.6.5.11 (28 May 2015)
*EC 1.7.3.6 hydroxylamine oxidase (cytochrome) (28 May 2015)
EC 1.10.5 With a quinone or related compound as acceptor (28 May 2015)
EC 1.10.5.1 ribosyldihydronicotinamide dehydrogenase (quinone) (28 May 2015)
EC 1.10.99.2 transferred now EC 1.10.5.1 (28 May 2015)
EC 1.10.99.3 transferred now EC 1.23.5.1 (28 May 2015)
*EC 1.11.1.19 dye decolorizing peroxidase (28 May 2015)
EC 1.13.11.80 (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase (28 May 2015)
EC 1.13.12.22 deoxynogalonate monooxygenase (28 May 2015)
EC 1.14.11.48 xanthine dioxygenase (28 May 2015)
EC 1.14.13.201 β-amyrin 28-monooxygenase (28 May 2015)
EC 1.14.13.202 methyl farnesoate epoxidase (28 May 2015)
EC 1.14.13.203 farnesoate epoxidase (28 May 2015)
EC 1.14.19.10 icosanoyl-CoA 5-desaturase (28 May 2015)
*EC 1.17.99.1 4-methylphenol dehydrogenase (hydroxylating) (28 May 2015)
*EC 1.20.4.1 arsenate reductase (glutaredoxin) (28 May 2015)
EC 1.20.4.4 arsenate reductase (thioredoxin) (28 May 2015)
EC 1.23 Reducing C-O-C group as acceptor (28 May 2015)
EC 1.23.5.1 violaxanthin de-epoxidase (28 May 2015)
*EC 2.1.1.98 diphthine synthase (28 May 2015)
EC 2.1.1.314 diphthine methyl ester synthase (28 May 2015)
EC 2.1.1.315 27-O-demethylrifamycin SV methyltransferase (28 May 2015)
*EC 2.3.1.161 lovastatin nonaketide synthase (28 May 2015)
EC 2.3.1.244 2-methylbutanoate polyketide synthase (28 May 2015)
EC 2.3.1.245 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase (28 May 2015)
EC 2.3.1.246 3,5-dihydroxyphenylacetyl-CoA synthase (28 May 2015)
*EC 2.3.3.5 2-methylcitrate synthase (28 May 2015)
EC 2.7.1.187 acarbose 7IV-phosphotransferase (28 May 2015)
EC 2.7.1.188 2-epi-5-epi-valiolone 7-kinase (28 May 2015)
EC 2.7.4.29 Kdo2-lipid A phosphotransferase (28 May 2015)
EC 3.1.2.31 dihydromonacolin L-[lovastatin nonaketide synthase] thioesterase (28 May 2015)
EC 3.1.3.97 3',5'-nucleoside bisphosphate phosphatase (28 May 2015)
EC 3.3.2.14 2,4-dinitroanisole O-demethylase (28 May 2015)
EC 3.4.14.13 γ-D-glutamyl-L-lysine dipeptidyl-peptidase (28 May 2015)
EC 3.5.1.118 γ-glutamyl hercynylcysteine S-oxide hydrolase (28 May 2015)
EC 4.1.1.100 prephenate decarboxylase (28 May 2015)
EC 4.1.99.21 (5-formylfuran-3-yl)methyl phosphate synthase (28 May 2015)
EC 4.2.1.155 methylthioacryloyl-CoA hydratase (28 May 2015)
EC 4.2.3.152 2-epi-5-epi-valiolone synthase (28 May 2015)
EC 4.4.1.29 phycobiliprotein cysteine-84 phycobilin lyase (28 May 2015)
EC 4.4.1.30 phycobiliprotein β-cysteine-155 phycobilin lyase (28 May 2015)
EC 4.4.1.31 phycoerythrocyanin α-cysteine-84 phycoviolobilin lyase/isomerase (28 May 2015)
EC 4.4.1.32 C-phycocyanin α-cysteine-84 phycocyanobilin lyase (28 May 2015)
EC 4.4.1.33 R-phycocyanin α-cysteine-84 phycourobilin lyase/isomerase (28 May 2015)
EC 5.1.1.20 L-Ala-D/L-Glu epimerase (28 May 2015)
EC 5.3.1.32 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase (28 May 2015)
EC 5.5.1.26 nogalonic acid methyl ester cyclase (28 May 2015)
*EC 6.3.2.37 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase (28 May 2015)
EC 6.3.2.46 fumarate—(S)-2,3-diaminopropanoate ligase (28 May 2015)
EC 6.3.2.47 dapdiamide A synthase (28 May 2015)

*EC 1.1.1.86

Accepted name: ketol-acid reductoisomerase (NADP+)

Reaction: (2R)-2,3-dihydroxy-3-methylbutanoate + NADP+ = (2S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH + H+

For diagram of reaction click here.

Glossary: (2S)-2-hydroxy-2-methyl-3-oxobutanoate = (2S)-2-acetolactate

Other name(s): dihydroxyisovalerate dehydrogenase (isomerizing); acetohydroxy acid isomeroreductase; ketol acid reductoisomerase; α-keto-β-hydroxylacyl reductoisomerase; 2-hydroxy-3-keto acid reductoisomerase; acetohydroxy acid reductoisomerase; acetolactate reductoisomerase; dihydroxyisovalerate (isomerizing) dehydrogenase; isomeroreductase; reductoisomerase; ketol-acid reductoisomerase; (R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing)

Systematic name: (2R)-2,3-dihydroxy-3-methylbutanoate:NADP+ oxidoreductase (isomerizing)

Comments: Also catalyses the reduction of 2-ethyl-2-hydroxy-3-oxobutanoate to 2,3-dihydroxy-3-methylpentanoate. The enzyme, found in many bacteria and archaea, is specific for NADPH (cf. EC 1.1.1.382, ketol-acid reductoisomerase (NAD+) and EC 1.1.1.383, ketol-acid reductoisomerase [NAD(P)+]).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-02-9

References:

1. Arfin, S.M. and Umbarger, H.E. Purification and properties of the acetohydroxy acid isomeroreductase of Salmonella typhimurium. J. Biol. Chem. 244 (1969) 1118-1127. [PMID: 4388025]

2. Hill, R.K., Sawada, S. and Arfin, S.M. Stereochemistry of valine and isoleucine biosynthesis. IV. Synthesis, configuration, and enzymatic specificity of α-acetolactate and α-aceto-α-hydroxybutyrate. Bioorg. Chem. 8 (1979) 175-189.

3. Kiritani, K., Narise, S. and Wagner, R.P. The reductoisomerase of Neurospora crassa. J. Biol. Chem. 241 (1966) 2047-2051.

4. Satyanarayana, T. and Radhakrishnan, A.N. Biosynthesis of valine and isoleucine in plants. 3. Reductoisomerase of Phaseolus radiatus. Biochim. Biophys. Acta 110 (1965) 380-388. [PMID: 5866387]

5. Brinkmann-Chen, S., Cahn, J.K. and Arnold, F.H. Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab. Eng. 26C (2014) 17-22. [PMID: 25172159]

[EC 1.1.1.86 created 1972, modified 1976, modified 1981 (EC 1.1.1.89 created 1972, incorporated 1976), modified 2015]

EC 1.1.1.382

Accepted name: ketol-acid reductoisomerase (NAD+)

Reaction: (2R)-2,3-dihydroxy-3-methylbutanoate + NAD+ = (2S)-2-hydroxy-2-methyl-3-oxobutanoate + NADH + H+

Glossary: (2S)-2-hydroxy-2-methyl-3-oxobutanoate = (2S)-2-acetolactate

Systematic name: (2R)-2,3-dihydroxy-3-methylbutanoate:NAD+ oxidoreductase (isomerizing)

Comments: The enzyme, characterized from the bacteria Thermacetogenium phaeum and Desulfococcus oleovorans and from the archaeon Archaeoglobus fulgidus, is specific for NADH [cf. EC 1.1.1.86, ketol-acid reductoisomerase (NADP+) and EC 1.1.1.383, ketol-acid reductoisomerase [NAD(P)+]].

References:

1. Brinkmann-Chen, S., Cahn, J.K. and Arnold, F.H. Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab. Eng. 26C (2014) 17-22. [PMID: 25172159]

[EC 1.1.1.382 created 2015]

EC 1.1.1.383

Accepted name: ketol-acid reductoisomerase [NAD(P)+]

Reaction: (2R)-2,3-dihydroxy-3-methylbutanoate + NAD(P)+ = (2S)-2-hydroxy-2-methyl-3-oxobutanoate + NAD(P)H + H+

Glossary: (2S)-2-hydroxy-2-methyl-3-oxobutanoate = (2S)-2-acetolactate

Systematic name: (2R)-2,3-dihydroxy-3-methylbutanoate:NAD(P)+ oxidoreductase (isomerizing)

Comments: The enzyme, characterized from the bacteria Hydrogenobaculum sp. and Syntrophomonas wolfei subsp. wolfei and from the archaea Metallosphaera sedula and Ignisphaera aggregans, can use both NADH and NADPH with similar efficiency [cf. EC 1.1.1.86, ketol-acid reductoisomerase (NADP+) and EC 1.1.1.382, ketol-acid reductoisomerase (NAD+)].

References:

1. Brinkmann-Chen, S., Cahn, J.K. and Arnold, F.H. Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab. Eng. 26C (2014) 17-22. [PMID: 25172159]

[EC 1.1.1.383 created 2015]

EC 1.1.1.384

Accepted name: dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose 3-reductase

Reaction: dTDP-4-dehydro-2,6-dideoxy-α-D-glucose + NADP+ = dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose + NADPH + H+

Glossary: dTDP-4-dehydro-2,6-dideoxy-α-D-glucose = dTDP-2,6-dideoxy-α-D-threo-hexopyranos-4-ulose
dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose = thymidine 5'-[(2R,6R)-6-methyl-4,5-dioxotetrahydro-2H-pyran-2-yl] diphosphate

Other name(s): KijD10; dTDP-4-keto-2,6-dideoxy-D-glucose 3-oxidoreductase; dTDP-4-dehydro-2,6-dideoxy-α-D-glucose 3-oxidoreductase

Systematic name: dTDP-4-dehydro-2,6-dideoxy-α-D-glucose:NADP+ 3-oxidoreductase

Comments: The enzyme is involved in the biosynthesis of several deoxysugars, including L-digitoxose, L- and D-olivose, L-oliose, D-mycarose and forosamine.

References:

1. Aguirrezabalaga, I., Olano, C., Allende, N., Rodriguez, L., Brana, A.F., Mendez, C. and Salas, J.A. Identification and expression of genes involved in biosynthesis of L-oleandrose and its intermediate L-olivose in the oleandomycin producer Streptomyces antibioticus. Antimicrob. Agents Chemother. 44 (2000) 1266-1275. [PMID: 10770761]

2. Wang, L., White, R.L. and Vining, L.C. Biosynthesis of the dideoxysugar component of jadomycin B: genes in the jad cluster of Streptomyces venezuelae ISP5230 for L-digitoxose assembly and transfer to the angucycline aglycone. Microbiology 148 (2002) 1091-1103. [PMID: 11932454]

3. Hong, L., Zhao, Z., Melancon, C.E., 3rd, Zhang, H. and Liu, H.W. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130 (2008) 4954-4967. [PMID: 18345667]

4. Kubiak, R.L. and Holden, H.M. Combined structural and functional investigation of a C-3''-ketoreductase involved in the biosynthesis of dTDP-L-digitoxose. Biochemistry 50 (2011) 5905-5917. [PMID: 21598943]

[EC 1.1.1.384 created 2015]

EC 1.1.1.385

Accepted name: dihydroanticapsin dehydrogenase

Reaction: L-dihydroanticapsin + NAD+ = L-anticapsin + NADH + H+

For diagram of reaction click here.

Glossary: L-dihydroanticapsin = 3-[(1R,2S,5R,6S)-5-hydroxy-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine
L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine

Other name(s): BacC; ywfD (gene name)

Systematic name: L-dihydroanticapsin:NAD+ oxidoreductase

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.

References:

1. 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 1.1.1.385 created 2015]

EC 1.1.1.386

Accepted name: ipsdienol dehydrogenase

Reaction: (R)-ipsdienol + NAD(P)+ = ipsdienone + NAD(P)H + H+

For diagram of reaction click here.

Glossary: ipsdienone = 2-methyl-6-methyleneocta-2,7-dien-4-one
(R)-ipsdienol = (4R)-2-methyl-6-methyleneocta-2,7-dien-4-ol

Other name(s): IDOLDH

Systematic name: (R)-ipsdienol:NAD(P)+ oxidoreductase

Comments: The enzyme is involved in pheromone production by the pine engraver beetle, Ips pini.

References:

1. Figueroa-Teran, R., Welch, W.H., Blomquist, G.J. and Tittiger, C. Ipsdienol dehydrogenase (IDOLDH): a novel oxidoreductase important for Ips pini pheromone production. Insect Biochem. Mol. Biol. 42 (2012) 81-90. [PMID: 22101251]

[EC 1.1.1.386 created 2015]

EC 1.2.5.2

Accepted name: aldehyde dehydrogenase (quinone)

Reaction: an aldehyde + a quinone + H2O = a carboxylate + a quinol

Other name(s): aldehyde dehydrogenase (acceptor)

Systematic name: aldehyde:quinone oxidoreductase

Comments: Wide specificity; acts on straight-chain aldehydes up to C10, aromatic aldehydes, glyoxylate and glyceraldehyde. The enzymes contains a PQQ cofactor and multiple hemes that deliver the electrons to the membrane quinone pool.

References:

1. Ameyama, M. and Adachi, O. Aldehyde dehydrogenase from acetic acid bacteria, membrane-bound. Methods Enzymol. 89 (1982) 491-497.

2. Ameyama, M., Osada, K., Shinagawa, E., Matsushita, K. and Adachi, O. Purification and characterization of aldehyde dehydrogenase of Acetobacter aceti. Agric. Biol. Chem. 45 (1981) 1189-1890.

3. Patel, R.N., Hou, C.T., Derelanko, P. and Felix, A. Purification and properties of a heme-containing aldehyde dehydrogenase from Methylosinus trichosporium. Arch. Biochem. Biophys. 203 (1980) 654-662. [PMID: 6779711]

4. Gomez-Manzo, S., Chavez-Pacheco, J.L., Contreras-Zentella, M., Sosa-Torres, M.E., Arreguin-Espinosa, R., Perez de la Mora, M., Membrillo-Hernandez, J. and Escamilla, J.E. Molecular and catalytic properties of the aldehyde dehydrogenase of Gluconacetobacter diazotrophicus, a quinoheme protein containing pyrroloquinoline quinone, cytochrome b, and cytochrome c. J. Bacteriol. 192 (2010) 5718-5724. [PMID: 20802042]

[EC 1.2.5.2 created 1983 as EC 1.2.99.3, modified 1989, transferred 2015 to EC 1.2.5.2 ]

EC 1.2.98.1

Accepted name: formaldehyde dismutase

Reaction: 2 formaldehyde + H2O = formate + methanol

Other name(s): aldehyde dismutase; cannizzanase; nicotinoprotein aldehyde dismutase

Systematic name: formaldehyde:formaldehyde oxidoreductase

Comments: The enzyme contains a tightly but noncovalently bound NADP(H) cofactor, as well as Zn2+ and Mg2+. The enzyme from the bacterium Mycobacterium sp. DSM 3803 also catalyses the reactions of EC 1.1.99.36, alcohol dehydrogenase (nicotinoprotein) and EC 1.1.99.37, methanol dehydrogenase (nicotinoprotein) [3]. Formaldehyde and acetaldehyde can act as donors; formaldehyde, acetaldehyde and propanal can act as acceptors [1,2].

References:

1. Kato, N., Shirakawa, K., Kobayashi, H. and Sakazawa, C. The dismutation of aldehydes by a bacterial enzyme. Agric. Biol. Chem. 47 (1983) 39-46.

2. Kato, N., Yamagami, T., Shimao, M. and Sakazawa, C. Formaldehyde dismutase, a novel NAD-binding oxidoreductase from Pseudomonas putida F61. Eur. J. Biochem. 156 (1986) 59-64. [PMID: 3514215]

3. Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N'-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463-471. [PMID: 19875438]

[EC 1.2.98.1 created 1986 as EC 1.2.99.4, modified 2012, transferred 2015 to EC 1.2.98.1]

[EC 1.2.99.3 Transferred entry: aldehyde dehydrogenase (pyrroloquinoline-quinone). Now EC 1.2.5.2, aldehyde dehydrogenase (quinone) (EC 1.2.99.3 created 1983, modified 1989, deleted 2014)]

[EC 1.2.99.4 Transferred entry: formaldehyde dismutase. Now EC 1.2.98.1, formaldehyde dismutase. (EC 1.2.99.4 created 1986, modified 2012, deleted 2015)]

EC 1.3.8.12

Accepted name: (2S)-methylsuccinyl-CoA dehydrogenase

Reaction: (2S)-methylsuccinyl-CoA + electron-transfer flavoprotein = 2-methylfumaryl-CoA + reduced electron-transfer flavoprotein

Glossary: 2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA

Other name(s): Mcd

Systematic name: (2S)-methylsuccinyl-CoA:electron-transfer flavoprotein oxidoreductase

Comments: The enzyme, characterized from the bacterium Rhodobacter sphaeroides, is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. The enzyme contains FAD.

References:

1. Erb, T.J., Fuchs, G. and Alber, B.E. (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Mol. Microbiol. 73 (2009) 992-1008. [PMID: 19703103]

[EC 1.3.8.12 created 2015]

*EC 1.5.1.1

Accepted name: 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H]

Reaction: (1) L-pipecolate + NAD(P)+ = 1-piperideine-2-carboxylate + NAD(P)H + H+
(2) L-proline + NAD(P)+ = 1-pyrroline-2-carboxylate + NAD(P)H + H+

Other name(s): Δ1-pyrroline-2-carboxylate reductase; DELTA1-pyrroline-2-carboxylate reductase; DELTA1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (ambiguous); AbLhpI; pyrroline-2-carboxylate reductase; L-proline:NAD(P)+ 2-oxidoreductase

Systematic name: L-pipecolate/L-proline:NAD(P)+ 2-oxidoreductase

Comments: The enzymes, characterized from the bacterium Azospirillum brasilense, is involved in trans-3-hydroxy-L-proline metabolism. In contrast to EC 1.5.1.21, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH), which is specific for NADPH, this enzyme shows similar activity with NADPH and NADH.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9029-16-7

References:

1. Meister, A., Radhakrishnan, A.N. and Buckley, S.D. Enzymatic synthesis of L-pipecolic acid and L-proline. J. Biol. Chem. 229 (1957) 789-800. [PMID: 13502341]

2. Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ1-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240-250. [PMID: 24649405]

[EC 1.5.1.1 created 1961, modified 2015]

*EC 1.5.1.21

Accepted name: 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH)

Reaction: (1) L-pipecolate + NADP+ = 1-piperideine-2-carboxylate + NADPH + H+
(2) L-proline + NADP+ = 1-pyrroline-2-carboxylate + NADPH + H+

Glossary: 1-piperideine-2-carboxylate = 3,4,5,6-tetrahydropyridine-2-carboxylate

Other name(s): Pyr2C reductase; 1,2-didehydropipecolate reductase; P2C reductase; 1,2-didehydropipecolic reductase; DELTA1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (ambiguous); L-pipecolate:NADP+ 2-oxidoreductase; DELTA1-piperideine-2-carboxylate reductase; Δ1-piperideine-2-carboxylate reductase

Systematic name: L-pipecolate/L-proline:NADP+ 2-oxidoreductase

Comments: The enzyme is involved in the catabolism of D-lysine and D-proline in bacteria that belong to the Pseudomonas genus. In contrast to EC 1.5.1.1, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H], which shows similar activity with NADPH and NADH, this enzyme is specific for NADPH.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 52037-88-4

References:

1. Payton, C.W. and Chang, Y.-F. Δ1-Piperideine-2-carboxylate reductase of Pseudomonas putida. J. Bacteriol. 149 (1982) 864-871. [PMID: 6801013]

2. Muramatsu, H., Mihara, H., Kakutani, R., Yasuda, M., Ueda, M., Kurihara, T. and Esaki, N. The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent Δ1-piperideine-2-carboxylate/Δ1-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-proline. J. Biol. Chem. 280 (2005) 5329-5335. [PMID: 15561717]

3. Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ1-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240-250. [PMID: 24649405]

[EC 1.5.1.21 created 1984 (EC 1.5.1.14 created 1976, incorporated 1989), modified 2015]

EC 1.5.1.49

Accepted name: 1-pyrroline-2-carboxylate reductase [NAD(P)H]

Reaction: L-proline + NAD(P)+ = 1-pyrroline-2-carboxylate + NAD(P)H + H+

Systematic name: L-proline:NAD(P)+ 2-oxidoreductase

Comments: The enzyme from the bacterium Colwellia psychrerythraea is involved in trans-3-hydroxy-L-proline metabolism. In contrast to EC 1.5.1.1, 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H], which shows similar activity with 1-piperideine-2-carboxylate and 1-pyrroline-2-carboxylate, this enzyme is specific for the latter. While the enzyme is active with both NADH and NADPH, activity is higher with NADPH.

References:

1. Watanabe, S., Tanimoto, Y., Yamauchi, S., Tozawa, Y., Sawayama, S. and Watanabe, Y. Identification and characterization of trans-3-hydroxy-L-proline dehydratase and Δ1-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-L-proline metabolism of bacteria. FEBS Open Bio 4 (2014) 240-250. [PMID: 24649405]

[EC 1.5.1.49 created 2015]

EC 1.6.5.11

Accepted name: NADH dehydrogenase (quinone)

Reaction: NADH + H+ + a quinone = NAD+ + a quinol

Other name(s): reduced nicotinamide adenine dinucleotide (quinone) dehydrogenase; NADH-quinone oxidoreductase; DPNH-menadione reductase; D-diaphorase; NADH2 dehydrogenase (quinone)

Systematic name: NADH:(quinone-acceptor) oxidoreductase

Comments: Menaquinone can act as acceptor. Inhibited by AMP and 2,4-dinitrophenol but not by dicoumarol or folic acid derivatives.

References:

1. Koli, A.K., Yearby, C., Scott, W. and Donaldson, K.O. Purification and properties of three separate menadione reductases from hog liver. J. Biol. Chem. 244 (1969) 621-629. [PMID: 4388793]

[EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11]

[EC 1.6.99.5 Transferred entry: NADH dehydrogenase (quinone). Transferred to EC 1.6.5.11, NADH dehydrogenase (quinone) (EC 1.6.99.5 created 1972, deleted 2014)]

*EC 1.7.3.6

Accepted name: hydroxylamine oxidase (cytochrome)

Reaction: hydroxylamine + O2 = nitrite + H2O + H+ (overall reaction)
(1a) hydroxylamine + 2 ferricytochrome c = nitroxyl + 2 ferrocytochrome c + 2 H+
(1b) nitroxyl + 2 ferrocytochrome c + O2 + H+ = nitrite + 2 ferricytochrome c + H2O (spontaneous)

Other name(s): HAO (ambiguous); hydroxylamine oxidoreductase (ambiguous); hydroxylamine oxidase (misleading)

Systematic name: hydroxylamine:oxygen oxidoreductase

Comments: The enzyme from the heterotrophic nitrifying bacterium Paracoccus denitrificans contains three to five non-heme, non-iron-sulfur iron atoms and interacts with cytochrome c556 and pseudoazurin [2,3]. Under anaerobic conditions in vitro only nitrous oxide is formed [3]. Presumably nitroxyl is released and combines with a second nitroxyl to give nitrous oxide and water. When oxygen is present, nitrite is formed.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-43-8

References:

1. Kurokawa, M, Fukumori, Y and Yamanaka, T A hydroxylamine - cytochrome c reductase occurs in the heterotrophic nitrifier Arthrobacter globiformis. Plant Cell Physiol 26 (1985) 1439-1442.

2. Wehrfritz, J.M., Reilly, A., Spiro, S. and Richardson, D.J. Purification of hydroxylamine oxidase from Thiosphaera pantotropha. Identification of electron acceptors that couple heterotrophic nitrification to aerobic denitrification. FEBS Lett 335 (1993) 246-250. [PMID: 8253206]

3. Moir, J.W., Wehrfritz, J.M., Spiro, S. and Richardson, D.J. The biochemical characterization of a novel non-haem-iron hydroxylamine oxidase from Paracoccus denitrificans GB17. Biochem. J. 319 (1996) 823-827. [PMID: 8920986]

4. Wehrfritz, J., Carter, J.P., Spiro, S. and Richardson, D.J. Hydroxylamine oxidation in heterotrophic nitrate-reducing soil bacteria and purification of a hydroxylamine-cytochrome c oxidoreductase from a Pseudomonas species. Arch. Microbiol. 166 (1996) 421-424. [PMID: 9082922]

[EC 1.7.3.6 created 1972 as EC 1.7.3.4, part transferred 2013 to EC 1.7.3.6, modified 2015]

EC 1.10.5 With a quinone or related compound as acceptor

EC 1.10.5.1

Accepted name: ribosyldihydronicotinamide dehydrogenase (quinone)

Reaction: 1-(β-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone = 1-(β-D-ribofuranosyl)nicotinamide + a quinol

For diagram of reaction click here.

Other name(s): NRH:quinone oxidoreductase 2; NQO2; NAD(P)H:quinone oxidoreductase-2 (misleading); QR2; quinone reductase 2; N-ribosyldihydronicotinamide dehydrogenase (quinone); NAD(P)H:quinone oxidoreductase2 (misleading)

Systematic name: 1-(β-D-ribofuranosyl)-1,4-dihydronicotinamide:quinone oxidoreductase

Comments: A flavoprotein. Unlike EC 1.6.5.2, NAD(P)H dehydrogenase (quinone), this quinone reductase cannot use NADH or NADPH; instead it uses N-ribosyl- and N-alkyldihydronicotinamides. Polycyclic aromatic hydrocarbons, such as benz[a]anthracene, and the estrogens 17β-estradiol and diethylstilbestrol are potent inhibitors, but dicoumarol is only a very weak inhibitor [2]. This enzyme can catalyse both 2-electron and 4-electron reductions, but one-electron acceptors, such as potassium ferricyanide, cannot be reduced [3].

References:

1. Liao, S., Dulaney, J.T. and Williams-Ashman, H.G. Purification and properties of a flavoprotein catalyzing the oxidation of reduced ribosyl nicotinamide. J. Biol. Chem. 237 (1962) 2981-2987. [PMID: 14465018]

2. Zhao, Q., Yang, X.L., Holtzclaw, W.D. and Talalay, P. Unexpected genetic and structural relationships of a long-forgotten flavoenzyme to NAD(P)H:quinone reductase (DT-diaphorase). Proc. Natl. Acad. Sci. USA 94 (1997) 1669-1674. [PMID: 9050836]

3. Wu, K., Knox, R., Sun, X.Z., Joseph, P., Jaiswal, A.K., Zhang, D., Deng, P.S. and Chen, S. Catalytic properties of NAD(P)H:quinone oxidoreductase-2 (NQO2), a dihydronicotinamide riboside dependent oxidoreductase. Arch. Biochem. Biophys. 347 (1997) 221-228. [PMID: 9367528]

4. Jaiswal, A.K. Human NAD(P)H:quinone oxidoreductase2. Gene structure, activity, and tissue-specific expression. J. Biol. Chem. 269 (1994) 14502-14508. [PMID: 8182056]

[EC 1.10.5.1 created 2005 as EC 1.10.99.2, transfered 2015 to EC 1.10.5.1]

[EC 1.10.99.2 Transferred entry: ribosyldihydronicotinamide dehydrogenase (quinone). Now classified as EC 1.10.5.1, ribosyldihydronicotinamide dehydrogenase (quinone). (EC 1.10.99.2 created 2005, deleted 2014)]

[EC 1.10.99.3 Transferred entry: violaxanthin de-epoxidase. Now classified as EC 1.23.5.1, violaxanthin de-epoxidase. (EC 1.10.99.3 created 2005, deleted 2014)]

*EC 1.11.1.19

Accepted name: dye decolorizing peroxidase

Reaction: Reactive Blue 5 + 2 H2O2 = phthalate + 2,2'-disulfonyl azobenzene + 3-[(4-amino-6-chloro-1,3,5-triazin-2-yl)amino]benzenesulfonate + 2 H2O

Glossary: Reactive Blue 5 = 1-amino-4-{[3-({4-chloro-6-[(3-sulfophenyl)amino]-1,3,5-triazin-2-yl}amino)-4-sulfophenyl]amino}-9,10-dihydro-9,10-dioxoanthracene-2-sulfonic acid

Other name(s): DyP; DyP-type peroxidase

Systematic name: Reactive-Blue-5:hydrogen-peroxide oxidoreductase

Comments: Heme proteins with proximal histidine secreted by basidiomycetous fungi and eubacteria. They are similar to EC 1.11.1.16 versatile peroxidase (oxidation of Reactive Black 5, phenols, veratryl alcohol), but differ from the latter in their ability to efficiently oxidize a number of recalcitrant anthraquinone dyes, and inability to oxidize Mn(II). The model substrate Reactive Blue 5 is converted with high efficiency via a so far unique mechanism that combines oxidative and hydrolytic steps and leads to the formation of phthalic acid. Bacterial TfuDyP catalyses sulfoxidation.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Kim, S.J. and Shoda, M. Purification and characterization of a novel peroxidase from Geotrichum candidum dec 1 involved in decolorization of dyes. Appl. Environ. Microbiol. 65 (1999) 1029-1035. [PMID: 10049859]

2. Sugano, Y., Ishii, Y. and Shoda, M. Role of H164 in a unique dye-decolorizing heme peroxidase DyP. Biochem. Biophys. Res. Commun. 322 (2004) 126-132. [PMID: 15313183]

3. Zubieta, C., Joseph, R., Krishna, S.S., McMullan, D., Kapoor, M., Axelrod, H.L., Miller, M.D., Abdubek, P., Acosta, C., Astakhova, T., Carlton, D., Chiu, H.J., Clayton, T., Deller, M.C., Duan, L., Elias, Y., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Kumar, A., Marciano, D., Morse, A.T., Murphy, K.D., Nigoghossian, E., Okach, L., Oommachen, S., Reyes, R., Rife, C.L., Schimmel, P., Trout, C.V., van den Bedem, H., Weekes, D., White, A., Xu, Q., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA. Proteins 69 (2007) 234-243. [PMID: 17654547]

4. Sugano, Y., Matsushima, Y., Tsuchiya, K., Aoki, H., Hirai, M. and Shoda, M. Degradation pathway of an anthraquinone dye catalyzed by a unique peroxidase DyP from Thanatephorus cucumeris Dec 1. Biodegradation 20 (2009) 433-440. [PMID: 19009358]

5. Sugano, Y. DyP-type peroxidases comprise a novel heme peroxidase family. Cell. Mol. Life Sci. 66 (2009) 1387-1403. [PMID: 19099183]

6. Ogola, H.J., Kamiike, T., Hashimoto, N., Ashida, H., Ishikawa, T., Shibata, H. and Sawa, Y. Molecular characterization of a novel peroxidase from the cyanobacterium Anabaena sp. strain PCC 7120. Appl. Environ. Microbiol. 75 (2009) 7509-7518. [PMID: 19801472]

7. van Bloois, E., Torres Pazmino, D.E., Winter, R.T. and Fraaije, M.W. A robust and extracellular heme-containing peroxidase from Thermobifida fusca as prototype of a bacterial peroxidase superfamily. Appl. Microbiol. Biotechnol. 86 (2010) 1419-1430. [PMID: 19967355]

8. Liers, C., Bobeth, C., Pecyna, M., Ullrich, R. and Hofrichter, M. DyP-like peroxidases of the jelly fungus Auricularia auricula-judae oxidize nonphenolic lignin model compounds and high-redox potential dyes. Appl. Microbiol. Biotechnol. 85 (2010) 1869-1879. [PMID: 19756587]

9. Hofrichter, M., Ullrich, R., Pecyna, M.J., Liers, C. and Lundell, T. New and classic families of secreted fungal heme peroxidases. Appl. Microbiol. Biotechnol. 87 (2010) 871-897. [PMID: 20495915]

[EC 1.11.1.19 created 2011, modified 2015]

EC 1.13.11.80

Accepted name: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase

Reaction: (3,5-dihydroxyphenyl)acetyl-CoA + O2 = 2-(3,5-dihydroxyphenyl)-2-oxoacetate + CoA

Glossary: (3,5-dihydroxyphenyl)acetyl-CoA = 2-(3,5-dihydroxyphenyl)acetyl-CoA

Other name(s): DpgC

Systematic name: (3,5-dihydroxyphenyl)acetyl-CoA:oxygen oxidoreductase

Comments: The enzyme, characterized from bacteria Streptomyces toyocaensis and Amycolatopsis orientalis, is involved in the biosynthesis of (3,5-dihydroxyphenyl)glycine, a component of the glycopeptide antibiotic vancomycin.

References:

1. Chen, H., Tseng, C.C., Hubbard, B.K. and Walsh, C.T. Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine. Proc. Natl. Acad. Sci. USA 98 (2001) 14901-14906. [PMID: 11752437]

2. Widboom, P.F., Fielding, E.N., Liu, Y. and Bruner, S.D. Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis. Nature 447 (2007) 342-345. [PMID: 17507985]

3. Fielding, E.N., Widboom, P.F. and Bruner, S.D. Substrate recognition and catalysis by the cofactor-independent dioxygenase DpgC. Biochemistry 46 (2007) 13994-14000. [PMID: 18004875]

[EC 1.13.11.80 created 2015]

EC 1.13.12.22

Accepted name: deoxynogalonate monooxygenase

Reaction: deoxynogalonate + O2 = nogalonate + H2O

For diagram of reaction click here.

Glossary: deoxynogalonate = [4,5-dihydroxy-10-oxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate
nogalonate = [4,5-dihydroxy-9,10-dioxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate

Other name(s): SnoaB (gene name); 12-deoxynogalonic acid oxidoreductase; [4,5-dihydroxy-10-oxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate oxidase; [4,5-dihydroxy-10-oxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate monooxygenase; deoxynogalonate oxidoreductase

Systematic name: deoxynogalonate:oxygen oxidoreductase

Comments: The enzyme, characterized from the bacterium Streptomyces nogalater, is involved in the biosynthesis of the aromatic polyketide nogalamycin.

References:

1. Koskiniemi, H., Grocholski, T., Schneider, G. and Niemi, J. Expression, purification and crystallization of the cofactor-independent monooxygenase SnoaB from the nogalamycin biosynthetic pathway. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 256-259. [PMID: 19255477]

2. Grocholski, T., Koskiniemi, H., Lindqvist, Y., Mantsala, P., Niemi, J. and Schneider, G. Crystal structure of the cofactor-independent monooxygenase SnoaB from Streptomyces nogalater: implications for the reaction mechanism. Biochemistry 49 (2010) 934-944. [PMID: 20052967]

[EC 1.13.12.22 created 2015]

EC 1.14.11.48

Accepted name: xanthine dioxygenase

Reaction: xanthine + 2-oxoglutarate + O2 = urate + succinate + CO2

For diagram click here.

Other name(s): XanA; α-ketoglutarate-dependent xanthine hydroxylase

Systematic name: xanthine,2-oxoglutarate:oxygen oxidoreductase

Comments: Requires Fe2+ and L-ascorbate. The enzyme, which was characterized from fungi, is specific for xanthine.

References:

1. Cultrone, A., Scazzocchio, C., Rochet, M., Montero-Moran, G., Drevet, C. and Fernandez-Martin, R. Convergent evolution of hydroxylation mechanisms in the fungal kingdom: molybdenum cofactor-independent hydroxylation of xanthine via α-ketoglutarate-dependent dioxygenases. Mol. Microbiol. 57 (2005) 276-290. [PMID: 15948966]

2. Montero-Moran, G.M., Li, M., Rendon-Huerta, E., Jourdan, F., Lowe, D.J., Stumpff-Kane, A.W., Feig, M., Scazzocchio, C. and Hausinger, R.P. Purification and characterization of the FeII- and α-ketoglutarate-dependent xanthine hydroxylase from Aspergillus nidulans. Biochemistry 46 (2007) 5293-5304. [PMID: 17429948]

3. Li, M., Muller, T.A., Fraser, B.A. and Hausinger, R.P. Characterization of active site variants of xanthine hydroxylase from Aspergillus nidulans. Arch. Biochem. Biophys. 470 (2008) 44-53. [PMID: 18036331]

[EC 1.14.11.48 created 2015]

EC 1.14.13.201

Accepted name: β-amyrin 28-monooxygenase

Reaction: β-amyrin + 3 NADPH + 3 H+ + 3 O2 = oleanolate + 3 NADP+ + 4 H2O (overall reaction)
(1a) β-amyrin + NADPH + H+ + O2 = erythrodiol + NADP+ + H2O
(1b) erythrodiol + NADPH + H+ + O2 = oleanolic aldehyde + NADP+ + 2 H2O
(1c) oleanolic aldehyde + NADPH + H+ + O2 = oleanolate + NADP+ + H2O

For diagram click here.

Other name(s): CYP716A52v2; CYP716A12; β-amyrin 28-oxidase

Systematic name: β-amyrin,NADPH:oxygen oxidoreductase (28-hydroxylating)

Comments: The enzyme, found in plants, is involved in the biosynthesis of oleanane-type triterpenoids, such as ginsenoside Ro. The enzyme from Medicago trunculata (CYP716A12) can also convert α-amyrin and lupeol to ursolic acid and betulinic acid, respectively.

References:

1. Fukushima, E.O., Seki, H., Ohyama, K., Ono, E., Umemoto, N., Mizutani, M., Saito, K. and Muranaka, T. CYP716A subfamily members are multifunctional oxidases in triterpenoid biosynthesis. Plant Cell Physiol 52 (2011) 2050-2061. [PMID: 22039103]

2. Han, J.Y., Kim, M.J., Ban, Y.W., Hwang, H.S. and Choi, Y.E. The involvement of β-amyrin 28-oxidase (CYP716A52v2) in oleanane-type ginsenoside biosynthesis in Panax ginseng. Plant Cell Physiol 54 (2013) 2034-2046. [PMID: 24092881]

[EC 1.14.13.201 created 2015]

EC 1.14.13.202

Accepted name: methyl farnesoate epoxidase

Reaction: methyl (2E,6E)-farnesoate + NADPH + H+ + O2 = juvenile hormone III + NADP+ + H2O

For diagram of reaction click here.

Glossary: juvenile hormone III = methyl (2E,6E,10R)-10,11-epoxy-3,7,11-trimethyldodeca-2,6-dienoate

Other name(s): CYP15A1

Systematic name: methyl (2E,6E)-farnesoate,NADPH:oxygen oxidoreductase

Comments: A heme-thiolate protein (cytochrome P-450). The enzyme, found in insects except for Lepidoptera (moths and butterflies) is specific for methyl farnesoate (cf. EC 1.14.13.203, farnesoate epoxidase) [1,2].

References:

1. Helvig, C., Koener, J.F., Unnithan, G.C. and Feyereisen, R. CYP15A1, the cytochrome P450 that catalyzes epoxidation of methyl farnesoate to juvenile hormone III in cockroach corpora allata. Proc. Natl. Acad. Sci. USA 101 (2004) 4024-4029. [PMID: 15024118]

2. Daimon, T. and Shinoda, T. Function, diversity, and application of insect juvenile hormone epoxidases (CYP15). Biotechnol. Appl. Biochem. 60 (2013) 82-91. [PMID: 23586995]

[EC 1.14.13.202 created 2015]

EC 1.14.13.203

Accepted name: farnesoate epoxidase

Reaction: (2E,6E)-farnesoate + NADPH + H+ + O2 = juvenile-hormone-III carboxylate + NADP+ + H2O

For diagram of reaction click here.

Glossary: juvenile-hormone-III carboxylate = (2E,6E,10R)-10,11-epoxy-3,7,11-trimethyldodeca-2,6-dienoate

Other name(s): CYP15C1

Systematic name: (2E,6E)-farnesoate,NADPH:oxygen oxidoreductase

Comments: A heme-thiolate protein (cytochrome P-450). The enzyme, found in Lepidoptera (moths and butterflies), is specific for farnesoate (cf. EC 1.14.13.202, methyl farnesoate epoxidase) [1,2]. It is involved in the synthesis of juvenile hormone.

References:

1. Daimon, T., Kozaki, T., Niwa, R., Kobayashi, I., Furuta, K., Namiki, T., Uchino, K., Banno, Y., Katsuma, S., Tamura, T., Mita, K., Sezutsu, H., Nakayama, M., Itoyama, K., Shimada, T. and Shinoda, T. Precocious metamorphosis in the juvenile hormone-deficient mutant of the silkworm, Bombyx mori. PLoS Genet 8 (2012) e1002486. [PMID: 22412378]

2. Daimon, T. and Shinoda, T. Function, diversity, and application of insect juvenile hormone epoxidases (CYP15). Biotechnol. Appl. Biochem. 60 (2013) 82-91. [PMID: 23586995]

[EC 1.14.13.203 created 2015]

EC 1.14.19.10

Accepted name: icosanoyl-CoA 5-desaturase

Reaction: icosanoyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = (Z)-icos-5-enoyl-CoA + 2 ferricytochrome b5 + 2 H2O

Other name(s): acyl-CoA Δ5-desaturase (ambiguous)

Systematic name: icosanoyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (5,6 cis-dehydrogenating)

Comments: The enzyme, characterized from the plant Limnanthes douglasii (meadowfoam), is involved in the biosynthesis of (5Z)-icos-5-enoate, an unusual monounsaturated fatty acid that makes up to 60% of the total fatty acids in Limnanthes sp. seed oil. The enzyme only acts on saturated fatty acids.

References:

1. Cahoon, E.B., Marillia, E.F., Stecca, K.L., Hall, S.E., Taylor, D.C. and Kinney, A.J. Production of fatty acid components of meadowfoam oil in somatic soybean embryos. Plant Physiol. 124 (2000) 243-251. [PMID: 10982439]

[EC 1.14.19.10 created 2015]

*EC 1.17.99.1

Accepted name: 4-methylphenol dehydrogenase (hydroxylating)

Reaction: 4-methylphenol + 2 acceptor + H2O = 4-hydroxybenzaldehyde + 2 reduced acceptor

Glossary: 4-methylphenol = 4-cresol = p-cresol

Other name(s): p-cresol-(acceptor) oxidoreductase (hydroxylating); p-cresol methylhydroxylase; 4-cresol dehydrogenase (hydroxylating)

Systematic name: 4-methylphenol:acceptor oxidoreductase (methyl-hydroxylating)

Comments: A flavocytochrome c (FAD). Phenazine methosulfate can act as acceptor. A quinone methide is probably formed as intermediate. The first hydroxylation forms 4-hydroxybenzyl alcohol; a second hydroxylation converts this into 4-hydroxybenzaldehyde.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 66772-07-4

References:

1. Hopper, D.J. and Taylor, D.G. The purification and properties of p-cresol-(acceptor) oxidoreductase (hydroxylating), a flavocytochrome from Pseudomonas putida. Biochem. J. 167 (1977) 155-162. [PMID: 588247]

2. McIntire, W., Edmondson, D.E. and Singer, T.P. 8α-O-Tyrosyl-FAD: a new form of covalently bound flavin from p-cresol methylhydroxylase. J. Biol. Chem. 255 (1980) 6553-6555. [PMID: 7391034]

[EC 1.17.99.1 created 1983, modified 2001, modified 2011, modified 2015]

*EC 1.20.4.1

Accepted name: arsenate reductase (glutaredoxin)

Reaction: arsenate + glutaredoxin = arsenite + glutaredoxin disulfide + H2O

For diagram of reaction click here.

Other name(s): ArsC (ambiguous)

Systematic name: arsenate:glutaredoxin oxidoreductase

Comments: A molybdoenzyme. The enzyme is part of a system for detoxifying arsenate. Although the arsenite formed is more toxic than arsenate, it can be extruded from some bacteria by EC 3.6.3.16, arsenite-transporting ATPase; in other organisms, arsenite can be methylated by EC 2.1.1.137, arsenite methyltransferase, in a pathway that produces non-toxic organoarsenical compounds. cf. EC 1.20.4.4, arsenate reductase (thioredoxin).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 146907-46-2

References:

1. Gladysheva, T., Liu, J.Y. and Rosen, B.P. His-8 lowers the pKa of the essential Cys-12 residue of the ArsC arsenate reductase of plasmid R773. J. Biol. Chem. 271 (1996) 33256-33260. [PMID: 8969183]

2. Gladysheva, T.B., Oden, K.L. and Rosen, B.P. Properties of the arsenate reductase of plasmid R773. Biochemistry 33 (1994) 7288-7293. [PMID: 8003492]

3. Holmgren, A. and Aslund, F. Glutaredoxin. Methods Enzymol. 252 (1995) 283-292. [PMID: 7476363]

4. Krafft, T. and Macy, J.M. Purification and characterization of the respiratory arsenate reductase of Chrysiogenes arsenatis. Eur. J. Biochem. 255 (1998) 647-653. [PMID: 9738904]

5. Martin, J.L. Thioredoxin - a fold for all reasons. Structure 3 (1995) 245-250. [PMID: 7788290]

6. Radabaugh, T.R. and Aposhian, H.V. Enzymatic reduction of arsenic compounds in mammalian systems: reduction of arsenate to arsenite by human liver arsenate reductase. Chem. Res. Toxicol. 13 (2000) 26-30. [PMID: 10649963]

7. Sato, T. and Kobayashi, Y. The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J. Bacteriol. 180 (1998) 1655-1661. [PMID: 9537360]

8. Shi, J., Vlamis-Gardikas, V., Aslund, F., Holmgren, A. and Rosen, B.P. Reactivity of glutaredoxins 1, 2, and 3 from Escherichia coli shows that glutaredoxin 2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction. J. Biol. Chem. 274 (1999) 36039-36042. [PMID: 10593884]

[EC 1.20.4.1 created 2000 as EC 1.97.1.5, transferred 2001 to EC 1.20.4.1, modified 2015]

EC 1.20.4.4

Accepted name: arsenate reductase (thioredoxin)

Reaction: arsenate + thioredoxin = arsenite + thioredoxin disulfide + H2O

For diagram of reaction click here.

Other name(s): ArsC (ambiguous)

Systematic name: arsenate:thioredoxin oxidoreductase

Comments: The enzyme, characterized in bacteria of the Firmicutes phylum, is specific for thioredoxin [1]. It has no activity with glutaredoxin [cf. EC 1.20.4.1, arsenate reductase (glutaredoxin)]. Although the arsenite formed is more toxic than arsenate, it can be extruded from some bacteria by EC 3.6.3.16, arsenite-transporting ATPase; in other organisms, arsenite can be methylated by EC 2.1.1.137, arsenite methyltransferase, in a pathway that produces non-toxic organoarsenical compounds. The enzyme also has the activity of EC 3.1.3.48, protein-tyrosine-phosphatase [3].

References:

1. Ji, G., Garber, E.A., Armes, L.G., Chen, C.M., Fuchs, J.A. and Silver, S. Arsenate reductase of Staphylococcus aureus plasmid pI258. Biochemistry 33 (1994) 7294-7299. [PMID: 8003493]

2. Messens, J., Hayburn, G., Desmyter, A., Laus, G. and Wyns, L. The essential catalytic redox couple in arsenate reductase from Staphylococcus aureus. Biochemistry 38 (1999) 16857-16865. [PMID: 10606519]

3. Zegers, I., Martins, J.C., Willem, R., Wyns, L. and Messens, J. Arsenate reductase from S. aureus plasmid pI258 is a phosphatase drafted for redox duty. Nat. Struct. Biol. 8 (2001) 843-847. [PMID: 11573087]

4. Messens, J., Martins, J.C., Van Belle, K., Brosens, E., Desmyter, A., De Gieter, M., Wieruszeski, J.M., Willem, R., Wyns, L. and Zegers, I. All intermediates of the arsenate reductase mechanism, including an intramolecular dynamic disulfide cascade. Proc. Natl. Acad. Sci. USA 99 (2002) 8506-8511. [PMID: 12072565]

[EC 1.20.4.4 created 2015]

EC 1.23 Reducing C-O-C group as acceptor

EC 1.23.5.1

Accepted name: violaxanthin de-epoxidase

Reaction: violaxanthin + 2 L-ascorbate = zeaxanthin + 2 L-dehydroascorbate + 2 H2O (overall reaction)
(1a) violaxanthin + L-ascorbate = antheraxanthin + L-dehydroascorbate + H2O
(1b) antheraxanthin + L-ascorbate = zeaxanthin + L-dehydroascorbate + H2O

For diagram of reaction click here.

Glossary: violaxanthin = (3S,3'S,5R,5'R,6S,6'S)-5,6:5',6'-diepoxy-5,5',6,6'-tetrahydro-β,β-carotene-3,3'-diol
antheraxanthin = (3R,3'S,5'R,6'S)-5',6'-epoxy-5',6'-dihydro-β,β-carotene-3,3'-diol
zeaxanthin = (3R,3'R)-β,β-carotene-3,3'-diol

Other name(s): VDE

Systematic name: violaxanthin:ascorbate oxidoreductase

Comments: Along with EC 1.14.13.90, zeaxanthin epoxidase, this enzyme forms part of the xanthophyll (or violaxanthin) cycle for controlling the concentration of zeaxanthin in chloroplasts. It is activated by a low pH of the thylakoid lumen (produced by high light intensity). Zeaxanthin induces the dissipation of excitation energy in the chlorophyll of the light-harvesting protein complex of photosystem II. In higher plants the enzyme reacts with all-trans-diepoxides, such as violaxanthin, and all-trans-monoepoxides, but in the alga Mantoniella squamata, only the diepoxides are good substrates.

References:

1. Yamamoto, H.Y. and Higashi, R.M. Violaxanthin de-epoxidase. Lipid composition and substrate specificity. Arch. Biochem. Biophys. 190 (1978) 514-522. [PMID: 102251]

2. Rockholm, D.C. and Yamamoto, H.Y. Violaxanthin de-epoxidase. Plant Physiol. 110 (1996) 697-703. [PMID: 8742341]

3. Bugos, R.C., Hieber, A.D. and Yamamoto, H.Y. Xanthophyll cycle enzymes are members of the lipocalin family, the first identified from plants. J. Biol. Chem. 273 (1998) 15321-15324. [PMID: 9624110]

4. Kuwabara, T., Hasegawa, M., Kawano, M. and Takaichi, S. Characterization of violaxanthin de-epoxidase purified in the presence of Tween 20: effects of dithiothreitol and pepstatin A. Plant Cell Physiol. 40 (1999) 1119-1126. [PMID: 10635115]

5. Latowski, D., Kruk, J., Burda, K., Skrzynecka-Jaskierm, M., Kostecka-Gugala, A. and Strzalka, K. Kinetics of violaxanthin de-epoxidation by violaxanthin de-epoxidase, a xanthophyll cycle enzyme, is regulated by membrane fluidity in model lipid bilayers. Eur. J. Biochem. 269 (2002) 4656-4665. [PMID: 12230579]

6. Goss, R. Substrate specificity of the violaxanthin de-epoxidase of the primitive green alga Mantoniella squamata (Prasinophyceae). Planta 217 (2003) 801-812. [PMID: 12748855]

7. Latowski, D., Akerlund, H.E. and Strzalka, K. Violaxanthin de-epoxidase, the xanthophyll cycle enzyme, requires lipid inverted hexagonal structures for its activity. Biochemistry 43 (2004) 4417-4420. [PMID: 15078086]

[EC 1.23.5.1 created 2005 as EC 1.10.99.3, transfered 2015 to EC 1.23.5.1]

*EC 2.1.1.98

Accepted name: diphthine synthase

Reaction: 3 S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = 3 S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2] (overall reaction)
(1a) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2]
(1b) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2]
(1c) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2]

For diagram of reaction click here.

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

Other name(s): S-adenosyl-L-methionine:elongation factor 2 methyltransferase (ambiguous); diphthine methyltransferase (ambiguous); S-adenosyl-L-methionine:2-(3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] methyltransferase; Dph5 (ambiguous)

Systematic name: S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine-[translation elongation factor 2]-forming)

Comments: This archaeal enzyme produces the trimethylated product diphthine, which is converted into diphthamide by EC 6.3.1.14, diphthine—ammonia ligase. Different from the eukaryotic enzyme, which produces diphthine methyl ester (cf. EC 2.1.1.314). In the archaeon Pyrococcus horikoshii the enzyme acts on His600 of elongation factor 2.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 114514-25-9

References:

1. Zhu, X., Kim, J., Su, X. and Lin, H. Reconstitution of diphthine synthase activity in vitro. Biochemistry 49 (2010) 9649-9657. [PMID: 20873788]

[EC 2.1.1.98 created 1990, modified 2013, modified 2015]

EC 2.1.1.314

Accepted name: diphthine methyl ester synthase

Reaction: 4 S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = 4 S-adenosyl-L-homocysteine + diphthine methyl ester-[translation elongation factor 2]

For diagram of reaction click here.

Glossary: diphthine methyl ester = 2-[(3S)-4-methoxy-4-oxo-3-(trimethylammonio)butyl]-L-histidine

Other name(s): S-adenosyl-L-methionine:elongation factor 2 methyltransferase (ambiguous); diphthine methyltransferase (ambiguous); Dph5 (ambiguous)

Systematic name: S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine methyl ester-[translation elongation factor 2]-forming)

Comments: This eukaryotic enzyme is part of the biosynthetic pathway of diphthamide. Different from the archaeal enzyme, which performs only 3 methylations, producing diphthine (cf. EC 2.1.1.98). The relevant histidine of elongation factor 2 is His715 in mammals and His699 in yeast. The order of the 4 methylations is not known.

References:

1. Chen, J.-Y.C. and Bodley, J.W. Biosynthesis of diphthamide in Saccharomyces cerevisiae. Partial purification and characterization of a specific S-adenosylmethionine:elongation factor 2 methyltransferase. J. Biol. Chem. 263 (1988) 11692-11696. [PMID: 3042777]

2. Moehring, J.M. and Moehring, T.J. The post-translational trimethylation of diphthamide studied in vitro. J. Biol. Chem. 263 (1988) 3840-3844. [PMID: 3346227]

3. 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 2.1.1.314 created 2015]

EC 2.1.1.315

Accepted name: 27-O-demethylrifamycin SV methyltransferase

Reaction: S-adenosyl-L-methionine + 27-O-demethylrifamycin SV = S-adenosyl-L-homocysteine + rifamycin SV

Glossary: rifamycin SV = (7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-2,15,17,27,29-pentahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-6,23-dioxo-8,30-dioxa-24-azatetracyclo[23.3.1.14,7.05,28]triaconta-1(28),2,4,9, 19,21,25(29),26-octaen-13-yl acetate

Other name(s): AdoMet:27-O-demethylrifamycin SV methyltransferase

Systematic name: S-adenosyl-L-methionine:27-O-demethylrifamycin-SV 27-O-methyltransferase

Comments: The enzyme, characterized from the bacterium Amycolatopsis mediterranei, is involved in biosynthesis of the antitubercular drug rifamycin B.

References:

1. Xu, J., Mahmud, T. and Floss, H.G. Isolation and characterization of 27-O-demethylrifamycin SV methyltransferase provides new insights into the post-PKS modification steps during the biosynthesis of the antitubercular drug rifamycin B by Amycolatopsis mediterranei S699. Arch. Biochem. Biophys. 411 (2003) 277-288. [PMID: 12623077]

[EC 2.1.1.315 created 2015]

*EC 2.3.1.161

Accepted name: lovastatin nonaketide synthase

Reaction: acetyl-CoA + 8 malonyl-CoA + 11 NADPH + 10 H+ + S-adenosyl-L-methionine + holo-[lovastatin nonaketide synthase] = dihydromonacolin L-[lovastatin nonaketide synthase] + 9 CoA + 8 CO2 + 11 NADP+ + S-adenosyl-L-homocysteine + 6 H2O

For diagram of reaction click here.

Glossary: dihydromonacolin L acid = (3R,5R)-7-[(1S,2S,4aR,6R,8aS)-2,6-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate

Other name(s): LNKS; LovB; LovC; acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing, thioester-hydrolysing)

Systematic name: acyl-CoA:malonyl-CoA C-acyltransferase (dihydromonacolin L acid-forming)

Comments: This fungal enzyme system comprises a multi-functional polyketide synthase (PKS) and an enoyl reductase. The PKS catalyses many of the chain building reactions of EC 2.3.1.85, fatty-acid synthase, as well as a reductive methylation and a Diels-Alder reaction, while the reductase is responsible for three enoyl reductions that are necessary for dihydromonacolin L acid production.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 235426-97-8

References:

1. Ma, S.M., Li, J.W., Choi, J.W., Zhou, H., Lee, K.K., Moorthie, V.A., Xie, X., Kealey, J.T., Da Silva, N.A., Vederas, J.C. and Tang, Y. Complete reconstitution of a highly reducing iterative polyketide synthase. Science 326 (2009) 589-592. [PMID: 19900898]

2. Kennedy, J., Auclair, K., Kendrew, S.G., Park, C., Vederas, J.C. and Hutchinson, C.R. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284 (1999) 1368-1372. [PMID: 10334994]

3. Auclair, K., Sutherland, A., Kennedy, J., Witter, D.J., van der Heever, J.P., Hutchinson, C.R. and Vederas, J.C. Lovastatin nonaketide synthase catalyses an intramolecular Diels-Alder reaction of a substrate analogue. J. Am. Chem. Soc. 122 (2000) 11519-11520.

[EC 2.3.1.161 created 2002, modified 2015]

EC 2.3.1.244

Accepted name: 2-methylbutanoate polyketide synthase

Reaction: acetyl-CoA + malonyl-CoA + [2-methylbutanoate polyketide synthase] + 2 NADPH + 2 H+ + S-adenosyl-L-methionine = (S)-2-methylbutanoyl-[2-methylbutanoate polyketide synthase] + 2 CoA + CO2 + 2 NADP+ + S-adenosyl-L-homocysteine + H2O

For diagram of reaction click here.

Other name(s): LovF

Systematic name: acyl-CoA:malonyl-CoA C-acyltransferase (2-methylbutanoate-forming)

Comments: This polyketide synthase enzyme forms the (S)-2-methylbutanoate side chain during lovastatin biosynthesis by the filamentous fungus Aspergillus terreus. The overall reaction comprises a single condensation reaction followed by α-methylation, β-ketoreduction, dehydration, and α,β enoyl reduction.

References:

1. Kennedy, J., Auclair, K., Kendrew, S.G., Park, C., Vederas, J.C. and Hutchinson, C.R. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284 (1999) 1368-1372. [PMID: 10334994]

2. Meehan, M.J., Xie, X., Zhao, X., Xu, W., Tang, Y. and Dorrestein, P.C. FT-ICR-MS characterization of intermediates in the biosynthesis of the α-methylbutyrate side chain of lovastatin by the 277 kDa polyketide synthase LovF. Biochemistry 50 (2011) 287-299. [PMID: 21069965]

[EC 2.3.1.244 created 2015]

EC 2.3.1.245

Accepted name: 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase

Reaction: glycerone phosphate + acetyl-CoA = 3-hydroxy-5-phosphonooxypentane-2,4-dione + coenzyme A

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

Other name(s): lsrF (gene name)

Systematic name: acetyl-CoA:glycerone phosphate C-acetyltransferase

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

References:

1. Diaz, Z., Xavier, K.B. and Miller, S.T. The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF. PLoS One 4 (2009) e6820. [PMID: 19714241]

2. Marques, J.C., Oh, I.K., Ly, D.C., Lamosa, P., Ventura, M.R., Miller, S.T. and Xavier, K.B. LsrF, a coenzyme A-dependent thiolase, catalyzes the terminal step in processing the quorum sensing signal autoinducer-2. Proc. Natl. Acad. Sci. USA 111 (2014) 14235-14240. [PMID: 25225400]

[EC 2.3.1.245 created 2015]

EC 2.3.1.246

Accepted name: 3,5-dihydroxyphenylacetyl-CoA synthase

Reaction: 4 malonyl-CoA = (3,5-dihydroxyphenylacetyl)-CoA + 3 CoA + 4 CO2 + H2O

Other name(s): DpgA

Systematic name: malonyl-CoA:malonyl-CoA malonyltransferase (3,5-dihydroxyphenylacetyl-CoA-forming)

Comments: The enzyme, characterized from the bacterium Amycolatopsis mediterranei, is involved in biosynthesis of the nonproteinogenic amino acid (S)-3,5-dihydroxyphenylglycine, a component of the vancomycin-type antibiotic balhimycin.

References:

1. Pfeifer, V., Nicholson, G.J., Ries, J., Recktenwald, J., Schefer, A.B., Shawky, R.M., Schroder, J., Wohlleben, W. and Pelzer, S. A polyketide synthase in glycopeptide biosynthesis: the biosynthesis of the non-proteinogenic amino acid (S)-3,5-dihydroxyphenylglycine. J. Biol. Chem. 276 (2001) 38370-38377. [PMID: 11495926]

2. Chen, H., Tseng, C.C., Hubbard, B.K. and Walsh, C.T. Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine. Proc. Natl. Acad. Sci. USA 98 (2001) 14901-14906. [PMID: 11752437]

3. Tseng, C.C., McLoughlin, S.M., Kelleher, N.L. and Walsh, C.T. Role of the active site cysteine of DpgA, a bacterial type III polyketide synthase. Biochemistry 43 (2004) 970-980. [PMID: 14744141]

4. Wu, H.C., Li, Y.S., Liu, Y.C., Lyu, S.Y., Wu, C.J. and Li, T.L. Chain elongation and cyclization in type III PKS DpgA. Chembiochem 13 (2012) 862-871. [PMID: 22492619]

[EC 2.3.1.246 created 2015]

*EC 2.3.3.5

Accepted name: 2-methylcitrate synthase

Reaction: propanoyl-CoA + H2O + oxaloacetate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate + CoA

For diagram of reaction click here.

Glossary: 2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate

Other name(s): 2-methylcitrate oxaloacetate-lyase; MCS; methylcitrate synthase; methylcitrate synthetase

Systematic name: propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming)

Comments: The enzyme acts on acetyl-CoA, propanoyl-CoA, butanoyl-CoA and pentanoyl-CoA. The relative rate of condensation of acetyl-CoA and oxaloacetate is 140% of that of propanoyl-CoA and oxaloacetate, but the enzyme is distinct from EC 2.3.3.1, citrate (Si)-synthase. Oxaloacetate cannot be replaced by glyoxylate, pyruvate or 2-oxoglutarate.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 57827-78-8

References:

1. Uchiyama, H. and Tabuchi, T. Properties of methylcitrate synthase from Candida lipolytica. Agric. Biol. Chem. 40 (1976) 1411-1418.

2. Textor, S., Wendisch, V.F., De Graaf, A.A., Muller, U., Linder, M.I., Linder, D. and Buckel, W. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168 (1997) 428-436. [PMID: 9325432]

3. Horswill, A.R. and Escalante-Semerena, J.C. Salmonella typhimurium LT2 catabolizes propionate via the 2-methylcitric acid cycle. J. Bacteriol. 181 (1999) 5615-5623. [PMID: 10482501]

4. Brock, M., Maerker, C., Schütz, A., Völker, U. and Buckel, W. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur. J. Biochem. 269 (2002) 6184-6194. [PMID: 12473114]

5. Domin, N., Wilson, D. and Brock, M. Methylcitrate cycle activation during adaptation of Fusarium solani and Fusarium verticillioides to propionyl-CoA-generating carbon sources. Microbiology 155 (2009) 3903-3912. [PMID: 19661181]

[EC 2.3.3.5 created 1978 as EC 4.1.3.31, transferred 2002 to EC 2.3.3.5, modified 2015]

EC 2.7.1.187

Accepted name: acarbose 7IV-phosphotransferase

Reaction: ATP + acarbose = ADP + acarbose 7IV-phosphate

Glossary: acarbose = 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)-2-cyclohexen-1-yl]amino}-α-D-glucopyranosyl-(1→4)-α-D-glucopyranosyl-(1→4)-β-D-glucopyranose

Other name(s): acarbose 7-kinase; AcbK

Systematic name: ATP:acarbose 7IV-phosphotransferase

Comments: The enzyme, characterized from the bacterium Actinoplanes sp. SE50/110, is specific for acarbose.

References:

1. Drepper, A. and Pape, H. Acarbose 7-phosphotransferase from Actinoplanes sp.: purification, properties, and possible physiological function. J. Antibiot. (Tokyo) 49 (1996) 664-668. [PMID: 8784428]

2. Goeke, K., Drepper, A. and Pape, H. Formation of acarbose phosphate by a cell-free extract from the acarbose producer Actinoplanes sp. J. Antibiot. (Tokyo) 49 (1996) 661-663. [PMID: 8784426]

3. Zhang, C.S., Stratmann, A., Block, O., Bruckner, R., Podeschwa, M., Altenbach, H.J., Wehmeier, U.F. and Piepersberg, W. Biosynthesis of the C7-cyclitol moiety of acarbose in Actinoplanes species SE50/110. 7-O-phosphorylation of the initial cyclitol precursor leads to proposal of a new biosynthetic pathway. J. Biol. Chem. 277 (2002) 22853-22862. [PMID: 11937512]

[EC 2.7.1.187 created 2015]

EC 2.7.1.188

Accepted name: 2-epi-5-epi-valiolone 7-kinase

Reaction: ATP + 2-epi-5-epi-valiolone = ADP + 2-epi-5-epi-valiolone 7-phosphate

For diagram of reaction click here.

Glossary: 2-epi-5-epi-valiolone = (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexan-1-one

Other name(s): AcbM

Systematic name: ATP:2-epi-5-epi-valiolone 7-phosphotransferase

Comments: The enzyme, characterized from the bacterium Actinoplanes sp. SE50/110, is involved in the biosynthesis of the oligosaccharide acarbose.

References:

1. Zhang, C.S., Stratmann, A., Block, O., Bruckner, R., Podeschwa, M., Altenbach, H.J., Wehmeier, U.F. and Piepersberg, W. Biosynthesis of the C7-cyclitol moiety of acarbose in Actinoplanes species SE50/110. 7-O-phosphorylation of the initial cyclitol precursor leads to proposal of a new biosynthetic pathway. J. Biol. Chem. 277 (2002) 22853-22862. [PMID: 11937512]

[EC 2.7.1.188 created 2015]

EC 2.7.4.29

Accepted name: Kdo2-lipid A phosphotransferase

Reaction: ditrans-octacis-undecaprenyl diphosphate + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A = ditrans-octacis-undecaprenyl phosphate + α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid A 1-diphosphate

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 A 1-diphosphate =
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

Other name(s): lipid A undecaprenyl phosphotransferase; LpxT; YeiU

Systematic name: ditrans-octacis-undecaprenyl diphosphate:α-D-Kdo-(2→4)-α-D-Kdo-(2→6)-lipid-A phosphotransferase

Comments: An inner-membrane protein. The activity of the enzyme is regulated by PmrA. In vitro the enzyme can use diacylglycerol 3-diphosphate as the phosphate donor.

References:

1. Touze, T., Tran, A.X., Hankins, J.V., Mengin-Lecreulx, D. and Trent, M.S. Periplasmic phosphorylation of lipid A is linked to the synthesis of undecaprenyl phosphate. Mol. Microbiol. 67 (2008) 264-277. [PMID: 18047581]

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]

[EC 2.7.4.29 created 2015]

EC 3.1.2.31

Accepted name: dihydromonacolin L-[lovastatin nonaketide synthase] thioesterase

Reaction: dihydromonacolin L-[lovastatin nonaketide synthase] + H2O = holo-[lovastatin nonaketide synthase] + dihydromonacolin L acid

For diagram of reaction click here.

Glossary: dihydromonacolin L acid = (3R,5R)-7-[(1S,2S,4aR,6R,8aS)-2,6-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate

Other name(s): LovG

Systematic name: dihydromonacolin L-[lovastatin nonaketide synthase] hydrolase

Comments: Dihydromonacolin L acid is synthesized while bound to an acyl-carrier protein domain of the lovastatin nonaketide synthase (EC 2.3.1.161). Since that enzyme lacks a thioesterase domain, release of the dihydromonacolin L acid moiety from the polyketide synthase requires this dedicated enzyme.

References:

1. Xu, W., Chooi, Y.H., Choi, J.W., Li, S., Vederas, J.C., Da Silva, N.A. and Tang, Y. LovG: the thioesterase required for dihydromonacolin L release and lovastatin nonaketide synthase turnover in lovastatin biosynthesis. Angew. Chem. Int. Ed. Engl. 52 (2013) 6472-6475. [PMID: 23653178]

[EC 3.1.2.31 created 2015]

EC 3.1.3.97

Accepted name: 3',5'-nucleoside bisphosphate phosphatase

Reaction: nucleoside 3',5'-bisphosphate + H2O = nucleoside 5'-phosphate + phosphate

Systematic name: nucleoside-3',5'-bisphosphate 3'-phosphohydrolase

Comments: The enzyme, characterized from the bacterium Chromobacterium violaceum, has similar catalytic efficiencies with all the bases. The enzyme has similar activity with ribonucleoside and 2'-deoxyribonucleoside 3',5'-bisphosphates, but shows no activity with nucleoside 2',5'-bisphosphates (cf. EC 3.1.3.7, 3'(2'),5'-bisphosphate nucleotidase).

References:

1. Cummings, J.A., Vetting, M., Ghodge, S.V., Xu, C., Hillerich, B., Seidel, R.D., Almo, S.C. and Raushel, F.M. Prospecting for unannotated enzymes: discovery of a 3',5'-nucleotide bisphosphate phosphatase within the amidohydrolase superfamily. Biochemistry 53 (2014) 591-600. [PMID: 24401123]

[EC 3.1.3.97 created 2015]

EC 3.3.2.14

Accepted name: 2,4-dinitroanisole O-demethylase

Reaction: 2,4-dinitroanisole + H2O = methanol + 2,4-dinitrophenol

Glossary: 2,4-dinitroanisole = 1-methoxy-2,4-dinitrobenzene

Other name(s): 2,4-dinitroanisole ether hydrolase; dnhA (gene name); dnhB (gene name); DNAN demethylase

Systematic name: 2,4-dinitroanisole methanol hydrolase

Comments: The enzyme, characterized from the bacterium Nocardioides sp. JS1661, is involved in the degradation of 2,4-dinitroanisole. Unlike other known O-demethylases, such as EC 1.14.99.15, 4-methoxybenzoate monooxygenase (O-demethylating), or EC 1.14.11.32, codeine 3-O-demethylase, it does not require oxygen or electron donors, and produces methanol rather than formaldehyde.

References:

1. Fida, T.T., Palamuru, S., Pandey, G. and Spain, J.C. Aerobic biodegradation of 2,4-dinitroanisole by Nocardioides sp. strain JS1661. Appl. Environ. Microbiol. 80 (2014) 7725-7731. [PMID: 25281383]

[EC 3.3.2.14 created 2015]

EC 3.4.14.13

Accepted name: γ-D-glutamyl-L-lysine dipeptidyl-peptidase

Reaction: The enzyme releases L-Ala-γ-D-Glu dipeptides from cell wall peptides via cleavage of an L-Ala-γ-D-Glu┼L-Lys bond.

Other name(s): YkfC

Comments: The enzyme, characterized from the bacterium Bacillus subtilis, is involved in the recycling of the murein peptide.

References:

1. Schmidt, D.M., Hubbard, B.K. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases. Biochemistry 40 (2001) 15707-15715. [PMID: 11747447]

2. Xu, Q., Abdubek, P., Astakhova, T., Axelrod, H.L., Bakolitsa, C., Cai, X., Carlton, D., Chen, C., Chiu, H.J., Chiu, M., Clayton, T., Das, D., Deller, M.C., Duan, L., Ellrott, K., Farr, C.L., Feuerhelm, J., Grant, J.C., Grzechnik, A., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Krishna, S.S., Kumar, A., Lam, W.W., Marciano, D., Miller, M.D., Morse, A.T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Tien, H.J., Trame, C.B., van den Bedem, H., Weekes, D., Wooten, T., Yeh, A., Hodgson, K.O., Wooley, J., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (2010) 1354-1364. [PMID: 20944232]

[EC 3.4.14.13 created 2015]

EC 3.5.1.118

Accepted name: γ-glutamyl hercynylcysteine S-oxide hydrolase

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

Glossary: hercynine = Nα,Nα,Nα-trimethyl-L-histidine = 3-(1H-imidazol-5-yl)-2-(trimethylamino)propanoate
S-(hercyn-2-yl)-L-cysteine S-oxide = S-(N,N,N-trimethyl-L-histidin-2-yl)-L-cysteine S-oxide

Other name(s): EgtC

Systematic name: S-γ-glutamyl hercynylcysteine S-oxide amidohydrolase

Comments: The enzyme is part of the biosynthesis pathway of ergothioneine in mycobacteria.

References:

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

[EC 3.5.1.118 created 2015]

EC 4.1.1.100

Accepted name: prephenate decarboxylase

Reaction: prephenate = 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate + CO2

For diagram of reaction click here.

Glossary: L-anticapsin = 3-[(1R,2S,6R)-5-oxo-7-oxabicyclo[4.1.0]hept-2-yl]-L-alanine

Other name(s): BacA; AerD; SalX; non-aromatizing prephenate decarboxylase

Systematic name: prephenate carboxy-lyase (3-[(4S)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate-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 isomerizes only the pro-R double bond in prephenate.

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. Mahlstedt, S., Fielding, E.N., Moore, B.S. and Walsh, C.T. Prephenate decarboxylases: a new prephenate-utilizing enzyme family that performs nonaromatizing decarboxylation en route to diverse secondary metabolites. Biochemistry 49 (2010) 9021-9023. [PMID: 20863139]

3. 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]

[EC 4.1.1.100 created 2015]

EC 4.1.99.21

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

Reaction: (5-formylfuran-3-yl)methyl phosphate + phosphate + 2 H2O = 2 D-glyceraldehyde 3-phosphate

Glossary: 2-furaldehyde phosphate = 4-(hydroxymethyl)-2-furancarboxaldehyde phosphate

Other name(s): mfnB (gene name); 4-HFC-P synthase; 2-furaldehyde phosphate synthase

Systematic name: 4-(hydroxymethyl)-2-furancarboxaldehyde phosphate lyase

Comments: The enzyme catalyses the reaction in the direction of producing (5-formylfuran-3-yl)methyl phosphate, an intermediate in the biosynthesis of methanofuran. Methanofuran is a carbon-carrier cofactor involved in the first step of the methanogenic reduction of carbon dioxide by methanogenic archaea.

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]

2. Wang, Y., Xu, H., Harich, K.C. and White, R.H. Identification and characterization of a tyramine-glutamate ligase (MfnD) Involved in methanofuran biosynthesis. Biochemistry 53 (2014) 6220-6230. [PMID: 25211225]

[EC 4.1.99.21 created 2015]

EC 4.2.1.155

Accepted name: (methylthio)acryloyl-CoA hydratase

Reaction: 3-(methylthio)acryloyl-CoA + 2 H2O = acetaldehyde + methanethiol + CoA + CO2 (overall reaction)
(1a) 3-(methylthio)acryloyl-CoA + H2O = 3-hydroxy-3-(methylthio)propanoyl-CoA
(1b) 3-hydroxy-3-(methylthio)propanoyl-CoA = 3-oxopropanoyl-CoA + methanethiol
(1c) 3-oxopropanoyl-CoA + H2O = 3-oxopropanoate + CoA
(1d) 3-oxopropanoate = acetaldehyde + CO2

Glossary: 3-(methylthio)acryloyl-CoA = 3-(methylsulfanyl)prop-2-enoyl-CoA

Other name(s): DmdD

Systematic name: 3-(methylsulfanyl)prop-2-enoyl-CoA hydro-lyase (acetaldehyde-forming)

Comments: The enzyme is involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton. Isolated from the bacterium Ruegeria pomeroyi.

References:

1. Tan, D., Crabb, W.M., Whitman, W.B. and Tong, L. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PLoS One 8 (2013) e63870. [PMID: 23704947]

[EC 4.2.1.155 created 2015]

EC 4.2.3.152

Accepted name: 2-epi-5-epi-valiolone synthase

Reaction: α-D-sedoheptulopyranose 7-phosphate = 2-epi-5-epi-valiolone + phosphate

For diagram of reaction click here.

Glossary: 2-epi-5-epi-valiolone = (2S,3S,4S,5R)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexan-1-one

Other name(s): AcbC; ValA; CetA; SalQ; C7-cyclitol synthase

Systematic name: α-D-sedoheptulopyranose 7-phosphate phosphate-lyase (cyclizing; 2-epi-5-epi-valiolone-forming)

Comments: The cyclization product, 2-epi-5-epi-valiolone, is a precursor of the valienamine moiety of acarbose. The enzyme from actinobacteria is highly specificity for α-D-sedoheptulopyranose 7-phosphate. It requires a divalent metal ion (Zn2+ or Co2+) and an NAD+ cofactor, which is transiently reduced during the reaction.

References:

1. Stratmann, A., Mahmud, T., Lee, S., Distler, J., Floss, H.G. and Piepersberg, W. The AcbC protein from Actinoplanes species is a C7-cyclitol synthase related to 3-dehydroquinate synthases and is involved in the biosynthesis of the α-glucosidase inhibitor acarbose. J. Biol. Chem. 274 (1999) 10889-10896. [PMID: 10196166]

2. Wu, X., Flatt, P.M., Schlorke, O., Zeeck, A., Dairi, T. and Mahmud, T. A comparative analysis of the sugar phosphate cyclase superfamily involved in primary and secondary metabolism. Chembiochem 8 (2007) 239-248. [PMID: 17195255]

3. Choi, W.S., Wu, X., Choeng, Y.H., Mahmud, T., Jeong, B.C., Lee, S.H., Chang, Y.K., Kim, C.J. and Hong, S.K. Genetic organization of the putative salbostatin biosynthetic gene cluster including the 2-epi-5-epi-valiolone synthase gene in Streptomyces albus ATCC 21838. Appl. Microbiol. Biotechnol. 80 (2008) 637-645. [PMID: 18648803]

4. Kean, K.M., Codding, S.J., Asamizu, S., Mahmud, T. and Karplus, P.A. Structure of a sedoheptulose 7-phosphate cyclase: ValA from Streptomyces hygroscopicus. Biochemistry 53 (2014) 4250-4260. [PMID: 24832673]

[EC 4.2.3.152 created 2015]

EC 4.4.1.29

Accepted name: phycobiliprotein cysteine-84 phycobilin lyase

Reaction: (1) [C-phycocyanin β-subunit]-Cys84-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys84-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin
(3) [allophycocyanin α-subunit]-Cys84-phycocyanobilin = apo-[allophycocyanin α-subunit] + (2R,3E)-phycocyanobilin
(4) [allophycocyanin β-subunit]-Cys84-phycocyanobilin = apo-[allophycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(5) [C-phycoerythrin α-subunit]-Cys84-phycoerythrobilin = apo-[C-phycoerythrin α-subunit] + (2R,3E)-phycoerythrobilin
(6) [C-phycoerythrin β-subunit]-Cys84-phycoerythrobilin = apo-[C-phycoerythrin β-subunit] + (2R,3E)-phycoerythrobilin

Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
phycoerythrobilin = 3,31,181,182-tetradehydro-2,3,15,16-tetrahydromesobiliverdin

Other name(s): cpcS (gene name); cpeS (gene name); cpcS1 (gene name); cpcU (gene name); phycocyanobilin:Cys-β84-phycobiliprotein lyase

Systematic name: [phycobiliprotein]-Cys84-phycobilin:phycobilin lyase

Comments: The enzyme, found in cyanobacteria and red algae, catalyses the attachment of phycobilin chromophores to cysteine 84 of several phycobiliproteins (the numbering used here corresponds to the enzyme from Anabaena, in other organisms the number may vary slightly). It can attach phycocyanobilin to the β subunits of C-phycocyanin and phycoerythrocyanin and to both subunits of allophycocyanin. In addition, it can attach phycoerythrobilin to both subunits of C-phycoerythrin.

References:

1. Zhao, K.H., Su, P., Li, J., Tu, J.M., Zhou, M., Bubenzer, C. and Scheer, H. Chromophore attachment to phycobiliprotein β-subunits: phycocyanobilin:cysteine-β84 phycobiliprotein lyase activity of CpeS-like protein from Anabaena Sp. PCC7120. J. Biol. Chem. 281 (2006) 8573-8581. [PMID: 16452471]

2. Zhao, K.H., Su, P., Tu, J.M., Wang, X., Liu, H., Ploscher, M., Eichacker, L., Yang, B., Zhou, M. and Scheer, H. Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins. Proc. Natl. Acad. Sci. USA 104 (2007) 14300-14305. [PMID: 17726096]

3. Saunee, N.A., Williams, S.R., Bryant, D.A. and Schluchter, W.M. Biogenesis of phycobiliproteins: II. CpcS-I and CpcU comprise the heterodimeric bilin lyase that attaches phycocyanobilin to Cys-82 of β-phycocyanin and Cys-81 of allophycocyanin subunits in Synechococcus sp. PCC 7002. J. Biol. Chem. 283 (2008) 7513-7522. [PMID: 18199753]

4. Kupka, M., Zhang, J., Fu, W.L., Tu, J.M., Bohm, S., Su, P., Chen, Y., Zhou, M., Scheer, H. and Zhao, K.H. Catalytic mechanism of S-type phycobiliprotein lyase: chaperone-like action and functional amino acid residues. J. Biol. Chem. 284 (2009) 36405-36414. [PMID: 19864423]

[EC 4.4.1.29 created 2015]

EC 4.4.1.30

Accepted name: phycobiliprotein β-cysteine-155 phycobilin lyase

Reaction: (1) [C-phycocyanin β-subunit]-Cys155-phycocyanobilin = apo-[C-phycocyanin β-subunit] + (2R,3E)-phycocyanobilin
(2) [phycoerythrocyanin β-subunit]-Cys155-phycocyanobilin = apo-[phycoerythrocyanin β-subunit] + (2R,3E)-phycocyanobilin

Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin

Other name(s): cpcT (gene name); cpeT1 (gene name); cpcT1 (gene name)

Systematic name: [phycobiliprotein β-subunit]-Cys155-phycocyanobilin:phycocyanobilin lyase

Comments: The enzyme, found in cyanobacteria and red algae, catalyses the attachment of the phycobilin chromophore phycocyanobilin to cysteine 155 of the β subunits of the phycobiliproteins C-phycocyanin and phycoerythrocyanin. The numbering used here corresponds to the enzyme from Anabaena, and could vary slightly in other organisms.

References:

1. Zhao, K.H., Zhang, J., Tu, J.M., Bohm, S., Ploscher, M., Eichacker, L., Bubenzer, C., Scheer, H., Wang, X. and Zhou, M. Lyase activities of CpcS- and CpcT-like proteins from Nostoc PCC7120 and sequential reconstitution of binding sites of phycoerythrocyanin and phycocyanin β-subunits. J. Biol. Chem. 282 (2007) 34093-34103. [PMID: 17895251]

2. Zhang, R., Feng, X.T., Wu, F., Ding, Y., Zang, X.N., Zhang, X.C., Yuan, D.Y. and Zhao, B.R. Molecular cloning and expression analysis of a new bilin lyase: the cpcT gene encoding a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the β-subunit of phycocyanin in Arthrospira platensis FACHB314. Gene 544 (2014) 191-197. [PMID: 24768724]

3. Zhou, W., Ding, W.L., Zeng, X.L., Dong, L.L., Zhao, B., Zhou, M., Scheer, H., Zhao, K.H. and Yang, X. Structure and mechanism of the phycobiliprotein lyase CpcT. J. Biol. Chem. 289 (2014) 26677-26689. [PMID: 25074932]

[EC 4.4.1.30 created 2015]

EC 4.4.1.31

Accepted name: phycoerythrocyanin α-cysteine-84 phycoviolobilin lyase/isomerase

Reaction: [phycoerythrocyanin α-subunit]-Cys84-phycoviolobilin = apo-[phycoerythrocyanin α-subunit] + (2R,3E)-phycocyanobilin

Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin
phycoviolobilin = 15,16-dihydrobiliverdin IIIa

Other name(s): pecE (gene name); pecF (gene name); phycoviolobilin phycoerythrocyanin-α84-cystein-lyase; PecE/PecF; PEC-Cys-R84 PCB lyase/isomerase

Systematic name: [phycoerythrocyanin α-subunit]-Cys84-phycoviolobilin:(2R,3E)-phycocyanobilin lyase/isomerase

Comments: The enzyme, characterized from the cyanobacteria Nostoc sp. PCC 7120 and Mastigocladus laminosus, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the β subunit of the phycobiliprotein phycoerythrocyanin and its isomerization to phycoviolobilin.

References:

1. Jung, L.J., Chan, C.F. and Glazer, A.N. Candidate genes for the phycoerythrocyanin α subunit lyase. Biochemical analysis of pecE and pecF interposon mutants. J. Biol. Chem. 270 (1995) 12877-12884. [PMID: 7759546]

2. Zhao, K.H., Deng, M.G., Zheng, M., Zhou, M., Parbel, A., Storf, M., Meyer, M., Strohmann, B. and Scheer, H. Novel activity of a phycobiliprotein lyase: both the attachment of phycocyanobilin and the isomerization to phycoviolobilin are catalyzed by the proteins PecE and PecF encoded by the phycoerythrocyanin operon. FEBS Lett 469 (2000) 9-13. [PMID: 10708746]

3. Storf, M., Parbel, A., Meyer, M., Strohmann, B., Scheer, H., Deng, M.G., Zheng, M., Zhou, M. and Zhao, K.H. Chromophore attachment to biliproteins: specificity of PecE/PecF, a lyase-isomerase for the photoactive 31-cys-α 84-phycoviolobilin chromophore of phycoerythrocyanin. Biochemistry 40 (2001) 12444-12456. [PMID: 11591166]

4. Zhao, K.H., Wu, D., Wang, L., Zhou, M., Storf, M., Bubenzer, C., Strohmann, B. and Scheer, H. Characterization of phycoviolobilin phycoerythrocyanin-α 84-cystein-lyase-(isomerizing) from Mastigocladus laminosus. Eur. J. Biochem. 269 (2002) 4542-4550. [PMID: 12230566]

[EC 4.4.1.31 created 2015]

EC 4.4.1.32

Accepted name: C-phycocyanin α-cysteine-84 phycocyanobilin lyase

Reaction: [C-phycocyanin α-subunit]-Cys84-phycocyanobilin = apo-[C-phycocyanin α-subunit] + (2R,3E)-phycocyanobilin

Glossary: phycocyanobilin = 3,31-didehydro-2,3-dihydromesobiliverdin

Other name(s): cpcE (gene name); cpcF (gene name)

Systematic name: [C-phycocyanin α-subunit]-Cys84-phycocyanobilin:(2R,3E)-phycocyanobilin lyase

Comments: The enzyme, characterized from the cyanobacterium Synechococcus elongatus PCC 7942, catalyses the covalent attachment of the phycobilin chromophore phycocyanobilin to cysteine 84 of the α subunit of the phycobiliprotein C-phycocyanin.

References:

1. Fairchild, C.D., Zhao, J., Zhou, J., Colson, S.E., Bryant, D.A. and Glazer, A.N. Phycocyanin α-subunit phycocyanobilin lyase. Proc. Natl. Acad. Sci. USA 89 (1992) 7017-7021. [PMID: 1495995]

2. Fairchild, C.D. and Glazer, A.N. Oligomeric structure, enzyme kinetics, and substrate specificity of the phycocyanin α subunit phycocyanobilin lyase. J. Biol. Chem. 269 (1994) 8686-8694. [PMID: 8132596]

3. Bhalerao, R.P., Lind, L.K. and Gustafsson, P. Cloning of the cpcE and cpcF genes from Synechococcus sp. PCC 6301 and their inactivation in Synechococcus sp. PCC 7942. Plant Mol. Biol. 26 (1994) 313-326. [PMID: 7524727]

[EC 4.4.1.32 created 2015]

EC 4.4.1.33

Accepted name: R-phycocyanin α-cysteine-84 phycourobilin lyase/isomerase

Reaction: [R-phycocyanin α-subunit]-Cys-84-phycourobilin = apo-[R-phycocyanin α-subunit] + (2R,3E)-phycoerythrobilin

Other name(s): rpcG (gene name)

Systematic name: [R-phycocyanin α-subunit]-Cys84-phycourobilin:(2R,3E)-phycoerythrobilin lyase/isomerase

Comments: The enzyme, characterized from the cyanobacterium Synechococcus sp. WH8102, catalyses the covalent attachment of the phycobilin chromophore phycoerythrobilin to cysteine 84 of the α subunit of the phycobiliprotein R-phycocyanin and its isomerization to phycourobilin.

References:

1. Blot, N., Wu, X.J., Thomas, J.C., Zhang, J., Garczarek, L., Bohm, S., Tu, J.M., Zhou, M., Ploscher, M., Eichacker, L., Partensky, F., Scheer, H. and Zhao, K.H. Phycourobilin in trichromatic phycocyanin from oceanic cyanobacteria is formed post-translationally by a phycoerythrobilin lyase-isomerase. J. Biol. Chem. 284 (2009) 9290-9298. [PMID: 19182270]

[EC 4.4.1.33 created 2015]

EC 5.1.1.20

Accepted name: L-Ala-D/L-Glu epimerase

Reaction: L-alanyl-D-glutamate = L-alanyl-L-glutamate

Other name(s): YkfB; YcjG; AEE; AE epimerase

Systematic name: L-alanyl-D-glutamate epimerase

Comments: The enzyme, characterized from the bacteria Escherichia coli and Bacillus subtilis, is involved in the recycling of the murein peptide, of which L-Ala-D-Glu is a component. In vitro the enzyme from Escherichia coli epimerizes several L-Ala-L-X dipeptides with broader specificity than the enzyme from Bacillus subtilis.

References:

1. Schmidt, D.M., Hubbard, B.K. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: functional assignment of unknown proteins in Bacillus subtilis and Escherichia coli as L-Ala-D/L-Glu epimerases. Biochemistry 40 (2001) 15707-15715. [PMID: 11747447]

2. Gulick, A.M., Schmidt, D.M., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activities in the enolase superfamily: crystal structures of the L-Ala-D/L-Glu epimerases from Escherichia coli and Bacillus subtilis. Biochemistry 40 (2001) 15716-15724. [PMID: 11747448]

[EC 5.1.1.20 created 2015]

EC 5.3.1.32

Accepted name: (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase

Reaction: (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione = 3-hydroxy-5-phosphonooxypentane-2,4-dione

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

Other name(s): lsrG (gene name); phospho-AI-2 isomerase

Systematic name: (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione aldose-ketose-isomerase

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. Marques, J.C., Lamosa, P., Russell, C., Ventura, R., Maycock, C., Semmelhack, M.F., Miller, S.T. and Xavier, K.B. Processing the interspecies quorum-sensing signal autoinducer-2 (AI-2): characterization of phospho-(S)-4,5-dihydroxy-2,3-pentanedione isomerization by LsrG protein. J. Biol. Chem. 286 (2011) 18331-18343. [PMID: 21454635]

[EC 5.3.1.32 created 2015]

EC 5.5.1.26

Accepted name: nogalonic acid methyl ester cyclase

Reaction: nogalaviketone = methyl nogalonate

For diagram of reaction click here.

Glossary: methyl nogalonate = methyl [4,5-dihydroxy-9,10-dioxo-3-(3-oxobutanoyl)-9,10-dihydroanthracen-2-yl]acetate
nogalaviketone = methyl 5,7-dihydroxy-2-methyl-4,6,11-trioxo-3,4,6,11-tetrahydrotetracene-1-carboxylate

Other name(s): methyl nogalonate cyclase; SnoaL (gene name)

Systematic name: methyl nogalonate lyase (cyclizing)

Comments: The enzyme, characterized from the bacterium Streptomyces nogalater, is involved in the biosynthesis of the aromatic polyketide nogalamycin.

References:

1. Sultana, A., Kallio, P., Jansson, A., Wang, J.S., Niemi, J., Mantsala, P. and Schneider, G. Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. EMBO J. 23 (2004) 1911-1921. [PMID: 15071504]

2. Sultana, A., Kallio, P., Jansson, A., Niemi, J., Mantsala, P. and Schneider, G. Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1118-1120. [PMID: 15159574]

[EC 5.5.1.26 created 2015]

*EC 6.3.2.37

Accepted name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—D-lysine ligase

Reaction: ATP + UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate + D-lysine = ADP + phosphate + N6-(UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl)-D-lysine

Glossary: muramic acid = 2-amino-3-O-[(R)-1-carboxyethyl]-2-deoxy-D-glucose

Other name(s): UDP-MurNAc-L-Ala-D-Glu:D-Lys ligase; D-lysine-adding enzyme

Systematic name: UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate:D-lysine γ-ligase (ADP-forming)

Comments: Involved in the synthesis of cell-wall peptidoglycan. The D-lysine is attached to the peptide chain at the N6 position. The enzyme from Thermotoga maritima also performs the reaction of EC 6.3.2.7, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate—L-lysine ligase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Boniface, A., Bouhss, A., Mengin-Lecreulx, D. and Blanot, D. The MurE synthetase from Thermotoga maritima is endowed with an unusual D-lysine adding activity. J. Biol. Chem. 281 (2006) 15680-15686. [PMID: 16595662]

[EC 6.3.2.37 created 2011, modified 2015]

EC 6.3.2.46

Accepted name: fumarate—(S)-2,3-diaminopropanoate ligase

Reaction: ATP + fumarate + (S)-2,3-diaminopropanoate = AMP + diphosphate + N3-fumaroyl-(S)-2,3-diaminopropanoate

Glossary: N3-fumaroyl-(S)-2,3-diaminopropanoate = (2E)-4-{[(2S)-2-amino-2-carboxyethyl]amino}-4-oxobut-2-enoate

Other name(s): DdaG

Systematic name: fumarate:(S)-2,3-diaminopropanoate ligase (AMP-forming)

Comments: The enzyme, characterized from the bacterium Enterobacter agglomerans, is involved in biosynthesis of dapdiamide tripeptide antibiotics, a family of fumaramoyl- and epoxysuccinamoyl-peptides named for the presence of an (S)-2,3-diaminopropanoate (DAP) moiety and two amide linkages in their scaffold.

References:

1. Hollenhorst, M.A., Clardy, J. and Walsh, C.T. The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics. Biochemistry 48 (2009) 10467-10472. [PMID: 19807062]

[EC 6.3.2.46 created 2015]

EC 6.3.2.47

Accepted name: dapdiamide A synthase

Reaction: (1) ATP + 3-({[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl}amino)-L-alanine + L-valine = ADP + phosphate + 3-({[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl}amino)-L-alanyl-L-valine
(2) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-valine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-valine
(3) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-isoleucine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-isoleucine
(4) ATP + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine + L-leucine = ADP + phosphate + 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-leucine

Glossary: dapdiamide A = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-valine
dapdiamide B = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-isoleucine
dapdiamide C = 3-{[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanyl-L-leucine
dapdiamide E = 3-({[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl}amino)-L-alanyl-L-valine

Other name(s): DdaF; 3-[[[(2R,3R)-3-carboxyoxiran-2-yl]carbonyl]amino]-L-alanine—L-valine ligase

Systematic name: {[(2E)-4-amino-4-oxobut-2-enoyl]amino}-L-alanine:L-valine ligase (ADP-forming)

Comments: The enzyme, characterized from the bacterium Enterobacter agglomerans, is involved in biosynthesis of dapdiamide tripeptide antibiotics, a family of fumaramoyl- and epoxysuccinamoyl-peptides named for the presence of an (S)-2,3-diaminopropanoate (DAP) moiety and two amide linkages in their scaffold.

References:

1. Hollenhorst, M.A., Clardy, J. and Walsh, C.T. The ATP-dependent amide ligases DdaG and DdaF assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics. Biochemistry 48 (2009) 10467-10472. [PMID: 19807062]

2. Hollenhorst, M.A., Bumpus, S.B., Matthews, M.L., Bollinger, J.M., Jr., Kelleher, N.L. and Walsh, C.T. The nonribosomal peptide synthetase enzyme DdaD tethers N(β)-fumaramoyl-L-2,3-diaminopropionate for Fe(II)/α-ketoglutarate-dependent epoxidation by DdaC during dapdiamide antibiotic biosynthesis. J. Am. Chem. Soc. 132 (2010) 15773-15781. [PMID: 20945916]

[EC 6.3.2.47 created 2015]


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