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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.374 UDP-N-acetylglucosamine 3-dehydrogenase (10 November 2014)
EC 1.1.1.375 L-2-hydroxycarboxylate dehydrogenase [NAD(P)+] (10 November 2014)
EC 1.1.1.376 L-arabinose 1-dehydrogenase [NAD(P)+] (10 November 2014)
EC 1.1.1.377 L-rhamnose 1-dehydrogenase (NADP+) (10 November 2014)
EC 1.1.1.378 L-rhamnose 1-dehydrogenase [NAD(P)+] (10 November 2014)
*EC 1.1.98.3 decaprenylphospho-β-D-ribofuranose 2-dehydrogenase (10 November 2014)
EC 1.2.99.9 formate dehydrogenase (coenzyme F420) (10 November 2014)
*EC 1.3.1.48 13,14-dehydro-15-oxoprostaglandin 13-reductase (10 November 2014)
EC 1.3.1.107 sanguinarine reductase (10 November 2014)
EC 1.3.4 With a disulfide as acceptor (10 November 2014)
EC 1.3.4.1 fumarate reductase (CoM/CoB) (10 November 2014)
*EC 1.3.7.5 phycocyanobilin:ferredoxin oxidoreductase (10 November 2014)
EC 1.3.98.2 transferred (10 November 2014)
*EC 1.5.1.47 dihydromethanopterin reductase [NAD(P)+] (10 November 2014)
EC 1.5.99.15 dihydromethanopterin reductase (acceptor) (10 November 2014)
EC 1.8.98.3 sulfite reductase (coenzyme F420) (10 November 2014)
EC 1.14.11.47 50S ribosomal protein L16 3-hydroxylase (10 November 2014)
EC 1.14.13.195 L-ornithine N5-monooxygenase (NADPH) (10 November 2014)
EC 1.14.13.196 L-ornithine N5-monooxygenase [NAD(P)H] (10 November 2014)
EC 1.14.13.197 dihydromonacolin L hydroxylase (10 November 2014)
EC 1.14.13.198 monacolin L hydroxylase (10 November 2014)
EC 1.14.13.199 docosahexaenoic acid ω-hydroxylase (10 November 2014)
EC 1.14.13.200 tetracenomycin A2 monooxygenase-dioxygenase (10 November 2014)
EC 1.14.14.7 transferred (10 November 2014)
*EC 1.14.15.4 steroid 11β-monooxygenase (10 November 2014)
*EC 1.14.15.6 cholesterol monooxygenase (side-chain-cleaving) (10 November 2014)
EC 1.14.19.9 tryptophan 7-halogenase (10 November 2014)
EC 1.14.99.49 2-hydroxy-5-methyl-1-naphthoate 7-hydroxylase (10 November 2014)
*EC 2.4.1.109 dolichyl-phosphate-mannose—protein mannosyltransferase (10 November 2014)
EC 2.4.1.329 sucrose 6F-phosphate phosphorylase (10 November 2014)
EC 2.4.1.330 β-D-glucosyl crocetin β-1,6-glucosyltransferase (10 November 2014)
EC 2.4.1.331 8-demethyltetracenomycin C L-rhamnosyltransferase (10 November 2014)
EC 2.5.1.124 6-linalyl-2-O,3-dimethylflaviolin synthase (10 November 2014)
EC 2.5.1.125 7-geranyloxy-5-hydroxy-2-methoxy-3-methylnaphthalene-1,4-dione synthase (10 November 2014)
EC 2.5.1.126 norspermine synthase (10 November 2014)
EC 2.5.1.127 caldopentamine synthase (10 November 2014)
*EC 2.7.1.8 glucosamine kinase (10 November 2014)
EC 2.7.1.185 mevalonate 3-kinase (10 November 2014)
EC 2.7.1.186 mevalonate-3-phosphate 5-kinase (10 November 2014)
EC 2.7.14 Protein-arginine kinases (10 November 2014)
EC 2.7.14.1 protein arginine kinase (10 November 2014)
*EC 2.8.4.4 [ribosomal protein S12] (aspartate89-C3)-methylthiotransferase (10 November 2014)
*EC 2.9.1.2 O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase (10 November 2014)
EC 3.1.2.15 deleted (10 November 2014)
EC 3.5.4.41 5'-deoxyadenosine deaminase (10 November 2014)
EC 3.9.1.2 protein arginine phosphatase (10 November 2014)
EC 4.1.1.99 phosphomevalonate decarboxylase (10 November 2014)
*EC 4.2.1.121 colneleate synthase (10 November 2014)
EC 4.2.3.147 pimaradiene synthase (10 November 2014)
EC 5.1.3.30 D-psicose 3-epimerase (10 November 2014)
EC 5.1.3.31 D-tagatose 3-epimerase (10 November 2014)
EC 5.1.3.32 L-rhamnose mutarotase (10 November 2014)
EC 5.4.99.62 D-ribose pyranase (10 November 2014)
EC 6.1.1.28 deleted
EC 6.2.1.44 3-(methylthio)propionyl—CoA ligase (10 November 2014)
*EC 6.3.2.1 pantoate—β-alanine ligase (AMP-forming) (10 November 2014)
EC 6.3.2.43 [lysine-biosynthesis-protein LysW]—L-2-aminoadipate ligase (10 November 2014)
EC 6.3.2.44 pantoate—β-alanine ligase (ADP-forming) (10 November 2014)
EC 6.5.1.6 DNA ligase (ATP or NAD+) (10 November 2014)
EC 6.5.1.7 DNA ligase (ATP, ADP or GTP) (10 November 2014)

EC 1.1.1.374

Reaction: UDP-N-acetyl-α-D-glucosamine + NAD+ = UDP-2-acetamido-3-dehydro-2-deoxy-α-D-glucopyranose + NADH + H+

Systematic name: UDP-N-acetyl-α-D-glucosamine:NAD+ 3-oxidoreductase

Comments: The enzyme from the archaeon Methanococcus maripaludis is is activated by KCl (200 mM).

References:

1. Namboori, S.C. and Graham, D.E. Enzymatic analysis of uridine diphosphate N-acetyl-D-glucosamine. Anal. Biochem. 381 (2008) 94-100. [PMID: 18634748]

[EC 1.1.1.374 created 2014]

EC 1.1.1.375

Accepted name: L-2-hydroxycarboxylate dehydrogenase [NAD(P)+]

Reaction: a (2S)-2-hydroxycarboxylate + NAD(P)+ = a 2-oxocarboxylate + NAD(P)H + H+

Other name(s): MdhII; lactate/malate dehydrogenase

Systematic name: (2S)-2-hydroxycarboxylate:NAD(P)+ oxidoreductase

Comments: The enzyme from the archaeon Methanocaldococcus jannaschii catalyses the reversible oxidation of (2R)-3-sulfolactate and (S)-malate to 3-sulfopyruvate and oxaloacetate, respectively (note that (2R)-3-sulfolactate has the same stereochemical configuration as (2S)-2-hydroxycarboxylates) [1]. The enzyme can use both NADH and NADPH, although activity is higher with NADPH [1-3]. The oxidation of (2R)-3-sulfolactate was observed only in the presence of NADP+ [1]. The same organism also possesses an NAD+-specific enzyme with similar activity, cf. EC 1.1.1.337, L-2-hydroxycarboxylate dehydrogenase (NAD+).

References:

1. Graupner, M., Xu, H. and White, R.H. Identification of an archaeal 2-hydroxy acid dehydrogenase catalyzing reactions involved in coenzyme biosynthesis in methanoarchaea. J. Bacteriol. 182 (2000) 3688-3692. [PMID: 10850983]

2. Lee, B.I., Chang, C., Cho, S.J., Eom, S.H., Kim, K.K., Yu, Y.G. and Suh, S.W. Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases. J. Mol. Biol. 307 (2001) 1351-1362. [PMID: 11292347]

3. Madern, D. The putative L-lactate dehydrogenase from Methanococcus jannaschii is an NADPH-dependent L-malate dehydrogenase. Mol. Microbiol. 37 (2000) 1515-1520. [PMID: 10998181]

[EC 1.1.1.375 created 2014]

EC 1.1.1.376

Accepted name: L-arabinose 1-dehydrogenase [NAD(P)+]

Reaction: L-arabinose + NAD(P)+ = L-arabinono-1,4-lactone + NAD(P)H + H+

Other name(s): L-arabino-aldose dehydrogenase

Systematic name: L-arabinose:NAD+ 1-oxidoreductase

Comments: The enzymes from the bacterium Azospirillum brasilense and the archaeon Haloferax volcanii are part of the L-arabinose degradation pathway and prefer NADP+ over NAD+. In vitro the enzyme from Azospirillum brasilense shows also high catalytic efficiency with D-galactose.

References:

1. Novick, N.J. and Tyler, M.E. Partial purification and properties of an L-arabinose dehydrogenase from Azospirillum brasilense. Can. J. Microbiol. 29 (1983) 242-246.

2. Watanabe, S., Kodaki, T. and Makino, K. Cloning, expression, and characterization of bacterial L-arabinose 1-dehydrogenase involved in an alternative pathway of L-arabinose metabolism. J. Biol. Chem. 281 (2006) 2612-2623. [PMID: 16326697]

3. Johnsen, U., Sutter, J.M., Zaiss, H. and Schonheit, P. L-Arabinose degradation pathway in the haloarchaeon Haloferax volcanii involves a novel type of L-arabinose dehydrogenase. Extremophiles 17 (2013) 897-909. [PMID: 23949136]

[EC 1.1.1.376 created 2014]

EC 1.1.1.377

Accepted name: L-rhamnose 1-dehydrogenase (NADP+)

Reaction: L-rhamnose + NADP+ = L-rhamnono-1,4-lactone + NADPH + H+

Systematic name: L-rhamnose:NADP+ 1-oxidoreductase

Comments: The enzyme from the archaeon Thermoplasma acidophilum is part of the non-phosphorylative degradation pathway for L-rhamnose. The enzyme differs in cofactor specificity from EC 1.1.1.173, L-rhamnose 1-dehydrogenase, which is specific for NAD+.

References:

1. Kim, S.M., Paek, K.H. and Lee, S.B. Characterization of NADP+-specific L-rhamnose dehydrogenase from the thermoacidophilic Archaeon Thermoplasma acidophilum. Extremophiles 16 (2012) 447-454. [PMID: 22481639]

[EC 1.1.1.377 created 2014]

EC 1.1.1.378

Accepted name: L-rhamnose 1-dehydrogenase [NAD(P)+]

Reaction: L-rhamnose + NAD(P)+ = L-rhamnono-1,4-lactone + NAD(P)H + H+

Systematic name: L-rhamnose:NAD(P)+ 1-oxidoreductase

Comments: The enzyme, which occurs in the bacteria Azotobacter vinelandii and Sphingomonas sp. SKA58, is part of the non-phosphorylative degradation pathway for L-rhamnose. The enzyme differs in cofactor specificity from EC 1.1.1.173, L-rhamnose 1-dehydrogenase, which is specific for NAD+ and EC 1.1.1.377, L-rhamnose 1-dehydrogenase (NADP+).

References:

1. Watanabe, S., Saimura, M. and Makino, K. Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism. J. Biol. Chem. 283 (2008) 20372-20382. [PMID: 18505728]

2. Watanabe, S. and Makino, K. Novel modified version of nonphosphorylated sugar metabolism - an alternative L-rhamnose pathway of Sphingomonas sp. FEBS J. 276 (2009) 1554-1567. [PMID: 19187228]

[EC 1.1.1.378 created 2014]

*EC 1.1.98.3

Accepted name: decaprenylphospho-β-D-ribofuranose 2-dehydrogenase

Reaction: trans,octacis-decaprenylphospho-β-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-β-D-erythro-pentofuranosid-2-ulose + FADH2

For diagram of reaction click here.

Other name(s): decaprenylphosphoryl-β-D-ribofuranose 2'-epimerase; Rv3790; DprE1; decaprenylphospho-β-D-ribofuranose 2-oxidase

Systematic name: trans,octacis-decaprenylphospho-β-D-ribofuranose:FAD 2-oxidoreductase

Comments: The enzyme, isolated from the bacterium Mycobacterium smegmatis, is involved, along with EC 1.1.1.333, decaprenylphospho-D-erythro-pentofuranosid-2-ulose 2-reductase, in the epimerization of trans,octacis-decaprenylphospho-β-D-ribofuranose to trans,octacis-decaprenylphospho-β-D-arabinofuranose, the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers.

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

References:

1. Ribeiro, A.L., Degiacomi, G., Ewann, F., Buroni, S., Incandela, M.L., Chiarelli, L.R., Mori, G., Kim, J., Contreras-Dominguez, M., Park, Y.S., Han, S.J., Brodin, P., Valentini, G., Rizzi, M., Riccardi, G. and Pasca, M.R. Analogous mechanisms of resistance to benzothiazinones and dinitrobenzamides in Mycobacterium smegmatis. PLoS One 6 (2011) e26675. [PMID: 22069462]

2. Trefzer, C., Škovierová, H., Buroni, S., Bobovská, A., Nenci, S., Molteni, E., Pojer, F., Pasca, M.R., Makarov, V., Cole, S.T., Riccardi, G., Mikušová, K. and Johnsson, K. Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-β-D-ribofuranose 2'-oxidase DprE1. J. Am. Chem. Soc. 134 (2012) 912-915. [PMID: 22188377]

[EC 1.1.98.3 created 2012, modified 2014]

EC 1.2.99.9

Accepted name: formate dehydrogenase (coenzyme F420)

Reaction: formate + oxidized coenzyme F420 = CO2 + reduced coenzyme F420

Other name(s): coenzyme F420 reducing formate dehydrogenase; coenzyme F420-dependent formate dehydrogenase

Systematic name: formate:coenzyme-F420 oxidoreductase

Comments: The enzyme from methanogenic archaea is a involved in formate-dependent H2 production. It contains noncovalently bound FAD [1].

References:

1. Schauer, N.L. and Ferry, J.G. FAD requirement for the reduction of coenzyme F420 by formate dehydrogenase from Methanobacterium formicicum. J. Bacteriol. 155 (1983) 467-472. [PMID: 6874636]

2. Schauer, N.L. and Ferry, J.G. Composition of the coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum. J. Bacteriol. 165 (1986) 405-411. [PMID: 3944055]

3. Lupa, B., Hendrickson, E.L., Leigh, J.A. and Whitman, W.B. Formate-dependent H2 production by the mesophilic methanogen Methanococcus maripaludis. Appl. Environ. Microbiol. 74 (2008) 6584-6590. [PMID: 18791018]

[EC 1.2.99.9 created 2014]

*EC 1.3.1.48

Accepted name: 13,14-dehydro-15-oxoprostaglandin 13-reductase

Reaction: 11α-hydroxy-9,15-dioxoprostanoate + NAD(P)+ = (13E)-11α-hydroxy-9,15-dioxoprost-13-enoate + NAD(P)H + H+

Other name(s): 15-oxo-Δ13-prostaglandin reductase; Δ13-15-ketoprostaglandin reductase; 15-ketoprostaglandin Δ13-reductase; prostaglandin Δ13-reductase; prostaglandin 13-reductase; (5Z)-(15S)-11α-hydroxy-9,15-dioxoprostanoate:NAD(P)+ Δ13-oxidoreductase; (5Z)-11α-hydroxy-9,15-dioxoprost-5-enoate:NAD(P)+ Δ13-oxidoreductase

Systematic name: 11α-hydroxy-9,15-dioxoprostanoate:NAD(P)+ Δ13-oxidoreductase

Comments: Reduces 13,14-dehydro-15-oxoprostaglandins to 13,14-dihydro derivatives. The enzyme from placenta is specific for NAD+.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 57406-74-3

References:

1. Hansen, H.S. Purification and assay of 15-ketoprostaglandin Δ13-reductase from bovine lung. Methods Enzymol. 86 (1982) 156-163. [PMID: 6290839]

2. Jarabak, J. Isolation and properties of a 15-ketoprostaglandin Δ13-reductase from human placenta. Methods Enzymol. 86 (1982) 163-167. [PMID: 7132753]

[EC 1.3.1.48 created 1990, modified 2014]

EC 1.3.1.107

Accepted name: sanguinarine reductase

Reaction: (1) dihydrosanguinarine + NAD(P)+ = sanguinarine + NAD(P)H + H+
(2) dihydrochelirubine + NAD(P)+ = chelirubine + NAD(P)H + H+

For diagram of reaction click here.

Glossary: sanguinarine = 13-methyl-2H,10H-[1,3]dioxolo[4,5-i][1,3]dioxolo[4',5':4,5]benzo[1,2-c]phenanthridinium
dihydrosanguinarine = 13-methyl-13,14-dihydro-2H,10H-[1,3]dioxolo[4,5-i][1,3]dioxolo[4',5':4,5]benzo[1,2-c]phenanthridine
chelirubine = 5-methoxy-13-methyl-2H,10H-[1,3]dioxolo[4,5-i][1,3]dioxolo[4',5':4,5]benzo[1,2-c]phenanthridinium
dihydrochelirubine = 5-methoxy-13-methyl-13,14-dihydro-2H,10H-[1,3]dioxolo[4,5-i][1,3]dioxolo[4',5':4,5]benzo[1,2-c]phenanthridinium

Systematic name: dihydrosanguinarine:NAD(P)+ oxidoreductase

Comments: The enzyme, purified from the California poppy (Eschscholzia californica), is involved in detoxifying the phytoalexin sanguinarine produced by poppy itself (cf. EC 1.5.3.12, dihydrobenzophenanthridine oxidase), when it binds to the cell wall of the poppy cell. The reaction with NADPH is up to three times faster than that with NADH at low concentrations (<10 uM) of the dinucleotide. At higher concentrations the reaction with NADPH is inhibited but not that with NADH [1].

References:

1. Weiss, D., Baumert, A., Vogel, M. and Roos, W. Sanguinarine reductase, a key enzyme of benzophenanthridine detoxification. Plant Cell Environ 29 (2006) 291-302. [PMID: 17080644]

2. Vogel, M., Lawson, M., Sippl, W., Conrad, U. and Roos, W. Structure and mechanism of sanguinarine reductase, an enzyme of alkaloid detoxification. J. Biol. Chem. 285 (2010) 18397-18406. [PMID: 20378534]

[EC 1.3.1.107 created 2014]

EC 1.3.4 With a disulfide as acceptor

EC 1.3.4.1

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 1.3.4.1 created 2014 as EC 1.3.98.2, transferred 2014 to EC 1.3.4.1]

*EC 1.3.7.5

Accepted name: phycocyanobilin:ferredoxin oxidoreductase

Reaction: (3Z)-phycocyanobilin + 4 oxidized ferredoxin = biliverdin IXα + 4 reduced ferredoxin

For diagram of reaction click here.

Systematic name: (3Z)-phycocyanobilin:ferredoxin oxidoreductase

Comments: Catalyses the four-electron reduction of biliverdin IXα (2-electron reduction at both the A and D rings). Reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin. Flavodoxins can be used instead of ferredoxin. The direct conversion of biliverdin IXα (BV) to (3Z)-phycocyanolbilin (PCB) in the cyanobacteria Synechocystis sp. PCC 6803, Anabaena sp. PCC7120 and Nostoc punctiforme is in contrast to the proposed pathways of PCB biosynthesis in the red alga Cyanidium caldarium, which involves (3Z)-phycoerythrobilin (PEB) as an intermediate [2] and in the green alga Mesotaenium caldariorum, in which PCB is an isolable intermediate.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 347401-12-1

References:

1. Frankenberg, N., Mukougawa, K., Kohchi, T. and Lagarias, J.C. Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms. Plant Cell 13 (2001) 965-978. [PMID: 11283349]

2. Beale, S.I. Biosynthesis of phycobilins. Chem. Rev. 93 (1993) 785-802.

3. Wu, S.-H., McDowell, M.T. and Lagarias, J.C. Phycocyanobilin is the natural chromophore precursor of phytochrome from the green alga Mesotaenium caldariorum. J. Biol. Chem. 272 (1997) 25700-25705. [PMID: 9325294]

[EC 1.3.7.5 created 2002, modified 2014]

[EC 1.3.98.2 Transferred entry: fumarate reductase (CoM/CoB). Now EC 1.3.4.1, fumarate reductase (CoM/CoB) (EC 1.3.98.2 created 2014, deleted 2014)]

*EC 1.5.1.47

Accepted name: dihydromethanopterin reductase [NAD(P)+]

Reaction: 5,6,7,8-tetrahydromethanopterin + NAD(P)+ = 7,8-dihydromethanopterin + NAD(P)H + H+

For diagram of reaction click here.

Other name(s): DmrA; H2MPT reductase; 5,6,7,8-tetrahydromethanopterin 5,6-oxidoreductase; dihydromethanopterin reductase

Systematic name: 5,6,7,8-tetrahydromethanopterin:NAD(P)+ 5,6-oxidoreductase

Comments: The enzyme, characterized from the bacterium Methylobacterium extorquens, is involved in biosynthesis of dephospho-tetrahydromethanopterin. The specific activity with NADH is 15% of that with NADPH at the same concentration [1]. It does not reduce 7,8-dihydrofolate (cf. EC 1.5.1.3, dihydrofolate reductase).

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

References:

1. Caccamo, M.A., Malone, C.S. and Rasche, M.E. Biochemical characterization of a dihydromethanopterin reductase involved in tetrahydromethanopterin biosynthesis in Methylobacterium extorquens AM1. J. Bacteriol. 186 (2004) 2068-2073. [PMID: 15028691]

[EC 1.5.1.47 created 2013, modified 2014]

EC 1.5.99.15

Accepted name: dihydromethanopterin reductase (acceptor)

Reaction: 5,6,7,8-tetrahydromethanopterin + oxidized acceptor = 7,8-dihydromethanopterin + reduced acceptor

For diagram of reaction click here.

Other name(s): DmrX

Systematic name: 5,6,7,8-tetrahydromethanopterin:acceptor 5,6-oxidoreductase

Comments: This archaeal enzyme catalyses the last step in the biosynthesis of tetrahydromethanopterin, a coenzyme used in methanogenesis. The enzyme, characterized from the archaea Methanosarcina mazei and Methanocaldococcus jannaschii, is an iron-sulfur flavoprotein. cf. EC 1.5.1.47, dihydromethanopterin reductase [NAD(P)+].

References:

1. Wang, S., Tiongson, J. and Rasche, M.E. Discovery and characterization of the first archaeal dihydromethanopterin reductase, an iron-sulfur flavoprotein from Methanosarcina mazei. J. Bacteriol. 196 (2014) 203-209. [PMID: 23995635]

[EC 1.5.99.15 created 2014]

EC 1.8.98.3

Accepted name: sulfite reductase (coenzyme F420)

Reaction: hydrogen sulfide + 3 oxidized coenzyme F420 + 3 H2O = sulfite + 3 reduced coenzyme F420

Other name(s): coenzyme F420-dependent sulfite reductase; Fsr

Systematic name: hydrogen sulfide:coenzyme F420 oxidoreductase

Comments: The enzyme, isolated from the archaeon Methanocaldococcus jannaschii, is involved in sulfite detoxification and assimilation.

References:

1. Johnson, E.F. and Mukhopadhyay, B. A new type of sulfite reductase, a novel coenzyme F420-dependent enzyme, from the methanarchaeon Methanocaldococcus jannaschii. J. Biol. Chem. 280 (2005) 38776-38786. [PMID: 16048999]

2. Johnson, E.F. and Mukhopadhyay, B. Coenzyme F420-dependent sulfite reductase-enabled sulfite detoxification and use of sulfite as a sole sulfur source by Methanococcus maripaludis. Appl. Environ. Microbiol. 74 (2008) 3591-3595. [PMID: 18378657]

[EC 1.8.98.3 created 2014]

EC 1.14.11.47

Accepted name: 50S ribosomal protein L16 3-hydroxylase

Reaction: [50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2 = [50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2

Other name(s): ycfD (gene name)

Systematic name: [50S ribosomal protein L16]-L-Arg81,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)

Comments: The enzyme, characterized from the bacterium Escherichia coli, hydroxylates an arginine residue on the 50S ribosomal protein L16, and is involved in regulation of bacterial ribosome assembly.

References:

1. Ge, W., Wolf, A., Feng, T., Ho, C.H., Sekirnik, R., Zayer, A., Granatino, N., Cockman, M.E., Loenarz, C., Loik, N.D., Hardy, A.P., Claridge, T.D., Hamed, R.B., Chowdhury, R., Gong, L., Robinson, C.V., Trudgian, D.C., Jiang, M., Mackeen, M.M., McCullagh, J.S., Gordiyenko, Y., Thalhammer, A., Yamamoto, A., Yang, M., Liu-Yi, P., Zhang, Z., Schmidt-Zachmann, M., Kessler, B.M., Ratcliffe, P.J., Preston, G.M., Coleman, M.L. and Schofield, C.J. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat. Chem. Biol. 8 (2012) 960-962. [PMID: 23103944]

2. van Staalduinen, L.M., Novakowski, S.K. and Jia, Z. Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe2(+)-dependent oxygenase involved in translational regulation in Escherichia coli. J. Mol. Biol. 426 (2014) 1898-1910. [PMID: 24530688]

[EC 1.14.11.47 created 2014]

EC 1.14.13.195

Accepted name: L-ornithine N5-monooxygenase (NADPH)

Reaction: L-ornithine + NADPH + H+ + O2 = N5-hydroxy-L-ornithine + NADP+ + H2O

Other name(s): CchB; ornithine hydroxylase; EtcB; PvdA; Af-OMO; dffA (gene name)

Systematic name: L-ornithine,NADPH:oxygen oxidoreductase (N5-hydroxylating)

Comments: A flavoprotein (FAD). The enzyme is involved in biosynthesis of N5-hydroxy-L-ornithine, N5-formyl-N5-hydroxy-L-ornithine or N5-acetyl-N5-hydroxy-L-ornithine. These nonproteinogenic amino acids are building blocks of siderophores produced by some bacteria (e.g. Streptomyces coelicolor, Saccharopolyspora erythraea and Pseudomonas aeruginosa). The enzyme is specific for NADPH. cf. EC 1.14.13.196, L-ornithine N5-monooxygenase [NAD(P)H].

References:

1. Ge, L. and Seah, S.Y. Heterologous expression, purification, and characterization of an L-ornithine N5-hydroxylase involved in pyoverdine siderophore biosynthesis in Pseudomonas aeruginosa. J. Bacteriol. 188 (2006) 7205-7210. [PMID: 17015659]

2. Meneely, K.M. and Lamb, A.L. Biochemical characterization of a flavin adenine dinucleotide-dependent monooxygenase, ornithine hydroxylase from Pseudomonas aeruginosa, suggests a novel reaction mechanism. Biochemistry 46 (2007) 11930-11937. [PMID: 17900176]

3. Pohlmann, V. and Marahiel, M.A. δ-amino group hydroxylation of L-ornithine during coelichelin biosynthesis. Org. Biomol. Chem. 6 (2008) 1843-1848. [PMID: 18452021]

4. Robbel, L., Helmetag, V., Knappe, T.A. and Marahiel, M.A. Consecutive enzymatic modification of ornithine generates the hydroxamate moieties of the siderophore erythrochelin. Biochemistry 50 (2011) 6073-6080. [PMID: 21650455]

[EC 1.14.13.195 created 2014]

EC 1.14.13.196

Accepted name: L-ornithine N5-monooxygenase [NAD(P)H]

Reaction: L-ornithine + NAD(P)H + H+ + O2 = N5-hydroxy-L-ornithine + NAD(P)+ + H2O

Other name(s): SidA (ambiguous)

Systematic name: L-ornithine,NAD(P)H:oxygen oxidoreductase (N5-hydroxylating)

Comments: A flavoprotein (FAD). The enzyme from the pathogenic fungus Aspergillus fumigatus catalyses a step in the biosynthesis of the siderophores triacetylfusarinine and desferriferricrocin, while the enzyme from the bacterium Kutzneria sp. 744 is involved in the biosynthesis of piperazate, a building block of the kutzneride family of antifungal antibiotics. Activity of the fungal enzyme is higher with NADPH, due to the fact that following the reduction of the flavin, NADP+ (but not NAD+) stabilizes the C4a-hydroperoxyflavin intermediate that oxidizes the substrate [3]. cf. EC 1.14.13.195, L-ornithine N5-monooxygenase (NADPH).

References:

1. Chocklett, S.W. and Sobrado, P. Aspergillus fumigatus SidA is a highly specific ornithine hydroxylase with bound flavin cofactor. Biochemistry 49 (2010) 6777-6783. [PMID: 20614882]

2. Franceschini, S., Fedkenheuer, M., Vogelaar, N.J., Robinson, H.H., Sobrado, P. and Mattevi, A. Structural insight into the mechanism of oxygen activation and substrate selectivity of flavin-dependent N-hydroxylating monooxygenases. Biochemistry 51 (2012) 7043-7045. [PMID: 22928747]

3. Romero, E., Fedkenheuer, M., Chocklett, S.W., Qi, J., Oppenheimer, M. and Sobrado, P. Dual role of NADP(H) in the reaction of a flavin dependent N-hydroxylating monooxygenase. Biochim. Biophys. Acta 1824 (2012) 850-857. [PMID: 22465572]

4. Neumann, C.S., Jiang, W., Heemstra, J.R., Jr., Gontang, E.A., Kolter, R. and Walsh, C.T. Biosynthesis of piperazic acid via N5-hydroxy-ornithine in Kutzneria spp. 744. Chembiochem 13 (2012) 972-976. [PMID: 22522643]

[EC 1.14.13.196 created 2014]

EC 1.14.13.197

Accepted name: dihydromonacolin L hydroxylase

Reaction: dihydromonacolin L acid + O2 + NADPH + H+ = monacolin L acid + NADP+ + 2 H2O (overall reaction)
(1a) dihydromonacolin L acid + O2 + NADPH + H+ = 3α-hydroxy-3,5-dihydromonacolin L acid + NADP+ + H2O
(1b) 3α-hydroxy-3,5-dihydromonacolin L acid = monacolin L acid + H2O (spontaneous)

For diagram of reaction click here.

Glossary: dihydromonacolin L acid = (3R,5R)-7-[(1S,2S,4aR,6R,8aS)-2,6-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen1yl]-3,5-dihydroxyheptanoate
monacolin L acid = (3R,5R)-7-[(1S,2S,6R,8aR)-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate
3α-hydroxy-3,5-dihydromonacolin L = (3R,5R)-7-[(1R,2R,3S,6R,8aR)-3-hydroxy-2,6-dimethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate

Other name(s): LovA (ambiguous)

Systematic name: dihydromonacolin L acid,NADPH:oxygen oxidoreductase (3-hydroxylating)

Comments: A heme-thiolate protein (cytochrome P-450). The dehydration of 3α-hydroxy-3,5-dihydromonacolin L acid is believed to be spontaneous [1,2]. The enzyme from fungi also catalyses the reaction of EC 1.14.13.198, monacolin L hydroxylase [3].

References:

1. Treiber, L.R., Reamer, R.A., Rooney, C.S. and Ramjit, H.G. Origin of monacolin L from Aspergillus terreus cultures. J. Antibiot. (Tokyo) 42 (1989) 30-36. [PMID: 2921224]

2. Nakamura, T., Komagata, D., Murakawa, S., Sakai, K. and Endo, A. Isolation and biosynthesis of 3α-hydroxy-3,5-dihydromonacolin L. J. Antibiot. (Tokyo) 43 (1990) 1597-1600. [PMID: 2276977]

3. Barriuso, J., Nguyen, D.T., Li, J.W., Roberts, J.N., MacNevin, G., Chaytor, J.L., Marcus, S.L., Vederas, J.C. and Ro, D.K. Double oxidation of the cyclic nonaketide dihydromonacolin L to monacolin J by a single cytochrome P450 monooxygenase, LovA. J. Am. Chem. Soc. 133 (2011) 8078-8081. [PMID: 21495633]

[EC 1.14.13.197 created 2014]

EC 1.14.13.198

Accepted name: monacolin L hydroxylase

Reaction: monacolin L acid + O2 + NADPH + H+ = monacolin J acid + NADP+ + H2O

For diagram of reaction click here.

Glossary: monacolin L acid = (3R,5R)-7-[(1S,2S,6R,8aR)-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoic acid
monacolin J acid = (3R,5R)-7-[(1S,2S,6R,8S,8aR)-8-hydroxy-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoic acid

Other name(s): LovA (ambiguous)

Systematic name: monacolin L acid,NADPH:oxygen oxidoreductase (8-hydroxylating)

Comments: A heme-thiolate protein (cytochrome P-450). The enzyme from fungi also catalyses the reaction of EC 1.14.13.197, dihydromonacolin L hydroxylase.

References:

1. Barriuso, J., Nguyen, D.T., Li, J.W., Roberts, J.N., MacNevin, G., Chaytor, J.L., Marcus, S.L., Vederas, J.C. and Ro, D.K. Double oxidation of the cyclic nonaketide dihydromonacolin L to monacolin J by a single cytochrome P450 monooxygenase, LovA. J. Am. Chem. Soc. 133 (2011) 8078-8081. [PMID: 21495633]

[EC 1.14.13.198 created 2014]

EC 1.14.13.199

Accepted name: docosahexaenoic acid ω-hydroxylase

Reaction: docosahexaenoate + NADPH + H+ + O2 = 22-hydroxydocosahexaenoate + NADP+ + H2O

Glossary: docosahexaenoate = (4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoate
icosapentaenoate = (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoate

Other name(s): CYP4F3B; CYP4V2

Systematic name: docosahexaenoate,NADPH:O2 oxidoreductase (22-hydroxydocosahexaenoate forming)

Comments: Isolated from human eye tissue. Defects in the enzyme are associated with Bietti crystalline corneoretinal dystrophy. The enzyme also produces some 21-hydroxydocosahexaenoate. Acts in a similar way on icosapentaenoic acid.

References:

1. Nakano, M., Kelly, E.J., Wiek, C., Hanenberg, H. and Rettie, A.E. CYP4V2 in Bietti's crystalline dystrophy: ocular localization, metabolism of ω-3-polyunsaturated fatty acids, and functional deficit of the p.H331P variant. Mol. Pharmacol. 82 (2012) 679-686. [PMID: 22772592]

[EC 1.14.13.199 created 2014]

EC 1.14.13.200

Accepted name: tetracenomycin A2 monooxygenase-dioxygenase

Reaction: tetracenomycin A2 + 2 O2 + 2 NAD(P)H + 2 H+ = tetracenomycin C + 2 NAD(P)+ + H2O

For diagram of reaction click here and for mechanism click here.

Glossary: tetracenomycin A2 = methyl 10,12-dihydroxy-3,8-dimethoxy-1-methyl-6,11-dioxo-6,11-dihydrotetracene-2-carboxylate
tetracenomycin C = methyl (6aR,7S,10aR)-6a,7,10a,12-tetrahydroxy-3,8-dimethoxy-1-methyl-6,10,11-trioxo-6,6a,7,10,10a,11-hexahydrotetracene-2-carboxylate

Other name(s): TcmG; ElmG

Systematic name: tetracenomycin A2,NAD(P)H:O2 oxidoreductase (tetracenomycin C forming)

Comments: Isolated from the bacterium Streptomyces glaucescens. The enzyme was also isolated from the bacterium Streptomyces olivaceus, where it acts on 8-demethyltetracenomycin A2 (tetracenomycin B2) as part of elloramycin biosynthesis. The reaction involves a monooxygenase reaction which is followed by a dioxygenase reaction giving a gem-diol and an epoxide. Water opens the epoxide giving two hydroxy groups. The gem-diol eliminates water to give a ketone which is then reduced to a hydroxy group.

References:

1. Shen, B. and Hutchinson, C.R. Triple hydroxylation of tetracenomycin A2 to tetracenomycin C in Streptomyces glaucescens. Overexpression of the tcmG gene in Streptomyces lividans and characterization of the tetracenomycin A2 oxygenase. J. Biol. Chem. 269 (1994) 30726-30733. [PMID: 7982994]

2. Rafanan, E.R., Jr., Hutchinson, C.R. and Shen, B. Triple hydroxylation of tetracenomycin A2 to tetracenomycin C involving two molecules of O2 and one molecule of H2O. Org. Lett. 2 (2000) 3225-3227. [PMID: 11009387]

3. Beynon, J., Rafanan, E.R., Jr., Shen, B. and Fisher, A.J. Crystallization and preliminary X-ray analysis of tetracenomycin A2 oxygenase: a flavoprotein hydroxylase involved in polyketide biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 1647-1651. [PMID: 11092935]

[EC 1.14.13.200 created 2014]

[EC 1.14.14.7 Transferred entry: tryptophan 7-halogenase. As oxygen is completely reduced to H2O and is not incorporated into the donor chloride, the enzyme has been transferred to EC 1.14.19.9, tryptophan 7-halogenase (EC 1.14.14.7 created 2009, deleted 2014)]

*EC 1.14.15.4

Accepted name: steroid 11β-monooxygenase

Reaction: a steroid + 2 reduced adrenodoxin + O2 + 2 H+ = an 11β-hydroxysteroid + 2 oxidized adrenodoxin + H2O

Other name(s): steroid 11β-hydroxylase; steroid 11β/18-hydroxylase

Systematic name: steroid,reduced-adrenodoxin:oxygen oxidoreductase (11β-hydroxylating)

Comments: A heme-thiolate protein (P-450). Also hydroxylates steroids at the 18-position, and converts 18-hydroxycorticosterone into aldosterone.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9029-66-7

References:

1. Grant, J.K. and Brownie, A.C. The role of fumarate and TPN in steroid enzymic 11β-hydroxylation. Biochim. Biophys. Acta 18 (1955) 433-434. [PMID: 13276417]

2. Hayano, M. and Dorfman, R.I. On the mechanism of the C-11β-hydroxylation of steroids. J. Biol. Chem. 211 (1954) 227-235. [PMID: 13211659]

3. Tomkins, G.M., Michael, P.J. and Curran, J.F. Studies on the nature of steroid 11β-hydroxylation. Biochim. Biophys. Acta 23 (1957) 655-656. [PMID: 13426185]

4. Yanagibashi, K., Haniu, M., Shively, J.E., Shen, W.H. and Hall, P. The synthesis of aldosterone by the adrenal cortex. Two zones (fasciculata and glomerulosa) possess one enzyme for 11β-, 18-hydroxylation, and aldehyde synthesis. J. Biol. Chem. 261 (1986) 3556-3562. [PMID: 3485096]

5. Zuidweg, M.H.J. Hydroxylation of Reichstein's compound S with cell-free preparations from Curvularia lunata. Biochim. Biophys. Acta 152 (1968) 144-158. [PMID: 4967077]

[EC 1.14.15.4 created 1961 as EC 1.99.1.7, transferred 1965 to EC 1.14.1.6, transferred 1972 to EC 1.14.15.4, modified 1989, modified 2014]

*EC 1.14.15.6

Accepted name: cholesterol monooxygenase (side-chain-cleaving)

Reaction: cholesterol + 6 reduced adrenodoxin + 3 O2 + 6 H+ = pregnenolone + 4-methylpentanal + 6 oxidized adrenodoxin + 4 H2O (overall reaction)
(1a) cholesterol + 2 reduced adrenodoxin + O2 + 2 H+ = (22R)-22-hydroxycholesterol + 2 oxidized adrenodoxin + H2O
(1b) (22R)-22-hydroxycholesterol + 2 reduced adrenodoxin + O2 + 2 H+ = (20R,22R)-20,22-dihydroxycholesterol + 2 oxidized adrenodoxin + H2O
(1c) (20R,22R)-20,22-dihydroxy-cholesterol + 2 reduced adrenodoxin + O2 + 2 H+ = pregnenolone + 4-methylpentanal + 2 oxidized adrenodoxin + 2 H2O

Other name(s): cholesterol desmolase; cytochrome P-450scc; C27-side chain cleavage enzyme; cholesterol 20-22-desmolase; cholesterol C20-22 desmolase; cholesterol side-chain cleavage enzyme; cholesterol side-chain-cleaving enzyme; steroid 20-22 desmolase; steroid 20-22-lyase; CYP11A1 (gene name)

Systematic name: cholesterol,reduced-adrenodoxin:oxygen oxidoreductase (side-chain-cleaving)

Comments: A heme-thiolate protein (cytochrome P-450). The reaction proceeds in three stages, with two hydroxylations at C-22 and C-20 preceding scission of the side-chain between carbons 20 and 22. The initial source of the electrons is NADPH, which transfers the electrons to the adrenodoxin via EC 1.18.1.6, adrenodoxin-NADP+ reductase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37292-81-2, 440354-98-3

References:

1. Burstein, S., Middleditch, B.S. and Gut, M. Mass spectrometric study of the enzymatic conversion of cholesterol to (22R)-22-hydroxycholesterol, (20R,22R)-20,22-dihydroxycholesterol, and pregnenolone, and of (22R)-22-hydroxycholesterol to the lgycol and pregnenolone in bovine adrenocortical preparations. Mode of oxygen incorporation. J. Biol. Chem. 250 (1975) 9028-9037. [PMID: 1238395]

2. Hanukoglu, I., Spitsberg, V., Bumpus, J.A., Dus, K.M. and Jefcoate, C.R. Adrenal mitochondrial cytochrome P-450scc. Cholesterol and adrenodoxin interactions at equilibrium and during turnover. J. Biol. Chem. 256 (1981) 4321-4328. [PMID: 7217084]

3. Hanukoglu, I. and Hanukoglu, Z. Stoichiometry of mitochondrial cytochromes P-450, adrenodoxin and adrenodoxin reductase in adrenal cortex and corpus luteum. Implications for membrane organization and gene regulation. Eur. J. Biochem. 157 (1986) 27-31. [PMID: 3011431]

4. Strushkevich, N., MacKenzie, F., Cherkesova, T., Grabovec, I., Usanov, S. and Park, H.W. Structural basis for pregnenolone biosynthesis by the mitochondrial monooxygenase system. Proc. Natl. Acad. Sci. USA 108 (2011) 10139-10143. [PMID: 21636783]

5. Mast, N., Annalora, A.J., Lodowski, D.T., Palczewski, K., Stout, C.D. and Pikuleva, I.A. Structural basis for three-step sequential catalysis by the cholesterol side chain cleavage enzyme CYP11A1. J. Biol. Chem. 286 (2011) 5607-5613. [PMID: 21159775]

[EC 1.14.15.6 created 1983, modified 2013, modified 2014]

EC 1.14.19.9

Accepted name: tryptophan 7-halogenase

Reaction: tryptophan + FADH2 + chloride + O2 + H+ = 7-chloro-L-tryptophan + FAD + 2 H2O

For diagram of reaction click here.

Other name(s): PrnA; RebH

Systematic name: L-tryptophan:FADH2 oxidoreductase (7-halogenating)

Comments: In the bacterium Lechevalieria aerocolonigenes the enzyme catalyses the initial step in the biosynthesis of rebeccamycin [2]. Also acts on bromide ion.

References:

1. Dong, C., Kotzsch, A., Dorward, M., van Pee, K.H. and Naismith, J.H. Crystallization and X-ray diffraction of a halogenating enzyme, tryptophan 7-halogenase, from Pseudomonas fluorescens. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1438-1440. [PMID: 15272170]

2. Yeh, E., Garneau, S. and Walsh, C.T. Robust in vitro activity of RebF and RebH, a two-component reductase/halogenase, generating 7-chlorotryptophan during rebeccamycin biosynthesis. Proc. Natl. Acad. Sci. USA 102 (2005) 3960-3965. [PMID: 15743914]

3. Bitto, E., Huang, Y., Bingman, C.A., Singh, S., Thorson, J.S. and Phillips Jr., G.N. The structure of flavin-dependent tryptophan 7-halogenase RebH. Proteins Struct. Funct. Genet. 70 (2008) 289-293.

[EC 1.14.19.9 created 2009 as EC 1.14.14.7, transferred 2014 to EC 1.14.19.9]

EC 1.14.99.49

Accepted name: 2-hydroxy-5-methyl-1-naphthoate 7-hydroxylase

Reaction: 2-hydroxy-5-methyl-1-naphthoate + reduced acceptor + O2 = 2,7-dihydroxy-5-methyl-1-naphthoate + oxidized acceptor + H2O

For diagram of reaction click here.

Other name(s): NcsB3

Systematic name: 2-hydroxy-5-methyl-1-naphthoate,hydrogen-donor:oxygen oxidoreductase (7-hydroxylating)

Comments: A heme-thiolate protein (P-450) enzyme involved in the synthesis of neocarzinostatin in the bacterium Streptomyces carzinostaticus.

References:

1. Hang, V.T.T., Oh, T.J., Yamaguchi, T. and Sohng, J.K. In vivo characterization of NcsB3 to establish the complete biosynthesis of the naphthoic acid moiety of the neocarzinostatin chromophore. FEMS Microbiol. Lett. 311 (2010) 119-125. [PMID: 20735485]

[EC 1.14.99.49 created 2014]

*EC 2.4.1.109

Accepted name: dolichyl-phosphate-mannose—protein mannosyltransferase

Reaction: dolichyl D-mannosyl phosphate + protein = dolichyl phosphate + O-D-mannosylprotein

For diagram of reaction click here.

Other name(s): dolichol phosphomannose-protein mannosyltransferase; protein O-D-mannosyltransferase; dolichyl-phosphate-D-mannose:protein O-D-mannosyltransferase; dolichyl-phosphate-mannose-protein mannosyltransferase

Systematic name: dolichyl-D-mannosyl-phosphate:protein O-D-mannosyltransferase

Comments: The enzyme transfers mannosyl residues to the hydroxy group of serine or threonine residues, producing cell-wall mannoproteins. It acts only on long-chain α-dihydropolyprenyl derivatives, larger than C35.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 74315-99-4

References:

1. Babczinski, P., Haselbeck, A. and Tanner, W. Yeast mannosyl transferases requiring dolichyl phosphate and dolichyl phosphate mannose as substrate. Partial purification and characterization of the solubilized enzyme. Eur. J. Biochem. 105 (1980) 509-515. [PMID: 6989607]

2. Palamarczyk, G., Lehle, L., Mankowski, T., Chojnacki, T. and Tanner, W. Specificity of solubilized yeast glycosyl transferases for polyprenyl derivatives. Eur. J. Biochem. 105 (1980) 517-523. [PMID: 6445267]

[EC 2.4.1.109 created 1983, modified 2014]

EC 2.4.1.329

Accepted name: sucrose 6F-phosphate phosphorylase

Reaction: sucrose 6F-phosphate + phosphate = α-D-glucopyranose 1-phosphate + β-D-fructofuranose 6-phosphate

Other name(s): sucrose 6'-phosphate phosphorylase

Systematic name: sucrose 6F-phosphate:phosphate 1-α-D-glucosyltransferase

Comments: The enzyme, isolated from the thermophilic bacterium Thermoanaerobacterium thermosaccharolyticum, catalyses the reversible phosphorolysis of sucrose 6F-phosphate. It also acts on sucrose with lower activity.

References:

1. Verhaeghe, T., Aerts, D., Diricks, M., Soetaert, W. and Desmet, T. The quest for a thermostable sucrose phosphorylase reveals sucrose 6'-phosphate phosphorylase as a novel specificity. Appl. Microbiol. Biotechnol. 98 (2014) 7027-7037. [PMID: 24599311]

[EC 2.4.1.329 created 2014]

EC 2.4.1.330

Accepted name: β-D-glucosyl crocetin β-1,6-glucosyltransferase

Reaction: (1) UDP-α-D-glucose + β-D-glucosyl crocetin = UDP + β-D-gentiobiosyl crocetin
(2) UDP-α-D-glucose + bis(β-D-glucosyl) crocetin = UDP + β-D-gentiobiosyl β-D-glucosyl crocetin
(3) UDP-α-D-glucose + β-D-gentiobiosyl β-D-glucosyl crocetin = UDP + crocin

For diagram of reaction click here.

Glossary: crocin = bis(β-D-gentiobiosyl) crocetin
crocetin = (2E,4E,6E,8E,10E,12E,14E)-2,6,11,15-tetramethylhexadeca-2,4,6,8,10,12,14-heptaenedioate

Other name(s): UGT94E5; UDP-glucose:crocetin glucosyl ester glucosyltransferasee

Systematic name: UDP-α-D-glucose:β-D-glucosyl crocetin β-1,6-glucosyltransferase

Comments: The enzyme, characterized from the plant Gardenia jasminoides, adds a glucose to several crocetin glycosyl esters, but not to crocetin (cf. EC 2.4.1.271, crocetin glucosyltransferase).

References:

1. Nagatoshi, M., Terasaka, K., Owaki, M., Sota, M., Inukai, T., Nagatsu, A. and Mizukami, H. UGT75L6 and UGT94E5 mediate sequential glucosylation of crocetin to crocin in Gardenia jasminoides. FEBS Lett 586 (2012) 1055-1061. [PMID: 22569263]

[EC 2.4.1.330 created 2014]

EC 2.4.1.331

Accepted name: 8-demethyltetracenomycin C L-rhamnosyltransferase

Reaction: dTDP-β-L-rhamnose + 8-demethyltetracenomycin C = dTDP + 8-demethyl-8-α-L-rhamnosyltetracenomycin C

For diagram of reaction click here.

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

Other name(s): elmGT

Systematic name: dTDP-β-L-rhamnose:8-demethyltetracenomycin C 3-α-L-rhamnosyltransferase

Comments: Isolated from Streptomyces olivaceus Tü2353. Involved in elloramycin biosynthesis. In vitro it can also utilize other 6-deoxy D- or L-hexoses.

References:

1. Blanco, G., Patallo, E.P., Brana, A.F., Trefzer, A., Bechthold, A., Rohr, J., Mendez, C. and Salas, J.A. Identification of a sugar flexible glycosyltransferase from Streptomyces olivaceus, the producer of the antitumor polyketide elloramycin. Chem. Biol. 8 (2001) 253-263. [PMID: 11306350]

[EC 2.4.1.331 created 2014]

EC 2.5.1.124

Accepted name: 6-linalyl-2-O,3-dimethylflaviolin synthase

Reaction: geranyl diphosphate + 2-O,3-dimethylflaviolin = diphosphate + 6-linalyl-2-O,3-dimethylflaviolin

Glossary: flaviolin = 2,5,7-trihydroxy-1,4-naphthoquinone
2-O,3-dimethylflaviolin = 5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione
6-linalyl-2-O,3-dimethylflaviolin = 6-(3,7-dimethylocta-1,6-dien-3-yl)-5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione

Other name(s): Fur7; 6-(3,7-dimethylocta-1,6-dien-3-yl)-5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione synthase

Systematic name: geranyl diphosphate:2-O-methyl-3-methylflaviolin geranyltransferase (6-linalyl-2-O,3-dimethylflaviolin-forming)

Comments: The enzyme is involved in biosynthesis of the polyketide-isoprenoid furaquinocin D in the bacterium Streptomyces sp. KO-3988. It catalyses the transfer of a geranyl group to 2-O,3-dimethylflaviolin to yield 6-linalyl-2-O,3-dimethylflaviolin and 7-O-geranyl-2-O,3-dimethylflaviolin (cf. EC 2.5.1.125, 7-geranyloxy-5-hydroxy-2-methoxy-3-methylnaphthalene-1,4-dione synthase) in a 10:1 ratio.

References:

1. Kumano, T., Tomita, T., Nishiyama, M. and Kuzuyama, T. Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products. J. Biol. Chem. 285 (2010) 39663-39671. [PMID: 20937800]

[EC 2.5.1.124 created 2014]

EC 2.5.1.125

Accepted name: 7-geranyloxy-5-hydroxy-2-methoxy-3-methylnaphthalene-1,4-dione synthase

Reaction: geranyl diphosphate + 2-O,3-dimethylflaviolin = diphosphate + 7-O-geranyl-2-O,3-dimethylflaviolin

Glossary: flaviolin = 2,5,7-trihydroxy-1,4-naphthoquinone
2-O,3-dimethylflaviolin = 5,7-dihydroxy-2-methoxy-3-methylnaphthalene-1,4-dione
7-O-geranyl-2-O,3-dimethylflaviolin = 7-{[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-5-hydroxy-2-methoxy-3-methylnaphthalene-1,4-dione

Other name(s): Fur7

Systematic name: geranyl diphosphate:2-O,3-dimethylflaviolin geranyltransferase (7-O-geranyl-2-O,3-dimethylflaviolin-forming)

Comments: The enzyme is involved in furaquinocin biosynthesis in the bacterium Streptomyces sp. KO-3988. It catalyses the transfer of a geranyl group to 2-O,3-dimethylflaviolin to yield 7-O-geranyl-2-O,3-dimethylflaviolin and 6-linalyl-2-O,3-dimethylflaviolin (cf. EC 2.5.1.124, 6-linalyl-2-O,3-dimethylflaviolin synthase) in a 1:10 ratio.

References:

1. Kumano, T., Tomita, T., Nishiyama, M. and Kuzuyama, T. Functional characterization of the promiscuous prenyltransferase responsible for furaquinocin biosynthesis: identification of a physiological polyketide substrate and its prenylated reaction products. J. Biol. Chem. 285 (2010) 39663-39671. [PMID: 20937800]

[EC 2.5.1.125 created 2014]

EC 2.5.1.126

Accepted name: norspermine synthase

Reaction: S-adenosyl 3-(methylthio)propylamine + norspermidine = S-methyl-5'-thioadenosine + norspermine

Glossary: norspermidine = bis(3-aminopropyl)amine
norspermine = N,N'-bis(3-aminopropyl)-1,3-propanediamine
spermidine = N-(3-aminopropyl)-1,4-butanediamine
thermospermine = N-{3-[(3-aminopropyl)amino]propyl}-1,4-butanediamine

Other name(s): long-chain polyamine synthase (ambiguous)

Systematic name: S-adenosyl 3-(methylthio)propylamine:norspermidine 3-aminopropyltransferase

Comments: The enzyme, characterized from the thermophilic archaeon Pyrobaculum aerophilum, can also synthesize norspermidine from propane-1,3-diamine and thermospermine from spermidine (with lower activity). The long-chain polyamines stabilize double-stranded DNA at high temperatures. In contrast to EC 2.5.1.127, caldopentamine synthase, this enzyme does not accept norspermine as a substrate.

References:

1. Knott, J.M. Biosynthesis of long-chain polyamines by crenarchaeal polyamine synthases from Hyperthermus butylicus and Pyrobaculum aerophilum. FEBS Lett 583 (2009) 3519-3524. [PMID: 19822146]

[EC 2.5.1.126 created 2014]

EC 2.5.1.127

Accepted name: caldopentamine synthase

Reaction: S-adenosyl 3-(methylthio)propylamine + norspermine = S-methyl-5'-thioadenosine + caldopentamine

Glossary: caldopentamine = N-(3-aminopropyl)-N'-{3-[(3-aminopropyl)amino]propyl}-1,3-propanediamine
norspermidine = N-(3-aminopropyl)-1,4-butanediamine
norspermine = N,N'-bis(3-aminopropyl)-1,3-propanediamine
spermidine = N-(3-aminopropyl)-1,4-butanediamine
thermospermine = N-{3-[(3-aminopropyl)amino]propyl}-1,4-butanediamine

Other name(s): long-chain polyamine synthase (ambiguous)

Systematic name: S-adenosyl 3-(methylthio)propylamine:norspermine 3-aminopropyltransferase

Comments: The enzyme, characterized from the thermophilic archaeon Hyperthermus butylicus, can also synthesize norspermine from norspermidine and thermospermine from spermidine (with lower activity). The long-chain polyamines stabilize double-stranded DNA at high temperatures. In contrast to EC 2.5.1.23, sym-norspermidine synthase and EC 2.5.1.126, norspermine synthase, this enzyme shows no activity with propane-1,3-diamine.

References:

1. Knott, J.M. Biosynthesis of long-chain polyamines by crenarchaeal polyamine synthases from Hyperthermus butylicus and Pyrobaculum aerophilum. FEBS Lett 583 (2009) 3519-3524. [PMID: 19822146]

[EC 2.5.1.127 created 2014]

*EC 2.7.1.8

Accepted name: glucosamine kinase

Reaction: ATP + D-glucosamine = ADP + D-glucosamine 6-phosphate

Glossary: D-glucosamine 6-phosphate = 2-amino-2-deoxy-D-glucose 6-phosphate

Other name(s): glucosamine kinase (phosphorylating); ATP:2-amino-2-deoxy-D-glucose-6-phosphotransferase; aminodeoxyglucose kinase; ATP:D-glucosamine phosphotransferase

Systematic name: ATP:D-glucosamine 6-phosphotransferase

Comments: The enzyme has been studied in the bacterium Vibrio cholerae, where it participates in a chitin degradation pathway.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9031-90-7

References:

1. Bueding, E. and MacKinnon, J.A. Hexokinases of Schistosoma mansoni. J. Biol. Chem. 215 (1955) 495-506. [PMID: 13242546]

2. Park, J.K., Wang, L.X. and Roseman, S. Isolation of a glucosamine-specific kinase, a unique enzyme of Vibrio cholerae. J. Biol. Chem. 277 (2002) 15573-15578. [PMID: 11850417]

[EC 2.7.1.8 created 1961, modified 2014]

EC 2.7.1.185

Accepted name: mevalonate 3-kinase

Reaction: ATP + (R)-mevalonate = ADP + (R)-3-phosphomevalonate

For diagram of reaction click here.

Other name(s): ATP:(R)-MVA 3-phosphotransferase

Systematic name: ATP:(R)-mevalonate 3-phosphotransferase

Comments: Mevalonate 3-kinase and mevalonate-3-phosphate-5-kinase (EC 2.7.1.186) act sequentially in an alternate mevalonate pathway in the archaeon Thermoplasma acidophilum. Mevalonate 3-kinase is different from mevalonate kinase, EC 2.7.1.36, which transfers phosphate to position 5 of (R)-mevalonate and is part of the classical mevalonate pathway in eukaryotes and archaea.

References:

1. Vinokur, J.M., Korman, T.P., Cao, Z. and Bowie, J.U. Evidence of a novel mevalonate pathway in archaea. Biochemistry 53 (2014) 4161-4168. [PMID: 24914732]

2. Azami, Y., Hattori, A., Nishimura, H., Kawaide, H., Yoshimura, T. and Hemmi, H. (R)-Mevalonate 3-phosphate is an intermediate of the mevalonate pathway in Thermoplasma acidophilum. J. Biol. Chem. 289 (2014) 15957-15967. [PMID: 24755225]

[EC 2.7.1.185 created 2014]

EC 2.7.1.186

Accepted name: mevalonate-3-phosphate 5-kinase

Reaction: ATP + (R)-3-phosphomevalonate = ADP + 3,5-bisphosphomevalonate

For diagram of reaction click here.

Systematic name: ATP:(R)-3-phosphomevalonate 5-phosphotransferase

Comments: Mevalonate 3-kinase (EC 2.7.1.185) and mevalonate-3-phosphate-5-kinase act sequentially in an alternate mevalonate pathway in the archaeon Thermoplasma acidophilum.

References:

1. Vinokur, J.M., Korman, T.P., Cao, Z. and Bowie, J.U. Evidence of a novel mevalonate pathway in archaea. Biochemistry 53 (2014) 4161-4168. [PMID: 24914732]

[EC 2.7.1.186 created 2014]

EC 2.7.14 Protein-arginine kinases

EC 2.7.14.1

Accepted name: protein arginine kinase

Reaction: ATP + a [protein]-L-arginine = ADP + a [protein]-Nω-phospho-L-arginine

Other name(s): McsB

Systematic name: ATP:[protein]-L-arginine Nω-phosphotransferase

Comments: The enzyme, characterized from Gram-positive bacteria, is involved in the regulation of the bacterial stress response.

References:

1. Fuhrmann, J., Schmidt, A., Spiess, S., Lehner, A., Turgay, K., Mechtler, K., Charpentier, E. and Clausen, T. McsB is a protein arginine kinase that phosphorylates and inhibits the heat-shock regulator CtsR. Science 324 (2009) 1323-1327. [PMID: 19498169]

2. Elsholz, A.K., Turgay, K., Michalik, S., Hessling, B., Gronau, K., Oertel, D., Mader, U., Bernhardt, J., Becher, D., Hecker, M. and Gerth, U. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc. Natl. Acad. Sci. USA 109 (2012) 7451-7456. [PMID: 22517742]

3. Schmidt, A., Trentini, D.B., Spiess, S., Fuhrmann, J., Ammerer, G., Mechtler, K. and Clausen, T. Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response. Mol. Cell. Proteomics 13 (2014) 537-550. [PMID: 24263382]

[EC 2.7.14.1 created 2014]

*EC 2.8.4.4

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

Reaction: L-aspartate89-[ribosomal protein S12] + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced acceptor = 3-methylthio-L-aspartate89-[ribosomal protein S12] + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5'-deoxyadenosine + oxidized acceptor (overall reaction)
(1a) S-adenosyl-L-methionine + L-aspartate89-[ribosomal protein S12] + sulfur-(sulfur carrier) = S-adenosyl-L-homocysteine + L-aspartate89-[ribosomal protein S12]-methanethiol + (sulfur carrier)
(1b) L-aspartate89-[ribosomal protein S12]-methanethiol + S-adenosyl-L-methionine + reduced acceptor = 3-methylthio-L-aspartate89-[ribosomal protein S12] + L-methionine + 5'-deoxyadenosine + oxidized receptor

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

Systematic name: [ribosomal protein S12]-L-aspartate89:sulfur-(sulfur carrier),S-adenosyl-L-methionine C3-methylthiotransferase

Comments: This bacterial enzyme binds two [4Fe-4S] clusters [2,3]. A bridge of five sulfur atoms is formed between the free Fe atoms of the two [4Fe-4S] clusters [6]. In the first reaction the enzyme transfers a methyl group from AdoMet to the external sulfur ion of the sulfur bridge. In the second reaction the enzyme catalyses the reductive fragmentation of a second molecule of AdoMet, yielding a 5'-deoxyadenosine radical, which then attacks the methylated sulfur atom of the polysulfide bridge, resulting in the transfer of a methylthiol group to aspartate89 [5,6]. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes.

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

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]

6. Forouhar, F., Arragain, S., Atta, M., Gambarelli, S., Mouesca, J.M., Hussain, M., Xiao, R., Kieffer-Jaquinod, S., Seetharaman, J., Acton, T.B., Montelione, G.T., Mulliez, E., Hunt, J.F. and Fontecave, M. Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases. Nat. Chem. Biol. 9 (2013) 333-338. [PMID: 23542644]

[EC 2.8.4.4 created 2014, modified 2014]

*EC 2.9.1.2

Accepted name: O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase

Reaction: O-phospho-L-seryl-tRNASec + selenophosphate + H2O = L-selenocysteinyl-tRNASec + 2 phosphate

Other name(s): MMPSepSecS; SepSecS; SLA/LP; O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase; O-phospho-L-seryl-tRNA:L-selenocysteinyl-tRNA synthase

Systematic name: selenophosphate:O-phospho-L-seryl-tRNASec selenium transferase

Comments: A pyridoxal-phosphate protein [4]. In archaea and eukarya selenocysteine formation is achieved by a two-step process: EC 2.7.1.164 (O-phosphoseryl-tRNASec kinase) phosphorylates the endogenous L-seryl-tRNASec to O-phospho-L-seryl-tRNASec, and then this misacylated amino acid-tRNA species is converted to L-selenocysteinyl-tRNASec by Sep-tRNA:Sec-tRNA synthase.

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

References:

1. Palioura, S., Sherrer, R.L., Steitz, T.A., Soll, D. and Simonovic, M. The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. Science 325 (2009) 321-325. [PMID: 19608919]

2. Araiso, Y., Palioura, S., Ishitani, R., Sherrer, R.L., O'Donoghue, P., Yuan, J., Oshikane, H., Domae, N., Defranco, J., Soll, D. and Nureki, O. Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. Nucleic Acids Res. 36 (2008) 1187-1199. [PMID: 18158303]

3. Aeby, E., Palioura, S., Pusnik, M., Marazzi, J., Lieberman, A., Ullu, E., Soll, D. and Schneider, A. The canonical pathway for selenocysteine insertion is dispensable in Trypanosomes. Proc. Natl. Acad. Sci. USA 106 (2009) 5088-5092. [PMID: 19279205]

4. Yuan, J., Palioura, S., Salazar, J.C., Su, D., O'Donoghue, P., Hohn, M.J., Cardoso, A.M., Whitman, W.B. and Soll, D. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc. Natl. Acad. Sci. USA 103 (2006) 18923-18927. [PMID: 17142313]

[EC 2.9.1.2 created 2009, modified 2014]

[EC 3.1.2.15 Deleted entry: This activity is covered by EC 3.4.19.12, ubiquitinyl hydrolase 1 (EC 3.1.2.15 created 1986, deleted 2014)]

EC 3.5.4.41

Accepted name: 5'-deoxyadenosine deaminase

Reaction: 5'-deoxyadenosine + H2O = 5'-deoxyinosine + NH3

Other name(s): MJ1541 (gene name); DadD

Systematic name: 5'-deoxyadenosine aminohydrolase

Comments: The enzyme from the archaeon Methanocaldococcus jannaschii is involved in the recycling of 5'-deoxyadenosine.

References:

1. Miller, D., O'Brien, K., Xu, H. and White, R.H. Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine. J. Bacteriol. 196 (2014) 1064-1072. [PMID: 24375099]

[EC 3.5.4.41 created 2014]

EC 3.9.1.2

Accepted name: protein arginine phosphatase

Reaction: a [protein]-Nω-phospho-L-arginine + H2O = a [protein]-L-arginine + phosphate

Other name(s): YwlE

Systematic name: [protein]-Nω-phospho-L-arginine phosphohydrolase

Comments: The enzyme, characterized from Gram-positive bacteria, hydrolyses the phosphoramidate (P-N) bond of Nω-phospho-L-arginine residues in proteins and peptides that were phosphorylated by EC 2.7.14.1, protein-arginine-kinase.

References:

1. Fuhrmann, J., Mierzwa, B., Trentini, D.B., Spiess, S., Lehner, A., Charpentier, E. and Clausen, T. Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria. Cell Rep 3 (2013) 1832-1839. [PMID: 23770242]

2. Trentini, D.B., Fuhrmann, J., Mechtler, K. and Clausen, T. Chasing phosphoarginine proteins: development of a selective enrichment method using a phosphatase trap. LID - mcp.O113.035790 [pii. Mol. Cell. Proteomics (2014) . [PMID: 24825175]

3. Elsholz, A.K., Turgay, K., Michalik, S., Hessling, B., Gronau, K., Oertel, D., Mader, U., Bernhardt, J., Becher, D., Hecker, M. and Gerth, U. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc. Natl. Acad. Sci. USA 109 (2012) 7451-7456. [PMID: 22517742]

[EC 3.9.1.2 created 2014]

EC 4.1.1.99

Accepted name: phosphomevalonate decarboxylase

Reaction: ATP + (R)-5-phosphomevalonate = ADP + phosphate + isopentenyl phosphate + CO2

For diagram of reaction click here.

Systematic name: ATP:phosphomevalonate carboxy-lyase (adding ATP; isopentenyl-phosphate-forming)

Comments: The enzyme is part of the mevalonate pathway in archaea.

References:

1. Vannice, J.C., Skaff, D.A., Keightley, A., Addo, J.K., Wyckoff, G.J. and Miziorko, H.M. Identification in Haloferax volcanii of phosphomevalonate decarboxylase and isopentenyl phosphate kinase as catalysts of the terminal enzyme reactions in an archaeal alternate mevalonate pathway. J. Bacteriol. 196 (2014) 1055-1063. [PMID: 24375100]

[EC 4.1.1.99 created 2014]

*EC 4.2.1.121

Accepted name: colneleate synthase

Reaction: (9S,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate + H2O

Glossary: colneleate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate

Other name(s): 9-divinyl ether synthase; 9-DES; CYP74D; CYP74D1; CYP74 cytochrome P-450; DES1; (8E)-9-[(1E,3E)-nona-1,3-dien-1-yloxy]non-8-enoate synthase

Systematic name: (9S,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate hydro-lyase

Comments: A heme-thiolate protein (P-450) [2]. It catalyses the selective removal of pro-R hydrogen at C-8 in the biosynthesis of colneleic acid [4]. It forms also (8E)-9-[(1E,3Z,6Z)-nona-1,3,6-trien-1-yloxy]non-8-enoic acid (i.e. colnelenate) from (9S,10E,12Z,15Z)-9-hydroperoxy-10,12,15-octadecatrienoate. The corresponding 13-hydroperoxides are poor substrates [1,3]. The divinyl ethers colneleate and colnelenate have antimicrobial activity.

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

References:

1. Stumpe, M., Kandzia, R., Gobel, C., Rosahl, S. and Feussner, I. A pathogen-inducible divinyl ether synthase (CYP74D) from elicitor-treated potato suspension cells. FEBS Lett. 507 (2001) 371-376. [PMID: 11696374]

2. Itoh, A. and Howe, G.A. Molecular cloning of a divinyl ether synthase. Identification as a CYP74 cytochrome P-450. J. Biol. Chem. 276 (2001) 3620-3627. [PMID: 11060314]

3. Fammartino, A., Cardinale, F., Gobel, C., Mene-Saffrane, L., Fournier, J., Feussner, I. and Esquerre-Tugaye, M.T. Characterization of a divinyl ether biosynthetic pathway specifically associated with pathogenesis in tobacco. Plant Physiol. 143 (2007) 378-388. [PMID: 17085514]

4. Hamberg, M. Hidden stereospecificity in the biosynthesis of divinyl ether fatty acids. FEBS J. 272 (2005) 736-743. [PMID: 15670154]

[EC 4.2.1.121 created 2011, modified 2014]

EC 4.2.3.147

Accepted name: pimaradiene synthase

Reaction: (+)-copalyl diphosphate = pimara-8(14),15-diene + diphosphate

For diagram of reaction click here.

Other name(s): PbmPIM1; PcmPIM1

Systematic name: (+)-copalyl diphosphate-lyase (pimara-8(14),15-diene-forming)

Comments: Isolated from the plants Pinus banksiana (jack pine) and Pinus contorta (lodgepole pine).

References:

1. Hall, D.E., Zerbe, P., Jancsik, S., Quesada, A.L., Dullat, H., Madilao, L.L., Yuen, M. and Bohlmann, J. Evolution of conifer diterpene synthases: diterpene resin acid biosynthesis in lodgepole pine and jack pine involves monofunctional and bifunctional diterpene synthases. Plant Physiol. 161 (2013) 600-616. [PMID: 23370714]

[EC 4.2.3.147 created 2014]

EC 5.1.3.30

Accepted name: D-psicose 3-epimerase

Reaction: D-psicose = D-fructose

Glossary: D-psicose = D-ribo-hex-2-ulose

Other name(s): DPEase (ambiguous)

Systematic name: D-psicose 3-epimerase

Comments: The enzyme is highly specific for D-psicose and shows very low activity with D-tagatose (cf. EC 5.1.3.31, D-tagatose 3-epimerase). The enzyme from the bacterium Clostridium scindens requires Mn2+ [1], whereas the enzymes from the bacteria Clostridium cellulolyticum [2,5], Clostridium sp. BNL1100 [3], and Clostridium bolteae [4] require Co2+ as optimum cofactor. The enzyme from Ruminococcus sp. [6] is not dependent on the presence of metal ions, but its activity is enhanced by Mn2+.

References:

1. Mu, W., Chu, F., Xing, Q., Yu, S., Zhou, L. and Jiang, B. Cloning, expression, and characterization of a D-psicose 3-epimerase from Clostridium cellulolyticum H10. J. Agric. Food Chem. 59 (2011) 7785-7792. [PMID: 21663329]

2. Chan, H.C., Zhu, Y., Hu, Y., Ko, T.P., Huang, C.H., Ren, F., Chen, C.C., Ma, Y., Guo, R.T. and Sun, Y. Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars. Protein Cell 3 (2012) 123-131. [PMID: 22426981]

3. Zhu, Y., Men, Y., Bai, W., Li, X., Zhang, L., Sun, Y. and Ma, Y. Overexpression of D-psicose 3-epimerase from Ruminococcus sp. in Escherichia coli and its potential application in D-psicose production. Biotechnol. Lett. 34 (2012) 1901-1906. [PMID: 22760176]

4. Zhang, W., Fang, D., Xing, Q., Zhou, L., Jiang, B. and Mu, W. Characterization of a novel metal-dependent D-psicose 3-epimerase from Clostridium scindens 35704. PLoS One 8 (2013) e62987. [PMID: 23646168]

5. Mu, W., Zhang, W., Fang, D., Zhou, L., Jiang, B. and Zhang, T. Characterization of a D-psicose-producing enzyme, D-psicose 3-epimerase, from Clostridium sp. Biotechnol. Lett. 35 (2013) 1481-1486. [PMID: 23660703]

6. Jia, M., Mu, W., Chu, F., Zhang, X., Jiang, B., Zhou, L.L. and Zhang, T. A D-psicose 3-epimerase with neutral pH optimum from Clostridium bolteae for D-psicose production: cloning, expression, purification, and characterization. Appl. Microbiol. Biotechnol. 98 (2014) 717-725. [PMID: 23644747]

[EC 5.1.3.30 created 2014]

EC 5.1.3.31

Accepted name: D-tagatose 3-epimerase

Reaction: (1) D-tagatose = D-sorbose
(2) D-psicose = D-fructose

Glossary: D-psicose = D-ribo-hex-2-ulose

Other name(s): L-ribulose 3-epimerase; ketose 3-epimerase

Systematic name: D-tagatose 3-epimerase

Comments: The enzymes isolated from the bacteria Pseudomonas cichorii [2], Pseudomonas sp. ST-24 [1], Rhodobacter sphaeroides [3] and Mesorhizobium loti [4] catalyse the epimerization of various ketoses at the C3 position, interconverting D-fructose and D-psicose, D-tagatose and D-sorbose, D-ribulose and D-xylulose, and L-ribulose and L-xylulose. The specificity depends on the species. The enzymes from Pseudomonas cichorii and Rhodobacter sphaeroides require Mn2+ [2,3].

References:

1. Itoh, H., Okaya, H., Khan, A. R., Tajima, S., Hayakawa, S., Izumori, K. Purification and characterization of D-tagatose 3-epimerase from Pseudomonas sp. ST-24. Biosci. Biotechnol. Biochem. 58 (1994) 2168-2171.

2. Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K. and Kamitori, S. Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose. J. Mol. Biol. 374 (2007) 443-453. [PMID: 17936787]

3. Zhang, L., Mu, W., Jiang, B. and Zhang, T. Characterization of D-tagatose-3-epimerase from Rhodobacter sphaeroides that converts D-fructose into D-psicose. Biotechnol. Lett. 31 (2009) 857-862. [PMID: 19205890]

4. Uechi, K., Takata, G., Fukai, Y., Yoshihara, A. and Morimoto, K. Gene cloning and characterization of L-ribulose 3-epimerase from Mesorhizobium loti and its application to rare sugar production. Biosci. Biotechnol. Biochem. 77 (2013) 511-515. [PMID: 23470755]

[EC 5.1.3.31 created 2014]

EC 5.1.3.32

Accepted name: L-rhamnose mutarotase

Reaction: α-L-rhamnopyranose = β-L-rhamnopyranose

Other name(s): rhamnose 1-epimerase; type-3 mutarotase; YiiL

Systematic name: L-rhamnopyranose 1-epimerase

Comments: The enzyme is specific for L-rhamnopyranose.

References:

1. Ryu, K.S., Kim, C., Kim, I., Yoo, S., Choi, B.S. and Park, C. NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration. J. Biol. Chem. 279 (2004) 25544-25548. [PMID: 15060078]

2. Ryu, K.S., Kim, J.I., Cho, S.J., Park, D., Park, C., Cheong, H.K., Lee, J.O. and Choi, B.S. Structural insights into the monosaccharide specificity of Escherichia coli rhamnose mutarotase. J. Mol. Biol. 349 (2005) 153-162. [PMID: 15876375]

[EC 5.1.3.32 created 2014]

EC 5.4.99.62

Accepted name: D-ribose pyranase

Reaction: β-D-ribopyranose = β-D-ribofuranose

Other name(s): RbsD

Systematic name: D-ribopyranose furanomutase

Comments: The enzyme also catalyses the conversion between β-allopyranose and β-allofuranose.

References:

1. Kim, M.S., Shin, J., Lee, W., Lee, H.S. and Oh, B.H. Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture. J. Biol. Chem. 278 (2003) 28173-28180. [PMID: 12738765]

2. Ryu, K.S., Kim, C., Kim, I., Yoo, S., Choi, B.S. and Park, C. NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration. J. Biol. Chem. 279 (2004) 25544-25548. [PMID: 15060078]

[EC 5.4.99.62 created 2014]

[EC 6.1.1.28 Deleted entry: proline/cysteine—tRNA ligase. Later published work having demonstrated that this was not a genuine enzyme, EC 6.1.1.28 was withdrawn at the public-review stage before being made official. (EC 6.1.1.28 created 2014, deleted 2014)]

EC 6.2.1.44

Accepted name: 3-(methylthio)propionyl—CoA ligase

Reaction: ATP + 3-(methylthio)propanoate + CoA = AMP + diphosphate + 3-(methylthio)propanoyl-CoA

For diagram of reaction click here.

Other name(s): DmdB; MMPA-CoA ligase; methylmercaptopropionate-coenzyme A ligase; 3-methylmercaptopropionyl-CoA ligase

Systematic name: 3-(methylthio)propanoate:CoA ligase (AMP-forming)

Comments: The enzyme is part of a dimethylsulfoniopropanoate demethylation pathway in the marine bacteria Ruegeria pomeroyi and Pelagibacter ubique. It also occurs in some nonmarine bacteria capable of metabolizing dimethylsulfoniopropionate (e.g. Burkholderia thailandensis, Pseudomonas aeruginosa, and Silicibacter lacuscaerulensis). It requires Mg2+ [2].

References:

1. Reisch, C.R., Stoudemayer, M.J., Varaljay, V.A., Amster, I.J., Moran, M.A. and Whitman, W.B. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473 (2011) 208-211. [PMID: 21562561]

2. Bullock, H.A., Reisch, C.R., Burns, A.S., Moran, M.A. and Whitman, W.B. Regulatory and functional diversity of methylmercaptopropionate coenzyme A ligases from the dimethylsulfoniopropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria. J. Bacteriol. 196 (2014) 1275-1285. [PMID: 24443527]

[EC 6.2.1.44 created 2014]

*EC 6.3.2.1

Accepted name: pantoate—β-alanine ligase (AMP-forming)

Reaction: ATP + (R)-pantoate + β-alanine = AMP + diphosphate + (R)-pantothenate

For diagram of reaction click here.

Glossary: (R)-pantoate = (2R)-2,4-dihydroxy-3,3-dimethylbutanoate
(R)-pantothenate = 3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanoate

Other name(s): pantothenate synthetase; pantoate activating enzyme; pantoic-activating enzyme; D-pantoate:β-alanine ligase (AMP-forming); pantoate—β-alanine ligase (ambiguous)

Systematic name: (R)-pantoate:β-alanine ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-49-8

References:

1. Ginoza, H.S. and Altenbern, R.A. The pantothenate-synthesizing enzyme cell-free extracts of Brucella abortus, strain 19. Arch. Biochem. Biophys. 56 (1955) 537-541. [PMID: 14377603]

2. Maas, W.K. Pantothenate studies. III. Description of the extracted pantothenate-synthesizing enzyme of Escherichia coli. J. Biol. Chem. 198 (1952) 23-32. [PMID: 12999714]

3. Maas, W.K. Mechanism of the enzymatic synthesis of pantothenate from β-alanine and pantoate. Fed. Proc. 15 (1956) 305-306.

[EC 6.3.2.1 created 1961, modified 2014]

EC 6.3.2.43

Accepted name: [lysine-biosynthesis-protein LysW]—L-2-aminoadipate ligase

Reaction: ATP + [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-2-aminoadipate = ADP + phosphate + [lysine-biosynthesis-protein LysW]-C-terminal-γ-(L-2-aminoadip-2-yl)-L-glutamate

Other name(s): α-aminoadipate-lysW ligase lysX (gene name); LysX (ambiguous); AAA—LysW ligase

Systematic name: [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate:L-2-aminoadipate ligase (ADP-forming)

Comments: The enzymes from the thermophilic bacterium Thermus thermophilus and the thermophilic archaea Sulfolobus acidocaldarius and Sulfolobus tokodaii protect the amino group of L-2-aminoadipate by conjugation to the carrier protein LysW. This reaction is part of the lysine biosynthesis pathway in these organisms.

References:

1. Vassylyeva, M.N., Sakai, H., Matsuura, T., Sekine, S., Nishiyama, M., Terada, T., Shirouzu, M., Kuramitsu, S., Vassylyev, D.G. and Yokoyama, S. Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 1651-1652. [PMID: 12925802]

2. Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol. 5 (2009) 673-679. [PMID: 19620981]

3. Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277-283. [PMID: 23434852]

[EC 6.3.2.43 created 2014]

EC 6.3.2.44

Accepted name: pantoate—β-alanine ligase (ADP-forming)

Reaction: ATP + (R)-pantoate + β-alanine = ADP + phosphate + (R)-pantothenate

For diagram of reaction click here.

Glossary: (R)-pantoate = (2R)-2,4-dihydroxy-3,3-dimethylbutanoate
(R)-pantothenate = 3-[(2R)-2,4-dihydroxy-3,3-dimethylbutanamido]propanoate

Other name(s): pantothenate synthetase (ambiguous); pantoate—β-alanine ligase (ambiguous)

Systematic name: (R)-pantoate:β-alanine ligase (ADP-forming)

Comments: The enzyme, characterized from the archaeon Methanosarcina mazei, is involved in the biosynthesis of pantothenate. It is different from EC 6.3.2.1, the AMP-forming pantoate-β-alanine ligase found in bacteria and eukaryota.

References:

1. Ronconi, S., Jonczyk, R. and Genschel, U. A novel isoform of pantothenate synthetase in the Archaea. FEBS J. 275 (2008) 2754-2764. [PMID: 18422645]

[EC 6.3.2.44 created 2014]

EC 6.5.1.6

Accepted name: DNA ligase (ATP or NAD+)

Reaction: (1) ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m = AMP + diphosphate + (deoxyribonucleotide)n+m
(2) NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m = AMP + β-nicotinamide D-ribonucleotide + (deoxyribonucleotide)n+m

Systematic name: poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (ATP or NAD+)

Comments: The enzymes from the archaea Thermococcus fumicolans and Thermococcus onnurineus show high activity with either ATP or NAD+, and significantly lower activity with TTP, GTP, and CTP. Different from EC 6.5.1.1, DNA ligase (ATP), EC 6.5.1.2, DNA ligase (NAD+) and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).

References:

1. Rolland, J.L., Gueguen, Y., Persillon, C., Masson, J.M. and Dietrich, J. Characterization of a thermophilic DNA ligase from the archaeon Thermococcus fumicolans. FEMS Microbiol. Lett. 236 (2004) 267-273. [PMID: 15251207]

2. Kim, Y.J., Lee, H.S., Bae, S.S., Jeon, J.H., Yang, S.H., Lim, J.K., Kang, S.G., Kwon, S.T. and Lee, J.H. Cloning, expression, and characterization of a DNA ligase from a hyperthermophilic archaeon Thermococcus sp. Biotechnol. Lett. 28 (2006) 401-407. [PMID: 16614906]

[EC 6.5.1.6 created 2014]

EC 6.5.1.7

Accepted name: DNA ligase (ATP, ADP or GTP)

Reaction: (1) ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m = AMP + diphosphate + (deoxyribonucleotide)n+m
(2) ADP + (deoxyribonucleotide)n + (deoxyribonucleotide)m = AMP + phosphate + (deoxyribonucleotide)n+m
(3) GTP + (deoxyribonucleotide)n + (deoxyribonucleotide)m = GMP + diphosphate + (deoxyribonucleotide)n+m

Systematic name: poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (ATP, ADP or GTP)

Comments: The enzymes from the archaea Hyperthermus butylicus and Sulfophobococcus zilligii are active with ATP, ADP or GTP. They show no activity with NAD+. Different from EC 6.5.1.1, DNA ligase (ATP), which is specific for ATP, and EC 6.5.1.6, DNA ligase (ATP or NAD+) which can utilize either ATP or NAD+.

References:

1. Sun, Y., Seo, M.S., Kim, J.H., Kim, Y.J., Kim, G.A., Lee, J.I., Lee, J.H. and Kwon, S.T. Novel DNA ligase with broad nucleotide cofactor specificity from the hyperthermophilic crenarchaeon Sulfophobococcus zilligii: influence of ancestral DNA ligase on cofactor utilization. Environ Microbiol 10 (2008) 3212-3224. [PMID: 18647334]

2. Kim, J.H., Lee, K.K., Sun, Y., Seo, G.J., Cho, S.S., Kwon, S.H. and Kwon, S.T. Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance. Extremophiles 17 (2013) 515-522. [PMID: 23546841]

[EC 6.5.1.7 created 2014]


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