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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.367 UDP-2-acetamido-2,6-β-L-arabino-hexul-4-ose reductase (17 March 2014)
EC 1.1.1.368 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase (17 March 2014)
EC 1.1.1.369 D-chiro-inositol 1-dehydrogenase (17 March 2014)
EC 1.1.1.370 scyllo-inositol 2-dehydrogenase (NAD+) (17 March 2014)
EC 1.1.1.371 scyllo-inositol 2-dehydrogenase (NADP+) (17 March 2014)
EC 1.1.5.10 D-2-hydroxyacid dehydrogenase (quinone) (17 March 2014)
EC 1.2.1.89 D-glyceraldehyde dehydrogenase (NADP+) (17 March 2014)
*EC 1.3.1.74 2-alkenal reductase [NAD(P)+] (17 March 2014)
EC 1.3.1.106 cobalt-precorrin-6A reductase (17 March 2014)
*EC 1.3.5.1 succinate dehydrogenase (quinone) (17 March 2014)
EC 1.3.98.2 fumarate reductase (CoM/CoB) (17 March 2014)
EC 1.3.99.1 deleted, included with EC 1.3.5.1 (17 March 2014)
EC 1.3.99.35 chlorophyllide a reductase (17 March 2014)
EC 1.5.98 With another known acceptor
EC 1.5.98.1 methylenetetrahydromethanopterin dehydrogenase (17 March 2014)
EC 1.5.98.2 5,10-methylenetetrahydromethanopterin reductase (17 March 2014)
*EC 1.5.99 With an unknown acceptor
EC 1.5.99.9 transferred now EC 1.5.98.1 (17 March 2014)
EC 1.5.99.11 transferred now EC 1.5.98.2 (17 March 2014)
EC 1.6.3.5 renalase (17 March 2014)
*EC 1.10.3.11 ubiquinol oxidase (non-electrogenic) (17 March 2014)
EC 1.10.3.14 ubiquinol oxidase (electrogenic, non H+-transporting) (17 March 2014)
EC 1.14.13.185 pikromycin synthase (17 March 2014)
EC 1.14.13.186 20-oxo-5-O-mycaminosyltylactone 23-monooxygenase (17 March 2014)
EC 1.14.13.187 L-evernosamine nitrososynthase (17 March 2014)
EC 1.14.13.188 6-deoxyerythronolide B hydroxylase (17 March 2014)
*EC 1.16.1.7 ferric-chelate reductase (NADH) (17 March 2014)
*EC 1.16.1.9 ferric-chelate reductase (NADPH) (17 March 2014)
EC 1.16.1.10 ferric-chelate reductase [NAD(P)H] (17 March 2014)
EC 1.21.99.2 cyclic dehypoxanthinyl futalosine synthase (17 March 2014)
*EC 2.1.1.57 methyltransferase cap1 (28 March 2014)
*EC 2.1.1.267 flavonoid 3',5'-methyltransferase (17 March 2014)
*EC 2.1.1.282 tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase (17 March 2014)
EC 2.1.1.294 3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase (17 March 2014)
EC 2.1.1.295 2-methyl-6-phytyl-1,4-hydroquinone methyltransferase (17 March 2014)
EC 2.1.1.296 methyltransferase cap2 (28 March 2014)
EC 2.1.1.297 peptide chain release factor N5-glutamine methyltransferase (17 March 2014)
EC 2.1.1.298 ribosomal protein L3 N5-glutamine methyltransferase (17 March 2014)
EC 2.1.1.299 protein N-terminal monomethyltransferase (17 March 2014)
EC 2.1.1.300 pavine N-methyltransferase (17 March 2014)
EC 2.3.1.232 methanol O-anthraniloyltransferase (17 March 2014)
*EC 2.3.3.1 citrate (Si)-synthase (17 March 2014)
EC 2.3.3.16 citrate synthase (unknown stereospecificity) (17 March 2014)
*EC 2.4.1.277 10-deoxymethynolide desosaminyltransferase (17 March 2014)
*EC 2.4.1.278 3-α-mycarosylerythronolide B desosaminyl transferase (17 March 2014)
EC 2.4.1.315 diglucosyl diacylglycerol synthase (1,6-linking) (17 March 2014)
EC 2.4.1.316 tylactone mycaminosyltransferase (17 March 2014)
EC 2.4.1.317 O-mycaminosyltylonolide 6-deoxyallosyltransferase (17 March 2014)
EC 2.4.1.318 demethyllactenocin mycarosyltransferase (17 March 2014)
EC 2.4.1.319 β-1,4-mannooligosaccharide phosphorylase (17 March 2014)
EC 2.4.1.320 1,4-β-mannosyl-N-acetylglucosamine phosphorylase (17 March 2014)
EC 2.4.1.321 cellobionic acid phosphorylase (17 March 2014)
EC 2.4.1.322 desvancosaminyl-vancomycin vancosaminetransferase (17 March 2014)
EC 2.4.1.323 7-deoxyloganetic acid glucosyltransferase (17 March 2014)
EC 2.4.1.324 7-deoxyloganetin glucosyltransferase (17 March 2014)
*EC 2.4.2.35 flavonol-3-O-glycoside xylosyltransferase (17 March 2014)
EC 2.4.2.57 AMP phosphorylase (17 March 2014)
EC 2.4.99.20 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase (17 March 2014)
EC 2.5.1.115 homogentisate phytyltransferase (17 March 2014)
EC 2.5.1.116 homogentisate geranylgeranyltransferase (17 March 2014)
EC 2.5.1.117 homogentisate solanesyltransferase (17 March 2014)
EC 2.5.1.118 β-(isoxazolin-5-on-2-yl)-L-alanine synthase (17 March 2014)
EC 2.5.1.119 β-(isoxazolin-5-on-4-yl)-L-alanine synthase (17 March 2014)
EC 2.5.1.120 aminodeoxyfutalosine synthase (17 March 2014)
EC 2.6.1.104 3-dehydro-glucose-6-phosphate—glutamate transaminase (17 March 2014)
EC 2.6.1.105 lysine—8-amino-7-oxononanoate transaminase (17 March 2014)
EC 2.6.1.106 dTDP-3-amino-3,4,6-trideoxy-α-D-glucose transaminase (17 March 2014)
EC 2.6.1.107 β-methylphenylalanine transaminase (17 March 2014)
EC 2.6.99.4 N6-L-threonylcarbamoyladenine synthase (17 March 2014)
EC 2.7.1.181 polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase (17 March 2014)
EC 2.7.1.182 phytol kinase (17 March 2014)
*EC 2.7.4.24 diphosphoinositol-pentakisphosphate kinase (17 March 2014)
EC 2.8.2.36 desulfo-A47934 sulfotransferase (17 March 2014)
EC 2.8.3.7 deleted now EC 2.8.3.20 and EC 2.8.3.22 (17 March 2014)
EC 2.8.3.20 succinyl-CoA—D-citramalate CoA-transferase (17 March 2014)
EC 2.8.3.21 L-carnitine CoA-transferase (17 March 2014)
EC 2.8.3.22 succinyl-CoA—L-malate CoA-transferase (17 March 2014)
EC 2.8.4.3 tRNA-2-methylthio-N6-dimethylallyladenosine synthase (17 March 2014)
EC 2.8.4.4 [ribosomal protein S12] (aspartate89-C3)-methylthiotransferase (17 March 2014)
EC 2.8.4.5 tRNA (N6-L-threonylcarbamoyladenosine37-C2)-methylthiotransferase (17 March 2014)
EC 3.1.2.30 (3S)-malyl-CoA thioesterase (17 March 2014)
EC 3.1.3.93 L-galactose 1-phosphate phosphatase (17 March 2014)
EC 3.1.3.94 D-galactose 1-phosphate phosphatase (17 March 2014)
EC 3.1.3.95 phosphatidylinositol-3,5-bisphosphate 3-phosphatase (17 March 2014)
*EC 3.1.21.2 deoxyribonuclease IV (17 March 2014)
EC 3.1.21.8 T4 deoxyribonuclease II (17 March 2014)
EC 3.1.21.9 T4 deoxyribonuclease IV (17 March 2014)
EC 3.1.27.9 transferred now EC 4.6.1.16 (17 March 2014)
EC 3.2.1.191 ginsenosidase type III (17 March 2014)
EC 3.2.1.192 ginsenoside Rb1 β-glucosidase (17 March 2014)
EC 3.2.1.193 ginsenosidase type I (17 March 2014)
EC 3.2.1.194 ginsenosidase type IV (17 March 2014)
EC 3.2.1.195 20-O-multi-glycoside ginsenosidase (17 March 2014)
*EC 3.2.2.6 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase (17 March 2014)
EC 3.2.2.30 aminodeoxyfutalosine nucleosidase (17 March 2014)
EC 3.5.1.116 ureidoglycolate amidohydrolase (17 March 2014)
EC 3.5.3.19 transferred now EC 3.5.1.116 (17 March 2014)
EC 3.5.4.40 aminodeoxyfutalosine deaminase (17 March 2014)
EC 3.5.99.10 2-iminobutanoate/2-iminopropanoate deaminase (17 March 2014)
EC 3.7.1.21 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase (17 March 2014)
EC 3.7.1.22 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing) (17 March 2014)
EC 4.1.1.97 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase (17 March 2014)
*EC 4.1.2.14 2-dehydro-3-deoxy-phosphogluconate aldolase (17 March 2014)
*EC 4.1.2.21 2-dehydro-3-deoxy-6-phosphogalactonate aldolase (17 March 2014)
EC 4.1.2.55 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase (17 March 2014)
EC 4.1.2.56 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate synthase (17 March 2014)
*EC 4.1.3.24 malyl-CoA lyase (17 March 2014)
*EC 4.1.3.25 (S)-citramalyl-CoA lyase (17 March 2014)
EC 4.1.3.46 (R)-citramalyl-CoA lyase (17 March 2014)
EC 4.2.1.89 deleted, due to EC 2.8.3.21 and EC 4.2.1.149 (17 March 2014)
EC 4.2.1.147 5,6,7,8-tetrahydromethanopterin hydro-lyase (17 March 2014)
EC 4.2.1.148 2-methylfumaryl-CoA hydratase (17 March 2014)
EC 4.2.1.149 crotonobetainyl-CoA hydratase (17 March 2014)
EC 4.2.1.150 short-chain-enoyl-CoA hydratase (17 March 2014)
EC 4.2.1.151 chorismate dehydratase (17 March 2014)
*EC 4.3.1.17 L-serine ammonia-lyase (17 March 2014)
*EC 4.3.1.19 threonine ammonia-lyase (17 March 2014)
EC 4.3.1.30 dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase (17 March 2014)
*EC 4.3.2.3 ureidoglycolate lyase (17 March 2014)
EC 4.6.1.16 tRNA-intron lyase (17 March 2014)
EC 5.1.3.28 UDP-N-acetyl-L-fucosamine synthase (17 March 2014)
EC 5.3.1.30 5-deoxy-glucuronate isomerase (17 March 2014)
EC 5.3.99.11 2-keto-myo-inositol isomerase (17 March 2014)
EC 5.4.1.2 transferred now EC 5.4.99.61 (17 March 2014)
EC 5.4.1.3 2-methylfumaryl-CoA isomerase (17 March 2014)
EC 5.4.99.60 cobalt-precorrin-8 methylmutase (17 March 2014)
EC 5.4.99.61 precorrin-8X methylmutase (17 March 2014)
EC 6.2.1.40 4-hydroxybutyrate—CoA ligase (17 March 2014)
EC 6.3.1.17 β-citrylglutamate synthase (17 March 2014)
EC 6.3.2.41 N-acetylaspartylglutamate synthase (17 March 2014)
EC 6.3.2.42 N-acetylaspartylglutamylglutamate synthase (17 March 2014)

EC 1.1.1.367

Accepted name: UDP-2-acetamido-2,6-β-L-arabino-hexul-4-ose reductase

Reaction: UDP-2-acetamido-2,6-dideoxy-β-L-talose + NAD(P)+ = UDP-2-acetamido-2,6-β-L-arabino-hexul-4-ose + NAD(P)H + H+

For diagram of reaction click here.

Glossary: UDP-2-acetamido-2,6-dideoxy-β-L-talose = UDP-N-acetyl-β-L-pneumosamine

Other name(s): WbjC; Cap5F

Systematic name: UDP-2-acetamido-2,6-dideoxy-L-talose:NADP+ oxidoreductase

Comments: Part of the biosynthesis of UDP-N-acetyl-L-fucosamine. Isolated from the bacteria Pseudomonas aeruginosa and Staphylococcus aureus.

References:

1. Kneidinger, B., O'Riordan, K., Li, J., Brisson, J.R., Lee, J.C. and Lam, J.S. Three highly conserved proteins catalyze the conversion of UDP-N-acetyl-D-glucosamine to precursors for the biosynthesis of O antigen in Pseudomonas aeruginosa O11 and capsule in Staphylococcus aureus type 5. Implications for the UDP-N-acetyl-L-fucosamine biosynthetic pathway. J. Biol. Chem. 278 (2003) 3615-3627. [PMID: 12464616]

2. Mulrooney, E.F., Poon, K.K., McNally, D.J., Brisson, J.R. and Lam, J.S. Biosynthesis of UDP-N-acetyl-L-fucosamine, a precursor to the biosynthesis of lipopolysaccharide in Pseudomonas aeruginosa serotype O11. J. Biol. Chem. 280 (2005) 19535-19542. [PMID: 15778500]

3. Miyafusa, T., Tanaka, Y., Kuroda, M., Ohta, T. and Tsumoto, K. Expression, purification, crystallization and preliminary diffraction analysis of CapF, a capsular polysaccharide-synthesis enzyme from Staphylococcus aureus. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 512-515. [PMID: 18540063]

[EC 1.1.1.367 created 2014]

EC 1.1.1.368

Accepted name: 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase

Reaction: 6-hydroxycyclohex-1-ene-1-carbonyl-CoA + NAD+ = 6-oxocyclohex-1-ene-1-carbonyl-CoA + NADH + H+

For diagram of reaction click here.

Systematic name: 6-hydroxycyclohex-1-ene-1-carbonyl-CoA:NAD+ 6-oxidoreductase

Comments: The enzyme participates in the central benzoyl-CoA degradation pathway of some anaerobic bacteria such as Thauera aromatica.

References:

1. Laempe, D., Jahn, M. and Fuchs, G. 6-Hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase and 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, enzymes of the benzoyl-CoA pathway of anaerobic aromatic metabolism in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 263 (1999) 420-429. [PMID: 10406950]

[EC 1.1.1.368 created 2014]

EC 1.1.1.369

Accepted name: D-chiro-inositol 1-dehydrogenase

Reaction: 1D-chiro-inositol + NAD+ = 2D-2,3,5/4,6-pentahydroxycyclohexanone + NADH + H+

For diagram of reaction click here.

Glossary: 1D-chiro-inositol = 1,2,4/3,5,6-cyclohexane-1,2,3,4,5,6-hexol

Other name(s): DCI 1-dehydrogenase; IolG

Systematic name: 1D-chiro-inositol:NAD+ 1-oxidoreductase

Comments: The enzyme, found in the bacterium Bacillus subtilis, also catalyses the reaction of EC 1.1.1.18, inositol 2-dehydrogenase, and can also use D-glucose and D-xylose. It shows trace activity with D-ribose and D-fructose [1]. It is part of a myo-inositol/D-chiro-inositol degradation pathway leading to acetyl-CoA.

References:

1. Ramaley, R., Fujita, Y. and Freese, E. Purification and properties of Bacillus subtilis inositol dehydrogenase. J. Biol. Chem. 254 (1979) 7684-7690. [PMID: 112095]

2. Yoshida, K., Yamaguchi, M., Morinaga, T., Ikeuchi, M., Kinehara, M. and Ashida, H. Genetic modification of Bacillus subtilis for production of D-chiro-inositol, an investigational drug candidate for treatment of type 2 diabetes and polycystic ovary syndrome. Appl. Environ. Microbiol. 72 (2006) 1310-1315. [PMID: 16461681]

[EC 1.1.1.369 created 2014]

EC 1.1.1.370

Accepted name: scyllo-inositol 2-dehydrogenase (NAD+)

Reaction: scyllo-inositol + NAD+ = 2,4,6/3,5-pentahydroxycyclohexanone + NADH + H+

For diagram of reaction click here.

Glossary: 2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose

Other name(s): iolX (gene name)

Systematic name: scyllo-inositol:NAD+ 2-oxidoreductase

Comments: The enzyme, found in the bacterium Bacillus subtilis, has no activity with NADP+ [cf. EC 1.1.1.371, scyllo-inositol 2-dehydrogenase (NADP+)]. It is part of a scyllo-inositol degradation pathway leading to acetyl-CoA.

References:

1. Morinaga, T., Ashida, H. and Yoshida, K. Identification of two scyllo-inositol dehydrogenases in Bacillus subtilis. Microbiology 156 (2010) 1538-1546. [PMID: 20133360]

[EC 1.1.1.370 created 2014]

EC 1.1.1.371

Accepted name: scyllo-inositol 2-dehydrogenase (NADP+)

Reaction: scyllo-inositol + NADP+ = 2,4,6/3,5-pentahydroxycyclohexanone + NADPH + H+

For diagram of reaction click here.

Glossary: 2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose

Other name(s): iolW (gene name)

Systematic name: scyllo-inositol:NADP+ 2-oxidoreductase

Comments: The enzyme, found in the bacterium Bacillus subtilis, has no activity with NAD+ [cf. EC 1.1.1.370, scyllo-inositol 2-dehydrogenase (NAD+)].

References:

1. Morinaga, T., Ashida, H. and Yoshida, K. Identification of two scyllo-inositol dehydrogenases in Bacillus subtilis. Microbiology 156 (2010) 1538-1546. [PMID: 20133360]

[EC 1.1.1.371 created 2014]

EC 1.1.5.10

Accepted name: D-2-hydroxyacid dehydrogenase (quinone)

Reaction: (R)-2-hydroxyacid + a quinone = 2-oxoacid + a quinol

Other name(s): (R)-2-hydroxy acid dehydrogenase; (R)-2-hydroxy-acid:(acceptor) 2-oxidoreductase; D-lactate dehydrogenase (ambiguous)

Systematic name: (R)-2-hydroxyacid:quinone oxidoreductase

Comments: The enzyme from mammalian kidney contains one mole of FAD per mole of enzyme.(R)-lactate, (R)-malate and meso-tartrate are good substrates. Ubiquinone-1 and the dye 2,6-dichloroindophenol can act as acceptors; NAD+ and NADP+ are not acceptors.

References:

1. Tubbs, P.K. and Greville, G.D. Dehydrogenation of D-lactate by a soluble enzyme from kidney mitochondria. Biochim. Biophys. Acta 34 (1959) 290-291. [PMID: 13839714]

2. Tubbs, P.K. and Greville, G.D. The oxidation of D-α-hydroxy acids in animal tissues. Biochem. J. 81 (1961) 104-114. [PMID: 13922962]

3. Cammack, R. Assay, purification and properties of mammalian D-2-hydroxy acid dehydrogenase. Biochem. J. 115 (1969) 55-64. [PMID: 5359443]

4. Cammack, R. D-2-hydroxy acid dehydrogenase from animal tissue. Methods Enzymol. 41 (1975) 323-329. [PMID: 236454]

[EC 1.1.5.10 created 2014]

EC 1.2.1.89

Accepted name: D-glyceraldehyde dehydrogenase (NADP+)

Reaction: D-glyceraldehyde + NADP+ + H2O = D-glycerate + NADPH + H+

Other name(s): glyceraldehyde dehydrogenase; GADH

Systematic name: D-glyceraldehyde:NADP+ oxidoreductase

Comments: The enzyme from the archaea Thermoplasma acidophilum and Picrophilus torridus is involved in the non-phosphorylative Entner-Doudoroff pathway. cf. EC 1.2.99.8, glyceraldehyde dehydrogenase (FAD-containing).

References:

1. Jung, J.H. and Lee, S.B. Identification and characterization of Thermoplasma acidophilum glyceraldehyde dehydrogenase: a new class of NADP+-specific aldehyde dehydrogenase. Biochem. J. 397 (2006) 131-138. [PMID: 16566751]

2. Reher, M. and Schonheit, P. Glyceraldehyde dehydrogenases from the thermoacidophilic euryarchaeota Picrophilus torridus and Thermoplasma acidophilum, key enzymes of the non-phosphorylative Entner-Doudoroff pathway, constitute a novel enzyme family within the aldehyde dehydrogenase superfamily. FEBS Lett 580 (2006) 1198-1204. [PMID: 16458304]

[EC 1.2.1.89 created 2014]

*EC 1.3.1.74

Accepted name: 2-alkenal reductase [NAD(P)+]

Reaction: a n-alkanal + NAD(P)+ = an alk-2-enal + NAD(P)H + H+

Other name(s): NAD(P)H-dependent alkenal/one oxidoreductase; NADPH:2-alkenal α,β-hydrogenase; 2-alkenal reductase

Systematic name: n-alkanal:NAD(P)+ 2-oxidoreductase

Comments: Highly specific for 4-hydroxynon-2-enal and non-2-enal. Alk-2-enals of shorter chain have lower affinities. Exhibits high activities also for alk-2-enones such as but-3-en-2-one and pent-3-en-2-one. Inactive with cyclohex-2-en-1-one and 12-oxophytodienoic acid. Involved in the detoxication of α,β-unsaturated aldehydes and ketones [cf. EC 1.3.1.102, 2-alkenal reductase (NADP+)].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 52227-95-9

References:

1. Mano, J., Torii, Y., Hayashi, S., Takimoto, K., Matsui, K., Nakamura, K., Inzé, D., Babiychuk, E., Kushnir, S. and Asada, K. The NADPH:quinone oxidoreductase P1-ζ-crystallin in Arabidopsis catalyzes the α,β-hydrogenation of 2-alkenals: detoxication of the lipid peroxide-derived reactive aldehydes. Plant Cell Physiol. 43 (2002) 1445-1455. [PMID: 12514241]

2. Dick, R.A., Kwak, M.K., Sutter, T.R. and Kensler, T.W. Antioxidative function and substrate specificity of NAD(P)H-dependent alkenal/one oxidoreductase. A new role for leukotriene B4 12-hydroxydehydrogenase/15-oxoprostaglandin 13-reductase. J. Biol. Chem. 276 (2001) 40803-40810. [PMID: 11524419]

[EC 1.3.1.74 created 2003, modified 2014]

EC 1.3.1.106

Accepted name: cobalt-precorrin-6A reductase

Reaction: cobalt-precorrin-6B + NAD+ = cobalt-precorrin-6A + NADH + H+

For diagram of reaction click here.

Other name(s): cbiJ (gene name)

Systematic name: cobalt-precorrin-6B:NAD+ oxidoreductase

Comments: The enzyme catalyses a step in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis. The enzyme from the bacterium Bacillus megaterium has no activity with NADPH. The equivalent enzyme in the aerobic pathway is EC 1.3.1.54, precorrin-6A reductase.

References:

1. Kim, W., Major, T.A. and Whitman, W.B. Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis. Archaea 1 (2005) 375-384. [PMID: 16243778]

2. Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Proc. Natl. Acad. Sci. USA 110 (2013) 14906-14911. [PMID: 23922391]

[EC 1.3.1.106 created 2014]

*EC 1.3.5.1

Accepted name: succinate dehydrogenase (quinone)

Reaction: succinate + a quinone = fumarate + a quinol

For diagram of reaction click here.

Other name(s): succinate dehydrogenase (ubiquinone); succinic dehydrogenase; complex II (ambiguous); succinate dehydrogenase complex; SDH; succinate:ubiquinone oxidoreductase

Systematic name: succinate:quinone oxidoreductase

Comments: A flavoprotein (FAD) complex containing iron-sulfur centres. The enzyme is found in the inner mitochondrial membrane in eukaryotes and the plasma membrane of many aerobic or facultative bacteria. It catalyses succinate oxidation in the citric acid cycle and transfers the electrons to quinones in the membrane, thus constituting a part of the aerobic respiratory chain (known as complex II). Eukaryotic enzymes utilize ubioquinone while bacterial enzymes utilize either ubiquinone or menaquinone, depending on the organism. cf. EC 1.3.5.4, fumarate reductase (quinone).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9028-11-9

References:

1. Kita, K., Vibat, C.R., Meinhardt, S., Guest, J.R. and Gennis, R.B. One-step purification from Escherichia coli of complex II (succinate: ubiquinone oxidoreductase) associated with succinate-reducible cytochrome b556. J. Biol. Chem. 264 (1989) 2672-2677. [PMID: 2644269]

2. Hatefi, Y., Ragan, C.I. and Galante, Y.M. The enzymes and the enzyme complexes of the mitochondrial oxidative phosphorylation system. In: Martonosi, A. (Ed.), The Enzymes of Biological Membranes, 2nd edn, vol. 4, Plenum Press, New York, 1985, pp. 1-70.

3. Figueroa, P., Leon, G., Elorza, A., Holuigue, L., Araya, A. and Jordana, X. The four subunits of mitochondrial respiratory complex II are encoded by multiple nuclear genes and targeted to mitochondria in Arabidopsis thaliana. Plant Mol. Biol. 50 (2002) 725-734. [PMID: 12374303]

4. Cecchini, G. Function and structure of complex II of the respiratory chain. Annu. Rev. Biochem. 72 (2003) 77-109. [PMID: 14527321]

5. Oyedotun, K.S. and Lemire, B.D. The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies. J. Biol. Chem. 279 (2004) 9424-9431. [PMID: 14672929]

6. Kurokawa, T. and Sakamoto, J. Purification and characterization of succinate:menaquinone oxidoreductase from Corynebacterium glutamicum. Arch. Microbiol. 183 (2005) 317-324. [PMID: 15883782]

[EC 1.3.5.1 created 1983, modified 2014]

EC 1.3.98.2

Accepted name: fumarate reductase (CoM/CoB)

Reaction: fumarate + CoM + CoB = succinate + CoM-S-S-CoB

Other name(s): thiol:fumarate reductase; Tfr

Systematic name: fumarate CoM:CoB oxidoreductase (succinate forming)

Comments: The enzyme, isolated from the archaeon Methanobacterium thermoautotrophicum, is very oxygen sensitive. It cannot use reduced flavins, reduced coenzyme F420, or NAD(P)H as an electron donor. Distinct from EC 1.3.1.6 [fumarate reductase (NADH)], EC 1.3.5.1 [succinate dehydrogenase (ubiquinone)], and EC 1.3.5.4 [fumarate reductase (quinol)].

References:

1. Khandekar, S.S. and Eirich, L.D. Purification and characterization of an anabolic fumarate reductase from Methanobacterium thermoautotrophicum. Appl. Environ. Microbiol. 55 (1989) 856-861. [PMID: 2499256]

2. Heim, S., Kunkel, A., Thauer, R.K. and Hedderich, R. Thiol:fumarate reductase (Tfr) from Methanobacterium thermoautotrophicum. Identification of the catalytic sites for fumarate reduction and thiol oxidation. Eur. J. Biochem. 253 (1998) 292-299. [PMID: 9578488]

[EC 1.3.98.2 created 2014]

[EC 1.3.99.1 Deleted entry: succinate dehydrogenase. The activty is included in EC 1.3.5.1, succinate dehydrogenase (quinone). (EC 1.3.99.1 created 1961, deleted 2013)]

EC 1.3.99.35

Accepted name: chlorophyllide a reductase

Reaction: 3-deacetyl-3-vinylbacteriochlorophyllide a + A + ADP + phosphate = chlorophyllide a + AH2 + ATP + H2O

For diagram of reaction click here.

Other name(s): BchX; BchY; BchZ

Systematic name: ATP-dependent acceptor:chlorophyllide-a 7,8-oxidoreductase

Comments: Binds a [4Fe-4S] cluster. Found in the purple non-sulfur bacterium Rhodobacter capsulatus. The enzyme catalyses trans-reduction of the B-ring of chlorophyllide a; the product has the (7R,8R)-configuration.

References:

1. Nomata, J., Mizoguchi, T., Tamiaki, H. and Fujita, Y. A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis: reconstitution of chlorophyllide a reductase with purified X-protein (BchX) and YZ-protein (BchY-BchZ) from Rhodobacter capsulatus. J. Biol. Chem. 281 (2006) 15021-15028. [PMID: 16571720]

[EC 1.3.99.35 created 2014]

EC 1.5.98 With another known acceptor

EC 1.5.98.1

Accepted name: methylenetetrahydromethanopterin dehydrogenase

Reaction: 5,10-methylenetetrahydromethanopterin + oxidized coenzyme F420 = 5,10-methenyltetrahydromethanopterin + reduced coenzyme F420

For diagram of reaction click here.

Other name(s): N5,N10-methylenetetrahydromethanopterin dehydrogenase; 5,10-methylenetetrahydromethanopterin dehydrogenase

Systematic name: 5,10-methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase

Comments: Coenzyme F420 is a 7,8-didemethyl-8-hydroxy-5-deazariboflavin derivative; methanopterin is a pterin analogue. The enzyme is involved in the formation of methane from CO2 in the methanogen Methanothermobacter thermautotrophicus.

References:

1. Hartzell, P.L., Zvilius, G., Escalante-Semerena, J.C. and Donnelly, M.I. Coenzyme F420 dependence of the methylenetetrahydromethanopterin dehydrogenase of Methanobacterium thermoautotrophicum. Biochem. Biophys. Res. Commun. 133 (1985) 884-890. [PMID: 4084309]

2. te Brömmelstroet, B.W., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F420-dependent enzymes, from Methanosarcina barkeri. Biochim. Biophys. Acta 1079 (1991) 293-302. [PMID: 1911853]

[EC 1.5.98.1 created 1989 as EC 1.5.99.9, modified 2004, transferred to EC 1.5.98.1 2013]

EC 1.5.98.2

Accepted name: 5,10-methylenetetrahydromethanopterin reductase

Reaction: 5-methyltetrahydromethanopterin + oxidized coenzyme F420 = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420

For diagram of reaction click here.

Other name(s): 5,10-methylenetetrahydromethanopterin cyclohydrolase; N5,N10-methylenetetrahydromethanopterin reductase; methylene-H4MPT reductase; coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase; N5,N10-methylenetetrahydromethanopterin:coenzyme-F420 oxidoreductase

Systematic name: 5-methyltetrahydromethanopterin:coenzyme-F420 oxidoreductase

Comments: Catalyses an intermediate step in methanogenesis from CO2 and H2 in methanogenic archaebacteria.

References:

1. Ma, K. and Thauer, R.K. Purification and properties of N5,N10-methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum (strain Marburg). Eur. J. Biochem. 191 (1990) 187-193. [PMID: 2379499]

2. te Brömmelstroet, B.W., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F420-dependent enzymes, from Methanosarcina barkeri. Biochim. Biophys. Acta 1079 (1991) 293-302. [PMID: 1911853]

3. Ma, K. and Thauer, R.K. Single step purification of methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum by specific binding to blue sepharose CL-6B. FEBS Lett. 268 (1990) 59-62. [PMID: 1696553]

4. te Brömmelstroet, B.W., Hensgens, C.M., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin reductase, a coenzyme F420-dependent enzyme, from Methanobacterium thermoautotrophicum strain ΔH*. J. Biol. Chem. 265 (1990) 1852-1857. [PMID: 2298726]

5. te Brömmelstroet, B.W., Hensgens, C.M., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methenyltetrahydromethanopterin cyclohydrolase from Methanosarcina barkeri. J. Bacteriol. 172 (1990) 564-571. [PMID: 2298699]

[EC 1.5.98.2 created 2000 as EC 1.5.99.11, modified 2004, transferred to EC 1.5.98.2 2013]

*EC 1.5.99 With an unknown acceptor

[EC 1.5.99.9 Transferred entry: methylenetetrahydromethanopterin dehydrogenase. As the acceptor is known the enzyme has been transferred to EC 1.5.98.1, methylenetetrahydromethanopterin dehydrogenase (EC 1.5.99.9 created 1989, modified 2004, deleted 2013)]

[EC 1.5.99.11 Transferred entry: methylenetetrahydromethanopterin dehydrogenase. As the acceptor is known the enzyme has been transferred to EC 1.5.98.2,5,10-methylenetetrahydromethanopterin reductase (EC 1.5.99.11 created 2000, modified 2004, deleted 2013)]

EC 1.6.3.5

Accepted name: renalase

Reaction: α-NAD(P)H + H+ + O2 = β-NAD(P)+ + H2O2

Other name(s): αNAD(P)H oxidase/anomerase

Systematic name: NAD(P)H:oxygen oxidoreductase (H2O2-forming, epimerising)

Comments: Requires FAD. Renalase is a flavoprotein hormone secreted into the blood by the kidney that is reported to lower blood pressure and slow heart rate.

References:

1. Beaupre, B.A., Carmichael, B.R., Hoag, M.R., Shah, D.D. and Moran, G.R. Renalase is an α-NAD(P)H oxidase/anomerase. J. Am. Chem. Soc. 135 (2013) 13980-13987. [PMID: 23964689]

[EC 1.6.3.5 created 2014]

*EC 1.10.3.11

Accepted name: ubiquinol oxidase (non-electrogenic)

Reaction: 2 ubiquinol + O2 = 2 ubiquinone + 2 H2O

Other name(s): plant alternative oxidase; cyanide-insensitive oxidase; AOX (gene name); ubiquinol oxidase

Systematic name: ubiquinol:O2 oxidoreductase (non-electrogenic)

Comments: The enzyme, described from the mitochondria of plants and some fungi and protists, is an alternative terminal oxidase that is not sensitive to cyanide inhibition and does not generate a proton motive force. Unlike the electrogenic terminal oxidases that contain hemes (cf. EC 1.10.3.10 and EC 1.10.3.14), this enzyme contains a dinuclear non-heme iron complex. The function of this oxidase is believed to be dissipating excess reducing power, minimizing oxidative stress, and optimizing photosynthesis in response to changing conditions.

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

References:

1. Bendall, D.S. and Bonner, W.D. Cyanide-insensitive respiration in plant mitochondria. Plant Physiol. 47 (1971) 236-245. [PMID: 16657603]

2. Siedow, J.N., Umbach, A.L. and Moore, A.L. The active site of the cyanide-resistant oxidase from plant mitochondria contains a binuclear iron center. FEBS Lett. 362 (1995) 10-14. [PMID: 7698344]

3. Berthold, D.A., Andersson, M.E. and Nordlund, P. New insight into the structure and function of the alternative oxidase. Biochim. Biophys. Acta 1460 (2000) 241-254. [PMID: 11106766]

4. Williams, B.A., Elliot, C., Burri, L., Kido, Y., Kita, K., Moore, A.L. and Keeling, P.J. A broad distribution of the alternative oxidase in microsporidian parasites. PLoS Pathog. 6 (2010) e1000761. [PMID: 20169184]

5. Gandin, A., Duffes, C., Day, D.A. and Cousins, A.B. The absence of alternative oxidase AOX1A results in altered response of photosynthetic carbon assimilation to increasing CO2 in Arabidopsis thaliana. Plant Cell Physiol 53 (2012) 1627-1637. [PMID: 22848123]

[EC 1.10.3.11 created 2011, modified 2014]

EC 1.10.3.14

Accepted name: ubiquinol oxidase (electrogenic, non H+-transporting)

Reaction: 2 ubiquinol + O2 + 4 H+[side 1] = 2 ubiquinone + 2 H2O + 4 H+[side 2]

Other name(s): cytochrome bd-I oxidase; cydA (gene name); cydB (gene name)

Systematic name: ubiquinol:O2 oxidoreductase (electrogenic, non H+-transporting)

Comments: This terminal oxidase enzyme is unable to pump protons but generates a proton motive force by transmembrane charge separation resulting from utilizing protons and electrons originating from opposite sides of the membrane to generate water. The bioenergetic efficiency (the number of charges driven across the membrane per electron used to reduce oxygen to water) is 1. The bd-I oxidase from the bacterium Escherichia coli is the predominant respiratory oxygen reductase that functions under microaerophilic conditions in that organism. cf. EC 1.10.3.10, ubiquinol oxidase (H+-transporting).

References:

1. Miller, M.J., Hermodson, M. and Gennis, R.B. The active form of the cytochrome d terminal oxidase complex of Escherichia coli is a heterodimer containing one copy of each of the two subunits. J. Biol. Chem. 263 (1988) 5235-5240. [PMID: 3281937]

2. Puustinen, A., Finel, M., Haltia, T., Gennis, R.B. and Wikstrom, M. Properties of the two terminal oxidases of Escherichia coli. Biochemistry 30 (1991) 3936-3942. [PMID: 1850294]

3. Belevich, I., Borisov, V.B., Zhang, J., Yang, K., Konstantinov, A.A., Gennis, R.B. and Verkhovsky, M.I. Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc. Natl. Acad. Sci. USA 102 (2005) 3657-3662. [PMID: 15728392]

4. Lenn, T., Leake, M.C. and Mullineaux, C.W. Clustering and dynamics of cytochrome bd-I complexes in the Escherichia coli plasma membrane in vivo. Mol. Microbiol. 70 (2008) 1397-1407. [PMID: 19019148]

[EC 1.10.3.14 created 2014]

EC 1.14.13.185

Accepted name: pikromycin synthase

Reaction: (1) narbomycin + NADPH + H+ + O2 = pikromycin + NADP+ + H2O
(2) narbomycin + NADPH + H+ + O2 = neopikromycin + NADP+ + H2O
(3) narbomycin + 2 NADPH + 2 H+ + 2 O2 = novapikromyin + 2 NADP+ + 2 H2O
(4) 10-deoxymethymycin + NADPH + H+ + O2 = methymycin + NADP+ + H2O
(5) 10-deoxymethymycin + NADPH + H+ + O2 = neomethymycin + NADP+ + H2O
(6) 10-deoxymethymycin + 2 NADPH + 2 H+ + 2 O2 = novamethymycin + 2 NADP+ + 2 H2O

For diagram of reaction click here.

Other name(s): PikC; CYP107L1

Systematic name: narbomycin,NADH:oxygen oxidoreductase (pikromycin-forming)

Comments: A heme-thiolate protein (cytochrome P-450). Involved in the biosynthesis of a number of bacterial macrolide antibiotics containing a desosamine glycoside unit. With narbomycin it hydroxylates at either C-12 to give pikromycin or C-14 to give neopikromycin or both positions to give narvopikromycin. With 10-deoxymethymycin it hydroxylates at either C-10 to give methymycin or C-12 to give neomethymycin or both positions to give novamethymycin.

References:

1. Xue, Y., Wilson, D., Zhao, L., Liu Hw and Sherman, D.H. Hydroxylation of macrolactones YC-17 and narbomycin is mediated by the pikC-encoded cytochrome P450 in Streptomyces venezuelae. Chem. Biol. 5 (1998) 661-667. [PMID: 9831532]

2. Sherman, D.H., Li, S., Yermalitskaya, L.V., Kim, Y., Smith, J.A., Waterman, M.R. and Podust, L.M. The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae. J. Biol. Chem. 281 (2006) 26289-26297. [PMID: 16825192]

3. Li, S., Ouellet, H., Sherman, D.H. and Podust, L.M. Analysis of transient and catalytic desosamine-binding pockets in cytochrome P-450 PikC from Streptomyces venezuelae. J. Biol. Chem. 284 (2009) 5723-5730. [PMID: 19124459]

[EC 1.14.13.185 created 2014]

EC 1.14.13.186

Accepted name: 20-oxo-5-O-mycaminosyltylactone 23-monooxygenase

Reaction: 20-oxo-5-O-β-mycaminosyltylactone + NADPH + H+ + O2 = 5-O-β-mycaminosyltylonolide + NADP+ + H2O

For diagram of reaction click here.

Glossary: tylactone = (4R,5S,6S,7S,9R,11E,13E,15S,16R)-7,16-diethyl-4,6-dihydroxy-5,9,13,15-tetramethyl-1-oxacyclohexadeca-11,13-diene-2,10-dione
α-D-mycaminose = 3-dimethylamino-3,6-dideoxy-α-D-glucopyranose
tylonolide = 2-[(4R,5S,6S,7R,9R,11E,13E,15R,16R)-16-ethyl-4,6-dihydroxy-15-(hydroxymethyl)-5,9,13-trimethyl-2,10-dioxo-1-oxacyclohexadeca-11,13-dien-7-yl]acetaldehyde

Other name(s): tylH1 (gene name)

Systematic name: 20-oxo-5-O-β-mycaminosyltylactone,NADPH:oxygen oxidoreductase (23-hydroxylating)

Comments: A heme thiolate (cytochrome p450) enzyme. Involved in the biosynthetic pathway of the macrolide antibiotic tylosin, which is produced by several species of Streptomyces bacteria.

References:

1. Baltz, R.H. and Seno, E.T. Properties of Streptomyces fradiae mutants blocked in biosynthesis of the macrolide antibiotic tylosin. Antimicrob. Agents Chemother. 20 (1981) 214-225. [PMID: 7283418]

2. Reeves, C.D., Ward, S.L., Revill, W.P., Suzuki, H., Marcus, M., Petrakovsky, O.V., Marquez, S., Fu, H., Dong, S.D. and Katz, L. Production of hybrid 16-membered macrolides by expressing combinations of polyketide synthase genes in engineered Streptomyces fradiae hosts. Chem. Biol. 11 (2004) 1465-1472. [PMID: 15489173]

[EC 1.14.13.186 created 2014]

EC 1.14.13.187

Accepted name: L-evernosamine nitrososynthase

Reaction: dTDP-β-L-evernosamine + 2 NADPH + 2 H+ + 2 O2 = dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-β-L-arabino-hexopyranose + 2 NADP+ + 3 H2O (overall reaction)
(1a) dTDP-β-L-evernosamine + NADPH + H+ + O2 = dTDP-N-hydroxy-β-L-evernosamine + NADP+ + H2O
(1b) dTDP-N-hydroxy-β-L-evernosamine + NADPH + H+ + O2 = dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-β-L-arabino-hexopyranose + NADP+ + 2 H2O

Glossary: dTDP-β-L-evernosamine = dTDP-3-amino-2,3,6-trideoxy-3-C-methyl-4-O-methyl-β-L-arabino-hexopyranose
dTDP-β-L-evernitrose = dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitro-β-L-arabino-hexopyranose

Systematic name: dTDP-β-L-evernosamine,NADPH:oxygen oxidoreductase (N-hydroxylating)

Comments: Requires FAD. Isolated from the bacterium Micromonospora carbonacea var. africana. The nitroso group is probably spontaneously oxidized to a nitro group giving dTDP-β-L-evernitrose, which is involved in the biosynthesis of the antibiotic everninomycin. The reaction was studied using dTDP-β-L-4-epi-vancosamine (dTDP-4-O-desmethyl-β-L-evernitrosamine).

References:

1. Hu, Y., Al-Mestarihi, A., Grimes, C.L., Kahne, D. and Bachmann, B.O. A unifying nitrososynthase involved in nitrosugar biosynthesis. J. Am. Chem. Soc. 130 (2008) 15756-15757. [PMID: 18983146]

2. Vey, J.L., Al-Mestarihi, A., Hu, Y., Funk, M.A., Bachmann, B.O. and Iverson, T.M. Structure and mechanism of ORF36, an amino sugar oxidizing enzyme in everninomicin biosynthesis. Biochemistry 49 (2010) 9306-9317. [PMID: 20866105]

[EC 1.14.13.187 created 2014]

EC 1.14.13.188

Accepted name: 6-deoxyerythronolide B hydroxylase

Reaction: 6-deoxyerythronolide B + NADPH + H+ + O2 = erythronolide B + NADP+ + H2O

Other name(s): DEB hydroxylase; eryF (gene name); P450(eryF); CYP107A1

Systematic name: 6-deoxyerythronolide-B,NADPH:oxygen oxidoreductase

Comments: A heme-thiolate protein (P-450). Isolated from the bacterium Saccharopolyspora erythraea. The enzyme is involved in the biosynthesis of the antibiotic erythromycin.

References:

1. Weber, J.M., Leung, J.O., Swanson, S.J., Idler, K.B. and McAlpine, J.B. An erythromycin derivative produced by targeted gene disruption in Saccharopolyspora erythraea. Science 252 (1991) 114-117. [PMID: 2011746]

2. Shafiee, A. and Hutchinson, C.R. Macrolide antibiotic biosynthesis: isolation and properties of two forms of 6-deoxyerythronolide B hydroxylase from Saccharopolyspora erythraea (Streptomyces erythreus). Biochemistry 26 (1987) 6204-6210. [PMID: 2446657]

3. Cupp-Vickery, J.R., Li, H. and Poulos, T.L. Preliminary crystallographic analysis of an enzyme involved in erythromycin biosynthesis: cytochrome P450eryF. Proteins: Struct., Funct., Bioinf. 20 (1994) 197-201. [PMID: 7846029]

4. Nagano, S., Cupp-Vickery, J.R. and Poulos, T.L. Crystal structures of the ferrous dioxygen complex of wild-type cytochrome P450eryF and its mutants, A245S and A245T: investigation of the proton transfer system in P450eryF. J. Biol. Chem. 280 (2005) 22102-22107. [PMID: 15824115]

[EC 1.14.13.188 created 2014]

*EC 1.16.1.7

Accepted name: ferric-chelate reductase (NADH)

Reaction: 2 Fe(II)-siderophore + NAD+ + H+ = 2 Fe(III)-siderophore + NADH

Other name(s): ferric chelate reductase (ambiguous); iron chelate reductase (ambiguous); NADH:Fe3+-EDTA reductase; NADH2:Fe3+ oxidoreductase; ferB (gene name); Fe(II):NAD+ oxidoreductase

Systematic name: Fe(II)-siderophore:NAD+ oxidoreductase

Comments: Contains FAD. The enzyme catalyses the reduction of bound ferric iron in a variety of iron chelators (siderophores), resulting in the release of ferrous iron. The plant enzyme is Involved in the transport of iron across plant plasma membranes. The enzyme from the bacterium Paracoccus denitrificans can also reduce chromate. cf. EC 1.16.1.9, ferric-chelate reductase (NADPH) and EC 1.16.1.10, ferric-chelate reductase [NAD(P)H].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 120720-17-4

References:

1. Askerlund, P., Larrson, C. and Widell, S. Localization of donor and acceptor sites of NADH dehydrogenase activities using inside-out and right-side-out plasma membrane vesicles from plants. FEBS Lett. 239 (1988) 23-28.

2. Brüggemann, W. and Moog, P.R. NADH-dependent Fe3+ EDTA and oxygen reduction by plasma membrane vesicles from barley roots. Physiol. Plant. 75 (1989) 245-254.

3. Brüggemann, W., Moog, P.R., Nakagawa, H., Janiesch, P. and Kuiper, P.J.C. Plasma membrane-bound NADH:Fe3+-EDTA reductase and iron deficiency in tomato (Lycopersicon esculentum). Is there a Turbo reductase ? Physiol. Plant. 79 (1990) 339-346.

4. Buckhout, T.J. and Hrubec, T.C. Pyridine nucleotide-dependent ferricyanide reduction associated with isolated plasma membranes of maize (Zea mays L.) roots. Protoplasma 135 (1986) 144-154.

5. Sandelius, A.S., Barr, R., Crane, F.L. and Morré, D.J. Redox reactions of plasma membranes isolated from soybean hypocotyls by phase partition. Plant Sci. 48 (1986) 1-10.

6. Mazoch, J., Tesarik, R., Sedlacek, V., Kucera, I. and Turanek, J. Isolation and biochemical characterization of two soluble iron(III) reductases from Paracoccus denitrificans. Eur. J. Biochem. 271 (2004) 553-562. [PMID: 14728682]

[EC 1.16.1.7 created 1992 as EC 1.6.99.13, transferred 2002 to EC 1.16.1.7, modified 2011, modified 2014]

*EC 1.16.1.9

Accepted name: ferric-chelate reductase (NADPH)

Reaction: 2 Fe(II)-siderophore + NADP+ + H+ = 2 Fe(III)-siderophore + NADPH

Other name(s): ferric chelate reductase (ambiguous); iron chelate reductase (ambiguous); NADPH:Fe3+-EDTA reductase; NADPH-dependent ferric reductase; yqjH (gene name); Fe(II):NADP+ oxidoreductase

Systematic name: Fe(II)-siderophore:NADP+ oxidoreductase

Comments: Contains FAD. The enzyme, which is widespread among bacteria, catalyses the reduction of ferric iron bound to a variety of iron chelators (siderophores), including ferric triscatecholates and ferric dicitrate, resulting in the release of ferrous iron. The enzyme from the bacterium Escherichia coli has the highest efficiency with the hydrolysed ferric enterobactin complex ferric N-(2,3-dihydroxybenzoyl)-L-serine [3]. cf. EC 1.16.1.7, ferric-chelate reductase (NADH) and EC 1.16.1.10, ferric-chelate reductase [NAD(P)H].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 120720-17-4

References:

1. Bamford, V.A., Armour, M., Mitchell, S.A., Cartron, M., Andrews, S.C. and Watson, K.A. Preliminary X-ray diffraction analysis of YqjH from Escherichia coli: a putative cytoplasmic ferri-siderophore reductase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 792-796. [PMID: 18765906]

2. Wang, S., Wu, Y. and Outten, F.W. Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli. J. Bacteriol. 193 (2011) 563-574. [PMID: 21097627]

3. Miethke, M., Hou, J. and Marahiel, M.A. The Siderophore-Interacting Protein YqjH Acts as a Ferric Reductase in Different Iron Assimilation Pathways of Escherichia coli. Biochemistry (2011) . [PMID: 22098718]

[EC 1.16.1.9 created 1992 as EC 1.6.99.13, transferred 2002 to EC 1.16.1.7, transferred 2011 to EC 1.16.1.9, modified 2012, modified 2014]

EC 1.16.1.10

Accepted name: ferric-chelate reductase [NAD(P)H]

Reaction: 2 Fe(II)-siderophore + NAD(P)+ + H+ = 2 Fe(III)-siderophore + NAD(P)H

Other name(s): ferric reductase (ambiguous)

Systematic name: Fe(II)-siderophore:NAD(P)+ oxidoreductase

Comments: A flavoprotein. The enzyme catalyses the reduction of bound ferric iron in a variety of iron chelators (siderophores), resulting in the release of ferrous iron. The enzyme from the hyperthermophilic archaeon Archaeoglobus fulgidus is not active with uncomplexed Fe(III). cf. EC 1.16.1.7, ferric-chelate reductase (NADH) and EC 1.16.1.9, ferric-chelate reductase (NADPH).

References:

1. Vadas, A., Monbouquette, H.G., Johnson, E. and Schroder, I. Identification and characterization of a novel ferric reductase from the hyperthermophilic Archaeon Archaeoglobus fulgidus. J. Biol. Chem. 274 (1999) 36715-36721. [PMID: 10593977]

2. Chiu, H.J., Johnson, E., Schroder, I. and Rees, D.C. Crystal structures of a novel ferric reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus and its complex with NADP+. Structure 9 (2001) 311-319. [PMID: 11525168]

[EC 1.16.1.10 created 2014]

EC 1.21.99.2

Accepted name: cyclic dehypoxanthinyl futalosine synthase

Reaction: dehypoxanthine futalosine + S-adenosyl-L-methionine = cyclic dehypoxanthinyl futalosine + 5'-deoxyadenosine + L-methionine

For diagram of reaction click here.

Glossary: dehypoxanthine futalosine = 3-{3-[(2R,3S,4R)-3,4,5-trihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
cyclic dehypoxanthinyl futalosine = (2R,3S,4R)-3,4,5-trihydroxy-4'-oxo-3',4,4',5-tetrahydro-2’H,3H-spiro[furan-2,1'-naphthalene]-6'-carboxylate

Other name(s): MqnC; dehypoxanthinyl futalosine cyclase

Systematic name: dehypoxanthine futalosine:S-adenosyl-L-methionine oxidoreductase (cyclizing)

Comments: This enzyme is a member of the 'AdoMet radical' (radical SAM) family. The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

References:

1. Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670-1673. [PMID: 18801996]

2. Cooper, L.E., Fedoseyenko, D., Abdelwahed, S.H., Kim, S.H., Dairi, T. and Begley, T.P. In vitro reconstitution of the radical S-adenosylmethionine enzyme MqnC involved in the biosynthesis of futalosine-derived menaquinone. Biochemistry 52 (2013) 4592-4594. [PMID: 23763543]

[EC 1.21.99.2 created 2014]

*EC 2.1.1.57

Accepted name: methyltransferase cap1

Reaction: S-adenosyl-L-methionine + a 5'-(N7-methyl 5'-triphosphoguanosine)-(purine-ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N7-methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)-[mRNA]

Other name(s): messenger ribonucleate nucleoside 2'-methyltransferase; messenger RNA (nucleoside-2'-)-methyltransferase; MTR1; cap1-MTase; mRNA (nucleoside-2'-O)-methyltransferase (ambiguous); S-adenosyl-L-methionine:mRNA (nucleoside-2'-O)-methyltransferase

Systematic name: S-adenosyl-L-methionine:5-(N7-methyl 5-triphosphoguanosine)-(purine-ribonucleotide)-[mRNA] 2-O-methyltransferase

Comments: This enzyme catalyses the methylation of the ribose on the first transcribed nucleotide of mRNA or snRNA molecules, which may be either guanosine or adenosine. This methylation event is known as cap1, and occurrs in all mRNAs and snRNAs of higher eukaryotes, including insects, vertebrates and their viruses. The human enzyme can also methylate mRNA molecules that lack methylation on the capping 5'-triphosphoguanosine [6].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61970-02-3

References:

1. Barbosa, E. and Moss, B. mRNA(nucleoside-2'-)-methyltransferase from vaccinia virus. Purification and physical properties. J. Biol. Chem. 253 (1978) 7692-7697. [PMID: 701281]

2. Barbosa, E. and Moss, B. mRNA(nucleoside-2'-)-methyltransferase from vaccinia virus. Characteristics and substrate specificity. J. Biol. Chem. 253 (1978) 7698-7702. [PMID: 701282]

3. Boone, R.F., Ensinger, M.J. and Moss, B. Synthesis of mRNA guanylyltransferase and mRNA methyltransferases in cells infected with vaccinia virus. J. Virol. 21 (1977) 475-483. [PMID: 833934]

4. Ensinger, M.J., Martin, S.A., Paoletti, E. and Moss, B. Modification of the 5'-terminus of mRNA by soluble guanylyl and methyl transferases from vaccinia virus. Proc. Natl. Acad. Sci. USA 72 (1975) 2525-2529. [PMID: 1058472]

5. Groner, Y., Gilbao, E. and Aviv, H. Methylation and capping of RNA polymerase II primary transcripts by HeLa nuclear homogenates. Biochemistry 17 (1978) 977-982. [PMID: 629955]

6. Werner, M., Purta, E., Kaminska, K.H., Cymerman, I.A., Campbell, D.A., Mittra, B., Zamudio, J.R., Sturm, N.R., Jaworski, J. and Bujnicki, J.M. 2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res. 39 (2011) 4756-4768. [PMID: 21310715]

[EC 2.1.1.57 created 1981 (EC 2.1.1.58 created 1981, incorporated 1984), modified 2014]

*EC 2.1.1.267

Accepted name: flavonoid 3',5'-methyltransferase

Reaction: (1) S-adenosyl-L-methionine + a 3'-hydroxyflavonoid = S-adenosyl-L-homocysteine + a 3'-methoxyflavonoid
(2) S-adenosyl-L-methionine + a 5'-hydroxy-3'-methoxyflavonoid = S-adenosyl-L-homocysteine + a 3',5'-dimethoxyflavonoid

For diagram of reaction click here.

Glossary: delphinidin = 3,3',4',5,5',7-hexahydroxyflavylium
cyanidin = 3,3',4',5,7-pentahydroxyflavylium
myricetin = 3,3',4',5,5',7-hexahydroxyflavone
quercetin = 3,3',4',5,7-pentahydroxyflavone

Other name(s): AOMT; CrOMT2

Systematic name: S-adenosyl-L-methionine:flavonoid 3'-O-methyltransferase

Comments: Isolated from Vitis vinifera (grape) [2]. Most active with delphinidin 3-glucoside but also acts on cyanidin 3-glucoside, cyanidin, myricetin, quercetin and quercetin 3-glucoside. The enzyme from Catharanthus roseus was most active with myricetin [1].

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

References:

1. Cacace, S., Schröder, G., Wehinger, E., Strack, D., Schmidt, J. and Schröder, J. A flavonol O-methyltransferase from Catharanthus roseus performing two sequential methylations. Phytochemistry 62 (2003) 127-137. [PMID: 12482447]

2. Hugueney, P., Provenzano, S., Verries, C., Ferrandino, A., Meudec, E., Batelli, G., Merdinoglu, D., Cheynier, V., Schubert, A. and Ageorges, A. A novel cation-dependent O-methyltransferase involved in anthocyanin methylation in grapevine. Plant Physiol. 150 (2009) 2057-2070. [PMID: 19525322]

[EC 2.1.1.267 created 2013, modified 2014]

*EC 2.1.1.282

Accepted name: tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase

Reaction: S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe = S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe

For diagram of reaction click here.

Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one

Other name(s): TYW3 (gene name); tRNA-yW synthesizing enzyme-3

Systematic name: S-adenosyl-L-methionine:tRNAPhe 7-[(3S)-(3-amino-3-carboxypropyl)-4-demethylwyosine-N4]-methyltransferase

Comments: The enzyme is involved in the biosynthesis of hypermodified tricyclic bases found at position 37 of certain tRNAs. These modifications are important for translational reading-frame maintenance. The enzyme is found in all eukaryotes and in some archaea, but not in bacteria. The eukaryotic enzyme is involved in the biosynthesis of wybutosine.

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

References:

1. Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142-2154. [PMID: 16642040]

[EC 2.1.1.282 created 2013, modified 2014]

EC 2.1.1.294

Accepted name: 3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Reaction: S-adenosyl-L-methionine + 3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = S-adenosyl-L-homocysteine + 3-O-methylphospho-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol

Other name(s): WbdD

Systematic name: S-adenosyl-L-methionine:3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-α-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Comments: The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the preceding phosphorylation of α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.7.1.181, α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-diphospho-ditrans,octacis-undecaprenol 3-kinase)

References:

1. Clarke, B.R., Cuthbertson, L. and Whitfield, C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J. Biol. Chem. 279 (2004) 35709-35718. [PMID: 15184370]

2. Clarke, B.R., Greenfield, L.K., Bouwman, C. and Whitfield, C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J. Biol. Chem. 284 (2009) 30662-30672. [PMID: 19734145]

3. Clarke, B.R., Richards, M.R., Greenfield, L.K., Hou, D., Lowary, T.L. and Whitfield, C. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J. Biol. Chem. 286 (2011) 41391-41401. [PMID: 21990359]

[EC 2.1.1.294 created 2014]

EC 2.1.1.295

Accepted name: 2-methyl-6-phytyl-1,4-hydroquinone methyltransferase

Reaction: (1) S-adenosyl-L-methionine + 2-methyl-6-phytylbenzene-1,4-diol = S-adenosyl-L-homocysteine + 2,3-dimethyl-6-phytylbenzene-1,4-diol
(2) S-adenosyl-L-methionine + 2-methyl-6-all-trans-nonaprenylbenzene-1,4-diol = S-adenosyl-L-homocysteine + plastoquinol
(3) S-adenosyl-L-methionine + 6-geranylgeranyl-2-methylbenzene-1,4-diol = S-adenosyl-L-homocysteine + 6-geranylgeranyl-2,3-dimethylbenzene-1,4-diol

For diagram of reaction click here or click here or click here.

Other name(s): VTE3 (gene name); 2-methyl-6-solanyl-1,4-hydroquinone methyltransferase; MPBQ/MSBQ methyltransferase; MPBQ/MSBQ MT

Systematic name: S-adenosyl-L-methionine:2-methyl-6-phytyl-1,4-benzoquinol C3-methyltransferase

Comments: Involved in the biosynthesis of plastoquinol, as well as vitamin E (tocopherols and tocotrienols).

References:

1. Shintani, D.K., Cheng, Z. and DellaPenna, D. The role of 2-methyl-6-phytylbenzoquinone methyltransferase in determining tocopherol composition in Synechocystis sp. PCC6803. FEBS Lett 511 (2002) 1-5. [PMID: 11821038]

2. Cheng, Z., Sattler, S., Maeda, H., Sakuragi, Y., Bryant, D.A. and DellaPenna, D. Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes. Plant Cell 15 (2003) 2343-2356. [PMID: 14508009]

3. Van Eenennaam, A.L., Lincoln, K., Durrett, T.P., Valentin, H.E., Shewmaker, C.K., Thorne, G.M., Jiang, J., Baszis, S.R., Levering, C.K., Aasen, E.D., Hao, M., Stein, J.C., Norris, S.R. and Last, R.L. Engineering vitamin E content: from Arabidopsis mutant to soy oil. Plant Cell 15 (2003) 3007-3019. [PMID: 14630966]

[EC 2.1.1.295 created 2014]

EC 2.1.1.296

Accepted name: methyltransferase cap2

Reaction: S-adenosyl-L-methionine + a 5'-(N7-methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N7-methyl 5'-triphosphoguanosine)-(2'-O-methyl-purine-ribonucleotide)-(2'-O-methyl-ribonucleotide)-[mRNA]

Other name(s): MTR2; cap2-MTase; mRNA (nucleoside-2'-O)-methyltransferase (ambiguous)

Systematic name: S-adenosyl-L-methionine:5'-(N7-methyl 5'-triphosphoguanosine)-(2′-O-methyl-purine-ribonucleotide)-ribonucleotide-[mRNA] 2'-O-methyltransferase

Comments: The enzyme, found in higher eukaryotes including insects and vertebrates, and their viruses, methylates the ribose of the ribonucleotide at the second transcribed position of mRNAs and snRNAs. This methylation event is known as cap2. The human enzyme can also methylate mRNA molecules where the upstream purine ribonucleotide is not methylated (see EC 2.1.1.57, methyltransferase cap1), but with lower efficiency [2].

References:

1. Arhin, G.K., Ullu, E. and Tschudi, C. 2'-O-methylation of position 2 of the trypanosome spliced leader cap 4 is mediated by a 48 kDa protein related to vaccinia virus VP39. Mol. Biochem. Parasitol. 147 (2006) 137-139. [PMID: 16516986]

2. Werner, M., Purta, E., Kaminska, K.H., Cymerman, I.A., Campbell, D.A., Mittra, B., Zamudio, J.R., Sturm, N.R., Jaworski, J. and Bujnicki, J.M. 2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res. 39 (2011) 4756-4768. [PMID: 21310715]

[EC 2.1.1.296 created 2014]

EC 2.1.1.297

Accepted name: peptide chain release factor N5-glutamine methyltransferase

Reaction: S-adenosyl-L-methionine + [peptide chain release factor 1 or 2]-L-glutamine = S-adenosyl-L-homocysteine + [peptide chain release factor 1 or 2]-N5-methyl-L-glutamine

Other name(s): N5-glutamine S-adenosyl-L-methionine dependent methyltransferase; N5-glutamine MTase; HemK; PrmC

Systematic name: S-adenosyl-L-methionine:[peptide chain release factor 1 or 2]-L-glutamine (N5-glutamine)-methyltransferase

Comments: Modifies the glutamine residue in the universally conserved glycylglycylglutamine (GGQ) motif of peptide chain release factor, resulting in almost complete loss of release activity.

References:

1. Nakahigashi, K., Kubo, N., Narita, S., Shimaoka, T., Goto, S., Oshima, T., Mori, H., Maeda, M., Wada, C. and Inokuchi, H. HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proc. Natl. Acad. Sci. USA 99 (2002) 1473-1478. [PMID: 11805295]

2. Heurgue-Hamard, V., Champ, S., Engstrom, A., Ehrenberg, M. and Buckingham, R.H. The hemK gene in Escherichia coli encodes the N5-glutamine methyltransferase that modifies peptide release factors. EMBO J. 21 (2002) 769-778. [PMID: 11847124]

3. Schubert, H.L., Phillips, J.D. and Hill, C.P. Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase. Biochemistry 42 (2003) 5592-5599. [PMID: 12741815]

4. Yoon, H.J., Kang, K.Y., Ahn, H.J., Shim, S.M., Ha, J.Y., Lee, S.K., Mikami, B. and Suh, S.W. X-ray crystallographic studies of HemK from Thermotoga maritima, an N5-glutamine methyltransferase. Mol. Cells 16 (2003) 266-269. [PMID: 14651272]

5. Yang, Z., Shipman, L., Zhang, M., Anton, B.P., Roberts, R.J. and Cheng, X. Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. J. Mol. Biol. 340 (2004) 695-706. [PMID: 15223314]

6. Pannekoek, Y., Heurgue-Hamard, V., Langerak, A.A., Speijer, D., Buckingham, R.H. and van der Ende, A. The N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase PrmC/HemK in Chlamydia trachomatis methylates class 1 release factors. J. Bacteriol. 187 (2005) 507-511. [PMID: 15629922]

[EC 2.1.1.297 created 2014]

EC 2.1.1.298

Accepted name: ribosomal protein L3 N5-glutamine methyltransferase

Reaction: S-adenosyl-L-methionine + [ribosomal protein L3]-L-glutamine = S-adenosyl-L-homocysteine + [ribosomal protein L3]-N5-methyl-L-glutamine

Other name(s): YfcB; PrmB

Systematic name: S-adenosyl-L-methionine:[ribosomal protein L3]-L-glutamine (N5-glutamine)-methyltransferase

Comments: Modifies the glutamine residue in the glycylglycylglutamine (GGQ) motif of ribosomal protein L3 (Gln150 in the protein from the bacterium Escherichia coli). The enzyme does not act on peptide chain release factor 1 or 2.

References:

1. Heurgue-Hamard, V., Champ, S., Engstrom, A., Ehrenberg, M. and Buckingham, R.H. The hemK gene in Escherichia coli encodes the N5-glutamine methyltransferase that modifies peptide release factors. EMBO J. 21 (2002) 769-778. [PMID: 11847124]

[EC 2.1.1.298 created 2014]

EC 2.1.1.299

Accepted name: protein N-terminal monomethyltransferase

Reaction: S-adenosyl-L-methionine + N-terminal-(A,P,S)PK-[protein] = S-adenosyl-L-homocysteine + N-terminal-N-methyl-N-(A,P,S)PK-[protein]

Other name(s): NRMT2 (gene name); METTL11B (gene name); N-terminal monomethylase

Systematic name: S-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] monomethyltransferase

Comments: This enzyme methylates the N-terminus of target proteins containing the N-terminal motif [Ala/Pro/Ser]-Pro-Lys after the initiator L-methionine is cleaved. In contrast to EC 2.1.1.244, protein N-terminal methyltransferase, the protein only adds one methyl group to the N-terminal.

References:

1. Petkowski, J.J., Bonsignore, L.A., Tooley, J.G., Wilkey, D.W., Merchant, M.L., Macara, I.G. and Schaner Tooley, C.E. NRMT2 is an N-terminal monomethylase that primes for its homologue NRMT1. Biochem. J. 456 (2013) 453-462. [PMID: 24090352]

[EC 2.1.1.299 created 2014]

EC 2.1.1.300

Accepted name: pavine N-methyltransferase

Reaction: S-adenosyl-L-methionine + (±)-pavine = S-adenosyl-L-homocysteine + N-methylpavine

Other name(s): PavNMT

Systematic name: S-adenosyl-L-methionine:(±)-pavine N-methyltransferase

Comments: The enzyme, isolated from the plant Thalictrum flavum, also methylates (R,S)-stylopine and (S)-scoulerine (11%) with lower activity (14% and 11%, respectively).

References:

1. Jain, A., Ziegler, J., Liscombe, D.K., Facchini, P.J., Tucker, P.A. and Panjikar, S. Purification, crystallization and X-ray diffraction analysis of pavine N-methyltransferase from Thalictrum flavum. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 1066-1069. [PMID: 18997344]

2. Liscombe, D.K., Ziegler, J., Schmidt, J., Ammer, C. and Facchini, P.J. Targeted metabolite and transcript profiling for elucidating enzyme function: isolation of novel N-methyltransferases from three benzylisoquinoline alkaloid-producing species. Plant J. 60 (2009) 729-743. [PMID: 19624470]

[EC 2.1.1.300 created 2014]

EC 2.3.1.232

Accepted name: methanol O-anthraniloyltransferase

Reaction: anthraniloyl-CoA + methanol = CoA + O-methyl anthranilate

Glossary: anthraniloyl-CoA = 2-aminobenzoyl-CoA

Other name(s): AMAT; anthraniloyl-coenzyme A (CoA):methanol acyltransferase

Systematic name: anthraniloyl-coenzyme A:methanol O-anthraniloyltransferase

Comments: The enzyme from Concord grape (Vitis labrusca) is solely responsible for the production of O-methyl anthranilate, an important aroma and flavor compound in the grape. The enzyme has a broad substrate specificity, and can use a range of alcohols with substantial activity, the best being butanol, benzyl alcohol, iso-pentanol, octanol and 2-propanol. It can use benzoyl-CoA and acetyl-CoA as acyl donors with lower efficiency. In addition to O-methyl anthranilate, the enzyme might be responsible for the production of ethyl butanoate, methyl-3-hydroxy butanoate and ethyl-3-hydroxy butanoate, which are present in large quantities in the grapes. Also catalyses EC 2.3.1.196, benzyl alcohol O-benzoyltransferase.

References:

1. Wang, J. and De Luca, V. The biosynthesis and regulation of biosynthesis of Concord grape fruit esters, including ’foxy’ methylanthranilate. Plant J. 44 (2005) 606-619. [PMID: 16262710]

[EC 2.3.1.232 created 2014]

*EC 2.3.3.1

Accepted name: citrate (Si)-synthase

Reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA

For diagram of reaction click here or click here.

Other name(s): (R)-citric synthase; citrate oxaloacetate-lyase [(pro-3S)-CH2COO-→acetyl-CoA]

Systematic name: acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-S)-carboxymethyl forming]

Comments: The stereospecificity of this enzyme is opposite to that of EC 2.3.3.3, citrate (Re)-synthase, which is found in some anaerobes. Citrate synthase for which the stereospecificity with respect to C2 of oxaloacetate has not been established are included in EC 2.3.3.16, citrate synthase.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-96-7

References:

1. Lenz, H., Buckel, W., Wunderwald, P., Biedermann, G., Buschmeier, V., Eggerer, H., Cornforth, J.W., Redmond, J.W. and Mallaby, R. Stereochemistry of si-citrate synthase and ATP-citrate-lyase reactions. Eur. J. Biochem. 24 (1971) 207-215. [PMID: 5157292]

2. Karpusas, M., Branchaud, B. and Remington, S.J. Proposed mechanism for the condensation reaction of citrate synthase: 1.9-Å structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A. Biochemistry 29 (1990) 2213-2219. [PMID: 2337600]

3. van Rooyen, J.P., Mienie, L.J., Erasmus, E., De Wet, W.J., Ketting, D., Duran, M. and Wadman, S.K. Identification of the stereoisomeric configurations of methylcitric acid produced by si-citrate synthase and methylcitrate synthase using capillary gas chromatography-mass spectrometry. J. Inherit. Metab. Dis. 17 (1994) 738-747. [PMID: 7707698]

[EC 2.3.3.1 created 1961 as EC 4.1.3.7, transferred 2002 to EC 2.3.3.1, modified 2014]

EC 2.3.3.16

Accepted name: citrate synthase (unknown stereospecificity)

Reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA

Other name(s): citrate condensing enzyme; citrate oxaloacetate-lyase; CoA-acetylating; citrate synthetase; citric synthase; citric-condensing enzyme; citrogenase; condensing enzyme; oxaloacetate transacetase; oxalacetic transacetase

Systematic name: acetyl-CoA:oxaloacetate C-acetyltransferase (thioester-hydrolysing)

Comments: This entry has been included to accommodate those citrate synthases for which the stereospecificity with respect to C2 of oxaloacetate has not been established [cf. EC 2.3.3.1, citrate (Si)-synthase and EC 2.3.3.3, citrate (Re)-synthase].

References:

1. Lohlein-Werhahn, G., Goepfert, P. and Eggerer, H. Purification and properties of an archaebacterial enzyme: citrate synthase from Sulfolobus solfataricus. Biol Chem Hoppe Seyler 369 (1988) 109-113. [PMID: 3130075]

2. Sievers, M., Stockli, M. and Teuber, M. Purification and properties of citrate synthase from Acetobacter europaeus. FEMS Microbiol. Lett. 146 (1997) 53-58. [PMID: 8997706]

3. Belova, L.L., Sokolov, A.P., Morgunov, I.G. and Trotsenko YuA. Purification and characterization of citrate synthase from Methylobacterium extorquens—a methylotrophic producer of polyhydroxybutyrate. Biochemistry (Mosc.) 62 (1997) 71-76. [PMID: 9113733]

4. Lee, S., Park, C. and Yim, J. Characterization of citrate synthase purified from Drosophila melanogaster. Mol. Cells 7 (1997) 599-604. [PMID: 9387145]

5. Maurus, R., Nguyen, N.T., Stokell, D.J., Ayed, A., Hultin, P.G., Duckworth, H.W. and Brayer, G.D. Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases. Biochemistry 42 (2003) 5555-5565. [PMID: 12741811]

[EC 2.3.3.16 created 2014]

*EC 2.4.1.277

Accepted name: 10-deoxymethynolide desosaminyltransferase

Reaction: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose + 10-deoxymethynolide = dTDP + 10-deoxymethymycin

For diagram of reaction click here.

Glossary: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose = dTDP-D-desosamine

Other name(s): glycosyltransferase DesVII; DesVII

Systematic name: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose:10-deoxymethynolide 3-dimethylamino-4,6-dideoxy-α-D-glucosyltransferase

Comments: DesVII is the glycosyltransferase responsible for the attachment of dTDP-D-desosamine to 10-deoxymethynolide or narbonolide during the biosynthesis of methymycin, neomethymycin, narbomycin, and pikromycin in the bacterium Streptomyces venezuelae. Activity requires an additional protein partner, DesVIII.

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

References:

1. Borisova, S.A. and Liu, H.W. Characterization of glycosyltransferase DesVII and its auxiliary partner protein DesVIII in the methymycin/picromycin biosynthetic pathway. Biochemistry 49 (2010) 8071-8084. [PMID: 20695498]

2. Borisova, S.A., Kim, H.J., Pu, X. and Liu, H.W. Glycosylation of acyclic and cyclic aglycone substrates by macrolide glycosyltransferase DesVII/DesVIII: analysis and implications. Chembiochem. 9 (2008) 1554-1558. [PMID: 18548476]

3. Hong, J.S., Park, S.J., Parajuli, N., Park, S.R., Koh, H.S., Jung, W.S., Choi, C.Y. and Yoon, Y.J. Functional analysis of desVIII homologues involved in glycosylation of macrolide antibiotics by interspecies complementation. Gene 386 (2007) 123-130. [PMID: 17049185]

[EC 2.4.1.277 created 2011, modified 2014]

*EC 2.4.1.278

Accepted name: 3-α-mycarosylerythronolide B desosaminyl transferase

Reaction: dTDP-D-desosamine + 3-α-L-mycarosylerythronolide B = dTDP + erythromycin D

For diagram of reaction click here.

Glossary: dTDP-D-desosamine = dTDP-3,4,6-trideoxy-3-(dimethylamino)-α-D-xylo-hexopyranose
erythromycin D = (3R,4S,5S,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-7,12-dihydroxy-6-[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyloxy]-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione
3-O-α-mycarosylerythronolide B = (3R,4S,5R,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-6,7,12-trihydroxy-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione

Other name(s): EryCIII; dTDP-3-dimethylamino-4,6-dideoxy-α-D-glucopyranose:3-α-mycarosylerythronolide B 3-dimethylamino-4,6-dideoxy-α-D-glucosyltransferase; desosaminyl transferase EryCIII

Systematic name: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose:3-α-mycarosylerythronolide B 3-dimethylamino-3,4,6-trideoxy-β-D-glucosyltransferase

Comments: The enzyme is involved in erythromycin biosynthesis.

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

References:

1. Yuan, Y., Chung, H.S., Leimkuhler, C., Walsh, C.T., Kahne, D. and Walker, S. In vitro reconstitution of EryCIII activity for the preparation of unnatural macrolides. J. Am. Chem. Soc. 127 (2005) 14128-14129. [PMID: 16218575]

2. Lee, H.Y., Chung, H.S., Hang, C., Khosla, C., Walsh, C.T., Kahne, D. and Walker, S. Reconstitution and characterization of a new desosaminyl transferase, EryCIII, from the erythromycin biosynthetic pathway. J. Am. Chem. Soc. 126 (2004) 9924-9925. [PMID: 15303858]

3. Moncrieffe, M.C., Fernandez, M.J., Spiteller, D., Matsumura, H., Gay, N.J., Luisi, B.F. and Leadlay, P.F. Structure of the glycosyltransferase EryCIII in complex with its activating P450 homologue EryCII. J. Mol. Biol. 415 (2012) 92-101. [PMID: 22056329]

[EC 2.4.1.278 created 2012, modified 2014]

EC 2.4.1.315

Accepted name: diglucosyl diacylglycerol synthase (1,6-linking)

Reaction: (1) UDP-α-D-glucose + 1,2-diacyl-3-O-(α-D-glucopyranosyl)-sn-glycerol = 1,2-diacyl-3-O-[α-D-glucopyranosyl-(1→6)-O-α-D-glucopyranosyl]-sn-glycerol + UDP
(2) UDP-α-D-glucose + 1,2-diacyl-3-O-[α-D-glucopyranosyl-(1→6)-O-α-D-glucopyranosyl]-sn-glycerol = 1,2-diacyl-3-O-[α-D-glucopyranosyl-(1→6)-α-D-glucopyranosyl-(1→6)-O-α-D-glucopyranosyl]-sn-glycerol + UDP

Other name(s): monoglucosyl diacylglycerol (1→6) glucosyltransferase; MGlcDAG (1→6) glucosyltransferase; DGlcDAG synthase (ambiguous); UGT106B1; ypfP (gene name)

Systematic name: UDP-α-D-glucose:1,2-diacyl-3-O-(α-D-glucopyranosyl)-sn-glycerol 6-glucosyltransferase

Comments: The enzyme is found in several bacterial species. The enzyme from Bacillus subtilis is specific for glucose and can form tetraglucosyl diacylglycerol in vitro [1]. The enzyme from Mycoplasma genitalium can incoporate galactose with similar efficiency, but forms mainly 1,2-diacyl-diglucopyranosyl-sn-glycerol in vivo [3]. The enzyme from Staphylococcus aureus can also form glucosyl-glycero-3-phospho-(1'-sn-glycerol) [2].

References:

1. Jorasch, P., Wolter, F.P., Zahringer, U. and Heinz, E. A UDP glucosyltransferase from Bacillus subtilis successively transfers up to four glucose residues to 1,2-diacylglycerol: expression of ypfP in Escherichia coli and structural analysis of its reaction products. Mol. Microbiol. 29 (1998) 419-430. [PMID: 9720862]

2. Jorasch, P., Warnecke, D.C., Lindner, B., Zahringer, U. and Heinz, E. Novel processive and nonprocessive glycosyltransferases from Staphylococcus aureus and Arabidopsis thaliana synthesize glycoglycerolipids, glycophospholipids, glycosphingolipids and glycosylsterols. Eur. J. Biochem. 267 (2000) 3770-3783. [PMID: 10848996]

3. Andres, E., Martinez, N. and Planas, A. Expression and characterization of a Mycoplasma genitalium glycosyltransferase in membrane glycolipid biosynthesis: potential target against mycoplasma infections. J. Biol. Chem. 286 (2011) 35367-35379. [PMID: 21835921]

[EC 2.4.1.315 created 2014]

EC 2.4.1.316

Accepted name: tylactone mycaminosyltransferase

Reaction: tylactone + dTDP-α-D-mycaminose = dTDP + 5-O-β-D-mycaminosyltylactone

For diagram of reaction click here.

Glossary: tylactone = (4R,5S,6S,7S,9R,11E,13E,15S,16R)-7,16-diethyl-4,6-dihydroxy-5,9,13,15-tetramethyloxacyclohexadeca-11,13-diene-2,10-dione
dTDP-α-D-mycaminose = dTDP-3,6-dideoxy-3-dimethylamino-α-D-glucopyranose

Other name(s): tylM2 (gene name)

Systematic name: dTDP-α-D-mycaminose:tylactone 5-O-β-D-mycaminosyltransferase

Comments: The enzyme participates in the biosynthetic pathway of the macrolide antibiotic tylosin, which is produced by several species of Streptomyces bacteria. Activity is significantly enhanced by the presence of an accessory protein encoded by the tylM3 gene.

References:

1. Gandecha, A.R., Large, S.L. and Cundliffe, E. Analysis of four tylosin biosynthetic genes from the tylLM region of the Streptomyces fradiae genome. Gene 184 (1997) 197-203. [PMID: 9031628]

2. Melancon, C.E., 3rd, Takahashi, H. and Liu, H.W. Characterization of tylM3/tylM2 and mydC/mycB pairs required for efficient glycosyltransfer in macrolide antibiotic biosynthesis. J. Am. Chem. Soc. 126 (2004) 16726-16727. [PMID: 15612702]

[EC 2.4.1.316 created 2014]

EC 2.4.1.317

Accepted name: O-mycaminosyltylonolide 6-deoxyallosyltransferase

Reaction: 5-O-β-D-mycaminosyltylonolide + dTDP-6-deoxy-α-D-allose = dTDP + demethyllactenocin

For diagram of reaction click here.

Glossary: mycaminose = 3,6-dideoxy-3-dimethylamino-glucopyranose
tylonolide = 2-[(4R,5S,6S,7R,9R,11E,13E,15R,16R)-16-ethyl-4,6-dihydroxy-15-(hydroxymethyl)-5,9,13-trimethyl-2,10-dioxooxacyclohexadeca-11,13-dien-7-yl]acetaldehyde
demethyllactenocin = [(2R,3R,4E,6E,9R,11R,12S,13S,14R)-12-{[3,6-dideoxy-3-(dimethylamino)-D-glucopyranosyl]oxy}-2-ethyl-14-hydroxy-5,9,13-trimethyl-8,16-dioxo-11-(2-oxoethyl)oxacyclohexadeca-4,6-dien-3-yl]methyl 6-deoxy-β-D-allopyranoside

Other name(s): tylN (gene name)

Systematic name: dTDP-6-deoxy-α-D-allose:5-O-β-D-mycaminosyltylonolide 23-O-6-deoxy-α-D-allosyltransferase

Comments: The enzyme participates in the biosynthetic pathway of the macrolide antibiotic tylosin, which is produced by several species of Streptomyces bacteria.

References:

1. Wilson, V.T. and Cundliffe, E. Characterization and targeted disruption of a glycosyltransferase gene in the tylosin producer, Streptomyces fradiae. Gene 214 (1998) 95-100. [PMID: 9651492]

[EC 2.4.1.317 created 2014]

EC 2.4.1.318

Accepted name: demethyllactenocin mycarosyltransferase

Reaction: dTDP-β-L-mycarose + demethyllactenocin = dTDP + demethylmacrocin

For diagram of reaction click here.

Glossary: dTDP-β-L-mycarose = dTDP-2,6-dideoxy-3-C-methyl-β-L-ribo-hexose
demethyllactenocin = [(2R,3R,4E,6E,9R,11R,12S,13S,14R)-12-{[3,6-dideoxy-3-(dimethylamino)-D-glucopyranosyl]oxy}-2-ethyl-14-hydroxy-5,9,13-trimethyl-8,16-dioxo-11-(2-oxoethyl)oxacyclohexadeca-4,6-dien-3-yl]methyl 6-deoxy-D-allopyranoside

Other name(s): tylCV (gene name); tylC5 (gene name)

Systematic name: dTDP-β-L-mycarose:demethyllactenocin 4'-O-α-L-mycarosyltransferase

Comments: The enzyme participates in the biosynthetic pathway of the macrolide antibiotic tylosin, which is produced by several species of Streptomyces bacteria.

References:

1. Bate, N., Butler, A.R., Smith, I.P. and Cundliffe, E. The mycarose-biosynthetic genes of Streptomyces fradiae, producer of tylosin. Microbiology 146 (2000) 139-146. [PMID: 10658660]

[EC 2.4.1.318 created 2014]

EC 2.4.1.319

Accepted name: β-1,4-mannooligosaccharide phosphorylase

Reaction: [(1→4)-β-D-mannosyl]n + phosphate = [(1→4)-β-D-mannosyl]n-1 + α-D-mannose 1-phosphate

Other name(s): RaMP2

Systematic name: 1,4-β-D-mannooligosaccharide::phosphate α-D-mannosyltransferase

Comments: The enzyme, isolated from the ruminal bacterium Ruminococcus albus, catalyses the reversible phosphorolysis of β-1,4-mannooligosaccharide with a minimum size of three monomers.

References:

1. Kawahara, R., Saburi, W., Odaka, R., Taguchi, H., Ito, S., Mori, H. and Matsui, H. Metabolic mechanism of mannan in a ruminal bacterium, Ruminococcus albus, involving two mannoside phosphorylases and cellobiose 2-epimerase: discovery of a new carbohydrate phosphorylase, β-1,4-mannooligosaccharide phosphorylase. J. Biol. Chem. 287 (2012) 42389-42399. [PMID: 23093406]

[EC 2.4.1.319 created 2014]

EC 2.4.1.320

Accepted name: 1,4-β-mannosyl-N-acetylglucosamine phosphorylase

Reaction: 4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine + phosphate = N-acetyl-D-glucosamine + α-D-mannose 1-phosphate

Other name(s): BT1033

Systematic name: 4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate α-D-mannosyltransferase

Comments: The enzyme isolated from the anaerobic bacterium Bacteroides thetaiotaomicron is involved in the degradation of host-derived N-glycans.

References:

1. Nihira, T., Suzuki, E., Kitaoka, M., Nishimoto, M., Ohtsubo, K. and Nakai, H. Discovery of β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans. J. Biol. Chem. 288 (2013) 27366-27374. [PMID: 23943617]

[EC 2.4.1.320 created 2014]

EC 2.4.1.321

Accepted name: cellobionic acid phosphorylase

Reaction: 4-O-β-D-glucopyranosyl-D-gluconate + phosphate = α-D-glucose 1-phosphate + D-gluconate

Glossary: 4-O-β-D-glucopyranosyl-D-gluconate = cellobionate

Systematic name: 4-O-β-D-glucopyranosyl-D-gluconate:phosphate α-D-glucosyltransferase

Comments: The enzyme occurs in cellulolytic bacteria and fungi. It catalyses the reversible phosphorolysis of cellobionic acid. In the synthetic direction it produces 4-O-β-D-glucopyranosyl-D-glucuronate from α-D-glucose 1-phosphate and D-glucuronate with low activity

References:

1. Nihira, T., Saito, Y., Nishimoto, M., Kitaoka, M., Igarashi, K., Ohtsubo, K. and Nakai, H. Discovery of cellobionic acid phosphorylase in cellulolytic bacteria and fungi. FEBS Lett 587 (2013) 3556-3561. [PMID: 24055472]

[EC 2.4.1.321 created 2014]

EC 2.4.1.322

Accepted name: desvancosaminyl-vancomycin vancosaminetransferase

Reaction: dTDP-β-L-vancosamine + desvancosaminyl-vancomycin = dTDP + vancomycin

For diagram of reaction click here.

Glossary: dTDP-β-L-vancosamine = dTDP-3-amino-2,3,6-trideoxy-3-C-methyl-β-L-lyxo-hexopyranose

Other name(s): desvancosamine-vancomycin TDP-vancosaminyltransferase; GtfD

Systematic name: dTDP-β-L-vancomycin:desvancosaminyl-vancomycin β-L-vancosaminetransferase

Comments: The enzyme, isolated from the bacterium Amycolatopsis orientalis, catalyses the ultimate step in the biosynthesis of the antibiotic vancomycin.

References:

1. Losey, H.C., Peczuh, M.W., Chen, Z., Eggert, U.S., Dong, S.D., Pelczer, I., Kahne, D. and Walsh, C.T. Tandem action of glycosyltransferases in the maturation of vancomycin and teicoplanin aglycones: novel glycopeptides. Biochemistry 40 (2001) 4745-4755. [PMID: 11294642]

2. Mulichak, A.M., Lu, W., Losey, H.C., Walsh, C.T. and Garavito, R.M. Crystal structure of vancosaminyltransferase GtfD from the vancomycin biosynthetic pathway: interactions with acceptor and nucleotide ligands. Biochemistry 43 (2004) 5170-5180. [PMID: 15122882]

[EC 2.4.1.322 created 2014]

EC 2.4.1.323

Accepted name: 7-deoxyloganetic acid glucosyltransferase

Reaction: UDP-α-D-glucose + 7-deoxyloganetate = UDP + 7-deoxyloganate

For diagram of reaction click here.

Other name(s): UGT8

Systematic name: UDP-α-D-glucose:7-deoxyloganetate O-D-glucosyltransferase

Comments: Isolated from the plant Catharanthus roseus (Madagascar periwinkle). Involved in loganin and secologanin biosynthesis. Does not react with 7-deoxyloganetin. cf. EC 2.4.1.324 7-deoxyloganetin glucosyltransferase.

References:

1. Asada, K., Salim, V., Masada-Atsumi, S., Edmunds, E., Nagatoshi, M., Terasaka, K., Mizukami, H. and De Luca, V. A 7-deoxyloganetic acid glucosyltransferase contributes a key step in secologanin biosynthesis in madagascar periwinkle. Plant Cell 25 (2013) 4123-4134. [PMID: 24104568]

[EC 2.4.1.323 created 2014]

EC 2.4.1.324

Accepted name: 7-deoxyloganetin glucosyltransferase

Reaction: UDP-α-D-glucose + 7-deoxyloganetin = UDP + 7-deoxyloganin

For diagram of reaction click here.

Other name(s): UDPglucose:iridoid glucosyltransferase; UGT6; UGT85A24

Systematic name: UDP-α-D-glucose:7-deoxyloganetin O-D-glucosyltransferase

Comments: Isolated from the plants Catharanthus roseus (Madagascar periwinkle) and Gardenia jasminoides (cape jasmine). With Gardenia it also acts on genipin. Involved in loganin and secologanin biosynthesis. Does not react with 7-deoxyloganetate. cf. EC 2.4.1.323 7-deoxyloganetic acid glucosyltransferase.

References:

1. Nagatoshi, M., Terasaka, K., Nagatsu, A. and Mizukami, H. Iridoid-specific glucosyltransferase from Gardenia jasminoides. J. Biol. Chem. 286 (2011) 32866-32874. [PMID: 21799001]

2. Asada, K., Salim, V., Masada-Atsumi, S., Edmunds, E., Nagatoshi, M., Terasaka, K., Mizukami, H. and De Luca, V. A 7-deoxyloganetic acid glucosyltransferase contributes a key step in secologanin biosynthesis in madagascar periwinkle. Plant Cell 25 (2013) 4123-4134. [PMID: 24104568]

[EC 2.4.1.324 created 2014]

*EC 2.4.2.35

Accepted name: flavonol-3-O-glycoside xylosyltransferase

Reaction: UDP-α-D-xylose + a flavonol 3-O-glycoside = UDP + a flavonol 3-[β-D-xylosyl-(1→2)-β-D-glycoside]

For diagram of reaction click here.

Other name(s): UDP-D-xylose:flavonol-3-O-glycoside 2''-O-β-D-xylosyltransferase

Systematic name: UDP-α-D-xylose:flavonol-3-O-glycoside 2''-O-β-D-xylosyltransferase

Comments: Flavonol 3-O-glucoside, flavonol 3-O-galactoside and, more slowly, rutin, can act as acceptors.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 83380-90-9

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.

[EC 2.4.2.35 created 1986, modified 2014]

EC 2.4.2.57

Accepted name: AMP phosphorylase

Reaction: (1) AMP + phosphate = adenine + α-D-ribose 1,5-bisphosphate
(2) CMP + phosphate = cytosine + α-D-ribose 1,5-bisphosphate
(3) UMP + phosphate = uracil + α-D-ribose 1,5-bisphosphate

For diagram of reaction click here.

Other name(s): AMPpase; nucleoside monophosphate phosphorylase; deoA (gene name)

Systematic name: AMP:phosphate α-D-ribosyl 5'-phosphate-transferase

Comments: The enzyme from archaea is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes. The activity with CMP and UMP requires activation by cAMP [2].

References:

1. Sato, T., Atomi, H. and Imanaka, T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315 (2007) 1003-1006. [PMID: 17303759]

2. Aono, R., Sato, T., Yano, A., Yoshida, S., Nishitani, Y., Miki, K., Imanaka, T. and Atomi, H. Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J. Bacteriol. 194 (2012) 6847-6855. [PMID: 23065974]

3. Nishitani, Y., Aono, R., Nakamura, A., Sato, T., Atomi, H., Imanaka, T. and Miki, K. Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. J. Mol. Biol. (2013) . [PMID: 23659790]

[EC 2.4.2.57 created 2014]

EC 2.4.99.20

Accepted name: 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase

Reaction: NADP+ + nicotinate = nicotinate-adenine dinucleotide phosphate + nicotinamide (overall reaction)
(1a) NADP+ = 2'-phospho-cyclic ADP-ribose + nicotinamide
(1b) 2'-phospho-cyclic ADP-ribose + nicotinate = nicotinate-adenine dinucleotide phosphate

For diagram of reaction click here.

Glossary: 2'-phospho-cyclic ADP-ribose = cADPRP
nicotinic acid-adenine dinucleotide phosphate = NAADP+

Other name(s): diphosphopyridine nucleosidase (ambiguous); CD38 (gene name); BST1 (gene name)

Systematic name: NADP+:nicotinate ADP-ribosyltransferase

Comments: This multiunctional enzyme catalyses both the removal of nicotinamide from NADP+, forming 2'-phospho-cyclic ADP-ribose, and the addition of nicotinate to the cyclic product, forming NAADP+, a calcium messenger that can mobilize intracellular Ca2+ stores and activate Ca2+ influx to regulate a wide range of physiological processes. In addition, the enzyme also catalyses EC 3.2.2.6, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.

References:

1. Chini, E.N., Chini, C.C., Kato, I., Takasawa, S. and Okamoto, H. CD38 is the major enzyme responsible for synthesis of nicotinic acid-adenine dinucleotide phosphate in mammalian tissues. Biochem. J. 362 (2002) 125-130. [PMID: 11829748]

2. Moreschi, I., Bruzzone, S., Melone, L., De Flora, A. and Zocchi, E. NAADP+ synthesis from cADPRP and nicotinic acid by ADP-ribosyl cyclases. Biochem. Biophys. Res. Commun. 345 (2006) 573-580. [PMID: 16690024]

[EC 2.4.99.20 created 2014]

EC 2.5.1.115

Accepted name: homogentisate phytyltransferase

Reaction: phytyl diphosphate + homogentisate = diphosphate + 2-methyl-6-phytylbenzene-1,4-diol + CO2

For diagram of reaction click here.

Glossary: 2-methyl-6-phytylbenzene-1,4-diol = MPBQ

Other name(s): HPT; VTE2 (gene name)

Systematic name: phytyl diphosphate:homogentisate phytyltransferase

Comments: Requires Mg2+ for activity [3]. Involved in the biosynthesis of the vitamin E tocopherols. While the enzyme from the cyanobacterium Synechocystis PCC 6803 has an appreciable activity with geranylgeranyl diphosphate (EC 2.5.1.116, homogentisate geranylgeranyltransferase), the enzyme from the plant Arabidopsis thaliana has only a low activity with that substrate [1,3,4].

References:

1. Collakova, E. and DellaPenna, D. Isolation and functional analysis of homogentisate phytyltransferase from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 127 (2001) 1113-1124. [PMID: 11706191]

2. Savidge, B., Weiss, J.D., Wong, Y.H., Lassner, M.W., Mitsky, T.A., Shewmaker, C.K., Post-Beittenmiller, D. and Valentin, H.E. Isolation and characterization of homogentisate phytyltransferase genes from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 129 (2002) 321-332. [PMID: 12011362]

3. Sadre, R., Gruber, J. and Frentzen, M. Characterization of homogentisate prenyltransferases involved in plastoquinone-9 and tocochromanol biosynthesis. FEBS Lett 580 (2006) 5357-5362. [PMID: 16989822]

4. Yang, W., Cahoon, R.E., Hunter, S.C., Zhang, C., Han, J., Borgschulte, T. and Cahoon, E.B. Vitamin E biosynthesis: functional characterization of the monocot homogentisate geranylgeranyl transferase. Plant J. 65 (2011) 206-217. [PMID: 21223386]

[EC 2.5.1.115 created 2014]

EC 2.5.1.116

Accepted name: homogentisate geranylgeranyltransferase

Reaction: geranylgeranyl diphosphate + homogentisate = diphosphate + 6-geranylgeranyl-2-methylbenzene-1,4-diol + CO2

For diagram of reaction click here.

Glossary: 6-geranylgeranyl-2-methylbenzene-1,4-diol = MGGBQ

Other name(s): HGGT; slr1736 (gene name)

Systematic name: geranylgeranyl diphosphate:homogentisate geranylgeranyltransferase

Comments: Requires Mg2+ for activity. Involved in the biosynthesis of the vitamin E, tocotrienols. While the enzyme from the bacterium Synechocystis PCC 6803 has higher activity with phytyl diphosphate (EC 2.5.1.115, homogentisate phytyltransferase), the enzymes from barley, rice and wheat have only a low activity with that substrate [2].

References:

1. Collakova, E. and DellaPenna, D. Isolation and functional analysis of homogentisate phytyltransferase from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 127 (2001) 1113-1124. [PMID: 11706191]

2. Cahoon, E.B., Hall, S.E., Ripp, K.G., Ganzke, T.S., Hitz, W.D. and Coughlan, S.J. Metabolic redesign of vitamin E biosynthesis in plants for tocotrienol production and increased antioxidant content. Nat. Biotechnol. 21 (2003) 1082-1087. [PMID: 12897790]

3. Yang, W., Cahoon, R.E., Hunter, S.C., Zhang, C., Han, J., Borgschulte, T. and Cahoon, E.B. Vitamin E biosynthesis: functional characterization of the monocot homogentisate geranylgeranyl transferase. Plant J. 65 (2011) 206-217. [PMID: 21223386]

[EC 2.5.1.116 created 2014]

EC 2.5.1.117

Accepted name: homogentisate solanesyltransferase

Reaction: all-trans-nonaprenyl diphosphate + homogentisate = diphosphate + 2-methyl-6-all-trans-nonaprenylbenzene-1,4-diol + CO2

For diagram of reaction click here.

Glossary: 2-methyl-6-all-trans-nonaprenylbenzene-1,4-diol = 2-methyl-6-solanesylbenzene-1,4-diol = MSBQ

Other name(s): HST; PDS2 (gene name)

Systematic name: all-trans-nonaprenyl diphosphate:homogentisate nonaprenyltransferase

Comments: Requires Mg2+ for activity. Part of the biosynthesis pathway of plastoquinol-9. The enzymes purified from the plant Arabidopsis thaliana and the alga Chlamydomonas reinhardtii are also active in vitro with unsaturated C10-C20 prenyl diphosphates, producing main products that are not decarboxylated [2].

References:

1. Sadre, R., Gruber, J. and Frentzen, M. Characterization of homogentisate prenyltransferases involved in plastoquinone-9 and tocochromanol biosynthesis. FEBS Lett 580 (2006) 5357-5362. [PMID: 16989822]

2. Sadre, R., Frentzen, M., Saeed, M. and Hawkes, T. Catalytic reactions of the homogentisate prenyl transferase involved in plastoquinone-9 biosynthesis. J. Biol. Chem. 285 (2010) 18191-18198. [PMID: 20400515]

[EC 2.5.1.117 created 2014]

EC 2.5.1.118

Accepted name: β-(isoxazolin-5-on-2-yl)-L-alanine synthase

Reaction: O3-acetyl-L-serine + isoxazolin-5-one = 3-(5-oxoisoxazolin-2-yl)-L-alanine + acetate

For diagram of reaction click here.

Systematic name: O3-acetyl-L-serine:isoxazolin-5-one 2-(2-amino-2-carboxyethyl)transferase

Comments: The enzyme from the plants Lathyrus odoratus (sweet pea) and L. sativus (grass pea) also forms 3-(5-oxoisoxazolin-4-yl)-L-alanine in vitro (cf. EC 2.5.1.119). However, only 3-(5-oxoisoxazolin-2-yl)-L-alanine is formed in vivo. 3-(5-oxoisoxazolin-2-yl)-L-alanine is the biosynthetic precursor of the neurotoxin N3-oxalyl-L-2,3-diaminopropanoic acid, the cause of lathyrism. Closely related and possibly identical to EC 2.5.1.47, cysteine synthase, and EC 2.5.1.51, β-pyrazolylalanine synthase.

References:

1. Ikegami, F., Kamiya, M., Kuo, Y.H., Lambein, F. and Murakoshi, I. Enzymatic synthesis of two isoxazolylalanine isomers by cysteine synthases in Lathyrus species. Biol. Pharm. Bull. 19 (1996) 1214-1215. [PMID: 8889043]

[EC 2.5.1.118 created 2014]

EC 2.5.1.119

Accepted name: β-(isoxazolin-5-on-4-yl)-L-alanine synthase

Reaction: O3-acetyl-L-serine + isoxazolin-5-one = 3-(5-oxoisoxazolin-4-yl)-L-alanine + acetate

For diagram of reaction click here.

Systematic name: O3-acetyl-L-serine:isoxazolin-5-one 4-(2-amino-2-carboxyethyl)transferase

Comments: 3-(5-Oxoisoxazolin-4-yl)-L-alanine is an antifungal antibiotic produced by the bacterium Streptomyces platensis. The enzymes from the plants Lathyrus odoratus (sweet pea) , L. sativus (grass pea) and Citrullus vulgaris (watermelon) that catalyse EC 2.5.1.118 (β-(isoxazolin-5-on-2-yl)-L-alanine synthase) also catalyse this reaction in vitro, but not in vivo. Closely related and possibly identical to EC 2.5.1.47, cysteine synthase, and EC 2.5.1.51, β-pyrazolylalanine synthase.

References:

1. Ikegami, F., Kamiya, M., Kuo, Y.H., Lambein, F. and Murakoshi, I. Enzymatic synthesis of two isoxazolylalanine isomers by cysteine synthases in Lathyrus species. Biol. Pharm. Bull. 19 (1996) 1214-1215. [PMID: 8889043]

[EC 2.5.1.119 created 2014]

EC 2.5.1.120

Accepted name: aminodeoxyfutalosine synthase

Reaction: S-adenosyl-L-methionine + 3-[(1-carboxyvinyl)oxy]benzoate + H2O = 6-amino-6-deoxyfutalosine + L-methionine + bicarbonate

For diagram of reaction click here.

Glossary: 6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate

Other name(s): MqnE; AFL synthase; aminofutalosine synthase

Systematic name: S-adenosyl-L-methionine:3-[(1-carboxyvinyl)-oxy]benzoate adenosyltransferase (bicarbonate-hydrolysing, 6-amino-6-deoxyfutalosine-forming)

Comments: This enzyme is a member of the ’AdoMet radical’ (radical SAM) family. S-Adenosyl-L-methionine acts as both a radical generator and as the source of the transferred adenosyl group. The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

References:

1. Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318-15321. [PMID: 24083939]

[EC 2.5.1.120 created 2014]

EC 2.6.1.104

Accepted name: 3-dehydro-glucose-6-phosphate—glutamate transaminase

Reaction: kanosamine 6-phosphate + 2-oxoglutarate = 3-dehydro-D-glucose 6-phosphate + L-glutamate

For diagram of reaction click here.

Glossary: kanosamine = 3-amino-3-deoxy-D-glucose

Other name(s): 3-oxo-glucose-6-phosphate:glutamate aminotransferase; ntdA (gene name)

Systematic name: kanosamine 6-phosphate:2-oxoglutarate aminotransferase

Comments: A pyridoxal-phosphate protein. The enzyme, found in the bacterium Bacillus subtilis, is involved in a kanosamine biosynthesis pathway.

References:

1. van Straaten, K.E., Langill, D.M., Palmer, D.R. and Sanders, D.A. Purification, crystallization and preliminary X-ray analysis of NtdA, a putative pyridoxal phosphate-dependent aminotransferase from Bacillus subtilis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 426-429. [PMID: 19342798]

2. Vetter, N.D., Langill, D.M., Anjum, S., Boisvert-Martel, J., Jagdhane, R.C., Omene, E., Zheng, H., van Straaten, K.E., Asiamah, I., Krol, E.S., Sanders, D.A. and Palmer, D.R. A previously unrecognized kanosamine biosynthesis pathway in Bacillus subtilis. J. Am. Chem. Soc. 135 (2013) 5970-5973. [PMID: 23586652]

[EC 2.6.1.104 created 2014]

EC 2.6.1.105

Accepted name: lysine—8-amino-7-oxononanoate transaminase

Reaction: L-lysine + 8-amino-7-oxononanoate = (S)-2-amino-6-oxohexanoate + 7,8-diaminononanoate

Glossary: (S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine

Other name(s): DAPA aminotransferase (ambiguous); bioA (gene name) (ambiguous); bioK (gene name)

Systematic name: L-lysine:8-amino-7-oxononanoate aminotransferase

Comments: A pyridoxal 5'-phosphate enzyme [2]. Participates in the pathway for biotin biosynthesis. The enzyme from the bacterium Bacillus subtilis cannot use S-adenosyl-L-methionine as amino donor and catalyses an alternative reaction for the conversion of 8-amino-7-oxononanoate to 7,8-diaminononanoate (cf. EC 2.6.1.62, adenosylmethionine—8-amino-7-oxononanoate transaminase).

References:

1. Van Arsdell, S.W., Perkins, J.B., Yocum, R.R., Luan, L., Howitt, C.L., Chatterjee, N.P. and Pero, J.G. Removing a bottleneck in the Bacillus subtilis biotin pathway: bioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction. Biotechnol. Bioeng. 91 (2005) 75-83. [PMID: 15880481]

2. Dey, S., Lane, J.M., Lee, R.E., Rubin, E.J. and Sacchettini, J.C. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase. Biochemistry 49 (2010) 6746-6760. [PMID: 20565114]

[EC 2.6.1.105 created 2014]

EC 2.6.1.106

Accepted name: dTDP-3-amino-3,4,6-trideoxy-α-D-glucose transaminase

Reaction: dTDP-3-amino-3,4,6-trideoxy-α-D-glucose + 2-oxoglutarate = dTDP-3-dehydro-4,6-deoxy-α-D-glucose + L-glutamate

For diagram of reaction click here.

Glossary: dTDP-α-D-desosamine = dTDP-3-(dimethylamino)-3,4,6-trideoxy-α-D-glucose

Other name(s): desV (gene name); megDII (gene name); eryCI (gene name)

Systematic name: dTDP-3-amino-3,4,6-trideoxy-α-D-glucose:2-oxoglutarate aminotransferase

Comments: A pyridoxal-phosphate protein. The enzyme is involved in the biosynthesis of dTDP-α-D-desosamine, a sugar found in several bacterial macrolide antibiotics including erythromycin, megalomicin A, mycinamicin II, and oleandomycin. The reaction occurs in the reverse direction.

References:

1. Burgie, E.S., Thoden, J.B. and Holden, H.M. Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Protein Sci. 16 (2007) 887-896. [PMID: 17456741]

[EC 2.6.1.106 created 2014]

EC 2.6.1.107

Accepted name: β-methylphenylalanine transaminase

Reaction: (2S,3S)-3-methylphenylalanine + 2-oxoglutarate = (3S)-2-oxo-3-phenylbutanoate + L-glutamate

Glossary: (3S)-2-oxo-3-phenylbutanoate = (3S)-β-methyl-phenylpyruvate

Other name(s): TyrB

Systematic name: (2S,3S)-3-methylphenylalanine:2-oxoglutarate aminotransferase

Comments: Requires pyridoxal phosphate. Isolated from the bacterium Streptomyces hygroscopicus NRRL3085. It is involved in the biosynthesis of the glycopeptide antibiotic mannopeptimycin.

References:

1. Huang, Y.T., Lyu, S.Y., Chuang, P.H., Hsu, N.S., Li, Y.S., Chan, H.C., Huang, C.J., Liu, Y.C., Wu, C.J., Yang, W.B. and Li, T.L. In vitro characterization of enzymes involved in the synthesis of nonproteinogenic residue (2S,3S)-β-methylphenylalanine in glycopeptide antibiotic mannopeptimycin. Chembiochem 10 (2009) 2480-2487. [PMID: 19731276]

[EC 2.6.1.107 created 2014]

EC 2.6.99.4

Accepted name: N6-L-threonylcarbamoyladenine synthase

Reaction: L-threonylcarbamoyladenylate + adenine37 in tRNA = AMP + N6-L-threonylcarbamoyladenine37 in tRNA

For diagram of reaction click here.

Glossary: N6-L-threonylcarbamoyladenine37 = t6A37

Other name(s): t6A synthase; Kae1; ygjD (gene name); Qri7

Systematic name: L-threonylcarbamoyladenylate:adenine37 in tRNA N6-L-threonylcarbamoyltransferase

Comments: The enzyme is involved in the synthesis of N6-threonylcarbamoyladenosine37 in tRNAs, which is found in tRNAs with the anticodon NNU, i.e. tRNAIle, tRNAThr, tRNAAsn, tRNALys, tRNASer and tRNAArg [3].

References:

1. Lauhon, C.T. Mechanism of N6-threonylcarbamoyladenonsine (t6A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 51 (2012) 8950-8963. [PMID: 23072323]

2. Deutsch, C., El Yacoubi, B., de Crecy-Lagard, V. and Iwata-Reuyl, D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J. Biol. Chem. 287 (2012) 13666-13673. [PMID: 22378793]

3. Perrochia, L., Crozat, E., Hecker, A., Zhang, W., Bareille, J., Collinet, B., van Tilbeurgh, H., Forterre, P. and Basta, T. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res. 41 (2013) 1953-1964. [PMID: 23258706]

4. Wan, L.C.K., Mao, D.Y.L., Neculai, D., Strecker, J., Chiovitti, D., Kurinov, I., Poda, G., Thevakumaran, N., Yuan, F., Szilard, R.K., Lissina, E., Nislow, C., Caudy, A.A., Durocher, D. and Sicheri, F. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res. 41 (2013) 6332-6346. [PMID: 23620299]

[EC 2.6.99.4 created 2014]

EC 2.7.1.181

Accepted name: polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase

Reaction: ATP + α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = ADP + 3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol

Other name(s): WbdD

Systematic name: ATP:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phosphotransferase

Comments: The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the methylation of 3-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-α-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.1.1.294, 3-phospho-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase)

References:

1. Clarke, B.R., Cuthbertson, L. and Whitfield, C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J. Biol. Chem. 279 (2004) 35709-35718. [PMID: 15184370]

2. Clarke, B.R., Greenfield, L.K., Bouwman, C. and Whitfield, C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J. Biol. Chem. 284 (2009) 30662-30672. [PMID: 19734145]

3. Clarke, B.R., Richards, M.R., Greenfield, L.K., Hou, D., Lowary, T.L. and Whitfield, C. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J. Biol. Chem. 286 (2011) 41391-41401. [PMID: 21990359]

[EC 2.7.1.181 created 2014]

EC 2.7.1.182

Accepted name: phytol kinase

Reaction: CTP + phytol = CDP + phytyl phosphate

Other name(s): VTE5 (gene name)

Systematic name: CTP:phytol O-phosphotransferase

Comments: The enzyme is found in plants and photosynthetic algae [2] and is involved in phytol salvage [1]. It can use UTP as an alternative phosphate donor with lower activity [2].

References:

1. Ischebeck, T., Zbierzak, A.M., Kanwischer, M. and Dormann, P. A salvage pathway for phytol metabolism in Arabidopsis. J. Biol. Chem. 281 (2006) 2470-2477. [PMID: 16306049]

2. Valentin, H.E., Lincoln, K., Moshiri, F., Jensen, P.K., Qi, Q., Venkatesh, T.V., Karunanandaa, B., Baszis, S.R., Norris, S.R., Savidge, B., Gruys, K.J. and Last, R.L. The Arabidopsis vitamin E pathway gene5-1 mutant reveals a critical role for phytol kinase in seed tocopherol biosynthesis. Plant Cell 18 (2006) 212-224. [PMID: 16361393]

[EC 2.7.1.182 created 2014]

*EC 2.7.4.24

Accepted name: diphosphoinositol-pentakisphosphate kinase

Reaction: (1) ATP + 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate = ADP + 1D-myo-inositol 1,5-bis(diphosphate) 2,3,4,6-tetrakisphosphate
(2) ATP + 1D-myo-inositol hexakisphosphate = ADP + 1D-myo-inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate

Other name(s): PP-IP5 kinase; diphosphoinositol pentakisphosphate kinase; ATP:5-diphospho-1D-myo-inositol-pentakisphosphate phosphotransferase; PP-InsP5 kinase; PPIP5K; PPIP5K1; PPIP5K2; VIP1; VIP2

Systematic name: ATP:1D-myo-inositol-5-diphosphate-pentakisphosphate phosphotransferase

Comments: This enzyme is activated by osmotic shock [4]. Ins(1,3,4,5,6)P5, 1D-myo-inositol diphosphate tetrakisphosphate and 1D-myo-inositol bisdiphosphate triphosphate are not substrates [4].

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

References:

1. Shears, S.B., Ali, N., Craxton, A. and Bembenek, M.E. Synthesis and metabolism of bis-diphosphoinositol tetrakisphosphate in vitro and in vivo. J. Biol. Chem. 270 (1995) 10489-10497. [PMID: 7737983]

2. Albert, C., Safrany, S.T., Bembenek, M.E., Reddy, K.M., Reddy, K.K., Falck, J.-R., Bröcker, M., Shears, S.B. and Mayr, G.W. Biological variability in the structures of diphosphoinositol polyphosphates in Dictyostelium discoideum and mammalian cells. Biochem. J. 327 (1997) 553-560. [PMID: 9359429]

3. Fridy, P.C., Otto, J.C., Dollins, D.E. and York, J.D. Cloning and characterization of two human VIP1-like inositol hexakisphosphate and diphosphoinositol pentakisphosphate kinases. J. Biol. Chem. 282 (2007) 30754-30762. [PMID: 17690096]

4. Choi, J.H., Williams, J., Cho, J., Falck, J.R. and Shears, S.B. Purification, sequencing, and molecular identification of a mammalian PP-InsP5 kinase that Is activated when cells are exposed to hyperosmotic stress. J. Biol. Chem. 282 (2007) 30763-30775. [PMID: 17702752]

5. Lin, H., Fridy, P.C., Ribeiro, A.A., Choi, J.H., Barma, D.K., Vogel, G., Falck, J.R., Shears, S.B., York, J.D. and Mayr, G.W. Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases. J. Biol. Chem. 284 (2009) 1863-1872. [PMID: 18981179]

6. Wang, H., Falck, J.R., Hall, T.M. and Shears, S.B. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat. Chem. Biol. 8 (2012) 111-116. [PMID: 22119861]

[EC 2.7.4.24 created 2003 as EC 2.7.1.155, transferred 2007 to EC 2.7.4.24, modified 2014]

EC 2.8.2.36

Accepted name: desulfo-A47934 sulfotransferase

Reaction: 3'-phosphoadenylyl sulfate + desulfo-A47934 = adenosine 3',5'-bisphosphate + A47934

Glossary: desulfo-A47934 = LY 154989 = 7-demethyl-64-O-demethyl-19-deoxy-22,31,45-trichloro-11-sulfo-ristomycin A aglycone

Other name(s): StaL

Systematic name: 3'-phosphoadenylyl-sulfate:desulfo-A47934 sulfotransferase

Comments: The enzyme from the bacterium Streptomyces toyocaensis catalyses the final step in the biosynthesis of the glycopeptide antibiotic A47934, a naturally occuring antibiotic of the vancomycin group.

References:

1. Lamb, S.S., Patel, T., Koteva, K.P. and Wright, G.D. Biosynthesis of sulfated glycopeptide antibiotics by using the sulfotransferase StaL. Chem. Biol. 13 (2006) 171-181. [PMID: 16492565]

2. Shi, R., Lamb, S.S., Bhat, S., Sulea, T., Wright, G.D., Matte, A. and Cygler, M. Crystal structure of StaL, a glycopeptide antibiotic sulfotransferase from Streptomyces toyocaensis. J. Biol. Chem. 282 (2007) 13073-13086. [PMID: 17329243]

[EC 2.8.2.36 created 2014]

[EC 2.8.3.7 Deleted entry: succinate—citramalate CoA-transferase. The activity has now been shown to be due to two separate enzymes described by EC 2.8.3.22, succinyl-CoA—L-malate CoA-transferase, and EC 2.8.3.20, succinyl-CoA—D-citramalate CoA-transferase (EC 2.8.3.7 created 1972, deleted 2013)]

EC 2.8.3.20

Accepted name: succinyl-CoA—D-citramalate CoA-transferase

Reaction: (1) succinyl-CoA + (R)-citramalate = succinate + (R)-citramalyl-CoA
(2) succinyl-CoA + (R)-malate = succinate + (R)-malyl-CoA

Glossary: (R)-citramalate = (2R)-2-hydroxy-2-methylbutanedioate
(R)-malate = (2R)-2-hydroxybutanedioate
(R)-malyl-CoA = (3R)-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s): Sct

Systematic name: succinyl-CoA:(R)-citramalate CoA-transferase

Comments: The enzyme, purified from the bacterium Clostridium tetanomorphum, can also accept itaconate as acceptor, with lower efficiency.

References:

1. Friedmann, S., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:D-citramalate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 6460-6468. [PMID: 16952935]

[EC 2.8.3.20 created 2014]

EC 2.8.3.21

Accepted name: L-carnitine CoA-transferase

Reaction: (1) (E)-4-(trimethylammonio)but-2-enoyl-CoA + L-carnitine = (E)-4-(trimethylammonio)but-2-enoate + L-carnitinyl-CoA
(2) 4-trimethylammoniobutanoyl-CoA + L-carnitine = 4-trimethylammoniobutanoate + L-carnitinyl-CoA

Glossary: L-carnitine = (3R)-3-hydroxy-4-(trimethylammonio)butanoate
(E)-4-(trimethylammonio)but-2-enoate = crotonobetaine
4-trimethylammoniobutanoate = γ-butyrobetaine

Other name(s): CaiB; crotonobetainyl/γ-butyrobetainyl-CoA:carnitine CoA-transferase

Systematic name: (E)-4-(trimethylammonio)but-2-enoyl-CoA:L-carnitine CoA-transferase

Comments: The enzyme is found in gammaproteobacteria such as Proteus sp. and Escherichia coli. It has similar activity with both substrates.

References:

1. Engemann, C., Elssner, T. and Kleber, H.P. Biotransformation of crotonobetaine to L-(-)-carnitine in Proteus sp. Arch. Microbiol. 175 (2001) 353-359. [PMID: 11409545]

2. Elssner, T., Engemann, C., Baumgart, K. and Kleber, H.P. Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli. Biochemistry 40 (2001) 11140-11148. [PMID: 11551212]

3. Stenmark, P., Gurmu, D. and Nordlund, P. Crystal structure of CaiB, a type-III CoA transferase in carnitine metabolism. Biochemistry 43 (2004) 13996-14003. [PMID: 15518548]

4. Engemann, C., Elssner, T., Pfeifer, S., Krumbholz, C., Maier, T. and Kleber, H.P. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch. Microbiol. 183 (2005) 176-189. [PMID: 15731894]

5. Rangarajan, E.S., Li, Y., Iannuzzi, P., Cygler, M. and Matte, A. Crystal structure of Escherichia coli crotonobetainyl-CoA: carnitine CoA-transferase (CaiB) and its complexes with CoA and carnitinyl-CoA. Biochemistry 44 (2005) 5728-5738. [PMID: 15823031]

[EC 2.8.3.21 created 2014]

EC 2.8.3.22

Accepted name: succinyl-CoA—L-malate CoA-transferase

Reaction: (1) succinyl-CoA + (S)-malate = succinate + (S)-malyl-CoA
(2) succinyl-CoA + (S)-citramalate = succinate + (S)-citramalyl-CoA

For diagram of reaction click here.

Glossary: (S)-citramalate = (2S)-2-hydroxy-2-methylbutanedioate
(S)-malate = (2S)-2-hydroxybutanedioate
(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s): SmtAB

Systematic name: succinyl-CoA:(S)-malate CoA-transferase

Comments: The enzyme, purified from the bacterium Chloroflexus aurantiacus, can also accept itaconate as acceptor, with lower efficiency. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.

References:

1. Friedmann, S., Steindorf, A., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 2646-2655. [PMID: 16547052]

[EC 2.8.3.22 created 2014]

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 = 2-methylthio-N6-dimethylallyladenine37 in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine (overall reaction)
(1a) N6-dimethylallyladenine37 in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine = 2-thio-N6-dimethylallyladenine37 in tRNA + (sulfur carrier) + L-methionine + 5'-deoxyadenosine
(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.

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]

EC 2.8.4.4

Accepted name: [ribosomal protein S12] (aspartate89-C3)-methylthiotransferase

Reaction: Asp89-[ribosomal protein S12] + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine = 3-methylthioaspartate89-[ribosomal protein S12] + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine (overall reaction)
(1a) Asp89-[ribosomal protein S12] + sulfur-(sulfur carrier) + S-adenosyl-L-methionine = 3-thioaspartate89-[ribosomal protein S12] + (sulfur carrier) + L-methionine + 5'-deoxyadenosine
(1b) S-adenosyl-L-methionine + 3-thioaspartate89-[ribosomal protein S12] = S-adenosyl-L-homocysteine + 3-methylthioaspartate89-[ribosomal protein S12]

Other name(s): RimO

Systematic name: [ribosomal protein S12]-Asp89:sulfur-(sulfur carrier),S-adenosyl-L-methionine C3-methylthiotransferase

Comments: This bacterial enzyme binds two [4Fe-4S] clusters as well as the transferred sulfur [2,3]. 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.

References:

1. Anton, B.P., Saleh, L., Benner, J.S., Raleigh, E.A., Kasif, S. and Roberts, R.J. RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc. Natl. Acad. Sci. USA 105 (2008) 1826-1831. [PMID: 18252828]

2. Lee, K.H., Saleh, L., Anton, B.P., Madinger, C.L., Benner, J.S., Iwig, D.F., Roberts, R.J., Krebs, C. and Booker, S.J. Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry 48 (2009) 10162-10174. [PMID: 19736993]

3. Arragain, S., Garcia-Serres, R., Blondin, G., Douki, T., Clemancey, M., Latour, J.M., Forouhar, F., Neely, H., Montelione, G.T., Hunt, J.F., Mulliez, E., Fontecave, M. and Atta, M. Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. J. Biol. Chem. 285 (2010) 5792-5801. [PMID: 20007320]

4. Strader, M.B., Costantino, N., Elkins, C.A., Chen, C.Y., Patel, I., Makusky, A.J., Choy, J.S., Court, D.L., Markey, S.P. and Kowalak, J.A. A proteomic and transcriptomic approach reveals new insight into β-methylthiolation of Escherichia coli ribosomal protein S12. Mol Cell Proteomics 10 (2011) M110.005199. [PMID: 21169565]

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 2.8.4.4 created 2014]

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 = 2-methylthio-N6-L-threonylcarbamoyladenine37 in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine (overall reaction)
(1a) N6-L-threonylcarbamoyladenine37 in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine = 2-thio-N6-L-threonylcarbamoyladenine37 in tRNA + (sulfur carrier) + L-methionine + 5-deoxyadenosine
(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.

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]

EC 3.1.2.30

Accepted name: (3S)-malyl-CoA thioesterase

Reaction: (S)-malyl-CoA + H2O = (S)-malate + CoA

Glossary: (S)-malate = (2S)-2-hydroxybutanedioate
(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s): mcl2 (gene name)

Systematic name: (S)-malyl-CoA hydrolase

Comments: Stimulated by Mg2+ or Mn2+. The enzyme has no activity with (2R,3S)-2-methylmalyl-CoA (cf. EC 4.1.3.24, malyl-CoA lyase) or other CoA esters.

References:

1. Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249-1258. [PMID: 20047909]

[EC 3.1.2.30 created 2014]

EC 3.1.3.93

Accepted name: L-galactose 1-phosphate phosphatase

Reaction: β-L-galactose 1-phosphate + H2O = L-galactose + phosphate

Other name(s): VTC4 (gene name) (ambiguous); IMPL2 (gene name) (ambiguous)

Systematic name: β-L-galactose-1-phosphate phosphohydrolase

Comments: The enzyme from plants also has the activity of EC 3.1.3.25, inositol-phosphate phosphatase. The enzymes have very low activity with D-galactose 1-phosphate (cf. EC 3.1.3.94, D-galactose 1-phosphate phosphatase).

References:

1. Laing, W.A., Bulley, S., Wright, M., Cooney, J., Jensen, D., Barraclough, D. and MacRae, E. A highly specific L-galactose-1-phosphate phosphatase on the path to ascorbate biosynthesis. Proc. Natl. Acad. Sci. USA 101 (2004) 16976-16981. [PMID: 15550539]

2. Torabinejad, J., Donahue, J.L., Gunesekera, B.N., Allen-Daniels, M.J. and Gillaspy, G.E. VTC4 is a bifunctional enzyme that affects myoinositol and ascorbate biosynthesis in plants. Plant Physiol. 150 (2009) 951-961. [PMID: 19339506]

3. Petersen, L.N., Marineo, S., Mandala, S., Davids, F., Sewell, B.T. and Ingle, R.A. The missing link in plant histidine biosynthesis: Arabidopsis myoinositol monophosphatase-like2 encodes a functional histidinol-phosphate phosphatase. Plant Physiol. 152 (2010) 1186-1196. [PMID: 20023146]

[EC 3.1.3.93 created 2014]

EC 3.1.3.94

Accepted name: D-galactose 1-phosphate phosphatase

Reaction: α-D-galactose 1-phosphate + H2O = D-galactose + phosphate

Systematic name: α-D-galactose-1-phosphate phosphohydrolase

Comments: The human enzyme also has the activity of EC 3.1.3.25, inositol-phosphate phosphatase. The enzyme has very low activity with L-galactose 1-phosphate (cf. EC 3.1.3.93, L-galactose 1-phosphate phosphatase).

References:

1. Parthasarathy, R., Parthasarathy, L. and Vadnal, R. Brain inositol monophosphatase identified as a galactose 1-phosphatase. Brain Res. 778 (1997) 99-106. [PMID: 9462881]

[EC 3.1.3.94 created 2014]

EC 3.1.3.95

Accepted name: phosphatidylinositol-3,5-bisphosphate 3-phosphatase

Reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate

Glossary: 1-phosphatidyl-1D-myo-inositol 5-phosphate = PtdIns5P
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate = PtdIns(3,5)P2

Other name(s): MTMR; PtdIns-3,5-P2 3-Ptase

Systematic name: 1-phosphatidyl-1D-myo-inositol-3,5-bisphosphate 3-phosphohydrolase

Comments: The enzyme is found in both plants and animals. It also has the activity of EC 3.1.3.64 (phosphatidylinositol-3-phosphatase).

References:

1. Walker, D.M., Urbe, S., Dove, S.K., Tenza, D., Raposo, G. and Clague, M.J. Characterization of MTMR3. an inositol lipid 3-phosphatase with novel substrate specificity. Curr. Biol. 11 (2001) 1600-1605. [PMID: 11676921]

2. Berger, P., Bonneick, S., Willi, S., Wymann, M. and Suter, U. Loss of phosphatase activity in myotubularin-related protein 2 is associated with Charcot-Marie-Tooth disease type 4B1. Hum. Mol. Genet. 11 (2002) 1569-1579. [PMID: 12045210]

3. Ding, Y., Lapko, H., Ndamukong, I., Xia, Y., Al-Abdallat, A., Lalithambika, S., Sadder, M., Saleh, A., Fromm, M., Riethoven, J.J., Lu, G. and Avramova, Z. The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and the response to drought. Plant Signal Behav 4 (2009) 1049-1058. [PMID: 19901554]

[EC 3.1.3.95 created 2014]

*EC 3.1.21.2

Accepted name: deoxyribonuclease IV

Reaction: Endonucleolytic cleavage of ssDNA at apurinic/apyrimidinic sites to 5'-phosphooligonucleotide end-products

Other name(s): deoxyribonuclease IV (phage-T4-induced) (misleading); endodeoxyribonuclease IV (phage T4-induced) (misleading); E. coli endonuclease IV; endodeoxyribonuclease (misleading); redoxyendonuclease; deoxriboendonuclease (misleading); endonuclease II; endonuclease IV; DNA-adenine-transferase; nfo (gene name)

Comments: The enzyme is an apurinic/apyrimidinic (AP) site endonuclease that primes DNA repair synthesis at AP sites. It specifically cleaves the DNA backbone at AP sites and also removes 3' DNA-blocking groups such as 3' phosphates, 3' phosphoglycolates, and 3' α,β-unsaturated aldehydes that arise from oxidative base damage and the activity of combined glycosylase/lyase enzymes. It is also the only known repair enzyme that is able to cleave the DNA backbone 5' of the oxidative lesion α-deoxyadenosine.The enzyme has a strong preference for single-stranded DNA.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 63363-78-0

References:

1. Friedberg, E.C. and Goldthwait, D.A. Endonuclease II of E. coli. I. Isolation and purification. Proc. Natl. Acad. Sci. USA 62 (1969) 934-940. [PMID: 4895219]

2. Friedberg, E.C., Hadi, S.-M. and Goldthwait, D.A. Endonuclease II of Escherichia coli. II. Enzyme properties and studies on the degradation of alkylated and native deoxyribonucleic acid. J. Biol. Chem. 244 (1969) 5879-5889. [PMID: 4981786]

3. Hadi, S.M. and Goldthwait, D.A. Endonuclease II of Escherichia coli. Degradation of partially depurinated deoxyribonucleic acid. Biochemistry 10 (1971) 4986-4993. [PMID: 4944066]

4. Cunningham, R.P., Saporito, S.M., Spitzer, S.G. and Weiss, B. Endonuclease IV (nfo) mutant of Escherichia coli. J. Bacteriol. 168 (1986) 1120-1127. [PMID: 2430946]

5. Ide, H., Tedzuka, K., Shimzu, H., Kimura, Y., Purmal, A.A., Wallace, S.S. and Kow, Y.W. Alpha-deoxyadenosine, a major anoxic radiolysis product of adenine in DNA, is a substrate for Escherichia coli endonuclease IV. Biochemistry 33 (1994) 7842-7847. [PMID: 7516707]

6. Hosfield, D.J., Guan, Y., Haas, B.J., Cunningham, R.P. and Tainer, J.A. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98 (1999) 397-408. [PMID: 10458614]

[EC 3.1.21.2 created 1972 as EC 3.1.4.30, transferred 1978 to EC 3.1.21.2, modified 2014]

EC 3.1.21.8

Accepted name: T4 deoxyribonuclease II

Reaction: Endonucleolytic nicking and cleavage of cytosine-containing double-stranded DNA.

Other name(s): T4 endonuclease II; EndoII (ambiguous); denA (gene name)

Comments: Requires Mg2+. This phage T4 enzyme is involved in degradation of host DNA. The enzyme primarily catalyses nicking of the bottom strand of double stranded DNA between the first and second base pair to the right of a top-strand CCGC motif. Double-stranded breaks are produced 5- to 10-fold less frequently [3]. It does not cleave the T4 native DNA, which contains 5-hydroxymethylcytosine instead of cytosine.

References:

1. Carlson, K., Krabbe, M., Nystrom, A.C. and Kosturko, L.D. DNA determinants of restriction. Bacteriophage T4 endonuclease II-dependent cleavage of plasmid DNA in vivo. J. Biol. Chem. 268 (1993) 8908-8918. [PMID: 8386173]

2. Carlson, K. and Kosturko, L.D. Endonuclease II of coliphage T4: a recombinase disguised as a restriction endonuclease. Mol. Microbiol. 27 (1998) 671-676. [PMID: 9515694]

3. Carlson, K., Kosturko, L.D. and Nystrom, A.C. Sequence-specific cleavage by bacteriophage T4 endonuclease II in vitro. Mol. Microbiol. 31 (1999) 1395-1405. [PMID: 10200960]

4. Andersson, C.E., Lagerback, P. and Carlson, K. Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme. J. Mol. Biol. 397 (2010) 1003-1016. [PMID: 20156453]

[EC 3.1.21.8 created 2014]

EC 3.1.21.9

Accepted name: T4 deoxyribonuclease IV

Reaction: Endonucleolytic cleavage of the 5' phosphodiester bond of deoxycytidine in single-stranded DNA.

Other name(s): T4 endonuclease IV; EndoIV (ambiguous); denB (gene name)

Comments: This phage T4 enzyme is involved in degradation of host DNA. The enzyme does not cleave double-stranded DNA or native T4 DNA, which contains 5-hydroxymethylcytosine instead of cytosine.

References:

1. Sadowski, P.D. and Hurwitz, J. Enzymatic breakage of deoxyribonucleic acid. II. Purification and properties of endonuclease IV from T4 phage-infected Escherichia coli. J. Biol. Chem. 244 (1969) 6192-6198. [PMID: 4900512]

2. Ling, V. Partial digestion of 32P-fd DNA with T4 endonuclease IV. FEBS Lett 19 (1971) 50-54. [PMID: 11946172]

3. Sadowski, P.D. and Bakyta, I. T4 endonuclease IV. Improved purification procedure and resolution from T4 endonuclease 3. J. Biol. Chem. 247 (1972) 405-412. [PMID: 4550601]

4. Bernardi, A., Maat, J., de Waard, A. and Bernardi, G. Preparation and specificity of endonuclease IV induced by bacteriophage T4. Eur. J. Biochem. 66 (1976) 175-179. [PMID: 782881]

5. Hirano, N., Ohshima, H. and Takahashi, H. Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis. Nucleic Acids Res. 34 (2006) 4743-4751. [PMID: 16971463]

6. Ohshima, H., Hirano, N. and Takahashi, H. A hexanucleotide sequence (dC1-dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4. Nucleic Acids Res. 35 (2007) 6681-6689. [PMID: 17940096]

[EC 3.1.21.9 created 2014]

[EC 3.1.27.9 Transferred entry: tRNA-intron endonuclease. Now EC 4.6.1.16, tRNA-intron lyase (EC 3.1.27.9 created 1992, deleted 2013)]

EC 3.2.1.191

Accepted name: ginsenosidase type III

Reaction: a protopanaxadiol-type ginsenoside with two glucosyl residues at position 3 + 2 H2O = a protopanaxadiol-type ginsenoside with no glycosidic modification at position 3 + 2 D-glucopyranose (overall reaction)
(1a) a protopanaxadiol-type ginsenoside with two glucosyl residues at position 3 + H2O a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + D-glucopyranose
(1b) a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + H2O = a protopanaxadiol-type ginsenoside with no glycosidic modification at position 3 + D-glucopyranose

For diagram of reaction click here.

Glossary: ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
gypenoside XVII = 3β-(β-D-glucopyranosyloxy)-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
gypenoside LXXV = 20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-ene-3β,12β-diol

Systematic name: protopanaxadiol-type ginsenoside 3-β-D-hydrolase

Comments: Ginsenosidase type III catalyses the sequential hydrolysis of the 3-O-β-D-(1→2)-glucopyranosyl bond followed by hydrolysis of the 3-O-β-D-glucopyranosyl bond of protopanaxadiol ginsenosides. When acting for example on ginsenoside Rb1 the enzyme first generates ginsenoside XVII, and subsequently ginsenoside LXXV.

References:

1. Jin, X.F., Yu, H.S., Wang, D.M., Liu, T.Q., Liu, C.Y., An, D.S., Im, W.T., Kim, S.G. and Jin, F.X. Kinetics of a cloned special ginsenosidase hydrolyzing 3-O-glucoside of multi-protopanaxadiol-type ginsenosides, named ginsenosidase type III. J Microbiol Biotechnol 22 (2012) 343-351. [PMID: 22450790]

2. An, D.S., Cui, C.H., Lee, H.G., Wang, L., Kim, S.C., Lee, S.T., Jin, F., Yu, H., Chin, Y.W., Lee, H.K., Im, W.T. and Kim, S.G. Identification and characterization of a novel Terrabacter ginsenosidimutans sp. nov. β-glucosidase that transforms ginsenoside Rb1 into the rare gypenosides XVII and LXXV. Appl. Environ. Microbiol. 76 (2010) 5827-5836. [PMID: 20622122]

3. Hong, H., Cui, C.H., Kim, J.K., Jin, F.X., Kim, S.C. and Im, W.T. Enzymatic Biotransformation of Ginsenoside Rb1 and Gypenoside XVII into Ginsenosides Rd and F2 by Recombinant β-glucosidase from Flavobacterium johnsoniae. J Ginseng Res 36 (2012) 418-424. [PMID: 23717145]

[EC 3.2.1.191 created 2014]

EC 3.2.1.192

Accepted name: ginsenoside Rb1 β-glucosidase

Reaction: ginsenoside Rb1 + 2 H2O = ginsenoside Rg3 + 2 D-glucopyranose (overall reaction)
(1a) ginsenoside Rb1 + H2O = ginsenoside Rd + D-glucopyranose
(1b) ginsenoside Rd + H2O = ginsenoside Rg3 + D-glucopyranose

For diagram of reaction click here.

Glossary: ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rd = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside F2 = 3β,20-bis(β-D-glucopyranosyloxy)dammar-24-en-12β-ol

Systematic name: ginsenoside Rb1 glucohydrolase

Comments: Ginsenosidases catalyse the hydrolysis of glycosyl moieties attached to the C-3, C-6 or C-20 position of ginsenosides. They are specific with respect to the nature of the glycosidic linkage, the position and the order in which the linkages are cleaved. Ginsenoside Rb1 β-glucosidase specifically and sequentially hydrolyses the 20-[β-D-glucopyranosyl-(1→6)-β-D glucopyranosyloxy] residues attached to position 20 by first hydrolysing the (1→6)-glucosidic bond to generate ginsenoside Rd as an intermediate, followed by hydrolysis of the remaining 20-O-β-D-glucosidic bond.

References:

1. Yan, Q., Zhou, W., Li, X., Feng, M. and Zhou, P. Purification method improvement and characterization of a novel ginsenoside-hydrolyzing β-glucosidase from Paecilomyces Bainier sp. 229. Biosci. Biotechnol. Biochem. 72 (2008) 352-359. [PMID: 18256474]

[EC 3.2.1.192 created 2014]

EC 3.2.1.193

Accepted name: ginsenosidase type I

Reaction: (1) a protopanaxadiol-type ginsenoside with two glucosyl residues at position 3 + H2O = a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + D-glucopyranose
(2) a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + H2O = a protopanaxadiol-type ginsenoside with no glycosidic modifications at position 3 + D-glucopyranose
(3) a protopanaxadiol-type ginsenoside with two glycosyl residues at position 20 + H2O = a protopanaxadiol-type ginsenoside with a single glucosyl residue at position 20 + a monosaccharide

For diagram of reaction click here.

Glossary: ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb2 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb3 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[β-D-xylopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rc = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinofuranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rd = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside F2 = 3β,20-bis(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside C-K = 20β-(β-D-glucopyranosyloxy)dammar-24-ene-3β,12β-diol
ginsenoside Rh2 = 3β-(β-D-glucopyranosyloxy)dammar-24-ene-12β,20-diol

Systematic name: ginsenoside glucohydrolase

Comments: Ginsenosidase type I is slightly activated by Mg2+ or Ca2+ [1]. The enzyme hydrolyses the 3-O-β-D-(1→2)-glucosidic bond, the 3-O-β-D-glucopyranosyl bond and the 20-O-β-D-(1→6)-glycosidic bond of protopanaxadiol-type ginsenosides. It usually leaves a single glucosyl residue attached at position 20 and one or no glucosyl residues at position 3. Starting with a ginsenoside that is glycosylated at both positions (e.g. ginsenoside Rb1, Rb2, Rb3, Rc or Rd), the most common products are ginsenoside F2 and ginsenoside C-K, with low amounts of ginsenoside Rh2.

References:

1. Yu, H., Zhang, C., Lu, M., Sun, F., Fu, Y. and Jin, F. Purification and characterization of new special ginsenosidase hydrolyzing multi-glycisides of protopanaxadiol ginsenosides, ginsenosidase type I. Chem Pharm Bull (Tokyo) 55 (2007) 231-235. [PMID: 17268094]

[EC 3.2.1.193 created 2014]

EC 3.2.1.194

Accepted name: ginsenosidase type IV

Reaction: a protopanaxatriol-type ginsenoside with two glycosyl residues at position 6 + 2 H2O = a protopanaxatriol-type ginsenoside with no glycosidic modification at position 6 + D-glucopyranose + a monosaccharide (overall reaction)
(1a) a protopanaxatriol-type ginsenoside with two glycosyl residues at position 6 + H2O = a protopanaxatriol-type ginsenoside with a single glucosyl at position 6 + a monosaccharide
(1b) a protopanaxatriol-type ginsenoside with a single glucosyl at position 6 + H2O = a protopanaxatriol-type ginsenoside with no glycosidic modification at position 6 + D-glucopyranose

For diagram of reaction click here.

Glossary: ginsenoside Re = 20-(β-D-glucopyranosyl)oxy-6α-[α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranosyloxy]dammar-24-en-3β,12β-diol
ginsenoside Rg1 = 6α,20-bis(β-D-glucopyranosyl)oxy-dammar-24-en-3β,12β-diol
ginsenoside F1 = 20-(β-D-glucopyranosyloxy)dammar-24-en-3β,6α,12β-triol

Systematic name: protopanaxatriol-type ginsenoside 6-β-D-glucohydrolase

Comments: Ginsenosidase type IV catalyses the sequential hydrolysis of the 6-O-β-D-(1→2)-glycosidic bond or the 6-O-α-D-(1→2)-glycosidic bond in protopanaxatriol-type ginsenosides with a disacchride attached to the C6 position, followed by the hydrolysis of the remaining 6-O-β-D-glycosidic bond (e.g. ginsenoside Re → ginsenoside Rg1 → ginsenoside F1).

References:

1. Wang, D.M., Yu, H.S., Song, J.G., Xu, Y.F., Liu, C.Y. and Jin, F.X. A novel ginsenosidase from an Aspergillus strain hydrolyzing 6-O-multi-glycosides of protopanaxatriol-type ginsenosides, named ginsenosidase type IV. J Microbiol Biotechnol 21 (2011) 1057-1063. [PMID: 22031031]

2. Wang, D, Yu, H., Song, J., Xu, Y., Jin, F. Enzyme kinetics of ginsenosidase type IV hydrolyzing 6-O-multi-glycosides of protopanaxatriol type ginsenosides. Process Biochem. 47 (2012) 133-138.

[EC 3.2.1.194 created 2014]

EC 3.2.1.195

Accepted name: 20-O-multi-glycoside ginsenosidase

Reaction: a protopanaxadiol-type ginsenoside with two glycosyl residues at position 20 + H2O = a protopanaxadiol-type ginsenoside with a single glucosyl residue at position 20 + a monosaccharide

For diagram of reaction click here.

Glossary: ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb2 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb3 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[β-D-xylopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rc = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinofuranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rd = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside Rg3 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-ene-12β,20-diol

Other name(s): ginsenosidase type II (erroneous)

Systematic name: protopanaxadiol-type ginsenoside 20-β-D-glucohydrolase

Comments: The 20-O-multi-glycoside ginsenosidase catalyses the hydrolysis of the 20-O-α-(1→6)-glycosidic bond and the 20-O-β-(1→6)-glycosidic bond of protopanaxadiol-type ginsenosides. The enzyme usually leaves a single glucosyl residue attached at position 20, although it can cleave the remaining glucosyl residue with a lower efficiency. Starting with a ginsenoside that is glycosylated at positions 3 and 20, such as ginsenosides Rb1, Rb2, Rb3 and Rc, the most common product is ginsenoside Rd, with a low amount of ginsenoside Rg3 also formed.

References:

1. Yu, H., Liu, Q., Zhang, C., Lu, M., Fu, Y., Im, W.-T., Lee, S.-T. and Jin, F. A new ginsenosidase from Aspergillus strain hydrolyzing 20-O-multi-glycoside of PPD ginsenoside. Process Biochem. 44 (2009) 772-775.

[EC 3.2.1.195 created 2014]

*EC 3.2.2.6

Accepted name: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

Reaction: NAD+ + H2O = ADP-D-ribose + nicotinamide (overall reaction)
(1a) NAD+ = cyclic ADP-ribose + nicotinamide
(1b) cyclic ADP-ribose + H2O = ADP-D-ribose

For diagram of reaction click here.

Glossary: ADP-D-ribose = adenosine 5'-(5-deoxy-D-ribofuranos-5-yl diphosphate)
cyclic ADP-ribose = N1-(β-D-ribosyl)adenosine 5'(P1),5''(P2)-cyclic diphosphate

Other name(s): NAD+ nucleosidase; NADase (ambiguous); DPNase (ambiguous); DPN hydrolase (ambiguous); NAD hydrolase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD glycohydrolase (misleading); NAD nucleosidase (ambiguous); nicotinamide adenine dinucleotide glycohydrolase (misleading); CD38 (gene name); BST1 (gene name)

Systematic name: NAD+ glycohydrolase (cyclic ADP-ribose-forming)

Comments: This multiunctional enzyme catalyses both the synthesis and hydrolysis of cyclic ADP-ribose, a calcium messenger that can mobilize intracellular Ca2+ stores and activate Ca2+ influx to regulate a wide range of physiological processes. In addition, the enzyme also catalyses EC 2.4.99.20, 2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase. cf. EC 3.2.2.5, NAD+ glycohydrolase.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9032-65-9

References:

1. Howard, M., Grimaldi, J.C., Bazan, J.F., Lund, F.E., Santos-Argumedo, L., Parkhouse, R.M., Walseth, T.F. and Lee, H.C. Formation and hydrolysis of cyclic ADP-ribose catalyzed by lymphocyte antigen CD38. Science 262 (1993) 1056-1059. [PMID: 8235624]

2. Takasawa, S., Tohgo, A., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Yonekura, H. and Okamoto, H. Synthesis and hydrolysis of cyclic ADP-ribose by human leukocyte antigen CD38 and inhibition of the hydrolysis by ATP. J. Biol. Chem. 268 (1993) 26052-26054. [PMID: 8253715]

3. Tohgo, A., Takasawa, S., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Furuya, Y., Yonekura, H. and Okamoto, H. Essential cysteine residues for cyclic ADP-ribose synthesis and hydrolysis by CD38. J. Biol. Chem. 269 (1994) 28555-28557. [PMID: 7961800]

4. Fryxell, K.B., O'Donoghue, K., Graeff, R.M., Lee, H.C. and Branton, W.D. Functional expression of soluble forms of human CD38 in Escherichia coli and Pichia pastoris. Protein Expr. Purif. 6 (1995) 329-336. [PMID: 7663169]

5. Yamamoto-Katayama, S., Ariyoshi, M., Ishihara, K., Hirano, T., Jingami, H. and Morikawa, K. Crystallographic studies on human BST-1/CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities. J. Mol. Biol. 316 (2002) 711-723. [PMID: 11866528]

6. Liu, Q., Kriksunov, I.A., Graeff, R., Munshi, C., Lee, H.C. and Hao, Q. Crystal structure of human CD38 extracellular domain. Structure 13 (2005) 1331-1339. [PMID: 16154090]

[EC 3.2.2.6 created 1961, modified 2004, modified 2014]

EC 3.2.2.30

Accepted name: aminodeoxyfutalosine nucleosidase

Reaction: 6-amino-6-deoxyfutalosine + H2O = dehypoxanthine futalosine + adenine

For diagram of reaction click here.

Glossary: 6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
dehypoxanthine futalosine = 3-{3-[(2R,3S,4R)-3,4,5-trihydroxytetrahydrofuran-2-yl]propanoyl}benzoate

Other name(s): AFL nucleosidase; aminofutalosine nucleosidase; methylthioadenosine nucleosidase; MqnB

Systematic name: 6-amino-6-deoxyfutalosine ribohydrolase

Comments: The enzyme, found in several bacterial species, also has the activity of EC 3.2.2.9, adenosylhomocysteine nucleosidase. It is part of a modified futalosine pathway for menaquinone biosynthesis.

References:

1. Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670-1673. [PMID: 18801996]

2. Li, X., Apel, D., Gaynor, E.C. and Tanner, M.E. 5'-methylthioadenosine nucleosidase is implicated in playing a key role in a modified futalosine pathway for menaquinone biosynthesis in Campylobacter jejuni. J. Biol. Chem. 286 (2011) 19392-19398. [PMID: 21489995]

3. Arakawa, C., Kuratsu, M., Furihata, K., Hiratsuka, T., Itoh, N., Seto, H. and Dairi, T. Diversity of the early step of the futalosine pathway. Antimicrob. Agents Chemother. 55 (2011) 913-916. [PMID: 21098241]

4. Wang, S., Haapalainen, A.M., Yan, F., Du, Q., Tyler, P.C., Evans, G.B., Rinaldo-Matthis, A., Brown, R.L., Norris, G.E., Almo, S.C. and Schramm, V.L. A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori. Biochemistry 51 (2012) 6892-6894. [PMID: 22891633]

5. Mishra, V. and Ronning, D.R. Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5'-alkylthio binding subsite. Biochemistry 51 (2012) 9763-9772. [PMID: 23148563]

6. Kim, R.Q., Offen, W.A., Davies, G.J. and Stubbs, K.A. Structural enzymology of Helicobacter pylori methylthioadenosine nucleosidase in the futalosine pathway. Acta Crystallogr. D Biol. Crystallogr. 70 (2014) 177-185. [PMID: 24419390]

[EC 3.2.2.30 created 2014]

EC 3.5.1.116

Accepted name: ureidoglycolate amidohydrolase

Reaction: (S)-ureidoglycolate + H2O = glyoxylate + 2 NH3 + CO2

For diagram of reaction click here.

Other name(s): ureidoglycolate hydrolase; UAH (gene name)

Systematic name: (S)-ureidoglycolate amidohydrolase (decarboxylating)

Comments: This plant enzyme is involved in the degradation of ureidoglycolate, an intermediate of purine degradation. Not to be confused with EC 4.3.2.3, ureidoglycolate lyase, which releases urea rather than ammonia.

References:

1. Winkler, R.G., Blevins, D.G. and Randall, D.D. Ureide catabolism in soybeans. III. Ureidoglycolate amidohydrolase and allantoate amidohydrolase are activities of an allantoate degrading enzyme complex. Plant Physiol. 86 (1988) 1084-1088. [PMID: 16666035]

2. Wells, X.E. and Lees, E.M. Ureidoglycolate amidohydrolase from developing French bean fruits (Phaseolus vulgaris [L.].). Arch. Biochem. Biophys. 287 (1991) 151-159. [PMID: 1910298]

3. Werner, A.K., Romeis, T. and Witte, C.P. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat. Chem. Biol. 6 (2010) 19-21. [PMID: 19935661]

[EC 3.5.1.116 created 1992 as EC 3.5.3.19, transferred 2014 to EC 3.5.1.116]

[EC 3.5.3.19 Transferred entry: ureidoglycolate hydrolase. Now classified as EC 3.5.1.116, ureidoglycolate amidohydrolase (EC 3.5.3.19 created 1992, deleted 2013)]

EC 3.5.4.40

Accepted name: aminodeoxyfutalosine deaminase

Reaction: 6-amino-6-deoxyfutalosine + H2O = futalosine + NH3

For diagram of reaction click here.

Glossary: 6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
futalosine = 3-{3-[(3S,4R)-3,4-dihydroxy-5-(6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-2-yl]propanoyl}benzoate

Other name(s): AFL deaminase; aminofutalosine deaminase; mqnX (gene name)

Systematic name: 6-amino-6-deoxyfutalosine deaminase

Comments: The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

References:

1. Arakawa, C., Kuratsu, M., Furihata, K., Hiratsuka, T., Itoh, N., Seto, H. and Dairi, T. Diversity of the early step of the futalosine pathway. Antimicrob. Agents Chemother. 55 (2011) 913-916. [PMID: 21098241]

2. Goble, A.M., Toro, R., Li, X., Ornelas, A., Fan, H., Eswaramoorthy, S., Patskovsky, Y., Hillerich, B., Seidel, R., Sali, A., Shoichet, B.K., Almo, S.C., Swaminathan, S., Tanner, M.E. and Raushel, F.M. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry 52 (2013) 6525-6536. [PMID: 23972005]

[EC 3.5.4.40 created 2014]

EC 3.5.99.10

Accepted name: 2-iminobutanoate/2-iminopropanoate deaminase

Reaction: (1) 2-iminobutanoate + H2O = 2-oxobutanoate + NH3
(2) 2-iminopropanoate + H2O = pyruvate + NH3

Other name(s): yjgF (gene name); ridA (gene name); enamine/imine deaminase (ambiguous)

Systematic name: 2-iminobutanoate aminohydrolase

Comments: This enzyme, which has been found in all species and tissues examined, catalyses the hydrolytic deamination of imine intermediates formed by several types of pyridoxal-5'-phosphate-dependent dehydratases, such as EC 4.3.1.19, threonine ammonia-lyase and EC 4.3.1.17, L-serine ammonia-lyase. The reactions, which can occur spontaneously, are accelerated to minimize the cellular damage that could be caused by these reactive intermediates.

References:

1. Lambrecht, J.A., Flynn, J.M. and Downs, D.M. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J. Biol. Chem. 287 (2012) 3454-3461. [PMID: 22094463]

[EC 3.5.99.10 created 2014]

EC 3.7.1.21

Accepted name: 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase

Reaction: 6-oxocyclohex-1-ene-1-carbonyl-CoA + 2 H2O = 3-hydroxypimeloyl-CoA (overall reaction)
(1a) 6-oxocyclohex-1-ene-1-carbonyl-CoA + H2O = 2-hydroxy-6-oxocyclohexane-1-carbonyl-CoA
(1b) 2-hydroxy-6-oxocyclohexane-1-carbonyl-CoA + H2O = 3-hydroxypimeloyl-CoA

For diagram of reaction click here.

Glossary: 3-hydroxypimeloyl-CoA = 3-hydroxy-6-carboxyhexanoyl-CoA

Other name(s): 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase

Systematic name: 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase (decyclizing)

Comments: The enzyme, which participates in the anaerobic benzoyl-CoA degradation pathway in certain organisms, catalyses the addition of one molecule of water to the double bound of 6-oxocyclohex-1-ene-1-carbonyl-CoA followed by the hydrolytic C-C cleavage of the alicyclic ring.

References:

1. Laempe, D., Jahn, M. and Fuchs, G. 6-Hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase and 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, enzymes of the benzoyl-CoA pathway of anaerobic aromatic metabolism in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 263 (1999) 420-429. [PMID: 10406950]

2. Kuntze, K., Shinoda, Y., Moutakki, H., McInerney, M.J., Vogt, C., Richnow, H.H. and Boll, M. 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. Environ Microbiol 10 (2008) 1547-1556. [PMID: 18312395]

[EC 3.7.1.21 created 2014]

EC 3.7.1.22

Accepted name: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)

Reaction: 3D-3,5/4-trihydroxycyclohexa-1,2-dione + H2O = 5-deoxy-D-glucuronate

For diagram of reaction click here.

Glossary: 3D-3,5/4-trihydroxycyclohexa-1,2-dione = (3R,4S,5R)-3,4,5-trihydroxycyclohexane-1,2-dione

Other name(s): IolD; THcHDO hydrolase

Systematic name: 3D-3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (decyclizing)

Comments: The enzyme, found in the bacterium Bacillus subtilis, is part of the myo-inositol degradation pathway leading to acetyl-CoA.

References:

1. Yoshida, K., Yamaguchi, M., Morinaga, T., Kinehara, M., Ikeuchi, M., Ashida, H. and Fujita, Y. myo-Inositol catabolism in Bacillus subtilis. J. Biol. Chem. 283 (2008) 10415-10424. [PMID: 18310071]

[EC 3.7.1.22 created 2014]

EC 4.1.1.97

Accepted name: 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase

Reaction: 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO2

For diagram of reaction click here.

Glossary: 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline

Other name(s): OHCU decarboxylase; hpxQ (gene name); PRHOXNB (gene name)

Systematic name: 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate carboxy-lyase [(S)-allantoin-forming]

Comments: This enzyme is part of the pathway from urate to (S)-allantoin, which is present in bacteria, plants and animals (but not in humans).

References:

1. Ramazzina, I., Folli, C., Secchi, A., Berni, R. and Percudani, R. Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes. Nat. Chem. Biol. 2 (2006) 144-148. [PMID: 16462750]

2. Cendron, L., Berni, R., Folli, C., Ramazzina, I., Percudani, R. and Zanotti, G. The structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase provides insights into the mechanism of uric acid degradation. J. Biol. Chem. 282 (2007) 18182-18189. [PMID: 17428786]

3. Kim, K., Park, J. and Rhee, S. Structural and functional basis for (S)-allantoin formation in the ureide pathway. J. Biol. Chem. 282 (2007) 23457-23464. [PMID: 17567580]

4. French, J.B. and Ealick, S.E. Structural and mechanistic studies on Klebsiella pneumoniae 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. J. Biol. Chem. 285 (2010) 35446-35454. [PMID: 20826786]

[EC 4.1.1.97 created 2014]

*EC 4.1.2.14

Accepted name: 2-dehydro-3-deoxy-phosphogluconate aldolase

Reaction: 2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate

For diagram of reaction click here.

Other name(s): phospho-2-keto-3-deoxygluconate aldolase; KDPG aldolase; phospho-2-keto-3-deoxygluconic aldolase; 2-keto-3-deoxy-6-phosphogluconic aldolase; 2-keto-3-deoxy-6-phosphogluconate aldolase; 6-phospho-2-keto-3-deoxygluconate aldolase; ODPG aldolase; 2-oxo-3-deoxy-6-phosphogluconate aldolase; 2-keto-3-deoxygluconate-6-P-aldolase; 2-keto-3-deoxygluconate-6-phosphate aldolase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Systematic name: 2-dehydro-3-deoxy-6-phosphate-D-gluconate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Comments: The enzyme shows no activity with 2-dehydro-3-deoxy-6-phosphate-D-galactonate. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase [2]. Also acts on 2-oxobutanoate [1].

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-53-7

References:

1. Meloche, H.P. and Wood, W.A. Crystallization and characteristics of 2-keto-3-deoxy-6-phosphogluconic aldolase. J. Biol. Chem. 239 (1964) 3515-3518. [PMID: 14245411]

2. Barran, L.R. and Wood, W.A. The mechanism of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Nature of the inactivation by fluorodinitrobenzene. J. Biol. Chem. 246 (1971) 4028-4035. [PMID: 5561473]

[EC 4.1.2.14 created 1965, modified 1976, modified 2014]

*EC 4.1.2.21

Accepted name: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Reaction: 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate

Other name(s): 6-phospho-2-keto-3-deoxygalactonate aldolase; phospho-2-keto-3-deoxygalactonate aldolase; 2-keto-3-deoxy-6-phosphogalactonic aldolase; phospho-2-keto-3-deoxygalactonic aldolase; 2-keto-3-deoxy-6-phosphogalactonic acid aldolase; (KDPGal)aldolase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Systematic name: 2-dehydro-3-deoxy-6-phospho-D-galactonate D-glyceraldehyde-3-phospho-lyase (pyruvate-forming)

Comments: The enzyme catalyses the last reaction in a D-galactose degradation pathway. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9030-99-3

References:

1. Shuster, C.W. 2-Keto-3-deoxy-6-phosphogalactonic acid aldolase. Methods Enzymol. 9 (1966) 524-528.

[EC 4.1.2.21 created 1972, modified 2014]

EC 4.1.2.55

Accepted name: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Reaction: (1) 2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
(2) 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate

For diagram of reaction click here.

Other name(s): 2-keto-3-deoxygluconate aldolase (ambiguous); KDGA (ambiguous)

Systematic name: 2-dehydro-3-deoxy-6-phosphate-D-gluconate/2-dehydro-3-deoxy-6-phosphate-D-galactonate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Comments: In the archaeon Sulfolobus solfataricus the enzyme is involved in glucose and galactose catabolism via the branched variant of the Entner-Doudoroff pathway. It utilizes 2-dehydro-3-deoxy-6-phosphate-D-gluconate and 2-dehydro-3-deoxy-6-phosphate-D-galactonate with similar catalytic efficiency. In vitro the enzyme can also catalyse the cleavage of the non-phosphorylated forms 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate with much lower catalytic efficiency. cf. EC 4.1.2.21, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, and EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.

References:

1. Buchanan, C.L., Connaris, H., Danson, M.J., Reeve, C.D. and Hough, D.W. An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates. Biochem. J. 343 (1999) 563-570. [PMID: 10527934]

2. Lamble, H.J., Theodossis, A., Milburn, C.C., Taylor, G.L., Bull, S.D., Hough, D.W. and Danson, M.J. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett 579 (2005) 6865-6869. [PMID: 16330030]

3. Wolterink-van Loo, S., van Eerde, A., Siemerink, M.A., Akerboom, J., Dijkstra, B.W. and van der Oost, J. Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem. J. 403 (2007) 421-430. [PMID: 17176250]

[EC 4.1.2.55 created 2014]

EC 4.1.2.56

Accepted name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate synthase

Reaction: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate = glycerone phosphate + L-aspartate 4-semialdehyde

For diagram of reaction click here and mechanism click here.

Other name(s): griI (gene name)

Systematic name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate L-aspartate 4-semialdehyde-lyase (glycerone phosphate-forming)

Comments: Part of the pathway for the biosynthesis of grixazone, a mixture of yellow pigments produced by the bacterium Streptomyces griseus.

References:

1. Suzuki, H., Ohnishi, Y., Furusho, Y., Sakuda, S. and Horinouchi, S. Novel benzene ring biosynthesis from C3 and C4 primary metabolites by two enzymes. J. Biol. Chem. 281 (2006) 36944-36951. [PMID: 17003031]

[EC 4.1.2.56 created 2014]

*EC 4.1.3.24

Accepted name: malyl-CoA lyase

Reaction: (1) (S)-malyl-CoA = acetyl-CoA + glyoxylate
(2) (2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate

For diagram of reaction click here.

Glossary: (S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
(2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s): malyl-coenzyme A lyase; (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase; mclA (gene name); mcl1 (gene name); (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase (acetyl-CoA-forming); L-malyl-CoA lyase

Systematic name: (S)-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)

Comments: The enzyme from the bacterium Chloroflexus aurantiacus, which participates in the 3-hydroxypropanoate cycle for carbon assimilation, also has the activity of EC 4.1.3.25, (3S)-citramalyl-CoA lyase [2,4]. The enzymes from Rhodobacter species are part of acetate assimilation pathways [3,5]. The reactions are reversible.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 37290-67-8

References:

1. Tuboi, S. and Kikuchi, G. Enzymic cleavage of malyl-Coenzyme A into acetyl-Coenzyme A and glyoxylic acid. Biochim. Biophys. Acta 96 (1965) 148-153. [PMID: 14285256]

2. Herter, S., Busch, A. and Fuchs, G. L-Malyl-coenzyme A lyase/β-methylmalyl-coenzyme A lyase from Chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic CO2 fixation. J. Bacteriol. 184 (2002) 5999-6006. [PMID: 12374834]

3. Meister, M., Saum, S., Alber, B.E. and Fuchs, G. L-malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. J. Bacteriol. 187 (2005) 1415-1425. [PMID: 15687206]

4. Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906-2914. [PMID: 17259315]

5. Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249-1258. [PMID: 20047909]

[EC 4.1.3.24 created 1972, modified 2014]

*EC 4.1.3.25

Accepted name: (S)-citramalyl-CoA lyase

Reaction: (3S)-citramalyl-CoA = acetyl-CoA + pyruvate

For diagram of reaction click here.

Other name(s): citramalyl coenzyme A lyase; (+)-CMA-CoA lyase; (3S)-citramalyl-CoA pyruvate-lyase; Mcl (ambiguous); citramalyl-CoA lyase

Systematic name: (3S)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)

Comments: Requires Mg2+ ions for activity [3]. The enzyme from the bacterium Clostridium tetanomorphum is a component of EC 4.1.3.22, citramalate lyase [2]. It also acts on (3S)-citramalyl thioacyl-carrier protein [2]. The enzyme from the bacterium Chloroflexus aurantiacus also has the activity of EC 4.1.3.24, malyl-CoA lyase [3]. It has no activity with (3R)-citramalyl-CoA (cf. EC 4.1.3.46, (R)-citramalyl-CoA lyase) [3].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37290-68-9

References:

1. Cooper, R.A. and Kornberg, H.L. The utilization of itaconate by Pseudomonas sp. Biochem. J. 91 (1964) 82-91. [PMID: 4284209]

2. Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469-477. [PMID: 923590]

3. Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906-2914. [PMID: 17259315]

[EC 4.1.3.25 created 1972, modified 2014]

EC 4.1.3.46

Accepted name: (R)-citramalyl-CoA lyase

Reaction: (3R)-citramalyl-CoA = acetyl-CoA + pyruvate

Other name(s): Ccl

Systematic name: (3R)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)

Comments: Requires Mn2+ ions for activity. The enzyme, purified from the bacterium Chloroflexus aurantiacus, has no activity with (3S)-citramalyl-CoA (cf. EC 4.1.3.25, (S)-citramalyl-CoA lyase).

References:

1. Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906-2914. [PMID: 17259315]

[EC 4.1.3.46 created 2014]

[EC 4.2.1.89 Deleted entry: carnitine dehydratase. The activity has now been shown to be due to EC 2.8.3.21, L-carnitine CoA-transferase and EC 4.2.1.149, crotonobetainyl-CoA hydratase. (EC 4.2.1.89 created 1989, deleted 2013)]

EC 4.2.1.147

Accepted name: 5,6,7,8-tetrahydromethanopterin hydro-lyase

Reaction: 5,6,7,8-tetrahydromethanopterin + formaldehyde = 5,10-methylenetetrahydromethanopterin + H2O

Other name(s): formaldehyde-activating enzyme

Systematic name: 5,6,7,8-tetrahydromethanopterin hydro-lyase (formaldehyde-adding, tetrahydromethanopterin-forming)

Comments: Found in methylotrophic bacteria and methanogenic archaea.

References:

1. Vorholt, J.A., Marx, C.J., Lidstrom, M.E. and Thauer, R.K. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J. Bacteriol. 182 (2000) 6645-6650. [PMID: 11073907]

2. Acharya, P., Goenrich, M., Hagemeier, C.H., Demmer, U., Vorholt, J.A., Thauer, R.K. and Ermler, U. How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. J. Biol. Chem. 280 (2005) 13712-13719. [PMID: 15632161]

[EC 4.2.1.147 created 2014]

EC 4.2.1.148

Accepted name: 2-methylfumaryl-CoA hydratase

Reaction: (2R,3S)-2-methylmalyl-CoA = 2-methylfumaryl-CoA + H2O

For diagram of reaction click here.

Glossary: (2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA

Other name(s): Mcd; erythro-β-methylmalonyl-CoA hydrolyase; mesaconyl-coenzyme A hydratase (ambiguous); mesaconyl-C1-CoA hydratase

Systematic name: (2R,3S)-2-methylmalyl-CoA hydro-lyase (2-methylfumaryl-CoA-forming)

Comments: The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.

References:

1. Zarzycki, J., Schlichting, A., Strychalsky, N., Muller, M., Alber, B.E. and Fuchs, G. Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. J. Bacteriol. 190 (2008) 1366-1374. [PMID: 18065535]

[EC 4.2.1.148 created 2014]

EC 4.2.1.149

Accepted name: crotonobetainyl-CoA hydratase

Reaction: L-carnitinyl-CoA = (E)-4-(trimethylammonio)but-2-enoyl-CoA + H2O

Glossary: L-carnitinyl-CoA = (3R)-3-hydroxy-4-(trimethylammonio)butanoyl-CoA
(E)-4-(trimethylammonio)but-2-enoyl-CoA = crotonobetainyl-CoA

Other name(s): CaiD; L-carnityl-CoA dehydratase

Systematic name: L-carnitinyl-CoA hydro-lyase [(E)-4-(trimethylammonio)but-2-enoyl-CoA-forming]

Comments: The enzyme is also able to use crotonyl-CoA as substrate, with low efficiency [2].

References:

1. Engemann, C., Elssner, T. and Kleber, H.P. Biotransformation of crotonobetaine to L-(-)-carnitine in Proteus sp. Arch. Microbiol. 175 (2001) 353-359. [PMID: 11409545]

2. Elssner, T., Engemann, C., Baumgart, K. and Kleber, H.P. Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli. Biochemistry 40 (2001) 11140-11148. [PMID: 11551212]

3. Engemann, C., Elssner, T., Pfeifer, S., Krumbholz, C., Maier, T. and Kleber, H.P. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch. Microbiol. 183 (2005) 176-189. [PMID: 15731894]

[EC 4.2.1.149 created 2014]

EC 4.2.1.150

Accepted name: short-chain-enoyl-CoA hydratase

Reaction: a short-chain (3S)-3-hydroxyacyl-CoA = a short-chain trans-2-enoyl-CoA + H2O

Other name(s): 3-hydroxybutyryl-CoA dehydratase; crotonase; crt (gene name)

Systematic name: short-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase

Comments: The enzyme from the bacterium Clostridium acetobutylicum is part of the central fermentation pathway and plays a key role in the production of both acids and solvents. It is specific for short, C4-C6, chain length substrates and exhibits an extremely high turnover number for crotonyl-CoA. cf. EC 4.2.1.17, enoyl-CoA hydratase and EC 4.2.1.74, long-chain-enoyl-CoA hydratase.

References:

1. Waterson, R.M., Castellino, F.J., Hass, G.M. and Hill, R.L. Purification and characterization of crotonase from Clostridium acetobutylicum. J. Biol. Chem. 247 (1972) 5266-5271. [PMID: 5057466]

2. Waterson, R.M. and Conway, R.S. Enoyl-CoA hydratases from Clostridium acetobutylicum and Escherichia coli. Methods Enzymol. 71 Pt C (1981) 421-430. [PMID: 7024731]

3. Boynton, Z.L., Bennet, G.N. and Rudolph, F.B. Cloning, sequencing, and expression of clustered genes encoding β-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 178 (1996) 3015-3024. [PMID: 8655474]

[EC 4.2.1.150 created 2014]

EC 4.2.1.151

Accepted name: chorismate dehydratase

Reaction: chorismate = 3-[(1-carboxyvinyl)oxy]benzoate + H2O

For diagram of reaction click here.

Other name(s): MqnA

Systematic name: chorismate hydro-lyase (3-[(1-carboxyvinyl)oxy]benzoate-forming)

Comments: The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

References:

1. Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318-15321. [PMID: 24083939]

[EC 4.2.1.151 created 2014]

*EC 4.3.1.17

Accepted name: L-serine ammonia-lyase

Reaction: L-serine = pyruvate + ammonia (overall reaction)
(1a) L-serine = 2-aminoprop-2-enoate + H2O
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + ammonia (spontaneous)

Other name(s): serine deaminase; L-hydroxyaminoacid dehydratase; L-serine deaminase; L-serine dehydratase; L-serine hydro-lyase (deaminating)

Systematic name: L-serine ammonia-lyase (pyruvate-forming)

Comments: Most enzymes that catalyse this reaction are pyridoxal-phosphate-dependent, although some enzymes contain an iron-sulfur cluster instead [6]. The reaction catalysed by both types of enzymes involves the initial elimination of water to form an enamine intermediate (hence the enzyme’s original classification as EC 4.2.1.13, L-serine dehydratase), followed by tautomerization to an imine form and hydrolysis of the C-N bond. The latter reaction, which can occur spontaneously, is also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. This reaction is also carried out by EC 4.3.1.19, threonine ammonia-lyase, from a number of sources.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9014-27-1

References:

1. Ramos, F. and Wiame, J.-M. Occurrence of a catabolic L-serine (L-threonine) deaminase in Saccharomyces cerevisiae. Eur. J. Biochem. 123 (1982) 571-576. [PMID: 7042346]

2. Simon, D., Hoshino, J. and Kröger, H. L-Serine dehydratase from rat liver. Purification and some properties. Biochim. Biophys. Acta 321 (1973) 361-368. [PMID: 4750769]

3. Suda, M. and Nakagawa, H. L-Serine dehydratase (rat liver). Methods Enzymol. 17B (1971) 346-351.

4. Sagers, R.D. and Carter, J. E. L-Serine dehydratase (Clostridium acidiurica). Methods Enzymol. 17B (1971) 351-356.

5. Robinson, W.G. and Labow, R. L-Serine dehydratase (Escherichia coli). Methods Enzymol. 17B (1971) 356-360.

6. Grabowski, R., Hofmeister, A.E. and Buckel, W. Bacterial L-serine dehydratases: a new family of enzymes containing iron-sulfur clusters. Trends Biochem. Sci. 18 (1993) 297-300. [PMID: 8236444]

7. Yamada, T., Komoto, J., Takata, Y., Ogawa, H., Pitot, H.C. and Takusagawa, F. Crystal structure of serine dehydratase from rat liver. Biochemistry 42 (2003) 12854-12865. [PMID: 14596599]

[EC 4.3.1.17 created 1961 as EC 4.2.1.13, transferred 2001 to EC 4.3.1.17, modified 2014]

*EC 4.3.1.19

Accepted name: threonine ammonia-lyase

Reaction: L-threonine = 2-oxobutanoate + ammonia (overall reaction)
(1a) L-threonine = 2-aminobut-2-enoate + H2O
(1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous)
(1c) 2-iminobutanoate + H2O = 2-oxobutanoate + ammonia (spontaneous)

For diagram of reaction click here.

Other name(s): threonine deaminase; L-serine dehydratase; serine deaminase; L-threonine dehydratase; threonine dehydrase; L-threonine deaminase; threonine dehydratase; L-threonine hydro-lyase (deaminating); L-threonine ammonia-lyase

Systematic name: L-threonine ammonia-lyase (2-oxobutanoate-forming)

Comments: Most enzymes that catalyse this reaction are pyridoxal-phosphate-dependent, although some enzymes contain an iron-sulfur cluster instead. The reaction catalysed by both types of enzymes involves the initial elimination of water to form an enamine intermediate (hence the enzyme’s original classification as EC 4.2.1.16, threonine dehydratase), followed by tautomerization to an imine form and hydrolysis of the C-N bond [3,5]. The latter reaction, which can occur spontaneously, is also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase [5]. The enzymes from a number of sources also act on L-serine, cf. EC 4.3.1.17, L-serine ammonia-lyase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 774231-81-1

References:

1. Cohn, M.S. and Phillips, A.T. Purification and characterization of a B6-independent threonine dehydratase from Pseudomonas putida. Biochemistry 13 (1974) 1208-1214. [PMID: 4814721]

2. Nishimura, J.S. and Greenberg, D.M. Purification and properties of L-threonine dehydrase of sheep liver. J. Biol. Chem. 236 (1961) 2684-2691. [PMID: 14479973]

3. Phillips, A.T. and Wood, W.A. The mechanism of action of 5'-adenylic acid-activated threonine dehydrase. J. Biol. Chem. 240 (1965) 4703-4709. [PMID: 5321308]

4. Shizuta, Y., Nakazawa, A., Tokushige, M. and Hayaishi, O. Studies on the interaction between regulatory enzymes and effectors. 3. Crystallization and characterization of adenosine 5'-monophosphate-dependent threonine deaminase from Escherichia coli. J. Biol. Chem. 244 (1969) 1883-1889. [PMID: 4889010]

5. Lambrecht, J.A., Flynn, J.M. and Downs, D.M. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. J. Biol. Chem. 287 (2012) 3454-3461. [PMID: 22094463]

[EC 4.3.1.19 created 1961 as EC 4.2.1.16, transferred 2001 to EC 4.3.1.19, modified 2014]

EC 4.3.1.30

Accepted name: dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase

Reaction: dTDP-4-amino-4,6-dideoxy-α-D-glucopyranose + S-adenosyl-L-methionine + reduced acceptor = dTDP-3-dehydro-4,6-dideoxy-α-D-glucopyranose + NH3 + L-methionine + 5'-deoxyadenosine + acceptor

For diagram of reaction click here.

Other name(s): desII (gene name); eryCV (gene name); MegCV

Systematic name: dTDP-4-amino-4,6-dideoxy-α-D-glucopyranose ammonia lyase (dTDP-3-dehydro-4,6-dideoxy-α-D-glucopyranose-forming)

Comments: The enzyme, which is a member of the ’AdoMet radical’ (radical SAM) family, is involved in biosynthesis of TDP-α-D-desosamine. The reaction starts by the transfer of an electron from the reduced form of the enzyme’s [4Fe-4S] cluster to S-adenosyl-L-methionine, spliting it into methionine and the radical 5-deoxyadenosin-5'-yl, which attacks the sugar substrate.

References:

1. Szu, P.H., Ruszczycky, M.W., Choi, S.H., Yan, F. and Liu, H.W. Characterization and mechanistic studies of DesII: a radical S-adenosyl-L-methionine enzyme involved in the biosynthesis of TDP-D-desosamine. J. Am. Chem. Soc. 131 (2009) 14030-14042. [PMID: 19746907]

2. Ruszczycky, M.W., Choi, S.H. and Liu, H.W. Stoichiometry of the redox neutral deamination and oxidative dehydrogenation reactions catalyzed by the radical SAM enzyme DesII. J. Am. Chem. Soc. 132 (2010) 2359-2369. [PMID: 20121093]

3. Ruszczycky, M.W., Choi, S.H., Mansoorabadi, S.O. and Liu, H.W. Mechanistic studies of the radical S-adenosyl-L-methionine enzyme DesII: EPR characterization of a radical intermediate generated during its catalyzed dehydrogenation of TDP-D-quinovose. J. Am. Chem. Soc. 133 (2011) 7292-7295. [PMID: 21513273]

[EC 4.3.1.30 created 2011]

*EC 4.3.2.3

Accepted name: ureidoglycolate lyase

Reaction: (S)-ureidoglycolate = glyoxylate + urea

For diagram of reaction click here.

Other name(s): ureidoglycolatase (ambiguous); ureidoglycolase (ambiguous); ureidoglycolate hydrolase (misleading); (S)-ureidoglycolate urea-lyase

Systematic name: (S)-ureidoglycolate urea-lyase (glyoxylate-forming)

Comments: This microbial enzyme is involved in the degradation of ureidoglycolate, an intermediate of purine degradation. Not to be confused with EC 3.5.1.116, ureidoglycolate amidohydrolase, which releases ammonia rather than urea.

Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9014-57-7

References:

1. Trijbels, F. and Vogels, G.D. Allantoate and ureidoglycolate degradation by Pseudomonas aeruginosa. Biochim. Biophys. Acta 132 (1967) 115-126. [PMID: 6030341]

2. Werner, A.K., Romeis, T. and Witte, C.P. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat. Chem. Biol. 6 (2010) 19-21. [PMID: 19935661]

[EC 4.3.2.3 created 1972, modified 2014]

EC 4.6.1.16

Accepted name: tRNA-intron lyase

Reaction: pretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus

Other name(s): transfer ribonucleate intron endoribonuclease; tRNA splicing endonuclease; splicing endonuclease; tRNATRPintron endonuclease; transfer splicing endonuclease

Systematic name: pretRNA lyase (intron-removing; 2',3'-cyclic-phosphate-forming)

Comments: The enzyme catalyses the final stage in the maturation of tRNA molecules.

References:

1. Attardi, D.G., Margarit, I. and Tocchini-Valentini, G.P. Structural alterations in mutant precursors of the yeast tRNALeu3 gene which behave as defective substrates for a highly purified splicing endoribonuclease. EMBO J. 4 (1985) 3289-3297. [PMID: 3937725]

2. Peebles, C.L., Gegenheimer, P. and Abelson, J. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell 32 (1983) 525-536. [PMID: 6186398]

3. Thompson, L.D., Brandon, L.D., Nieuwlandt, D.T. and Daniels, C.J. Transfer RNA intron processing in the halophilic archaebacteria. Can. J. Microbiol. 35 (1989) 36-42. [PMID: 2470486]

4. Thompson, L.D. and Daniels, C.J. A tRNA(Trp) intron endonuclease from Halobacterium volcanii. Unique substrate recognition properties. J. Biol. Chem. 263 (1988) 17951-17959. [PMID: 3192521]

[EC 4.6.1.16 created 1992 as EC 3.1.27.9, transferred 2014 to EC 4.6.1.16]

EC 5.1.3.28

Accepted name: UDP-N-acetyl-L-fucosamine synthase

Reaction: UDP-2-acetamido-2,6-dideoxy-β-L-talose = UDP-N-acetyl-β-L-fucosamine

For diagram of reaction click here.

Glossary: UDP-2-acetamido-2,6-dideoxy-β-L-talose = UDP-N-acetyl-β-L-pneumosamine

Other name(s): WbjD; Cap5G

Systematic name: UDP-2-acetamido-2,6-dideoxy-L-talose 2-epimerase

Comments: Isolated from the bacteria Pseudomonas aeruginosa and Staphylococcus aureus. Involved in bacterial polysaccharide biosynthesis.

References:

1. Kneidinger, B., O'Riordan, K., Li, J., Brisson, J.R., Lee, J.C. and Lam, J.S. Three highly conserved proteins catalyze the conversion of UDP-N-acetyl-D-glucosamine to precursors for the biosynthesis of O antigen in Pseudomonas aeruginosa O11 and capsule in Staphylococcus aureus type 5. Implications for the UDP-N-acetyl-L-fucosamine biosynthetic pathway. J. Biol. Chem. 278 (2003) 3615-3627. [PMID: 12464616]

2. Mulrooney, E.F., Poon, K.K., McNally, D.J., Brisson, J.R. and Lam, J.S. Biosynthesis of UDP-N-acetyl-L-fucosamine, a precursor to the biosynthesis of lipopolysaccharide in Pseudomonas aeruginosa serotype O11. J. Biol. Chem. 280 (2005) 19535-19542. [PMID: 15778500]

[EC 5.1.3.28 created 2014]

EC 5.3.1.30

Accepted name: 5-deoxy-glucuronate isomerase

Reaction: 5-deoxy-D-glucuronate = 5-dehydro-2-deoxy-D-gluconate

For diagram of reaction click here.

Glossary: 5-dehydro-2-deoxy-D-gluconate = 2-deoxy-D-threo-hex-5-ulosonic acid
5-deoxy-D-glucuronate = 5-deoxy-D-xylo-hexuronic acid

Other name(s): 5DG isomerase; IolB

Systematic name: 5-deoxy-D-glucuronate aldose-ketose-isomerase

Comments: The enzyme, found in the bacterium Bacillus subtilis, is part of a myo-inositol degradation pathway leading to acetyl-CoA.

References:

1. Yoshida, K., Yamaguchi, M., Morinaga, T., Kinehara, M., Ikeuchi, M., Ashida, H. and Fujita, Y. myo-Inositol catabolism in Bacillus subtilis. J. Biol. Chem. 283 (2008) 10415-10424. [PMID: 18310071]

[EC 5.3.1.30 created 2014]

EC 5.3.99.11

Accepted name: 2-keto-myo-inositol isomerase

Reaction: 2,4,6/3,5-pentahydroxycyclohexanone = 2D-2,3,5/4,6-pentahydroxycyclohexanone

For diagram of reaction click here.

Glossary: 2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose

Other name(s): IolI; inosose isomerase; 2KMI isomerase.

Systematic name: 2,4,6/3,5-pentahydroxycyclohexanone 2-isomerase

Comments: Requires a divalent metal ion for activity. Mn2+, Fe2+ and Co2+ can be used. The enzyme, found in the bacterium Bacillus subtilis, is part of the myo-inositol/D-chiro-inositol degradation pathway leading to acetyl-CoA.

References:

1. Zhang, R.G., Dementieva, I., Duke, N., Collart, F., Quaite-Randall, E., Alkire, R., Dieckman, L., Maltsev, N., Korolev, O. and Joachimiak, A. Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding. Proteins 48 (2002) 423-426. [PMID: 12112707]

2. Yoshida, K., Yamaguchi, M., Morinaga, T., Ikeuchi, M., Kinehara, M. and Ashida, H. Genetic modification of Bacillus subtilis for production of D-chiro-inositol, an investigational drug candidate for treatment of type 2 diabetes and polycystic ovary syndrome. Appl. Environ. Microbiol. 72 (2006) 1310-1315. [PMID: 16461681]

[EC 5.3.99.11 created 2014]

[EC 5.4.1.2 Transferred entry: precorrin-8X methylmutase. Now classified as EC 5.4.99.61, precorrin-8X methylmutase. (EC 5.4.1.2 created 1999, deleted 2014)]

EC 5.4.1.3

Accepted name: 2-methylfumaryl-CoA isomerase

Reaction: 2-methylfumaryl-CoA = 3-methylfumaryl-CoA

For diagram of reaction click here.

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

Other name(s): mesaconyl-CoA C1-C4 CoA transferase; Mct

Systematic name: 2-methylfumaryl-CoA 1,4-CoA-mutase

Comments: The enzyme, purified from the bacterium Chloroflexus aurantiacus, acts as an intramolecular CoA transferase and does not transfer CoA to free mesaconate. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.

References:

1. Zarzycki, J., Brecht, V., Muller, M. and Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. USA 106 (2009) 21317-21322. [PMID: 19955419]

[EC 5.4.1.3 created 2014]

EC 5.4.99.60

Accepted name: cobalt-precorrin-8 methylmutase

Reaction: cobalt-precorrin-8 = cobyrinate

For diagram of reaction click here.

Other name(s): cbiC (gene name)

Systematic name: precorrin-8 11,12-methylmutase

Comments: The enzyme catalyses the the conversion of cobalt-precorrin-8 to cobyrinate by methyl rearrangement, a step in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis. The equivalent enzyme in the aerobic pathway is EC 5.4.99.61, precorrin-8X methylmutase.

References:

1. Xue, Y., Wei, Z., Li, X. and Gong, W. The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis. J. Struct. Biol. 153 (2006) 307-311. [PMID: 16427313]

2. Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Proc. Natl. Acad. Sci. USA 110 (2013) 14906-14911. [PMID: 23922391]

[EC 5.4.99.60 created 2014]

EC 5.4.99.61

Accepted name: precorrin-8X methylmutase

Reaction: precorrin-8X = hydrogenobyrinate

For diagram of reaction click here.

Other name(s): precorrin isomerase; hydrogenobyrinic acid-binding protein; cobH (gene name)

Systematic name: precorrin-8X 11,12-methylmutase

Comments: The enzyme catalyses the the conversion of precorrin-8X to hydrogenobyrinate by methyl rearrangement, a step in the aerobic (late cobalt insertion) pathway of adenosylcobalamin biosynthesis. The equivalent enzyme in the anaerobic pathway is EC 5.4.99.60, precorrin-8X methylmutase.

References:

1. Thibaut, D., Couder, M., Famechon, A., Debussche, L., Cameron, B., Crouzet, J., Blanche, F. The final step in the biosynthesis of hydrogenobyrinic acid is catalyzed by the cobH gene product with precorrin-8X as the substrate. J. Bacteriol. 174 (1992) 1043-1049. [PMID: 1732194]

2. Roth, J.R., Lawrence, J.G., Rubenfield, M., Kieffer-Higgins, S., Church, G.M. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J. Bacteriol. 175 (1993) 3303-3316. [PMID: 8501034]

3. Roessner, C.A., Warren, M.J., Santander, P.J., Atshaves, B.P., Ozaki, S., Stolowich, N.J., Iida, K., Scott, A.I. Expression of Salmonella typhimurium enzymes for cobinamide synthesis. Identification of the 11-methyl and 20-methyl transferases of corrin biosynthesis. FEBS Lett. 301 (1992) 73-78. [PMID: 1451790]

4. Crouzet, J., Cameron, B., Cauchois, L., Rigault, S., Rouyez, M.C., Blanche, F. , Thibaut D., Debussche, L. Genetic and sequence analysis of an 8.7-kilobase Pseudomonas denitrificans fragment carrying eight genes involved in transformation of precorrin-2 to cobyrinic acid. J. Bacteriol. 172 (1990) 5980-5990. [PMID: 2211521]

5. Shipman, L.W., Li, D., Roessner, C.A., Scott, A.I. and Sacchettini, J.C. Crystal structure of precorrin-8x methyl mutase. Structure 9 (2001) 587-596. [PMID: 11470433]

[EC 5.4.99.61 created 1999 as EC 5.4.1.2, transferred 2014 to EC 5.4.99.61]

EC 6.2.1.40

Accepted name: 4-hydroxybutyrate—CoA ligase

Reaction: ATP + 4-hydroxybutanoate + CoA = AMP + diphosphate + 4-hydroxybutanoyl-CoA

Other name(s): 4-hydroxybutyrate-CoA synthetase

Systematic name: 4-hydroxybutyrate:CoA ligase (AMP formimg)

Comments: Isolated from the archaeon Metallosphaera sedula. Involved in the 3-hydroxypropionate/4-hydroxybutyrate cycle.

References:

1. Ramos-Vera, W.H., Weiss, M., Strittmatter, E., Kockelkorn, D. and Fuchs, G. Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota. J. Bacteriol. 193 (2011) 1201-1211. [PMID: 21169482]

2. Hawkins, A.S., Han, Y., Bennett, R.K., Adams, M.W. and Kelly, R.M. Role of 4-hydroxybutyrate-CoA synthetase in the CO2 fixation cycle in thermoacidophilic archaea. J. Biol. Chem. 288 (2013) 4012-4022. [PMID: 23258541]

[EC 6.2.1.40 created 2014]

EC 6.3.1.17

Accepted name: β-citrylglutamate synthase

Reaction: ATP + citrate + L-glutamate = ADP + phosphate + β-citryl-L-glutamate

Other name(s): NAAG synthetase I; NAAGS-I; RIMKLB (gene name) (ambiguous)

Systematic name: citrate:L-glutamate ligase (ADP-forming)

Comments: The enzyme, found in animals, also has the activity of EC 6.3.2.41, N-acetylaspartylglutamate synthase.

References:

1. Collard, F., Stroobant, V., Lamosa, P., Kapanda, C.N., Lambert, D.M., Muccioli, G.G., Poupaert, J.H., Opperdoes, F. and Van Schaftingen, E. Molecular identification of N-acetylaspartylglutamate synthase and β-citrylglutamate synthase. J. Biol. Chem. 285 (2010) 29826-29833. [PMID: 20657015]

[EC 6.3.1.17 created 2014]

EC 6.3.2.41

Accepted name: N-acetylaspartylglutamate synthase

Reaction: ATP + N-acetyl-L-aspartate + L-glutamate = ADP + phosphate + N-acetyl-L-aspartyl-L-glutamate

Other name(s): N-acetylaspartylglutamate synthetase; NAAG synthetase; NAAGS; RIMKLA (gene name) (ambiguous); RIMKLB (gene name) (ambiguous)

Systematic name: N-acetyl-L-aspartate:L-glutamate ligase (ADP, N-acetyl-L-aspartyl-L-glutamate-forming)

Comments: The enzyme, found in animals, produces the neurotransmitter N-acetyl-L-aspartyl-L-glutamate. One isoform also has the activity of EC 6.3.1.17, β-citrylglutamate synthase [2], while another isoform has the activity of EC 6.3.2.42, N-acetylaspartylglutamylglutamate synthase [3].

References:

1. Becker, I., Lodder, J., Gieselmann, V. and Eckhardt, M. Molecular characterization of N-acetylaspartylglutamate synthetase. J. Biol. Chem. 285 (2010) 29156-29164. [PMID: 20643647]

2. Collard, F., Stroobant, V., Lamosa, P., Kapanda, C.N., Lambert, D.M., Muccioli, G.G., Poupaert, J.H., Opperdoes, F. and Van Schaftingen, E. Molecular identification of N-acetylaspartylglutamate synthase and β-citrylglutamate synthase. J. Biol. Chem. 285 (2010) 29826-29833. [PMID: 20657015]

3. Lodder-Gadaczek, J., Becker, I., Gieselmann, V., Wang-Eckhardt, L. and Eckhardt, M. N-acetylaspartylglutamate synthetase II synthesizes N-acetylaspartylglutamylglutamate. J. Biol. Chem. 286 (2011) 16693-16706. [PMID: 21454531]

[EC 6.3.2.41 created 2014]

EC 6.3.2.42

Accepted name: N-acetylaspartylglutamylglutamate synthase

Reaction: 2 ATP + N-acetyl-L-aspartate + 2 L-glutamate = 2 ADP + 2 phosphate + N-acetyl-L-aspartyl-L-glutamyl-L-glutamate

Other name(s): N-acetylaspartylglutamylglutamate synthetase; NAAG(2) synthase; NAAG synthetase II; NAAGS-II; RIMKLA (gene name) (ambiguous)

Systematic name: N-acetyl-L-aspartate:L-glutamate ligase (ADP, N-acetyl-L-aspartyl-L-glutamyl-L-glutamate-forming)

Comments: The enzyme, found in mammals, also has the activity of EC 6.3.2.41, N-acetylaspartylglutamate synthase.

References:

1. Lodder-Gadaczek, J., Becker, I., Gieselmann, V., Wang-Eckhardt, L. and Eckhardt, M. N-acetylaspartylglutamate synthetase II synthesizes N-acetylaspartylglutamylglutamate. J. Biol. Chem. 286 (2011) 16693-16706. [PMID: 21454531]

[EC 6.3.2.42 created 2014]


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