The Enzyme Database

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EC 1.14.19.24     
Accepted name: acyl-CoA 11-(E)-desaturase
Reaction: an acyl-CoA + 2 ferrocytochrome b5 + O2 + 2 H+ = an (11E)-enoyl-CoA + 2 ferricytochrome b5 + 2 H2O
Systematic name: acyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (11,12 trans-dehydrogenating)
Comments: Involved in sex pheromone synthesis in the Lepidoptera (moths). The enzyme from the moth Spodoptera littoralis prefers 13:0 and 14:0 substrates. The product is formed by the stereospecific removal of the pro-R H at C-11 and the pro-S H at C-12. cf. EC 1.14.19.5, acyl-CoA 11-(Z)-desaturase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 199543-17-4
References:
1.  Foster, S. P. and Roelofs, W. L. Biosynthesis of a monoene and a conjugated diene sex pheromone component of the lightbrown apple moth by 11 desaturation. Experientia 46 (1990) 269–273.
2.  Martinez, T., Fabrias, G. and Camps, F. Sex pheromone biosynthetic pathway in Spodoptera littoralis and its activation by a neurohormone. J. Biol. Chem. 265 (1990) 1381–1387. [PMID: 2295634]
3.  Navarro, I., Font, I., Fabrias, G. and Camps, F. Stereospecificity of the (E)- and (Z)-11 myristoyl desaturases in the biosynthesis of Spodoptera littoralis sex pheromone. J. Am. Chem. Soc. 119 (1997) 11335–11336.
4.  Pinilla, A., Camps, F. and Fabrias, G. Cryptoregiochemistry of the Δ11-myristoyl-CoA desaturase involved in the biosynthesis of Spodoptera littoralis sex pheromone. Biochemistry 38 (1999) 15272–15277. [DOI] [PMID: 10563812]
[EC 1.14.19.24 created 2000 as EC 1.14.99.31, transferred 2015 to EC 1.14.19.24]
 
 
EC 1.14.19.30     
Accepted name: acyl-lipid (8-3)-desaturase
Reaction: (1) an (8Z,11Z,14Z)-icosa-8,11,14-trienoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (5Z,8Z,11Z,14Z)-icosatetra-5,8,11,14-tetraenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) an (8Z,11Z,14Z,17Z)-icosa-8,11,14,17-tetraenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
Glossary: (8Z,11Z,14Z)-icosa-8,11,14-trienoate = di-homo-γ-linolenate
(5Z,8Z,11Z,14Z)-icosa-8,11,14-trienoate = arachidonate
Other name(s): acyl-lipid 5-desaturase; Δ5-fatty-acid desaturase; DES5 (gene name); D5des (gene name); FADS1
Systematic name: Δ8 acyl-lipid,ferrocytochrome b5:oxygen oxidoreductase (5,6 cis-dehydrogenating)
Comments: The enzyme, which has been characterized from multiple organisms including the moss Physcomitrella patens, the marine microalga Rebecca salina, and the filamentous fungus Mortierella alpina, introduces a cis double bond at the 5-position in 20-carbon polyunsaturated fatty acids incorporated in a glycerolipid that contain a Δ8 double bond. The enzyme contains a cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase, and does not require an external cytochrome.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Michaelson, L.V., Lazarus, C.M., Griffiths, G., Napier, J.A. and Stobart, A.K. Isolation of a Δ5-fatty acid desaturase gene from Mortierella alpina. J. Biol. Chem. 273 (1998) 19055–19059. [DOI] [PMID: 9668087]
2.  Kaewsuwan, S., Cahoon, E.B., Perroud, P.F., Wiwat, C., Panvisavas, N., Quatrano, R.S., Cove, D.J. and Bunyapraphatsara, N. Identification and functional characterization of the moss Physcomitrella patens Δ5-desaturase gene involved in arachidonic and eicosapentaenoic acid biosynthesis. J. Biol. Chem. 281 (2006) 21988–21997. [DOI] [PMID: 16728405]
3.  Zhou, X.R., Robert, S.S., Petrie, J.R., Frampton, D.M., Mansour, M.P., Blackburn, S.I., Nichols, P.D., Green, A.G. and Singh, S.P. Isolation and characterization of genes from the marine microalga Pavlova salina encoding three front-end desaturases involved in docosahexaenoic acid biosynthesis. Phytochemistry 68 (2007) 785–796. [DOI] [PMID: 17291553]
[EC 1.14.19.30 created 2015]
 
 
EC 1.14.19.31     
Accepted name: acyl-lipid (7-3)-desaturase
Reaction: (1) a (7Z,10Z,13Z,16Z,19Z)-docosa-7,10,13,16,19-pentaenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
(2) a (7Z,10Z,13Z,16Z)-docosa-7,10,13,16-tetraenoyl-[glycerolipid] + 2 ferrocytochrome b5 + O2 + 2 H+ = a (4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyl-[glycerolipid] + 2 ferricytochrome b5 + 2 H2O
Glossary: (7Z,10Z,13Z,16Z)-docosa-7,10,13,16-tetraenoate = adrenate
Other name(s): D4Des (gene name); des1 (gene name); CrΔ4FAD (gene name); acyl-lipid 4-desaturase
Systematic name: Δ7 acyl-lipid,ferrocytochrome b5:oxygen oxidoreductase (4,5 cis-dehydrogenating)
Comments: The enzymes from several algae introduce a cis double bond at the 4-position in 22-carbon polyunsaturated fatty acids that contain a Δ7 double bond. The enzyme from the fresh water alga Chlamydomonas reinhardtii acts on the 16 carbon fatty acid (7Z,10Z,13Z)-hexadeca-7,10,13-trienoate [5]. The enzyme contains an N-terminal cytochrome b5 domain that acts as the direct electron donor to the active site of the desaturase, and does not require an external cytochrome.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Qiu, X., Hong, H. and MacKenzie, S.L. Identification of a Δ4 fatty acid desaturase from Thraustochytrium sp. involved in the biosynthesis of docosahexanoic acid by heterologous expression in Saccharomyces cerevisiae and Brassica juncea. J. Biol. Chem. 276 (2001) 31561–31566. [DOI] [PMID: 11397798]
2.  Tonon, T., Harvey, D., Larson, T.R. and Graham, I.A. Identification of a very long chain polyunsaturated fatty acid Δ4-desaturase from the microalga Pavlova lutheri. FEBS Lett. 553 (2003) 440–444. [DOI] [PMID: 14572666]
3.  Meyer, A., Cirpus, P., Ott, C., Schlecker, R., Zähringer, U. and Heinz, E. Biosynthesis of docosahexaenoic acid in Euglena gracilis: biochemical and molecular evidence for the involvement of a Δ4-fatty acyl group desaturase. Biochemistry 42 (2003) 9779–9788. [DOI] [PMID: 12911321]
4.  Zhou, X.R., Robert, S.S., Petrie, J.R., Frampton, D.M., Mansour, M.P., Blackburn, S.I., Nichols, P.D., Green, A.G. and Singh, S.P. Isolation and characterization of genes from the marine microalga Pavlova salina encoding three front-end desaturases involved in docosahexaenoic acid biosynthesis. Phytochemistry 68 (2007) 785–796. [DOI] [PMID: 17291553]
5.  Zäuner, S., Jochum, W., Bigorowski, T. and Benning, C. A cytochrome b5-containing plastid-located fatty acid desaturase from Chlamydomonas reinhardtii. Eukaryot Cell 11 (2012) 856–863. [DOI] [PMID: 22562471]
[EC 1.14.19.31 created 2015]
 
 
EC 1.14.19.41     
Accepted name: sterol 22-desaturase
Reaction: ergosta-5,7,24(28)-trien-3β-ol + NADPH + H+ + O2 = ergosta-5,7,22,24(28)-tetraen-3β-ol + NADP+ + 2 H2O
For diagram of sterol sidechain modification, click here
Other name(s): ERG5 (gene name); CYP710A (gene name)
Systematic name: ergosta-5,7,24(28)-trien-3β-ol,NADPH:oxygen oxidoreductase (22,23-dehydrogenating)
Comments: A heme-thiolate protein (P-450). The enzyme, found in yeast and plants, catalyses the introduction of a double bond between the C-22 and C-23 carbons of certain sterols. In yeast the enzyme acts on ergosta-5,7,24(28)-trien-3β-ol, a step in the biosynthesis of ergosterol. The enzyme from the plant Arabidopsis thaliana acts on sitosterol and 24-epi-campesterol, producing stigmasterol and brassicasterol, respectively.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kelly, S.L., Lamb, D.C., Corran, A.J., Baldwin, B.C., Parks, L.W. and Kelly, D.E. Purification and reconstitution of activity of Saccharomyces cerevisiae P450 61, a sterol Δ22-desaturase. FEBS Lett. 377 (1995) 217–220. [DOI] [PMID: 8543054]
2.  Skaggs, B.A., Alexander, J.F., Pierson, C.A., Schweitzer, K.S., Chun, K.T., Koegel, C., Barbuch, R. and Bard, M. Cloning and characterization of the Saccharomyces cerevisiae C-22 sterol desaturase gene, encoding a second cytochrome P-450 involved in ergosterol biosynthesis. Gene 169 (1996) 105–109. [DOI] [PMID: 8635732]
3.  Morikawa, T., Mizutani, M., Aoki, N., Watanabe, B., Saga, H., Saito, S., Oikawa, A., Suzuki, H., Sakurai, N., Shibata, D., Wadano, A., Sakata, K. and Ohta, D. Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato. Plant Cell 18 (2006) 1008–1022. [DOI] [PMID: 16531502]
[EC 1.14.19.41 created 2015]
 
 
EC 1.14.19.79     
Accepted name: 3β,22α-dihydroxysteroid 3-dehydrogenase
Reaction: (1) (22S)-22-hydroxycampesterol + [reduced NADPH-hemoprotein reductase] + O2 = (22S)-22-hydroxycampest-4-en-3-one + [oxidized NADPH-hemoprotein reductase] + 2 H2O
(2) 6-deoxoteasterone + [reduced NADPH-hemoprotein reductase] + O2 = 3-dehydro-6-deoxoteasterone + [oxidized NADPH-hemoprotein reductase] + 2 H2O
Glossary: 6-deoxoteasterone = (22R,23R)-5α-campestane-3β,22,23-triol
Other name(s): CYP90A1 (gene name)
Systematic name: 3β,22α-dihydroxysteroid,[reduced NADPH-hemoprotein reductase]:oxygen 3-oxidoreductase
Comments: This cytochrome P-450 (heme-thiolate) enzyme, characterized from the plant Arabidopsis thaliana, catalyses C-3 dehydrogenation of all 3β-hydroxy brassinosteroid synthesis intermediates with 22-hydroxylated or 22,23-dihydroxylated side chains.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ohnishi, T., Godza, B., Watanabe, B., Fujioka, S., Hategan, L., Ide, K., Shibata, K., Yokota, T., Szekeres, M. and Mizutani, M. CYP90A1/CPD, a brassinosteroid biosynthetic cytochrome P450 of Arabidopsis, catalyzes C-3 oxidation. J. Biol. Chem. 287 (2012) 31551–31560. [DOI] [PMID: 22822057]
[EC 1.14.19.79 created 2022]
 
 
EC 1.14.20.5     
Accepted name: flavone synthase I
Reaction: a flavanone + 2-oxoglutarate + O2 = a flavone + succinate + CO2 + H2O
For diagram of flavonoid biosynthesis, click here and for diagram of the biosynthesis of naringenin derivatives, click here
Other name(s): FNSI (gene name)
Systematic name: flavanone,2-oxoglutarate:oxygen oxidoreductase (dehydrating)
Comments: The enzyme, which has been found in rice and in members of the Apiaceae (a plant family), is a member of the 2-oxoglutarate-dependent dioxygenases, and requires ascorbate and Fe2+ for full activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 138263-98-6
References:
1.  Martens, S., Forkmann, G., Matern, U. and Lukačin, R. Cloning of parsley flavone synthase I. Phytochemistry 58 (2001) 43–46. [DOI] [PMID: 11524111]
2.  Lukačin, R., Matern, U., Junghanns, K.T., Heskamp, M.L., Britsch, L., Forkmann, G. and Martens, S. Purification and antigenicity of flavone synthase I from irradiated parsley cells. Arch. Biochem. Biophys. 393 (2001) 177–183. [DOI] [PMID: 11516175]
3.  Martens, S., Forkmann, G., Britsch, L., Wellmann, F., Matern, U. and Lukačin, R. Divergent evolution of flavonoid 2-oxoglutarate-dependent dioxygenases in parsley. FEBS Lett. 544 (2003) 93–98. [DOI] [PMID: 12782296]
[EC 1.14.20.5 created 2004 as EC 1.14.11.22, transferred 2018 to EC 1.14.20.5]
 
 
EC 1.14.99.31      
Transferred entry: myristoyl-CoA 11-(E) desaturase. Now classified as EC 1.14.19.24, myristoyl-CoA 11-(E) desaturase
[EC 1.14.99.31 created 2000, deleted 2015]
 
 
EC 1.14.99.32      
Transferred entry: myristoyl-CoA 11-(Z) desaturase. Now classified as EC 1.14.19.5, acyl-CoA 11-(Z)-desaturase.
[EC 1.14.99.32 created 2000, deleted 2015]
 
 
EC 1.14.99.65     
Accepted name: 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] 3-hydroxylase
Reaction: 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] + reduced acceptor + O2 = 2-(4-aminophenyl)-L-seryl-[CmlP-peptidyl-carrier-protein] + acceptor + H2O
Other name(s): cmlA (gene name)
Systematic name: 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein],acceptor:oxygen 3-oxidoreductase
Comments: The enzyme, characterized from the bacterium Streptomyces venezuelae, participates in the biosynthesis of the antibiotic chloramphenicol. It carries an oxygen-bridged dinuclear iron cluster. The native electron donor remains unknown, and the enzyme was assayed in vitro using sodium dithionite. The enzyme only acts on its substrate when it is loaded onto the peptidyl-carrier domain of the CmlP non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Makris, T.M., Chakrabarti, M., Munck, E. and Lipscomb, J.D. A family of diiron monooxygenases catalyzing amino acid β-hydroxylation in antibiotic biosynthesis. Proc. Natl. Acad. Sci. USA 107 (2010) 15391–15396. [PMID: 20713732]
[EC 1.14.99.65 created 2019]
 
 
EC 1.14.99.67     
Accepted name: α-N-dichloroacetyl-p-aminophenylserinol N-oxygenase
Reaction: α-N-dichloroacetyl-p-aminophenylserinol + reduced acceptor + 2 O2 = chloramphenicol + acceptor + 2 H2O
Glossary: α-N-dichloroacetyl-p-aminophenylserinol = N-[(1R,2R)-1-(4-aminophenyl)-1,3-dihydroxypropan-2-yl]-2,2-dichloroacetamide
Other name(s): cmlI (gene name)
Systematic name: α-N-dichloroacetyl-p-aminophenylserinol,acceptor:oxygen oxidoreductase (N-hydroxylating)
Comments: The enzyme, isolated from the bacterium Streptomyces venezuelae, is involved in the biosynthesis of the antibiotic chloramphenicol. It contains a carboxylate-bridged binuclear non-heme iron cluster. The components of the native electron chain have not been identified, although the immediate donor is likely to be an iron-sulfur protein. The reaction mechanism involves formation of an extremely stable peroxo intermediate that catalyses three individual two-electron oxidations via a hydroxylamine and a nitroso intermediates without releasing the intermediates. cf. EC 1.14.99.68, 4-aminobenzoate N-oxygenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Lu, H., Chanco, E. and Zhao, H. CmlI is an N-oxygenase in the biosynthesis of chloramphenicol. Tetrahedron 68 (2012) 7651–7654. [DOI] [PMID: 24347692]
2.  Makris, T.M., Vu, V.V., Meier, K.K., Komor, A.J., Rivard, B.S., Munck, E., Que, L., Jr. and Lipscomb, J.D. An unusual peroxo intermediate of the arylamine oxygenase of the chloramphenicol biosynthetic pathway. J. Am. Chem. Soc. 137 (2015) 1608–1617. [DOI] [PMID: 25564306]
3.  Komor, A.J., Rivard, B.S., Fan, R., Guo, Y., Que, L., Jr. and Lipscomb, J.D. CmlI N-oxygenase catalyzes the final three steps in chloramphenicol biosynthesis without dissociation of intermediates. Biochemistry 56 (2017) 4940–4950. [DOI] [PMID: 28823151]
[EC 1.14.99.67 created 2020]
 
 
EC 1.17.3.2     
Accepted name: xanthine oxidase
Reaction: xanthine + H2O + O2 = urate + H2O2
For diagram of AMP catabolism, click here
Glossary: 4-mercuribenzoate = (4-carboxylatophenyl)mercury
Other name(s): hypoxanthine oxidase; hypoxanthine:oxygen oxidoreductase; Schardinger enzyme; xanthine oxidoreductase; hypoxanthine-xanthine oxidase; xanthine:O2 oxidoreductase; xanthine:xanthine oxidase
Systematic name: xanthine:oxygen oxidoreductase
Comments: An iron-molybdenum flavoprotein (FAD) containing [2Fe-2S] centres. Also oxidizes hypoxanthine, some other purines and pterins, and aldehydes, but is distinct from EC 1.2.3.1, aldehyde oxidase. Under some conditions the product is mainly superoxide rather than peroxide: RH + H2O + 2 O2 = ROH + 2 O2.- + 2 H+. The mammalian enzyme predominantly exists as an NAD-dependent dehydrogenase (EC 1.17.1.4, xanthine dehydrogenase). During purification the enzyme is largely converted to the O2-dependent xanthine oxidase form (EC 1.17.3.2). The conversion can be triggered by several mechanisms, including the oxidation of cysteine thiols to form disulfide bonds [4,5,7,10] [which can be catalysed by EC 1.8.4.7, enzyme-thiol transhydrogenase (glutathione-disulfide) in the presence of glutathione disulfide] or limited proteolysis, which results in irreversible conversion. The conversion can also occur in vivo [4,6,10].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9002-17-9
References:
1.  Avis, P.G., Bergel, F. and Bray, R.C. Cellular constituents. The chemistry of xanthine oxidase. Part I. The preparation of a crystalline xanthine oxidase from cow's milk. J. Chem. Soc. (Lond.) (1955) 1100–1105.
2.  Battelli, M.G. and Lorenzoni, E. Purification and properties of a new glutathione-dependent thiol:disulphide oxidoreductase from rat liver. Biochem. J. 207 (1982) 133–138. [PMID: 6960894]
3.  Bray, R.C. Xanthine oxidase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 533–556.
4.  Della Corte, E. and Stirpe, F. The regulation of rat liver xanthine oxidase. Involvement of thiol groups in the conversion of the enzyme activity from dehydrogenase (type D) into oxidase (type O) and purification of the enzyme. Biochem. J. 126 (1972) 739–745. [PMID: 4342395]
5.  Ikegami, T. and Nishino, T. The presence of desulfo xanthine dehydrogenase in purified and crude enzyme preparations from rat liver. Arch. Biochem. Biophys. 247 (1986) 254–260. [DOI] [PMID: 3459393]
6.  Engerson, T.D., McKelvey, T.G., Rhyne, D.B., Boggio, E.B., Snyder, S.J. and Jones, H.P. Conversion of xanthine dehydrogenase to oxidase in ischemic rat tissues. J. Clin. Invest. 79 (1987) 1564–1570. [DOI] [PMID: 3294898]
7.  Saito, T., Nishino, T. and Tsushima, K. Interconversion between NAD-dependent and O2-dependent types of rat liver xanthine dehydrogenase and difference in kinetic and redox properties between them. Adv. Exp. Med. Biol. 253B (1989) 179–183. [PMID: 2610112]
8.  Carpani, G., Racchi, M., Ghezzi, P., Terao, M. and Garattini, E. Purification and characterization of mouse liver xanthine oxidase. Arch. Biochem. Biophys. 279 (1990) 237–241. [DOI] [PMID: 2350174]
9.  Eger, B.T., Okamoto, K., Enroth, C., Sato, M., Nishino, T., Pai, E.F. and Nishino, T. Purification, crystallization and preliminary X-ray diffraction studies of xanthine dehydrogenase and xanthine oxidase isolated from bovine milk. Acta Crystallogr. D Biol. Crystallogr. 56 (2000) 1656–1658. [PMID: 11092937]
10.  Nishino, T., Okamoto, K., Eger, B.T., Pai, E.F. and Nishino, T. Mammalian xanthine oxidoreductase - mechanism of transition from xanthine dehydrogenase to xanthine oxidase. FEBS J. 275 (2008) 3278–3289. [DOI] [PMID: 18513323]
[EC 1.17.3.2 created 1961 as EC 1.2.3.2, transferred 1984 to EC 1.1.3.22, modified 1989, transferred 2004 to EC 1.17.3.2, modified 2011]
 
 
EC 1.17.7.1     
Accepted name: (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase (ferredoxin)
Reaction: (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + 2 oxidized ferredoxin = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + 2 reduced ferredoxin
For diagram of Non-Mevalonate terpenoid biosynthesis, click here
Other name(s): 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ambiguous); (E)-4-hydroxy-3-methylbut-2-en-1-yl-diphosphate:protein-disulfide oxidoreductase (hydrating) (incorrect); (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (ambiguous); gcpE (gene name); ISPG (gene name); (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase
Systematic name: (E)-4-hydroxy-3-methylbut-2-en-1-yl-diphosphate:oxidized ferredoxin oxidoreductase
Comments: An iron-sulfur protein found in plant chloroplasts and cyanobacteria that contains a [4Fe-4S] cluster [1]. Forms part of an alternative non-mevalonate pathway for isoprenoid biosynthesis. Bacteria have a similar enzyme that uses flavodoxin rather than ferredoxin (cf. EC 1.17.7.3). The enzyme from the plant Arabidopsis thaliana is active with photoreduced 5-deazaflavin but not with flavodoxin [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Okada, K. and Hase, T. Cyanobacterial non-mevalonate pathway: (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase interacts with ferredoxin in Thermosynechococcus elongatus BP-1. J. Biol. Chem. 280 (2005) 20672–20679. [DOI] [PMID: 15792953]
2.  Seemann, M., Wegner, P., Schünemann, V., Tse Sum Bui, B., Wolff, M., Marquet, A., Trautwein, A.X. and Rohmer, M. Isoprenoid biosynthesis in chloroplasts via the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE) from Arabidopsis thaliana is a [4Fe-4S] protein. J. Biol. Inorg. Chem. 10 (2005) 131–137. [DOI] [PMID: 15650872]
3.  Seemann, M., Tse Sum Bui, B., Wolff, M., Tritsch, D., Campos, N., Boronat, A., Marquet, A. and Rohmer, M. Isoprenoid biosynthesis through the methylerythritol phosphate pathway: the (E)-4-hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE) is a [4Fe-4S] protein. Angew. Chem. Int. Ed. Engl. 41 (2002) 4337–4339. [DOI] [PMID: 12434382]
4.  Seemann, M., Tse Sum Bui, B., Wolff, M., Miginiac-Maslow, M. and Rohmer, M. Isoprenoid biosynthesis in plant chloroplasts via the MEP pathway: direct thylakoid/ferredoxin-dependent photoreduction of GcpE/IspG. FEBS Lett. 580 (2006) 1547–1552. [DOI] [PMID: 16480720]
[EC 1.17.7.1 created 2003 as EC 1.17.4.3, transferred 2009 to EC 1.17.7.1, modified 2014]
 
 
EC 1.17.99.3     
Accepted name: 3α,7α,12α-trihydroxy-5β-cholestanoyl-CoA 24-hydroxylase
Reaction: (25R)-3α,7α,12α-trihydroxy-5β-cholestan-26-oyl-CoA + H2O + acceptor = (24R,25R)-3α,7α,12α,24-tetrahydroxy-5β-cholestan-26-oyl-CoA + reduced acceptor
For diagram of cholic-acid biosynthesis (sidechain), click here
Other name(s): trihydroxycoprostanoyl-CoA oxidase; THC-CoA oxidase; THCA-CoA oxidase; 3α,7α,12α-trihydroxy-5β-cholestanoyl-CoA oxidase; 3α,7α,12α-trihydroxy-5β-cholestan-26-oate 24-hydroxylase
Systematic name: (25R)-3α,7α,12α-trihydroxy-5β-cholestan-26-oyl-CoA:acceptor 24-oxidoreductase (24R-hydroxylating)
Comments: Requires ATP. The reaction in mammals possibly involves dehydrogenation to give a 24(25)-double bond followed by hydration [1]. However, in amphibians such as the Oriental fire-bellied toad (Bombina orientalis), it is probable that the product is formed via direct hydroxylation of the saturated side chain of (25R)-3α,7α,12α-trihydroxy-5β-cholestan-26-oate and not via hydration of a 24(25) double bond [5]. In microsomes, the free acid is preferred to the coenzyme A ester, whereas in mitochondria, the coenzyme A ester is preferred to the free-acid form of the substrate [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 119799-47-2
References:
1.  Gustafsson, J. Biosynthesis of cholic acid in rat liver. 24-Hydroxylation of 3α,7α,12α-trihydroxy-5β-cholestanoic acid. J. Biol. Chem. 250 (1975) 8243–8247. [PMID: 240854]
2.  Schepers, L., Van Veldhoven, P.P., Casteels, M., Eyssen, H.J. and Mannaerts, G.P. Presence of three acyl-CoA oxidases in rat liver peroxisomes. An inducible fatty acyl-CoA oxidase, a noninducible fatty acyl-CoA oxidase, and a noninducible trihydroxycoprostanoyl-CoA oxidase. J. Biol. Chem. 265 (1990) 5242–5246. [PMID: 2156865]
3.  Dieuaide-Noubhani, M., Novikov, D., Baumgart, E., Vanhooren, J.C., Fransen, M., Goethals, M., Vandekerckhove, J., Van Veldhoven, P.P. and Mannaerts, G.P. Further characterization of the peroxisomal 3-hydroxyacyl-CoA dehydrogenases from rat liver. Relationship between the different dehydrogenases and evidence that fatty acids and the C27 bile acids di- and tri-hydroxycoprostanic acids are metabolized by separate multifunctional proteins. Eur. J. Biochem. 240 (1996) 660–666. [DOI] [PMID: 8856068]
4.  Dieuaide-Noubhani, M., Novikov, D., Baumgart, E., Vanhooren, J.C., Fransen, M., Goethals, M., Vandekerckhove, J., Van Veldhoven, P.P. and Mannaerts, G.P. Erratum report. Further characterization of the peroxisomal 3-hydroxyacyl-CoA dehydrogenases from rat liver. Relationship between the different dehydrogenases and evidence that fatty acids and the C27 bile acids di- and tri-hydroxycoprostanic acids are metabolized by separate multifunctional proteins. Eur. J. Biochem. 243 (1997) 537.
5.  Pedersen, J.I., Eggertsen, G., Hellman, U., Andersson, U. and Björkhem, I. Molecular cloning and expression of cDNA encoding 3α,7α,12α-trihydroxy-5β-cholestanoyl-CoA oxidase from rabbit liver. J. Biol. Chem. 272 (1997) 18481–18489. [DOI] [PMID: 9218493]
6.  Russell, D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137–174. [DOI] [PMID: 12543708]
[EC 1.17.99.3 created 2005]
 
 
EC 1.17.99.4     
Accepted name: uracil/thymine dehydrogenase
Reaction: (1) uracil + H2O + acceptor = barbiturate + reduced acceptor
(2) thymine + H2O + acceptor = 5-methylbarbiturate + reduced acceptor
For diagram of pyrimidine catabolism, click here
Other name(s): uracil oxidase; uracil-thymine oxidase; uracil dehydrogenase
Systematic name: uracil:acceptor oxidoreductase
Comments: Forms part of the oxidative pyrimidine-degrading pathway in some microorganisms, along with EC 3.5.2.1 (barbiturase) and EC 3.5.1.95 (N-malonylurea hydrolase). Mammals, plants and other microorganisms utilize the reductive pathway, comprising EC 1.3.1.1 [dihydrouracil dehydrogenase (NAD+)] or EC 1.3.1.2 [dihydropyrimidine dehydrogenase (NADP+)], EC 3.5.2.2 (dihydropyrimidinase) and EC 3.5.1.6 (β-ureidopropionase), with the ultimate degradation products being an L-amino acid, NH3 and CO2 [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9029-00-9
References:
1.  Hayaishi, O. and Kornberg, A. Metabolism of cytosine, thymine, uracil, and barbituric acid by bacterial enzymes. J. Biol. Chem. 197 (1952) 717–723. [PMID: 12981104]
2.  Wang, T.P. and Lampen, J.O. Metabolism of pyrimidines by a soil bacterium. J. Biol. Chem. 194 (1952) 775–783. [PMID: 14927671]
3.  Wang, T.P. and Lampen, J.O. Uracil oxidase and the isolation of barbituric acid from uracil oxidation. J. Biol. Chem. 194 (1952) 785–791. [PMID: 14927672]
4.  Lara, F.J.S. On the decomposition of pyrimidines by bacteria. II. Studies with cell-free enzyme preparations. J. Bacteriol. 64 (1952) 279–285. [PMID: 14955523]
5.  Soong, C.L., Ogawa, J. and Shimizu, S. Novel amidohydrolytic reactions in oxidative pyrimidine metabolism: analysis of the barbiturase reaction and discovery of a novel enzyme, ureidomalonase. Biochem. Biophys. Res. Commun. 286 (2001) 222–226. [DOI] [PMID: 11485332]
[EC 1.17.99.4 created 1961 as EC 1.2.99.1, transferred 1984 to EC 1.1.99.19, transferred 2006 to EC 1.17.99.4]
 
 
EC 1.18.1.1     
Accepted name: rubredoxin—NAD+ reductase
Reaction: 2 reduced rubredoxin + NAD+ + H+ = 2 oxidized rubredoxin + NADH
For diagram of camphor catabolism, click here
Glossary: rubredoxin = iron-containing protein found in sulfur-metabolizing bacteria and archaea, participating in electron transfer
Other name(s): rubredoxin reductase; rubredoxin-nicotinamide adenine dinucleotide reductase; dihydronicotinamide adenine dinucleotide-rubredoxin reductase; reduced nicotinamide adenine dinucleotide-rubredoxin reductase; NADH-rubredoxin reductase; rubredoxin-NAD reductase; NADH: rubredoxin oxidoreductase; DPNH-rubredoxin reductase; NADH-rubredoxin oxidoreductase
Systematic name: rubredoxin:NAD+ oxidoreductase
Comments: Requires FAD. The enzyme from Clostridium acetobutylicum reduces rubredoxin, ferricyanide and dichlorophenolindophenol, but not ferredoxin or flavodoxin. The reaction does not occur when NADPH is substituted for NADH. Contains iron at the redox centre.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9032-27-3
References:
1.  Peterson, J.A., Kusunose, M., Kusunose, E. and Coon, M.J. Enzymatic ω-oxidation. II. Function of rubredoxin as the electron carrier in ω-hydroxylation. J. Biol. Chem. 242 (1967) 4334–4340. [PMID: 4294330]
2.  Ueda, T., Lode, E.T. and Coon, M.J. Enzymatic ω-oxidation. VI. Isolation of homogeneous reduced diphosphopyridine nucleotide-rubredoxin reductase. J. Biol. Chem. 247 (1972) 2109–2116. [PMID: 4335861]
3.  Ueda, T., Lode, E.T. and Coon, M.J. Enzymatic oxidation. VII. Reduced diphosphopyridine nucleotide-rubredoxin reductase: properties and function as an electron carrier in hydroxylation. J. Biol. Chem. 247 (1972) 5010–5016. [PMID: 4403503]
4.  Petitdemange, H., Marczak, R., Blusson, H. and Gay, R. Isolation and properties of reduced nicotinamide adenine dinucleotide rubredoxin oxidoreductase of Clostridium acetobutylicum. Biochem. Biophys. Res. Commun. 91 (1979) 1258–1265. [DOI] [PMID: 526302]
[EC 1.18.1.1 created 1972 as EC 1.6.7.2, transferred 1978 to EC 1.18.1.1, modified 2001]
 
 
EC 1.18.1.5     
Accepted name: putidaredoxin—NAD+ reductase
Reaction: reduced putidaredoxin + NAD+ = oxidized putidaredoxin + NADH + H+
For diagram of camphor catabolism, click here
Other name(s): putidaredoxin reductase; camA (gene name)
Systematic name: putidaredoxin:NAD+ oxidoreductase
Comments: Requires FAD. The enzyme from Pseudomonas putida reduces putidaredoxin. It contains a [2Fe-2S] cluster. Involved in the camphor monooxygenase system (see EC 1.14.15.1, camphor 5-monooxygenase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Roome, P.W., Jr., Philley, J.C. and Peterson, J.A. Purification and properties of putidaredoxin reductase. J. Biol. Chem. 258 (1983) 2593–2598. [PMID: 6401738]
2.  Koga, H., Yamaguchi, E., Matsunaga, K., Aramaki, H. and Horiuchi, T. Cloning and nucleotide sequences of NADH-putidaredoxin reductase gene (camA) and putidaredoxin gene (camB) involved in cytochrome P-450cam hydroxylase of Pseudomonas putida. J. Biochem. 106 (1989) 831–836. [PMID: 2613690]
3.  Peterson, J.A., Lorence, M.C. and Amarneh, B. Putidaredoxin reductase and putidaredoxin. Cloning, sequence determination, and heterologous expression of the proteins. J. Biol. Chem. 265 (1990) 6066–6073. [PMID: 2180940]
4.  Sevrioukova, I.F. and Poulos, T.L. Putidaredoxin reductase, a new function for an old protein. J. Biol. Chem. 277 (2002) 25831–25839. [DOI] [PMID: 12011076]
5.  Sevrioukova, I.F., Garcia, C., Li, H., Bhaskar, B. and Poulos, T.L. Crystal structure of putidaredoxin, the [2Fe-2S] component of the P450cam monooxygenase system from Pseudomonas putida. J. Mol. Biol. 333 (2003) 377–392. [DOI] [PMID: 14529624]
6.  Sevrioukova, I.F., Li, H. and Poulos, T.L. Crystal structure of putidaredoxin reductase from Pseudomonas putida, the final structural component of the cytochrome P450cam monooxygenase. J. Mol. Biol. 336 (2004) 889–902. [DOI] [PMID: 15095867]
7.  Smith, N., Mayhew, M., Holden, M.J., Kelly, H., Robinson, H., Heroux, A., Vilker, V.L. and Gallagher, D.T. Structure of C73G putidaredoxin from Pseudomonas putida. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 816–822. [DOI] [PMID: 15103126]
[EC 1.18.1.5 created 2012]
 
 
EC 1.19.1.1     
Accepted name: flavodoxin—NADP+ reductase
Reaction: reduced flavodoxin + NADP+ = oxidized flavodoxin + NADPH + H+
Other name(s): FPR
Systematic name: flavodoxin:NADP+ oxidoreductase
Comments: A flavoprotein (FAD). This activity occurs in some prokaryotes and algae that possess flavodoxin, and provides low-potential electrons for a variety of reactions such as nitrogen fixation, sulfur assimilation and amino acid biosynthesis. In photosynthetic organisms it is involved in the photosynthetic electron transport chain. The enzyme also catalyses EC 1.18.1.2, ferredoxin—NADP+ reductase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9029-33-8
References:
1.  McIver, L., Leadbeater, C., Campopiano, D.J., Baxter, R.L., Daff, S.N., Chapman, S.K. and Munro, A.W. Characterisation of flavodoxin NADP+ oxidoreductase and flavodoxin; key components of electron transfer in Escherichia coli. Eur. J. Biochem. 257 (1998) 577–585. [DOI] [PMID: 9839946]
2.  Leadbeater, C., McIver, L., Campopiano, D.J., Webster, S.P., Baxter, R.L., Kelly, S.M., Price, N.C., Lysek, D.A., Noble, M.A., Chapman, S.K. and Munro, A.W. Probing the NADPH-binding site of Escherichia coli flavodoxin oxidoreductase. Biochem. J. 352 (2000) 257–266. [PMID: 11085917]
3.  Wan, J.T. and Jarrett, J.T. Electron acceptor specificity of ferredoxin (flavodoxin):NADP+ oxidoreductase from Escherichia coli. Arch. Biochem. Biophys. 406 (2002) 116–126. [DOI] [PMID: 12234497]
4.  Bortolotti, A., Perez-Dorado, I., Goni, G., Medina, M., Hermoso, J.A., Carrillo, N. and Cortez, N. Coenzyme binding and hydride transfer in Rhodobacter capsulatus ferredoxin/flavodoxin NADP(H) oxidoreductase. Biochim. Biophys. Acta 1794 (2009) 199–210. [DOI] [PMID: 18973834]
5.  Bortolotti, A., Sanchez-Azqueta, A., Maya, C.M., Velazquez-Campoy, A., Hermoso, J.A., Medina, M. and Cortez, N. The C-terminal extension of bacterial flavodoxin-reductases: involvement in the hydride transfer mechanism from the coenzyme. Biochim. Biophys. Acta 1837 (2014) 33–43. [DOI] [PMID: 24016470]
6.  Skramo, S., Hersleth, H.P., Hammerstad, M., Andersson, K.K. and Rohr, A.K. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of a ferredoxin/flavodoxin-NADP(H) oxidoreductase (Bc0385) from Bacillus cereus. Acta Crystallogr. F Struct. Biol. Commun. 70 (2014) 777–780. [DOI] [PMID: 24915092]
[EC 1.19.1.1 created 2016]
 
 
EC 2.1.1.57     
Accepted name: methyltransferase cap1
Reaction: S-adenosyl-L-methionine + a 5′-(N7-methyl 5′-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5′-(N7-methyl 5′-triphosphoguanosine)-(2′-O-methyl-ribonucleotide)-[mRNA]
Other name(s): FTSJD2 (gene name); 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)-(ribonucleotide)-[mRNA] 2-O-methyltransferase
Comments: This enzyme catalyses the methylation of the ribose on the first transcribed nucleotide of mRNA or snRNA molecules. This methylation event is known as cap1, and occurs 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. [DOI] [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. [DOI] [PMID: 21310715]
[EC 2.1.1.57 created 1981 (EC 2.1.1.58 created 1981, incorporated 1984), modified 2014, modified 2021]
 
 
EC 2.1.1.64     
Accepted name: 3-demethylubiquinol 3-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3-demethylubiquinol-n = S-adenosyl-L-homocysteine + ubiquinol-n
For diagram of ubiquinol biosynthesis, click here
Glossary: 3-demethylubiquinol-n = 3-hydroxy-2-methoxy-5-methyl-6-(all-trans-polyprenyl)-1,4-benzoquinol
Other name(s): 5-demethylubiquinone-9 methyltransferase; OMHMB-methyltransferase; 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase; S-adenosyl-L-methionine:2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone-O-methyltransferase; COQ3 (gene name); Coq3 O-methyltransferase; 3-demethylubiquinone-9 3-methyltransferase; ubiG (gene name, ambiguous)
Systematic name: S-adenosyl-L-methionine:3-hydroxy-2-methoxy-5-methyl-6-(all-trans-polyprenyl)-1,4-benzoquinol 3-O-methyltransferase
Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, the human COQ3 enzyme can restore biosynthesis of ubiquinone-6 in coq3 deletion mutants of yeast [3]. The enzymes from yeast, Escherichia coli and rat also catalyse the methylation of 3,4-dihydroxy-5-all-trans-polyprenylbenzoate [3] (a reaction that is classified as EC 2.1.1.114, polyprenyldihydroxybenzoate methyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 63774-48-1
References:
1.  Houser, R.M. and Olson, R.E. 5-Demethylubiquinone-9-methyltransferase from rat liver mitochondria. Characterization, localization, and solubilization. J. Biol. Chem. 252 (1977) 4017–4021. [PMID: 863914]
2.  Leppik, R.A., Stroobant, P., Shineberg, B., Young, I.G. and Gibson, F. Membrane-associated reactions in ubiquinone biosynthesis. 2-Octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase. Biochim. Biophys. Acta 428 (1976) 146–156. [DOI] [PMID: 769831]
3.  Poon, W.W., Barkovich, R.J., Hsu, A.Y., Frankel, A., Lee, P.T., Shepherd, J.N., Myles, D.C. and Clarke, C.F. Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis. J. Biol. Chem. 274 (1999) 21665–21672. [DOI] [PMID: 10419476]
4.  Jonassen, T. and Clarke, C.F. Isolation and functional expression of human COQ3, a gene encoding a methyltransferase required for ubiquinone biosynthesis. J. Biol. Chem. 275 (2000) 12381–12387. [DOI] [PMID: 10777520]
[EC 2.1.1.64 created 1982, modified 2011]
 
 
EC 2.1.1.78     
Accepted name: isoorientin 3′-O-methyltransferase
Reaction: S-adenosyl-L-methionine + isoorientin = S-adenosyl-L-homocysteine + isoscoparin
Other name(s): isoorientin 3′-methyltransferase
Systematic name: S-adenosyl-L-methionine:isoorientin 3′-O-methyltransferase
Comments: Also acts on isoorientin 2′′-O-rhamnoside. Involved in the biosynthesis of flavones.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 83061-51-2
References:
1.  van Brederode, J., Kamps-Heinsbroek, R. and Mastenbroek, O. Biochemical and ontogenetic evidence that the ferulic acid and isoscoparin formation in silene are catalyzed by different enzymes. Z. Pflanzenphysiol. 106 (1982) 43–53.
[EC 2.1.1.78 created 1986]
 
 
EC 2.1.1.85     
Accepted name: protein-histidine N-methyltransferase
Reaction: S-adenosyl-L-methionine + protein L-histidine = S-adenosyl-L-homocysteine + protein Nτ-methyl-L-histidine
Other name(s): protein methylase IV; protein (histidine) methyltransferase; actin-specific histidine methyltransferase; S-adenosyl methionine:protein-histidine N-methyltransferase
Systematic name: S-adenosyl-L-methionine:protein-L-histidine N-tele-methyltransferase
Comments: Highly specific for histidine residues, for example, in actin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 108022-17-9
References:
1.  Vijayasarathy, C. and Narasinga Rao, B.S. Partial purification and characterisation of S-adenosylmethionine:protein-histidine N-methyltransferase from rabbit skeletal muscle. Biochim. Biophys. Acta 923 (1987) 156–165. [DOI] [PMID: 3801515]
[EC 2.1.1.85 created 1989]
 
 
EC 2.1.1.92      
Deleted entry: bergaptol O-methyltransferase. Now included with EC 2.1.1.69, 5-hydroxyfuranocoumarin 5-O-methyltransferase. The reaction with bergaptol is a specific example of the general reaction associated with EC 2.1.1.69
[EC 2.1.1.92 created 1989, deleted 2006]
 
 
EC 2.1.1.114     
Accepted name: polyprenyldihydroxybenzoate methyltransferase
Reaction: S-adenosyl-L-methionine + 3,4-dihydroxy-5-all-trans-polyprenylbenzoate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-5-all-trans-polyprenylbenzoate
For diagram of ubiquinol biosynthesis, click here
Other name(s): 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase; dihydroxyhexaprenylbenzoate methyltransferase; COQ3 (gene name); Coq3 O-methyltransferase; DHHB O-methyltransferase
Systematic name: S-adenosyl-L-methionine:3,4-dihydroxy-5-all-trans-polyprenylbenzoate 3-O-methyltransferase
Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, the human COQ3 enzyme can restore biosynthesis of ubiquinone-6 in coq3 deletion mutants of yeast [3]. The enzymes from yeast and rat also catalyse the methylation of 3-demethylubiquinol-6 and 3-demethylubiquinol-9, respectively [2] (this activity is classified as EC 2.1.1.64, 3-demethylubiquinol 3-O-methyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 139569-31-6
References:
1.  Clarke, C.F., Williams, W., Teruya, J.H. Ubiquinone biosynthesis in Saccharomyces cerevisiae. Isolation and sequence of COQ3, the 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase gene. J. Biol. Chem. 266 (1991) 16636–16641. [PMID: 1885593]
2.  Poon, W.W., Barkovich, R.J., Hsu, A.Y., Frankel, A., Lee, P.T., Shepherd, J.N., Myles, D.C. and Clarke, C.F. Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis. J. Biol. Chem. 274 (1999) 21665–21672. [DOI] [PMID: 10419476]
3.  Jonassen, T. and Clarke, C.F. Isolation and functional expression of human COQ3, a gene encoding a methyltransferase required for ubiquinone biosynthesis. J. Biol. Chem. 275 (2000) 12381–12387. [DOI] [PMID: 10777520]
4.  Xing, L., Zhu, Y., Fang, P., Wang, J., Zeng, F., Li, X., Teng, M. and Li, X. Crystallization and preliminary crystallographic studies of UbiG, an O-methyltransferase from Escherichia coli. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67 (2011) 727–729. [DOI] [PMID: 21636923]
[EC 2.1.1.114 created 1999]
 
 
EC 2.1.1.190     
Accepted name: 23S rRNA (uracil1939-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil1939 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
Other name(s): RumA; RNA uridine methyltransferase A; YgcA
Systematic name: S-adenosyl-L-methionine:23S rRNA (uracil1939-C5)-methyltransferase
Comments: The enzyme specifically methylates uracil1939 at C5 in 23S rRNA [1]. The enzyme contains an [4Fe-4S] cluster coordinated by four conserved cysteine residues [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Agarwalla, S., Kealey, J.T., Santi, D.V. and Stroud, R.M. Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J. Biol. Chem. 277 (2002) 8835–8840. [DOI] [PMID: 11779873]
2.  Lee, T.T., Agarwalla, S. and Stroud, R.M. Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure 12 (2004) 397–407. [DOI] [PMID: 15016356]
3.  Madsen, C.T., Mengel-Jorgensen, J., Kirpekar, F. and Douthwaite, S. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738–4746. [PMID: 12907714]
4.  Persaud, C., Lu, Y., Vila-Sanjurjo, A., Campbell, J.L., Finley, J. and O'Connor, M. Mutagenesis of the modified bases, m5U1939 and Ψ2504, in Escherichia coli 23S rRNA. Biochem. Biophys. Res. Commun. 392 (2010) 223–227. [DOI] [PMID: 20067766]
5.  Agarwalla, S., Stroud, R.M. and Gaffney, B.J. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J. Biol. Chem. 279 (2004) 34123–34129. [DOI] [PMID: 15181002]
6.  Lee, T.T., Agarwalla, S. and Stroud, R.M. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120 (2005) 599–611. [DOI] [PMID: 15766524]
[EC 2.1.1.190 created 2010]
 
 
EC 2.1.1.197     
Accepted name: malonyl-[acyl-carrier protein] O-methyltransferase
Reaction: S-adenosyl-L-methionine + malonyl-[acyl-carrier protein] = S-adenosyl-L-homocysteine + malonyl-[acyl-carrier protein] methyl ester
Other name(s): BioC
Systematic name: S-adenosyl-L-methionine:malonyl-[acyl-carrier protein] O-methyltransferase
Comments: Involved in an early step of biotin biosynthesis in Gram-negative bacteria. This enzyme catalyses the transfer of a methyl group to the ω-carboxyl group of malonyl-[acyl-carrier protein] forming a methyl ester. The methyl ester is recognized by the fatty acid synthetic enzymes, which process it via the fatty acid elongation cycle to give pimelyl-[acyl-carrier-protein] methyl ester [5]. While the enzyme can also accept malonyl-CoA, it has a much higher activity with malonyl-[acyl-carrier protein] [6]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Del Campillo-Campbell, A., Kayajanian, G., Campbell, A. and Adhya, S. Biotin-requiring mutants of Escherichia coli K-12. J. Bacteriol. 94 (1967) 2065–2066. [PMID: 4864413]
2.  Rolfe, B. and Eisenberg, M.A. Genetic and biochemical analysis of the biotin loci of Escherichia coli K-12. J. Bacteriol. 96 (1968) 515–524. [PMID: 4877129]
3.  Otsuka, A.J., Buoncristiani, M.R., Howard, P.K., Flamm, J., Johnson, C., Yamamoto, R., Uchida, K., Cook, C., Ruppert, J. and Matsuzaki, J. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. J. Biol. Chem. 263 (1988) 19577–19585. [PMID: 3058702]
4.  Cleary, P.P. and Campbell, A. Deletion and complementation analysis of biotin gene cluster of Escherichia coli. J. Bacteriol. 112 (1972) 830–839. [PMID: 4563978]
5.  Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. 6 (2010) 682–688. [DOI] [PMID: 20693992]
6.  Lin, S. and Cronan, J.E. The BioC O-methyltransferase catalyzes methyl esterification of malonyl-acyl carrier protein, an essential step in biotin synthesis. J. Biol. Chem. 287 (2012) 37010–37020. [DOI] [PMID: 22965231]
[EC 2.1.1.197 created 2010, modified 2013]
 
 
EC 2.1.1.201     
Accepted name: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase
Reaction: S-adenosyl-L-methionine + 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol = S-adenosyl-L-homocysteine + 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol
For diagram of ubiquinol biosynthesis, click here
Other name(s): ubiE (gene name, ambiguous)
Systematic name: S-adenosyl-L-methionine:2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol 5-C-methyltransferase
Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, when the COQ5 gene from Saccharomyces cerevisiae is introduced into Escherichia coli, it complements the respiratory deficiency of an ubiE mutant [3]. The bifunctional enzyme from Escherichia coli also catalyses the methylation of demethylmenaquinol-8 (this activity is classified as EC 2.1.1.163) [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Lee, P.T., Hsu, A.Y., Ha, H.T. and Clarke, C.F. A C-methyltransferase involved in both ubiquinone and menaquinone biosynthesis: isolation and identification of the Escherichia coli ubiE gene. J. Bacteriol. 179 (1997) 1748–1754. [DOI] [PMID: 9045837]
2.  Young, I.G., McCann, L.M., Stroobant, P. and Gibson, F. Characterization and genetic analysis of mutant strains of Escherichia coli K-12 accumulating the biquinone precursors 2-octaprenyl-6-methoxy-1,4-benzoquinone and 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone. J. Bacteriol. 105 (1971) 769–778. [PMID: 4323297]
3.  Dibrov, E., Robinson, K.M. and Lemire, B.D. The COQ5 gene encodes a yeast mitochondrial protein necessary for ubiquinone biosynthesis and the assembly of the respiratory chain. J. Biol. Chem. 272 (1997) 9175–9181. [DOI] [PMID: 9083048]
4.  Barkovich, R.J., Shtanko, A., Shepherd, J.A., Lee, P.T., Myles, D.C., Tzagoloff, A. and Clarke, C.F. Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis. J. Biol. Chem. 272 (1997) 9182–9188. [DOI] [PMID: 9083049]
[EC 2.1.1.201 created 2011]
 
 
EC 2.1.1.251     
Accepted name: methylated-thiol—coenzyme M methyltransferase
Reaction: methanethiol + CoM = methyl-CoM + hydrogen sulfide (overall reaction)
(1a) methanethiol + a [Co(I) methylated-thiol-specific corrinoid protein] = a [methyl-Co(III) methylated-thiol-specific corrinoid protein] + hydrogen sulfide
(1b) a [methyl-Co(III) methylated-thiol-specific corrinoid protein] + CoM = methyl-CoM + a [Co(I) methylated-thiol-specific corrinoid protein]
Glossary: CoM = coenzyme M = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
Other name(s): mtsA (gene name)
Systematic name: methylated-thiol:CoM methyltransferase
Comments: The enzyme, which is involved in methanogenesis from methylated thiols, such as methane thiol, dimethyl sulfide, and 3-(methylsulfanyl)propanoate, catalyses two successive steps - the transfer of a methyl group from the substrate to the cobalt cofactor of a methylated-thiol-specific corrinoid protein (MtsB), and the subsequent transfer of the methyl group from the corrinoid protein to CoM. With most other methanogenesis substrates this process is carried out by two different enzymes (for example, EC 2.1.1.90, methanol—corrinoid protein Co-methyltransferase, and EC 2.1.1.246, [methyl-Co(III) methanol-specific corrinoid protein]—coenzyme M methyltransferase). The cobalt is oxidized during methylation from the Co(I) state to the Co(III) state, and is reduced back to the Co(I) form during demethylation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Paul, L. and Krzycki, J.A. Sequence and transcript analysis of a novel Methanosarcina barkeri methyltransferase II homolog and its associated corrinoid protein homologous to methionine synthase. J. Bacteriol. 178 (1996) 6599–6607. [DOI] [PMID: 8932317]
2.  Tallant, T.C. and Krzycki, J.A. Methylthiol:coenzyme M methyltransferase from Methanosarcina barkeri, an enzyme of methanogenesis from dimethylsulfide and methylmercaptopropionate. J. Bacteriol. 179 (1997) 6902–6911. [DOI] [PMID: 9371433]
3.  Tallant, T.C., Paul, L. and Krzycki, J.A. The MtsA subunit of the methylthiol:coenzyme M methyltransferase of Methanosarcina barkeri catalyses both half-reactions of corrinoid-dependent dimethylsulfide: coenzyme M methyl transfer. J. Biol. Chem. 276 (2001) 4485–4493. [DOI] [PMID: 11073950]
[EC 2.1.1.251 created 2012]
 
 
EC 2.1.1.296     
Accepted name: methyltransferase cap2
Reaction: S-adenosyl-L-methionine + a 5′-(N7-methyl 5′-triphosphoguanosine)-(2′-O-methyl-ribonucleotide)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5′-(N7-methyl 5′-triphosphoguanosine)-(2′-O-methyl-ribonucleotide)-(2′-O-methyl-ribonucleotide)-[mRNA]
Other name(s): CMTR2 (gene name); MTR2; cap2-MTase; mRNA (nucleoside-2′-O)-methyltransferase (ambiguous)
Systematic name: S-adenosyl-L-methionine:5′-(N7-methyl 5′-triphosphoguanosine)-(2′-O-methyl-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 ribonucleotide is not methylated (see EC 2.1.1.57, methyltransferase cap1), but with lower efficiency [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
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. [DOI] [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. [DOI] [PMID: 21310715]
[EC 2.1.1.296 created 2014, modified 2021]
 
 
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [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. [DOI] [PMID: 15629922]
[EC 2.1.1.297 created 2014]
 
 
EC 2.1.1.298     
Accepted name: ribosomal protein uL3 N5-glutamine methyltransferase
Reaction: S-adenosyl-L-methionine + [ribosomal protein uL3]-L-glutamine = S-adenosyl-L-homocysteine + [ribosomal protein uL3]-N5-methyl-L-glutamine
Other name(s): YfcB; PrmB
Systematic name: S-adenosyl-L-methionine:[ribosomal protein uL3]-L-glutamine (N5-glutamine)-methyltransferase
Comments: Modifies the glutamine residue in the glycylglycylglutamine (GGQ) motif of ribosomal protein uL3 (Gln150 in the protein from the bacterium Escherichia coli). The enzyme does not act on peptide chain release factor 1 or 2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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. [DOI] [PMID: 11847124]
[EC 2.1.1.298 created 2014, modified 2023]
 
 
EC 2.1.1.320     
Accepted name: type II protein arginine methyltransferase
Reaction: 2 S-adenosyl-L-methionine + [protein]-L-arginine = 2 S-adenosyl-L-homocysteine + [protein]-Nω,Nω′-dimethyl-L-arginine (overall reaction)
(1a) S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-Nω-methyl-L-arginine
(1b) S-adenosyl-L-methionine + [protein]-Nω-methyl-L-arginine = S-adenosyl-L-homocysteine + [protein]-Nω,Nω′-dimethyl-L-arginine
Other name(s): PRMT5 (gene name); PRMT9 (gene name)
Systematic name: S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nω,Nω′-dimethyl-L-arginine-forming)
Comments: The enzyme catalyses the methylation of one of the terminal guanidino nitrogen atoms in arginine residues within proteins, forming monomethylarginine, followed by the methylation of the second terminal nitrogen atom to form a symmetrical dimethylarginine. The mammalian enzyme is active in both the nucleus and the cytoplasm, and plays a role in the assembly of snRNP core particles by methylating certain small nuclear ribonucleoproteins. cf. EC 2.1.1.319, type I protein arginine methyltransferase, EC 2.1.1.321, type III protein arginine methyltransferase, and EC 2.1.1.322, type IV protein arginine methyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Branscombe, T.L., Frankel, A., Lee, J.H., Cook, J.R., Yang, Z., Pestka, S. and Clarke, S. PRMT5 (Janus kinase-binding protein 1) catalyzes the formation of symmetric dimethylarginine residues in proteins. J. Biol. Chem. 276 (2001) 32971–32976. [DOI] [PMID: 11413150]
2.  Wang, X., Zhang, Y., Ma, Q., Zhang, Z., Xue, Y., Bao, S. and Chong, K. SKB1-mediated symmetric dimethylation of histone H4R3 controls flowering time in Arabidopsis. EMBO J. 26 (2007) 1934–1941. [DOI] [PMID: 17363895]
3.  Lacroix, M., El Messaoudi, S., Rodier, G., Le Cam, A., Sardet, C. and Fabbrizio, E. The histone-binding protein COPR5 is required for nuclear functions of the protein arginine methyltransferase PRMT5. EMBO Rep. 9 (2008) 452–458. [DOI] [PMID: 18404153]
4.  Chari, A., Golas, M.M., Klingenhager, M., Neuenkirchen, N., Sander, B., Englbrecht, C., Sickmann, A., Stark, H. and Fischer, U. An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs. Cell 135 (2008) 497–509. [DOI] [PMID: 18984161]
5.  Antonysamy, S., Bonday, Z., Campbell, R.M., Doyle, B., Druzina, Z., Gheyi, T., Han, B., Jungheim, L.N., Qian, Y., Rauch, C., Russell, M., Sauder, J.M., Wasserman, S.R., Weichert, K., Willard, F.S., Zhang, A. and Emtage, S. Crystal structure of the human PRMT5:MEP50 complex. Proc. Natl. Acad. Sci. USA 109 (2012) 17960–17965. [DOI] [PMID: 23071334]
6.  Hadjikyriacou, A., Yang, Y., Espejo, A., Bedford, M.T. and Clarke, S.G. Unique features of human protein arginine methyltransferase 9 (PRMT9) and its substrate RNA splicing factor SF3B2. J. Biol. Chem. 290 (2015) 16723–16743. [DOI] [PMID: 25979344]
[EC 2.1.1.320 created 2015]
 
 
EC 2.1.1.326     
Accepted name: N-acetyldemethylphosphinothricin P-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + N-acetyldemethylphosphinothricin + reduced acceptor = S-adenosyl-L-homocysteine + 5′-deoxyadenosine + L-methionine + N-acetylphosphinothricin + oxidized acceptor
Glossary: N-acetyldemethylphosphinothricin = (2S)-2-acetamido-4-phosphinatobutanoate
Other name(s): phpK (gene name); bcpD (gene name); P-methylase
Systematic name: S-adenosyl-L-methionine:N-acetyldemethylphosphinothricin P-methyltransferase
Comments: The enzyme was originally characterized from bacteria that produce the tripeptides bialaphos and phosalacine, which inhibit plant and bacterial glutamine synthetases. It is a radical S-adenosyl-L-methionine (SAM) enzyme that contains a [4Fe-4S] center and a methylcob(III)alamin cofactor. According to the proposed mechanism, the reduced iron-sulfur center donates an electron to SAM, resulting in homolytic cleavage of the carbon-sulfur bond to form a 5′-deoxyadenosyl radical that abstracts the hydrogen atom from the P-H bond of the substrate, forming a phosphinate-centered radical. This radical reacts with methylcob(III)alamin to produce the methylated product and cob(II)alamin, which is reduced by an unknown donor to cob(I)alamin. A potential route for restoring the latter back to methylcob(III)alamin is a nucleophilic attack on a second SAM molecule. The enzyme acts in vivo on N-acetyldemethylphosphinothricin-L-alanyl-L-alanine or N-acetyl-demethylphosphinothricin-L-alanyl-L-leucine, the intermediates in the biosynthesis of bialaphos and phosalacine, respectively. This transformation produces the only example of a carbon-phosphorus-carbon linkage known to occur in nature.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kamigiri, K., Hidaka, T., Imai, S., Murakami, T. and Seto, H. Studies on the biosynthesis of bialaphos (SF-1293) 12. C-P bond formation mechanism of bialaphos: discovery of a P-methylation enzyme. J. Antibiot. (Tokyo) 45 (1992) 781–787. [PMID: 1624380]
2.  Hidaka, T., Hidaka, M., Kuzuyama, T. and Seto, H. Sequence of a P-methyltransferase-encoding gene isolated from a bialaphos-producing Streptomyces hygroscopicus. Gene 158 (1995) 149–150. [DOI] [PMID: 7789803]
3.  Werner, W.J., Allen, K.D., Hu, K., Helms, G.L., Chen, B.S. and Wang, S.C. In vitro phosphinate methylation by PhpK from Kitasatospora phosalacinea. Biochemistry 50 (2011) 8986–8988. [DOI] [PMID: 21950770]
4.  Allen, K.D. and Wang, S.C. Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217. Biochim. Biophys. Acta 1844 (2014) 2135–2144. [DOI] [PMID: 25224746]
5.  Hu, K., Werner, W.J., Allen, K.D. and Wang, S.C. Investigation of enzymatic C-P bond formation using multiple quantum HCP nuclear magnetic resonance spectroscopy. Magn. Reson. Chem. 53 (2015) 267–272. [DOI] [PMID: 25594737]
[EC 2.1.1.326 created 2016]
 
 
EC 2.1.1.344     
Accepted name: ornithine lipid N-methyltransferase
Reaction: 3 S-adenosyl-L-methionine + an ornithine lipid = 3 S-adenosyl-L-homocysteine + an N,N,N-trimethylornithine lipid (overall reaction)
(1a) S-adenosyl-L-methionine + an ornithine lipid = S-adenosyl-L-homocysteine + an N-methylornithine lipid
(1b) S-adenosyl-L-methionine + an N-methylornithine lipid = S-adenosyl-L-homocysteine + an N,N-dimethylornithine lipid
(1c) S-adenosyl-L-methionine + an N,N-dimethylornithine lipid = S-adenosyl-L-homocysteine + an N,N,N-trimethylornithine lipid
Glossary: an ornithine lipid = an Nα-[(3R)-3-(acyloxy)acyl]-L-ornithine
Other name(s): olsG (gene name)
Systematic name: S-adenosyl-L-methionine:ornithine lipid N-methyltransferase
Comments: The enzyme, characterized from the bacterium Singulisphaera acidiphila, catalyses three successive methylations of the terminal δ-nitrogen in ornithine lipids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Escobedo-Hinojosa, W.I., Vences-Guzman, M.A., Schubotz, F., Sandoval-Calderon, M., Summons, R.E., Lopez-Lara, I.M., Geiger, O. and Sohlenkamp, C. OlsG (Sinac_1600) is an ornithine lipid N-methyltransferase from the planctomycete Singulisphaera acidiphila. J. Biol. Chem. 290 (2015) 15102–15111. [DOI] [PMID: 25925947]
[EC 2.1.1.344 created 2017]
 
 
EC 2.1.1.355     
Accepted name: [histone H3]-lysine9 N-trimethyltransferase
Reaction: 3 S-adenosyl-L-methionine + a [histone H3]-L-lysine9 = 3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine9 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine9
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine9 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine9
(1c) S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
Other name(s): KMT1A (gene name); KMT1B (gene name); KMT1C (gene name); KMT1D (gene name); KMT1F (gene name); MT8 (gene name); SUV39H1 (gene name); G9A (gene name); EHMT1 (gene name); PRDM2 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine9 N6-trimethyltransferase
Comments: This entry describes several enzymes that successively methylate the L-lysine9 residue of histone H3 (H3K9), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. In general, the methylation of H3K9 leads to transcriptional repression of the affected target genes. cf. EC 2.1.1.367, [histone H3]-lysine9 N-methyltransferase, EC 2.1.1.368, [histone H3]-lysine9 N-dimethyltransferase, and EC 2.1.1.366, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  O'Carroll, D., Scherthan, H., Peters, A.H., Opravil, S., Haynes, A.R., Laible, G., Rea, S., Schmid, M., Lebersorger, A., Jerratsch, M., Sattler, L., Mattei, M.G., Denny, P., Brown, S.D., Schweizer, D. and Jenuwein, T. Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression. Mol. Cell Biol. 20 (2000) 9423–9433. [PMID: 11094092]
2.  Schotta, G., Ebert, A., Krauss, V., Fischer, A., Hoffmann, J., Rea, S., Jenuwein, T., Dorn, R. and Reuter, G. Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J. 21 (2002) 1121–1131. [PMID: 11867540]
3.  Tachibana, M., Sugimoto, K., Nozaki, M., Ueda, J., Ohta, T., Ohki, M., Fukuda, M., Takeda, N., Niida, H., Kato, H. and Shinkai, Y. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 16 (2002) 1779–1791. [PMID: 12130538]
4.  Schultz, D.C., Ayyanathan, K., Negorev, D., Maul, G.G. and Rauscher, F.J., 3rd. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 16 (2002) 919–932. [PMID: 11959841]
5.  Kim, K.C., Geng, L. and Huang, S. Inactivation of a histone methyltransferase by mutations in human cancers. Cancer Res. 63 (2003) 7619–7623. [PMID: 14633678]
6.  Wu, H., Min, J., Lunin, V.V., Antoshenko, T., Dombrovski, L., Zeng, H., Allali-Hassani, A., Campagna-Slater, V., Vedadi, M., Arrowsmith, C.H., Plotnikov, A.N. and Schapira, M. Structural biology of human H3K9 methyltransferases. PLoS One 5:e8570 (2010). [PMID: 20084102]
[EC 2.1.1.355 created 1976 as EC 2.1.1.43, modified 1982, modified 1983, part transferred 2019 to EC 2.1.1.355, modified 2020]
 
 
EC 2.1.3.5     
Accepted name: oxamate carbamoyltransferase
Reaction: carbamoyl phosphate + oxamate = phosphate + N-carbamoyl-2-oxoglycine
For diagram of AMP catabolism, click here
Other name(s): oxamic transcarbamylase
Systematic name: carbamoyl-phosphate:oxamate carbamoyltransferase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 62213-52-9
References:
1.  Bojanowski, R., Gaudy, E., Valentine, R.C. and Wolfe, R.S. Oxamic transcarbamylase of Streptococcus allantoicus. J. Bacteriol. 87 (1964) 75–80. [PMID: 14102876]
[EC 2.1.3.5 created 1976]
 
 
EC 2.1.3.9     
Accepted name: N-acetylornithine carbamoyltransferase
Reaction: carbamoyl phosphate + N2-acetyl-L-ornithine = phosphate + N-acetyl-L-citrulline
Glossary: N-acetyl-L-citrulline = N5-acetylcarbamoyl-L-ornithine
Other name(s): acetylornithine transcarbamylase; N-acetylornithine transcarbamylase; AOTC; carbamoyl-phosphate:2-N-acetyl-L-ornithine carbamoyltransferase; AOTCase
Systematic name: carbamoyl-phosphate:N2-acetyl-L-ornithine carbamoyltransferase
Comments: Differs from EC 2.1.3.3, ornithine carbamoyltransferase. This enzyme replaces EC 2.1.3.3 in the canonic arginine biosynthetic pathway of several Eubacteria and has no catalytic activity with L-ornithine as substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 890853-54-0
References:
1.  Shi, D., Morizono, H., Yu, X., Roth, L., Caldovic, L., Allewell, N.M., Malamy, M.H. and Tuchman, M. Crystal structure of N-acetylornithine transcarbamylase from Xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several Eubacteria. J. Biol. Chem. 280 (2005) 14366–14369. [DOI] [PMID: 15731101]
2.  Morizono, H., Cabrera-Luque, J., Shi, D., Gallegos, R., Yamaguchi, S., Yu, X., Allewell, N.M., Malamy, M.H. and Tuchman, M. Acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis. J. Bacteriol. 188 (2006) 2974–2982. [DOI] [PMID: 16585758]
[EC 2.1.3.9 created 2005]
 
 
EC 2.1.3.14      
Deleted entry: tobramycin carbamoyltransferase. The enzyme has been replaced by EC 6.1.2.2, nebramycin 5′ synthase
[EC 2.1.3.14 created 2013, deleted 2014]
 
 
EC 2.3.1.9     
Accepted name: acetyl-CoA C-acetyltransferase
Reaction: 2 acetyl-CoA = CoA + acetoacetyl-CoA (overall reaction)
(1a) acetyl-CoA + [acetyl-CoA C-acetyltransferase]-L-cysteine = [acetyl-CoA C-acetyltransferase]-S-acetyl-L-cysteine + CoA
(1b) [acetyl-CoA C-acetyltransferase]-S-acetyl-L-cysteine + acetyl-CoA = acetoacetyl-CoA + [acetyl-CoA C-acetyltransferase]-L-cysteine
For diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here and for diagram of mevalonate biosynthesis, click here
Other name(s): acetoacetyl-CoA thiolase; β-acetoacetyl coenzyme A thiolase; 2-methylacetoacetyl-CoA thiolase [misleading]; 3-oxothiolase; acetyl coenzyme A thiolase; acetyl-CoA acetyltransferase; acetyl-CoA:N-acetyltransferase; thiolase II; type II thiolase
Systematic name: acetyl-CoA:acetyl-CoA C-acetyltransferase
Comments: The enzyme, found in both eukaryotes and prokaryotes, catalyses the Claisen condensation of an acetyl-CoA and an acyl-CoA (often another acetyl-CoA), leading to the formation of an acyl-CoA that is longer by two carbon atoms. The reaction starts with the acylation of a nucleophilic cysteine at the active site, usually by acetyl-CoA but potentially by a different acyl-CoA, with concomitant release of CoA. In the second step the acyl group is transferred to an acetyl-CoA molecule. cf. EC 2.3.1.16, acetyl-CoA C-acyltransferase.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-46-7
References:
1.  Lynen, F. and Ochoa, S. Enzymes of fatty acid metabolism. Biochim. Biophys. Acta 12 (1953) 299–314. [DOI] [PMID: 13115439]
2.  Stern, J.R., Drummond, G.I., Coon, M.J. and del Campillo, A. Enzymes of ketone body metabolism. I. Purification of an acetoacetate-synthesizing enzyme from ox liver. J. Biol. Chem. 235 (1960) 313–317. [PMID: 13834445]
[EC 2.3.1.9 created 1961, modified 2019]
 
 
EC 2.3.1.16     
Accepted name: acetyl-CoA C-acyltransferase
Reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA (overall reaction)
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cysteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cysteine
(1b) acyl-CoA + [acetyl-CoA C-acyltransferase]-L-cysteine = [acetyl-CoA C-acyltransferase]-S-acyl-L-cysteine + CoA
For diagram of aerobic phenylacetate catabolism, click here and for diagram of Benzoyl-CoA catabolism, click here
Other name(s): β-ketothiolase; 3-ketoacyl-CoA thiolase; KAT; β-ketoacyl coenzyme A thiolase; β-ketoacyl-CoA thiolase; β-ketoadipyl coenzyme A thiolase; β-ketoadipyl-CoA thiolase; 3-ketoacyl CoA thiolase; 3-ketoacyl coenzyme A thiolase; 3-ketoacyl thiolase; 3-ketothiolase; 3-oxoacyl-CoA thiolase; 3-oxoacyl-coenzyme A thiolase; 6-oxoacyl-CoA thiolase; acetoacetyl-CoA β-ketothiolase; acetyl-CoA acyltransferase; ketoacyl-CoA acyltransferase; ketoacyl-coenzyme A thiolase; long-chain 3-oxoacyl-CoA thiolase; oxoacyl-coenzyme A thiolase; pro-3-ketoacyl-CoA thiolase; thiolase I; type I thiolase; 2-methylacetoacetyl-CoA thiolase [misleading]
Systematic name: acyl-CoA:acetyl-CoA C-acyltransferase
Comments: The enzyme, found in both eukaryotes and in prokaryotes, is involved in degradation pathways such as fatty acid β-oxidation. The enzyme acts on 3-oxoacyl-CoAs to produce acetyl-CoA and an acyl-CoA shortened by two carbon atoms. The reaction starts with the acylation of a nucleophilic cysteine at the active site by a 3-oxoacyl-CoA, with the concomitant release of acetyl-CoA. In the second step the acyl group is transferred to CoA. Most enzymes have a broad substrate range for the 3-oxoacyl-CoA. cf. EC 2.3.1.9, acetyl-CoA C-acetyltransferase.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9029-97-4
References:
1.  Beinert, H., Bock, R.M., Goldman, D.S., Green, D.E., Mahler, H.R., Mii, S., Stansly, P.G. and Wakil, S.J. A synthesis of dl-cortisone acetate. J. Am. Chem. Soc. 75 (1953) 4111–4112.
2.  Goldman, D.S. Studies on the fatty acid oxidizing system of animal tissue. VII. The β-ketoacyl coenzyme A cleavage enzyme. J. Biol. Chem. 208 (1954) 345–357. [PMID: 13174544]
3.  Stern, J.R., Coon, M.J. and del Campillo, A. Enzymatic breakdown and synthesis of acetoacetate. Nature 171 (1953) 28–30. [PMID: 13025466]
[EC 2.3.1.16 created 1961, modified 2019]
 
 
EC 2.3.1.28     
Accepted name: chloramphenicol O-acetyltransferase
Reaction: acetyl-CoA + chloramphenicol = CoA + chloramphenicol 3-acetate
Other name(s): chloramphenicol acetyltransferase; chloramphenicol acetylase; chloramphenicol transacetylase; CAT I; CAT II; CAT III
Systematic name: acetyl-CoA:chloramphenicol 3-O-acetyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9040-07-7
References:
1.  Shaw, W.V. The enzymatic acetylation of chloramphenicol by extracts of R factor-resistant Escherichia coli. J. Biol. Chem. 242 (1967) 687–693. [PMID: 5335032]
2.  Shaw, W.V. and Brodsky, R.F. Characterization of chloramphenicol acetyltransferase from chloramphenicol-resistant Staphylococcus aureus. J. Bacteriol. 95 (1968) 28–36. [PMID: 4965980]
[EC 2.3.1.28 created 1972]
 
 
EC 2.3.1.39     
Accepted name: [acyl-carrier-protein] S-malonyltransferase
Reaction: malonyl-CoA + an [acyl-carrier protein] = CoA + a malonyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): [acyl carrier protein]malonyltransferase; FabD; malonyl coenzyme A-acyl carrier protein transacylase; malonyl transacylase; malonyl transferase; malonyl-CoA-acyl carrier protein transacylase; malonyl-CoA:[acyl-carrier-protein] S-malonyltransferase; malonyl-CoA:ACP transacylase; malonyl-CoA:ACP-SH transacylase; malonyl-CoA:AcpM transacylase; malonyl-CoA:acyl carrier protein transacylase; malonyl-CoA:acyl-carrier-protein transacylase; malonyl-CoA/dephospho-CoA acyltransferase; MAT; MCAT; MdcH
Systematic name: malonyl-CoA:[acyl-carrier protein] S-malonyltransferase
Comments: This enzyme, along with EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, is essential for the initiation of fatty-acid biosynthesis in bacteria. This enzyme also provides the malonyl groups for polyketide biosynthesis [7]. The product of the reaction, malonyl-ACP, is an elongation substrate in fatty-acid biosynthesis. In Mycobacterium tuberculosis, holo-ACP (the product of EC 2.7.8.7, holo-[acyl-carrier-protein] synthase) is the preferred substrate [5]. This enzyme also forms part of the multienzyme complexes EC 4.1.1.88, biotin-independent malonate decarboxylase and EC 7.2.4.4, biotin-dependent malonate decarboxylase. Malonylation of ACP is immediately followed by decarboxylation within the malonate-decarboxylase complex to yield acetyl-ACP, the catalytically active species of the decarboxylase [12]. In the enzyme from Klebsiella pneumoniae, methylmalonyl-CoA can also act as a substrate but acetyl-CoA cannot [10] whereas the enzyme from Pseudomonas putida can use both as substrates [11]. The ACP subunit found in fatty-acid biosynthesis contains a pantetheine-4′-phosphate cofactor; that from malonate decarboxylase also contains pantetheine-4′-phosphate but in the form of a 2′-(5-triphosphoribosyl)-3′-dephospho-CoA cofactor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37257-17-3
References:
1.  Alberts, A.W., Majerus, P.W. and Vagelos, P.R. Acetyl-CoA acyl carrier protein transacylase. Methods Enzymol. 14 (1969) 50–53. [DOI]
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [PMID: 4561013]
3.  Williamson, I.P. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVII. Preparation and general properties of acetyl coenzyme A and malonyl coenzyme A-acyl carrier protein transacylases. J. Biol. Chem. 241 (1966) 2326–2332. [DOI] [PMID: 5330116]
4.  Joshi, V.C. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XXVI. Purification and properties of malonyl-coenzyme A--acyl carrier protein transacylase of Escherichia coli. Arch. Biochem. Biophys. 143 (1971) 493–505. [DOI] [PMID: 4934182]
5.  Kremer, L., Nampoothiri, K.M., Lesjean, S., Dover, L.G., Graham, S., Betts, J., Brennan, P.J., Minnikin, D.E., Locht, C. and Besra, G.S. Biochemical characterization of acyl carrier protein (AcpM) and malonyl-CoA:AcpM transacylase (mtFabD), two major components of Mycobacterium tuberculosis fatty acid synthase II. J. Biol. Chem. 276 (2001) 27967–27974. [DOI] [PMID: 11373295]
6.  Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J., O'Connell, J.D., 3rd, Khosla, C. and Stroud, R.M. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 11 (2003) 147–154. [DOI] [PMID: 12575934]
7.  Szafranska, A.E., Hitchman, T.S., Cox, R.J., Crosby, J. and Simpson, T.J. Kinetic and mechanistic analysis of the malonyl CoA:ACP transacylase from Streptomyces coelicolor indicates a single catalytically competent serine nucleophile at the active site. Biochemistry 41 (2002) 1421–1427. [DOI] [PMID: 11814333]
8.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [DOI] [PMID: 9208947]
9.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [DOI] [PMID: 10561613]
10.  Hoenke, S. and Dimroth, P. Formation of catalytically active acetyl-S-malonate decarboxylase requires malonyl-coenzyme A:acyl carrier protein transacylase as auxiliary enzyme. Eur. J. Biochem. 259 (1999) 181–187. [DOI] [PMID: 9914491]
11.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [DOI] [PMID: 9851033]
12.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 2.3.1.39 created 1972, modified 2006, modified 2008]
 
 
EC 2.3.1.47     
Accepted name: 8-amino-7-oxononanoate synthase
Reaction: pimeloyl-[acyl-carrier protein] + L-alanine = 8-amino-7-oxononanoate + CO2 + holo-[acyl-carrier protein]
Glossary: pimeloyl-[acyl-carrier protein] = 6-carboxyhexanoyl-[acyl-carrier protein]
Other name(s): 7-keto-8-aminopelargonic acid synthetase; 7-keto-8-aminopelargonic synthetase; 8-amino-7-oxopelargonate synthase; bioF (gene name)
Systematic name: 6-carboxyhexanoyl-[acyl-carrier protein]:L-alanine C-carboxyhexanoyltransferase (decarboxylating)
Comments: A pyridoxal-phosphate protein. The enzyme catalyses the decarboxylative condensation of L-alanine and pimeloyl-[acyl-carrier protein], a key step in the pathway for biotin biosynthesis. Pimeloyl-CoA can be used with lower efficiency [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-61-0
References:
1.  Eisenberg, M.A. and Star, C. Synthesis of 7-oxo-8-aminopelargonic acid, a biotin vitamer, in cell-free extracts of Escherichia coli biotin auxotrophs. J. Bacteriol. 96 (1968) 1291–1297. [PMID: 4879561]
2.  Alexeev, D., Alexeeva, M., Baxter, R.L., Campopiano, D.J., Webster, S.P. and Sawyer, L. The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme. J. Mol. Biol. 284 (1998) 401–419. [DOI] [PMID: 9813126]
3.  Ploux, O., Breyne, O., Carillon, S. and Marquet, A. Slow-binding and competitive inhibition of 8-amino-7-oxopelargonate synthase, a pyridoxal-5′-phosphate-dependent enzyme involved in biotin biosynthesis, by substrate and intermediate analogs. Kinetic and binding studies. Eur. J. Biochem. 259 (1999) 63–70. [PMID: 9914476]
4.  Webster, S.P. , Alexeev. D., Campopiano, D.J., Watt, R.M., Alexeeva, M., Sawyer, L. and Baxter, R. Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies. Biochemistry 39 (2000) 516–528. [DOI] [PMID: 10642176]
5.  Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. 6 (2010) 682–688. [DOI] [PMID: 20693992]
[EC 2.3.1.47 created 1976, modified 2013]
 
 
EC 2.3.1.73     
Accepted name: diacylglycerol—sterol O-acyltransferase
Reaction: a 1,2-diacyl-sn-glycerol + sterol = a 1-acyl-sn-glycerol + sterol ester
Other name(s): 1,2-diacyl-sn-glycerol:sterol acyl transferase
Systematic name: 1,2-diacyl-sn-glycerol:sterol O-acyltransferase
Comments: Cholesterol, sitosterol, campesterol and diacylglycerol can act as acceptors. Transfers a number of long-chain fatty acyl groups.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 79586-23-5
References:
1.  Bartlett, K., Keat, M.J. and Mercer, E.I. Biosynthesis of sterol esters in Phycomyces blakesleeanus. Phytochemistry 13 (1974) 1107–1113.
2.  Garcia, R.E. and Mudd, J.B. Metabolism of monoacylglycerol and diacylglycerol by enzyme preparations from spinach leaves. Arch. Biochem. Biophys. 191 (1978) 487–493. [DOI] [PMID: 742884]
3.  Garcia, R.E. and Mudd, J.B. 1,2-Diacyl-sn-glycerol:sterol acyl transferase from spinach leaves (Spinacia oleracea L.). Methods Enzymol. 71 (1981) 768–772.
[EC 2.3.1.73 created 1984]
 
 
EC 2.3.1.160     
Accepted name: vinorine synthase
Reaction: acetyl-CoA + 16-epivellosimine = CoA + vinorine
For diagram of ajmaline, vinorine, vomilenine and raucaffricine biosynthesis, click here
Systematic name: acyl-CoA:16-epivellosimine O-acetyltransferase (cyclizing)
Comments: The reaction proceeds in two stages. The indole nitrogen of 16-epivellosimine interacts with its aldehyde group giving an hydroxy-substituted new ring. This alcohol is then acetylated. Also acts on gardneral (11-methoxy-16-epivellosimine). Generates the ajmalan skeleton, which forms part of the route to ajmaline.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 88844-97-7
References:
1.  Pfitzner, A., Polz, L. and Stöckligt, J. Properties of vinorine synthase the Rauwolfia enzyme involved in the formation of the ajmaline skeleton. Z. Naturforsch. C: Biosci. 41 (1986) 103–114.
2.  Bayer, A., Ma, X. and Stöckigt, J. Acetyltransfer in natural product biosynthesis—functional cloning and molecular analysis of vinorine synthase. Bioorg. Med. Chem. 12 (2004) 2787–2795. [DOI] [PMID: 15110860]
3.  Ma, X., Koepke, J., Bayer, A., Linhard, V., Fritzsch, G., Zhang, B., Michel, H. and Stöckigt, J. Vinorine synthase from Rauvolfia: the first example of crystallization and preliminary X-ray diffraction analysis of an enzyme of the BAHD superfamily. Biochim. Biophys. Acta 1701 (2004) 129–132. [DOI] [PMID: 15450182]
4.  Ma, X., Koepke, J., Panjikar, S., Fritzsch, G. and Stöckigt, J. Crystal structure of vinorine synthase, the first representative of the BAHD superfamily. J. Biol. Chem. 280 (2005) 13576–13583. [DOI] [PMID: 15665331]
[EC 2.3.1.160 created 2002]
 
 
EC 2.3.1.175     
Accepted name: deacetylcephalosporin-C acetyltransferase
Reaction: acetyl-CoA + deacetylcephalosporin C = CoA + cephalosporin C
For diagram of cephalosporin biosynthesis, click here
Other name(s): acetyl-CoA:deacetylcephalosporin-C acetyltransferase; DAC acetyltransferase; cefG; deacetylcephalosporin C acetyltransferase; acetyl coenzyme A:DAC acetyltransferase; acetyl-CoA:DAC acetyltransferase; CPC acetylhydrolase; acetyl-CoA:DAC O-acetyltransferase; DAC-AT
Systematic name: acetyl-CoA:deacetylcephalosporin-C O-acetyltransferase
Comments: This enzyme catalyses the final step in the biosynthesis of cephalosporin C.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 57827-76-6
References:
1.  Matsuyama, K., Matsumoto, H., Matsuda, A., Sugiura, H., Komatsu, K. and Ichikawa, S. Purification of acetyl coenzyme A: deacetylacephalosporin C O-acetyltransferase from Acremonium chrysogenum. Biosci. Biotechnol. Biochem. 56 (1992) 1410–1412. [DOI] [PMID: 1368946]
2.  Gutiérrez, S., Velasco, J., Fernandez, F.J. and Martín, J.F. The cefG gene of Cephalosporium acremonium is linked to the cefEF gene and encodes a deacetylcephalosporin C acetyltransferase closely related to homoserine O-acetyltransferase. J. Bacteriol. 174 (1992) 3056–3064. [DOI] [PMID: 1569032]
3.  Matsuda, A., Sugiura, H., Matsuyama, K., Matsumoto, H., Ichikawa, S. and Komatsu, K. Cloning and disruption of the cefG gene encoding acetyl coenzyme A: deacetylcephalosporin C O-acetyltransferase from Acremonium chrysogenum. Biochem. Biophys. Res. Commun. 186 (1992) 40–46. [DOI] [PMID: 1632779]
4.  Gutiérrez, S., Velasco, J., Marcos, A.T., Fernández, F.J., Fierro, F., Barredo, J.L., Díez, B. and Martín, J.F. Expression of the cefG gene is limiting for cephalosporin biosynthesis in Acremonium chrysogenum. Appl. Microbiol. Biotechnol. 48 (1997) 606–614. [PMID: 9421924]
5.  Velasco, J., Gutierrez, S., Campoy, S. and Martin, J.F. Molecular characterization of the Acremonium chrysogenum cefG gene product: the native deacetylcephalosporin C acetyltransferase is not processed into subunits. Biochem. J. 337 (1999) 379–385. [PMID: 9895280]
6.  Martín, J.F., Gutiérrez, S., Fernández, F.J., Velasco, J., Fierro, F., Marcos, A.T. and Kosalkova, K. Expression of genes and processing of enzymes for the biosynthesis of penicillins and cephalosporins. Antonie Van Leeuwenhoek 65 (1994) 227–243. [PMID: 7847890]
[EC 2.3.1.175 created 2005]
 
 
EC 2.3.1.181     
Accepted name: lipoyl(octanoyl) transferase
Reaction: an octanoyl-[acyl-carrier protein] + a protein = a protein N6-(octanoyl)lysine + an [acyl-carrier protein]
Glossary: lipoyl group
Other name(s): LipB; lipoyl (octanoyl)-[acyl-carrier-protein]-protein N-lipoyltransferase; lipoyl (octanoyl)-acyl carrier protein:protein transferase; lipoate/octanoate transferase; lipoyltransferase; octanoyl-[acyl carrier protein]-protein N-octanoyltransferase; lipoyl(octanoyl)transferase; octanoyl-[acyl-carrier-protein]:protein N-octanoyltransferase
Systematic name: octanoyl-[acyl-carrier protein]:protein N-octanoyltransferase
Comments: This is the first committed step in the biosynthesis of lipoyl cofactor. Lipoylation is essential for the function of several key enzymes involved in oxidative metabolism, as it converts apoprotein into the biologically active holoprotein. Examples of such lipoylated proteins include pyruvate dehydrogenase (E2 domain), 2-oxoglutarate dehydrogenase (E2 domain), the branched-chain 2-oxoacid dehydrogenases and the glycine cleavage system (H protein) [2,3]. Lipoyl-ACP can also act as a substrate [4] although octanoyl-ACP is likely to be the true substrate [6]. The other enzyme involved in the biosynthesis of lipoyl cofactor is EC 2.8.1.8, lipoyl synthase. An alternative lipoylation pathway involves EC 6.3.1.20, lipoate—protein ligase, which can lipoylate apoproteins using exogenous lipoic acid (or its analogues).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 392687-64-8
References:
1.  Nesbitt, N.M., Baleanu-Gogonea, C., Cicchillo, R.M., Goodson, K., Iwig, D.F., Broadwater, J.A., Haas, J.A., Fox, B.G. and Booker, S.J. Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase. Protein Expr. Purif. 39 (2005) 269–282. [DOI] [PMID: 15642479]
2.  Vanden Boom, T.J., Reed, K.E. and Cronan, J.E., Jr. Lipoic acid metabolism in Escherichia coli: isolation of null mutants defective in lipoic acid biosynthesis, molecular cloning and characterization of the E. coli lip locus, and identification of the lipoylated protein of the glycine cleavage system. J. Bacteriol. 173 (1991) 6411–6420. [DOI] [PMID: 1655709]
3.  Jordan, S.W. and Cronan, J.E., Jr. A new metabolic link. The acyl carrier protein of lipid synthesis donates lipoic acid to the pyruvate dehydrogenase complex in Escherichia coli and mitochondria. J. Biol. Chem. 272 (1997) 17903–17906. [DOI] [PMID: 9218413]
4.  Zhao, X., Miller, J.R., Jiang, Y., Marletta, M.A. and Cronan, J.E. Assembly of the covalent linkage between lipoic acid and its cognate enzymes. Chem. Biol. 10 (2003) 1293–1302. [DOI] [PMID: 14700636]
5.  Wada, M., Yasuno, R., Jordan, S.W., Cronan, J.E., Jr. and Wada, H. Lipoic acid metabolism in Arabidopsis thaliana: cloning and characterization of a cDNA encoding lipoyltransferase. Plant Cell Physiol. 42 (2001) 650–656. [PMID: 11427685]
6.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
[EC 2.3.1.181 created 2006, modified 2016]
 
 
EC 2.3.1.189     
Accepted name: mycothiol synthase
Reaction: desacetylmycothiol + acetyl-CoA = CoA + mycothiol
For diagram of mycothiol biosynthesis, click here
Glossary: desacetylmycothiol = 1-O-[2-(L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
mycothiol = 1-O-[2-(N2-acetyl-L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
Other name(s): MshD
Systematic name: acetyl-CoA:desacetylmycothiol O-acetyltransferase
Comments: This enzyme catalyses the last step in the biosynthesis of mycothiol, the major thiol in most actinomycetes, including Mycobacterium [1]. The enzyme is a member of a large family of GCN5-related N-acetyltransferases (GNATs) [2]. The enzyme has been purified from Mycobacterium tuberculosis H37Rv. Acetyl-CoA is the preferred CoA thioester but propionyl-CoA is also a substrate [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Spies, H.S. and Steenkamp, D.J. Thiols of intracellular pathogens. Identification of ovothiol A in Leishmania donovani and structural analysis of a novel thiol from Mycobacterium bovis. Eur. J. Biochem. 224 (1994) 203–213. [DOI] [PMID: 8076641]
2.  Koledin, T., Newton, G.L. and Fahey, R.C. Identification of the mycothiol synthase gene (mshD) encoding the acetyltransferase producing mycothiol in actinomycetes. Arch. Microbiol. 178 (2002) 331–337. [DOI] [PMID: 12375100]
3.  Vetting, M.W., Roderick, S.L., Yu, M. and Blanchard, J.S. Crystal structure of mycothiol synthase (Rv0819) from Mycobacterium tuberculosis shows structural homology to the GNAT family of N-acetyltransferases. Protein Sci. 12 (2003) 1954–1959. [DOI] [PMID: 12930994]
[EC 2.3.1.189 created 2010]
 
 
EC 2.3.1.199     
Accepted name: very-long-chain 3-oxoacyl-CoA synthase
Reaction: a very-long-chain acyl-CoA + malonyl-CoA = a very-long-chain 3-oxoacyl-CoA + CO2 + CoA
Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.
Other name(s): very-long-chain 3-ketoacyl-CoA synthase; very-long-chain β-ketoacyl-CoA synthase; condensing enzyme (ambiguous); CUT1 (gene name); CER6 (gene name); FAE1 (gene name); KCS (gene name); ELO (gene name)
Systematic name: malonyl-CoA:very-long-chain acyl-CoA malonyltransferase (decarboxylating and thioester-hydrolysing)
Comments: This is the first component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long-chain acyl CoAs. Multiple forms exist with differing preferences for the substrate, and thus the specific form expressed determines the local composition of very-long-chain fatty acids [6,7]. For example, the FAE1 form from the plant Arabidopsis thaliana accepts only 16 and 18 carbon substrates, with oleoyl-CoA (18:1) being the preferred substrate [5], while CER6 from the same plant prefers substrates with chain length of C22 to C32 [4,8]. cf. EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, EC 4.2.1.134, very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] dehydratase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Toke, D.A. and Martin, C.E. Isolation and characterization of a gene affecting fatty acid elongation in Saccharomyces cerevisiae. J. Biol. Chem. 271 (1996) 18413–18422. [DOI] [PMID: 8702485]
2.  Oh, C.S., Toke, D.A., Mandala, S. and Martin, C.E. ELO2 and ELO3, homologues of the Saccharomyces cerevisiae ELO1 gene, function in fatty acid elongation and are required for sphingolipid formation. J. Biol. Chem. 272 (1997) 17376–17384. [DOI] [PMID: 9211877]
3.  Dittrich, F., Zajonc, D., Huhne, K., Hoja, U., Ekici, A., Greiner, E., Klein, H., Hofmann, J., Bessoule, J.J., Sperling, P. and Schweizer, E. Fatty acid elongation in yeast--biochemical characteristics of the enzyme system and isolation of elongation-defective mutants. Eur. J. Biochem. 252 (1998) 477–485. [DOI] [PMID: 9546663]
4.  Millar, A.A., Clemens, S., Zachgo, S., Giblin, E.M., Taylor, D.C. and Kunst, L. CUT1, an Arabidopsis gene required for cuticular wax biosynthesis and pollen fertility, encodes a very-long-chain fatty acid condensing enzyme. Plant Cell 11 (1999) 825–838. [PMID: 10330468]
5.  Ghanevati, M. and Jaworski, J.G. Engineering and mechanistic studies of the Arabidopsis FAE1 β-ketoacyl-CoA synthase, FAE1 KCS. Eur. J. Biochem. 269 (2002) 3531–3539. [DOI] [PMID: 12135493]
6.  Blacklock, B.J. and Jaworski, J.G. Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases. Biochem. Biophys. Res. Commun. 346 (2006) 583–590. [DOI] [PMID: 16765910]
7.  Denic, V. and Weissman, J.S. A molecular caliper mechanism for determining very long-chain fatty acid length. Cell 130 (2007) 663–677. [DOI] [PMID: 17719544]
8.  Tresch, S., Heilmann, M., Christiansen, N., Looser, R. and Grossmann, K. Inhibition of saturated very-long-chain fatty acid biosynthesis by mefluidide and perfluidone, selective inhibitors of 3-ketoacyl-CoA synthases. Phytochemistry 76 (2012) 162–171. [DOI] [PMID: 22284369]
[EC 2.3.1.199 created 2012]
 
 
EC 2.3.1.203     
Accepted name: UDP-N-acetylbacillosamine N-acetyltransferase
Reaction: acetyl-CoA + UDP-N-acetylbacillosamine = CoA + UDP-N,N′-diacetylbacillosamine
For diagram of legionaminic acid biosynthesis, click here
Glossary: UDP-N-acetylbacillosamine = UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine
UDP-N,N′-diacetylbacillosamine = UDP-2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose
Other name(s): UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase; pglD (gene name)
Systematic name: acetyl-CoA:UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase
Comments: The product, UDP-N,N′-diacetylbacillosamine, is an intermediate in protein glycosylation pathways in several bacterial species, including N-linked glycosylation of certain L-asparagine residues in Campylobacter species [1,2] and O-linked glycosylation of certain L-serine residues in Neisseria species [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N′-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659–13669. [DOI] [PMID: 17087520]
2.  Rangarajan, E.S., Ruane, K.M., Sulea, T., Watson, D.C., Proteau, A., Leclerc, S., Cygler, M., Matte, A. and Young, N.M. Structure and active site residues of PglD, an N-acetyltransferase from the bacillosamine synthetic pathway required for N-glycan synthesis in Campylobacter jejuni. Biochemistry 47 (2008) 1827–1836. [DOI] [PMID: 18198901]
3.  Hartley, M.D., Morrison, M.J., Aas, F.E., Borud, B., Koomey, M. and Imperiali, B. Biochemical characterization of the O-linked glycosylation pathway in Neisseria gonorrhoeae responsible for biosynthesis of protein glycans containing N,N′-diacetylbacillosamine. Biochemistry 50 (2011) 4936–4948. [DOI] [PMID: 21542610]
[EC 2.3.1.203 created 2012, modified 2013]
 
 
EC 2.3.1.222     
Accepted name: phosphate propanoyltransferase
Reaction: propanoyl-CoA + phosphate = CoA + propanoyl phosphate
Other name(s): PduL
Systematic name: propanoyl-CoA:phosphate propanoyltransferase
Comments: Part of the degradation pathway for propane-1,2-diol .
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Liu, Y., Leal, N.A., Sampson, E.M., Johnson, C.L., Havemann, G.D. and Bobik, T.A. PduL is an evolutionarily distinct phosphotransacylase involved in B12-dependent 1,2-propanediol degradation by Salmonella enterica serovar typhimurium LT2. J. Bacteriol. 189 (2007) 1589–1596. [DOI] [PMID: 17158662]
[EC 2.3.1.222 created 2013]
 
 


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