The Enzyme Database

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

Proposed Changes to the Enzyme List

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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

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


Contents

EC 1.1.1.372 D/L-glyceraldehyde reductase
EC 1.1.1.373 sulfolactaldehyde 3-reductase
EC 1.1.3.3 deleted
*EC 1.1.3.19 4-hydroxymandelate oxidase (decarboxylating)
EC 1.1.3.46 4-hydroxymandelate oxidase
*EC 1.2.1.27 methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
*EC 1.3.1.10 enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific)
EC 1.3.99.36 cypemycin cysteine dehydrogenase (decarboxylating)
EC 1.5.1.48 2-methyl-1-pyrroline reductase
*EC 1.5.4.1 pyrimidodiazepine synthase
*EC 1.10.3.10 ubiquinol oxidase (H+-transporting)
EC 1.10.3.15 grixazone synthase
EC 1.11.1.23 (S)-2-hydroxypropylphosphonic acid epoxidase
EC 1.11.2.5 3-methyl-L-tyrosine peroxygenase
EC 1.13.11.78 2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming)
EC 1.13.11.79 5,6-dimethylbenzimidazole synthase
EC 1.14.11.45 L-isoleucine 4-hydroxylase
EC 1.14.11.46 2-aminoethylphosphonate dioxygenase
EC 1.14.13.189 5-methyl-1-naphthoate 3-hydroxylase
EC 1.14.13.190 ferruginol synthase
EC 1.14.13.191 ent-sandaracopimaradiene 3-hydroxylase
EC 1.14.13.192 oryzalexin E synthase
EC 1.14.13.193 oryzalexin D synthase
EC 1.14.13.194 phylloquinone ω-hydroxylase
EC 1.14.14.15 (3S)-3-amino-3-(3-chloro-4-hydroxyphenyl)propanoyl-[peptidyl-carrier protein SgcC2] monooxygenase
EC 1.14.16.7 phenylalanine 3-monooxygenase
EC 1.14.19.7 transferred
EC 1.14.99.40 transferred
EC 1.16.3.2 bacterial non-heme ferritin
EC 2.1.1.301 cypemycin N-terminal methyltransferase
EC 2.1.1.302 3-hydroxy-5-methyl-1-naphthoate 3-O-methyltransferase
EC 2.1.1.303 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase
EC 2.1.1.304 L-tyrosine C3-methyltransferase
EC 2.1.1.305 8-demethyl-8-α-L-rhamnosyltetracenomycin-C 2′-O-methyltransferase
EC 2.1.1.306 8-demethyl-8-(2-methoxy-α-L-rhamnosyl)tetracenomycin-C 3′-O-methyltransferase
EC 2.1.1.307 8-demethyl-8-(2,3-dimethoxy-α-L-rhamnosyl)tetracenomycin-C 4′-O-methyltransferase
EC 2.1.3.13 deleted
EC 2.1.3.14 deleted
EC 2.3.1.233 1,3,6,8-tetrahydroxynaphthalene synthase
*EC 2.4.1.208 diglucosyl diacylglycerol synthase (1,2-linking)
EC 2.4.1.325 TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase
EC 2.4.1.326 aklavinone 7-L-rhodosaminyltransferase
EC 2.4.1.327 aclacinomycin-T 2-deoxy-L-fucose transferase
EC 2.4.1.328 erythronolide mycarosyltransferase
EC 2.5.1.121 5,10-dihydrophenazine-1-carboxylate 9-dimethylallyltransferase
EC 2.5.1.122 4-O-dimethylallyl-L-tyrosine synthase
EC 2.5.1.123 flaviolin linalyltransferase
EC 2.7.1.183 glycoprotein-mannosyl O6-kinase
EC 2.7.1.184 sulfofructose kinase
*EC 2.7.7.86 cyclic GMP-AMP synthase
EC 2.8.2.37 trehalose 2-sulfotransferase
EC 3.1.1.96 D-aminoacyl-tRNA deacylase
EC 3.1.4.57 phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase
EC 3.1.12 Exodeoxyribonucleases producing 3′-phosphomonoesters
EC 3.1.12.1 5′ to 3′ exodeoxyribonuclease (nucleoside 3′-phosphate-forming)
*EC 3.5.1.46 6-aminohexanoate-oligomer exohydrolase
EC 3.5.1.117 6-aminohexanoate-oligomer endohydrolase
*EC 3.5.4.17 adenosine-phosphate deaminase
*EC 3.5.99.7 1-aminocyclopropane-1-carboxylate deaminase
EC 3.13.1.4 3-sulfinopropanoyl-CoA desulfinase
EC 4.1.1.98 4-hydroxy-3-polyprenylbenzoate decarboxylase
EC 4.1.2.57 sulfofructosephosphate aldolase
*EC 4.2.1.134 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase
EC 4.2.1.152 hydroperoxy icosatetraenoate dehydratase
EC 4.2.1.153 3-methylfumaryl-CoA hydratase
EC 4.2.1.154 tetracenomycin F2 cyclase
EC 4.2.3.145 ophiobolin F synthase
EC 4.2.3.146 cyclooctat-9-en-7-ol synthase
EC 5.1.3.29 L-fucose mutarotase
EC 5.3.1.31 sulfoquinovose isomerase
*EC 5.4.2.11 phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
EC 5.4.4.7 hydroperoxy icosatetraenoate isomerase
*EC 5.5.1.23 aklanonic acid methyl ester cyclase
EC 6.1.2.2 nebramycin 5′ synthase
EC 6.2.1.41 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate—CoA ligase
EC 6.2.1.42 3-oxocholest-4-en-26-oate—CoA ligase
EC 6.2.1.43 2-hydroxy-7-methoxy-5-methyl-1-naphthoate—CoA ligase
*EC 6.3.1.9 trypanothione synthase
EC 6.3.1.18 γ-glutamylanilide synthase


EC 1.1.1.372
Accepted name: D/L-glyceraldehyde reductase
Reaction: (1) glycerol + NADP+ = L-glyceraldehyde + NADPH + H+
(2) glycerol + NADP+ = D-glyceraldehyde + NADPH + H+
Other name(s): gld1 (gene name); gaaD (gene name)
Systematic name: glycerol:NADP+ oxidoreductase (D/L-glyceraldehyde-forming)
Comments: The enzyme takes part in a D-galacturonate degradation pathway in the fungi Aspergillus niger and Trichoderma reesei (Hypocrea jecorina). It has equal activity with D- and L-glyceraldehyde, and can also reduce glyoxal and methylglyoxal. The reaction is only observed in the direction of glyceraldehyde reduction.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Liepins, J., Kuorelahti, S., Penttila, M. and Richard, P. Enzymes for the NADPH-dependent reduction of dihydroxyacetone and D-glyceraldehyde and L-glyceraldehyde in the mould Hypocrea jecorina. FEBS J. 273 (2006) 4229–4235. [PMID: 16930134]
2.  Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449–1457. [PMID: 18768163]
[EC 1.1.1.372 created 2014]
 
 
EC 1.1.1.373
Accepted name: sulfolactaldehyde 3-reductase
Reaction: 2,3-dihydroxypropane-1-sulfonate + NAD+ = 2-hydroxy-3-oxopropane-1-sulfonate + NADH + H+
For diagram of sulphoglycolysis of sulfoquinovose, click here
Glossary: 2-hydroxy-3-oxopropane-1-sulfonate = sulfolactaldehyde
Other name(s): yihU (gene name)
Systematic name: 2,3-dihydroxypropane-1-sulfonate:NAD+ 3-oxidoreductase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114–117. [PMID: 24463506]
[EC 1.1.1.373 created 2014]
 
 
EC 1.1.3.3
Deleted entry: malate oxidase. Now classified as EC 1.1.5.4, malate dehydrogenase (quinone).
[EC 1.1.3.3 created 1961, deleted 2014]
 
 
*EC 1.1.3.19
Accepted name: 4-hydroxymandelate oxidase (decarboxylating)
Reaction: (S)-4-hydroxymandelate + O2 = 4-hydroxybenzaldehyde + CO2 + H2O2
Glossary: (S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate
Other name(s): L-4-hydroxymandelate oxidase (decarboxylating); (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate:oxygen 1-oxidoreductase; (S)-4-hydroxymandelate:oxygen 1-oxidoreductase; 4-hydroxymandelate oxidase
Systematic name: (S)-4-hydroxymandelate:oxygen 1-oxidoreductase (decarboxylating)
Comments: A flavoprotein (FAD), requires Mn2+. The enzyme from the bacterium Pseudomonas putida is involved in the degradation of mandelate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 60976-30-9
References:
1.  Bhat, S.G. and Vaidyanathan, C.S. Purification and properties of L-4-hydroxymandelate oxidase from Pseudomonas convexa. Eur. J. Biochem. 68 (1976) 323–331. [PMID: 976259]
[EC 1.1.3.19 created 1984, modified 2014]
 
 
EC 1.1.3.46
Accepted name: 4-hydroxymandelate oxidase
Reaction: (S)-4-hydroxymandelate + O2 = 2-(4-hydroxyphenyl)-2-oxoacetate + H2O2
Glossary: (S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate
2-(4-hydroxyphenyl)-2-oxoacetate = 4-hydroxyphenylglyoxylate = (4-hydroxyphenyl)(oxo)acetate
L-(4-hydroxyphenyl)glycine = (S)-4-hydroxyphenylglycine
L-(3,5-dihydroxyphenyl)glycine = (S)-3,5-dihydroxyphenylglycine
Other name(s): 4HmO; HmO
Systematic name: (S)-4-hydroxymandelate:oxygen 1-oxidoreductase
Comments: A flavoprotein (FMN). The enzyme from the bacterium Amycolatopsis orientalis is involved in the biosynthesis of L-(4-hydroxyphenyl)glycine and L-(3,5-dihydroxyphenyl)glycine, two non-proteinogenic amino acids occurring in the vancomycin group of antibiotics.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hubbard, B.K., Thomas, M.G. and Walsh, C.T. Biosynthesis of L-p-hydroxyphenylglycine, a non-proteinogenic amino acid constituent of peptide antibiotics. Chem. Biol. 7 (2000) 931–942. [PMID: 11137816]
2.  Li, T.L., Choroba, O.W., Charles, E.H., Sandercock, A.M., Williams, D.H. and Spencer, J.B. Characterisation of a hydroxymandelate oxidase involved in the biosynthesis of two unusual amino acids occurring in the vancomycin group of antibiotics. Chem. Commun. (Camb.) (2001) 1752–1753. [PMID: 12240298]
[EC 1.1.3.46 created 2014]
 
 
*EC 1.2.1.27
Accepted name: methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
Reaction: 2-methyl-3-oxopropanoate + CoA + H2O + NAD+ = propanoyl-CoA + HCO3- + NADH
For diagram of inositol catabolism, click here
Glossary: methylmalonate semialdehyde = 2-methyl-3-oxopropanoate
Other name(s): MSDH; MMSA dehydrogenase; iolA (gene name); methylmalonate-semialdehyde dehydrogenase (acylating)
Systematic name: 2-methyl-3-oxopropanoate:NAD+ 3-oxidoreductase (CoA-propanoylating)
Comments: Also converts 3-oxopropanoate into acetyl-CoA [3]. The reaction occurs in two steps with the decarboxylation process preceding CoA-binding [3]. Bicarbonate rather than CO2 is released as a final product [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 37205-49-5
References:
1.  Sokatch, J.R., Sanders, L.E. and Marshall, V.P. Oxidation of methylmalonate semialdehyde to propionyl coenzyme A in Pseudomonas aeruginosa grown on valine. J. Biol. Chem. 243 (1968) 2500–2506. [PMID: 4297649]
2.  Dubourg, H., Stines-Chaumeil, C., Didierjean, C., Talfournier, F., Rahuel-Clermont, S., Branlant, G. and Aubry, A. Expression, purification, crystallization and preliminary X-ray diffraction data of methylmalonate-semialdehyde dehydrogenase from Bacillus subtilis. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1435–1437. [PMID: 15272169]
3.  Stines-Chaumeil, C., Talfournier, F. and Branlant, G. Mechanistic characterization of the MSDH (methylmalonate semialdehyde dehydrogenase) from Bacillus subtilis. Biochem. J. 395 (2006) 107–115. [PMID: 16332250]
[EC 1.2.1.27 created 1972, modified 2014]
 
 
*EC 1.3.1.10
Accepted name: enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific)
Reaction: an acyl-[acyl-carrier protein] + NADP+ = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH + H+
Other name(s): acyl-ACP dehydrogenase (ambiguous); enoyl-[acyl carrier protein] (reduced nicotinamide adenine dinucleotide phosphate) reductase; NADPH 2-enoyl Co A reductase; enoyl acyl-carrier-protein reductase (ambiguous); enoyl-ACP reductase (ambiguous); acyl-[acyl-carrier-protein]:NADP+ oxidoreductase (B-specific); acyl-[acyl-carrier protein]:NADP+ oxidoreductase (B-specific); enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific)
Systematic name: acyl-[acyl-carrier protein]:NADP+ oxidoreductase (Si-specific)
Comments: One of the activities of EC 2.3.1.86, fatty-acyl-CoA synthase, an enzyme found in yeasts (Ascomycota and the Basidiomycota). Catalyses the reduction of enoyl-acyl-[acyl-carrier protein] derivatives of carbon chain length from 4 to 16. The yeast enzyme is Si-specific with respect to NADP+. cf. EC 1.3.1.39, enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) and EC 1.3.1.104, enoyl-[acyl-carrier-protein] reductase (NADPH), which describes enzymes whose stereo-specificity towards NADPH is not known. See also EC 1.3.1.9, enoyl-[acyl-carrier-protein] reductase (NADH).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 37251-09-5
References:
1.  Seyama, T., Kasama, T., Yamakawa, T., Kawaguchi, A., Saito, K. and Okuda, S. Origin of hydrogen atoms in the fatty acids synthesized with yeast fatty acid synthetase. J. Biochem. (Tokyo) 82 (1977) 1325–1329. [PMID: 338601]
[EC 1.3.1.10 created 1972, modified 1986, modified 2013, modified 2014]
 
 
EC 1.3.99.36
Accepted name: cypemycin cysteine dehydrogenase (decarboxylating)
Reaction: cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys + acceptor = C3.19,S21-cyclocypemycin(1-18)-L-Ala-L-Leu-N-thioethenyl-L-valinamide + CO2 + H2S + reduced acceptor
For diagram of reaction, click here
Other name(s): cypemycin decarboxylase; CypD
Systematic name: cypemycin(1-18)-L-Cys-L-Leu-L-Val-L-Cys:acceptor oxidoreductase (decarboxylating, cyclizing)
Comments: Cypemycin, isolated from the bacterium Streptomyces sp. OH-4156, is a peptide antibiotic, member of the linaridins, a class of posttranslationally modified ribosomally synthesized peptides. The enzyme decarboxylates and reduces the C-terminal L-cysteine residue, producing a reactive ethenethiol group that reacts with a dethiolated cysteine upstream to form an aminovinyl-methyl-cysteine loop that is important for the antibiotic activity of the mature peptide.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Claesen, J. and Bibb, M. Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides. Proc. Natl. Acad. Sci. USA 107 (2010) 16297–16302. [PMID: 20805503]
[EC 1.3.99.36 created 2014]
 
 
EC 1.5.1.48
Accepted name: 2-methyl-1-pyrroline reductase
Reaction: (R)-2-methylpyrrolidine + NADP+ = 2-methyl-1-pyrroline + NADPH + H+
Other name(s): (R)-imine reductase (ambiguous)
Systematic name: (R)-2-methylpyrrolidine:NADP+ 2-oxidoreductase
Comments: The enzyme from the bacterium Streptomyces sp. GF3587 is highly specific for its substrate and forms only the (R) isomer.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Mitsukura, K., Suzuki, M., Shinoda, S., Kuramoto, T., Yoshida, T. and Nagasawa, T. Purification and characterization of a novel (R)-imine reductase from Streptomyces sp. GF3587. Biosci. Biotechnol. Biochem. 75 (2011) 1778–1782. [PMID: 21897027]
[EC 1.5.1.48 created 2014]
 
 
*EC 1.5.4.1
Accepted name: pyrimidodiazepine synthase
Reaction: 2-amino-6-acetyl-3,7,8,9-tetrahydro-3H-pyrimido[4,5-b][1,4]diazepin-4-one + glutathione disulfide + H2O = 6-pyruvoyltetrahydropterin + 2 glutathione
For diagram of 6-pyruvyltetrahydropterin metabolism, click here
Glossary: 2-amino-6-acetyl-3,7,8,9-tetrahydro-3H-pyrimido[4,5-b][1,4]diazepin-4-one = pyrimidodiazepine
Other name(s): PDA synthase; pyrimidodiazepine:oxidized-glutathione oxidoreductase (ring-opening, cyclizing); pyrimidodiazepine:glutathione-disulfide oxidoreductase (ring-opening, cyclizing)
Systematic name: 2-amino-6-acetyl-3,7,8,9-tetrahydro-3H-pyrimido[4,5-b][1,4]diazepin-4-one:glutathione-disulfide oxidoreductase (ring-opening, cyclizing)
Comments: In the reverse direction, the reduction of 6-pyruvoyl-tetrahydropterin is accompanied by the opening of the 6-membered pyrazine ring and the formation of the 7-membered diazepine ring. The pyrimidodiazepine formed is an acetyldihydro derivative. Involved in the formation of the eye pigment drosopterin in Drosophila melanogaster.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 93586-06-2
References:
1.  Wiederrecht, G.J. and Brown, G.M. Purification and properties of the enzymes from Drosophila melanogaster that catalyze the conversion of dihydroneopterin triphosphate to the pyrimidodiazepine precursor of the drosopterins. J. Biol. Chem. 259 (1984) 14121–14127. [PMID: 6438092]
2.  Kim, J., Suh, H., Kim, S., Kim, K., Ahn, C. and Yim, J. Identification and characteristics of the structural gene for the Drosophila eye colour mutant sepia, encoding PDA synthase, a member of the ω class glutathione S-transferases. Biochem. J. 398 (2006) 451–460. [PMID: 16712527]
[EC 1.5.4.1 created 1990, modified 2014]
 
 
*EC 1.10.3.10
Accepted name: ubiquinol oxidase (H+-transporting)
Reaction: 2 ubiquinol + O2 + n H+[side 1] = 2 ubiquinone + 2 H2O + n H+[side 2]
Other name(s): cytochrome bb3 oxidase; cytochrome bo oxidase; cytochrome bd-II oxidase; ubiquinol:O2 oxidoreductase (H+-transporting)
Systematic name: ubiquinol:oxygen oxidoreductase (H+-transporting)
Comments: Contains a dinuclear centre comprising two hemes, or heme and copper. This terminal oxidase enzyme generates proton motive force by two mechanisms: (1) transmembrane charge separation resulting from utilizing protons and electrons originating from opposite sides of the membrane to generate water, and (2) active pumping of protons across the membrane. The bioenergetic efficiency (the number of charges driven across the membrane per electron used to reduce oxygen to water) depends on the enzyme; for example, for the bo3 oxidase it is 2, while for the bd-II oxidase it is 1. cf. EC 1.10.3.14, ubiquinol oxidase (electrogenic, non H+-transporting).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Abramson, J., Riistama, S., Larsson, G., Jasaitis, A., Svensson-Ek, M., Laakkonen, L., Puustinen, A., Iwata, S. and Wikstrom, M. The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. Nat. Struct. Biol. 7 (2000) 910–917. [PMID: 11017202]
2.  Yap, L.L., Lin, M.T., Ouyang, H., Samoilova, R.I., Dikanov, S.A. and Gennis, R.B. The quinone-binding sites of the cytochrome bo3 ubiquinol oxidase from Escherichia coli. Biochim. Biophys. Acta 1797 (2010) 1924–1932. [PMID: 20416270]
3.  Shepherd, M., Sanguinetti, G., Cook, G.M. and Poole, R.K. Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism. J. Biol. Chem. 285 (2010) 18464–18472. [PMID: 20392690]
4.  Borisov, V.B., Murali, R., Verkhovskaya, M.L., Bloch, D.A., Han, H., Gennis, R.B. and Verkhovsky, M.I. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc. Natl. Acad. Sci. USA 108 (2011) 17320–17324. [PMID: 21987791]
[EC 1.10.3.10 created 2011, modified 2014]
 
 
EC 1.10.3.15
Accepted name: grixazone synthase
Reaction: 2 3-amino-4-hydroxybenzoate + N-acetyl-L-cysteine + 2 O2 = grixazone B + 4 H2O + CO2
For diagram of grixazone biosynthesis, click here
Glossary: grixazone B = 8-amino-9-(N-acetyl-L-cystein-S-yl)-7-oxo-7H-phenoxazine-2-carboxylic acid
Other name(s): GriF
Systematic name: 3-amino-4-hydroxybenzoate:N-acetyl-L-cysteine:oxygen oxidoreductase
Comments: A type 3 multi copper protein. The enzyme, isolated from the bacterium Streptomyces griseus, catalyses an 8 electron oxidation. Activation of the enzyme requires a copper chaperone (GriE). It also acts on 3-amino-4-hydroxybenzaldehyde, giving grixazone A. The second aldehyde group is presumably lost as formate. The enzyme also catalyses the reaction of EC 1.10.3.4 o-aminophenol oxidase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Suzuki, H., Ohnishi, Y., Furusho, Y., Sakuda, S. and Horinouchi, S. Novel benzene ring biosynthesis from C3 and C4 primary metabolites by two enzymes. J. Biol. Chem. 281 (2006) 36944–36951. [PMID: 17003031]
2.  Le Roes-Hill, M., Goodwin, C. and Burton, S. Phenoxazinone synthase: what’s in a name. Trends Biotechnol 27 (2009) 248–258. [PMID: 19268377]
[EC 1.10.3.15 created 2014]
 
 
EC 1.11.1.23
Accepted name: (S)-2-hydroxypropylphosphonic acid epoxidase
Reaction: (S)-2-hydroxypropylphosphonate + H2O2 = (1R,2S)-1,2-epoxypropylphosphonate + 2 H2O
For diagram of fosfomycin biosynthesis, click here
Glossary: (1R,2S)-1,2-epoxypropylphosphonate = fosfomycin = [(2R,3S)-3-methyloxiran-2-yl]phosphonate
Other name(s): HPP epoxidase; HppE; 2-hydroxypropylphosphonic acid epoxidase; Fom4; (S)-2-hydroxypropylphosphonate epoxidase
Systematic name: (S)-2-hydroxypropylphosphonate:hydrogen-peroxide epoxidase
Comments: This is the last enzyme in the biosynthetic pathway of fosfomycin, a broad-spectrum antibiotic produced by certain Streptomyces species. Contains non heme iron that forms a iron(IV)-oxo (ferryl) complex with hydrogen peroxide, which functions as a proton abstractor from the substrate [7].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Munos, J.W., Moon, S.J., Mansoorabadi, S.O., Chang, W., Hong, L., Yan, F., Liu, A. and Liu, H.W. Purification and characterization of the epoxidase catalyzing the formation of fosfomycin from Pseudomonas syringae. Biochemistry 47 (2008) 8726–8735. [PMID: 18656958]
2.  Yan, F., Moon, S.J., Liu, P., Zhao, Z., Lipscomb, J.D., Liu, A. and Liu, H.W. Determination of the substrate binding mode to the active site iron of (S)-2-hydroxypropylphosphonic acid epoxidase using 17O-enriched substrates and substrate analogues. Biochemistry 46 (2007) 12628–12638. [PMID: 17927218]
3.  Hidaka, T., Goda, M., Kuzuyama, T., Takei, N., Hidaka, M. and Seto, H. Cloning and nucleotide sequence of fosfomycin biosynthetic genes of Streptomyces wedmorensis. Mol. Gen. Genet. 249 (1995) 274–280. [PMID: 7500951]
4.  Liu, P., Mehn, M.P., Yan, F., Zhao, Z., Que, L., Jr. and Liu, H.W. Oxygenase activity in the self-hydroxylation of (S)-2-hydroxypropylphosphonic acid epoxidase involved in fosfomycin biosynthesis. J. Am. Chem. Soc. 126 (2004) 10306–10312. [PMID: 15315444]
5.  Higgins, L.J., Yan, F., Liu, P., Liu, H.W. and Drennan, C.L. Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme. Nature 437 (2005) 838–844. [PMID: 16015285]
6.  Cameron, S., McLuskey, K., Chamberlayne, R., Hallyburton, I. and Hunter, W.N. Initiating a crystallographic analysis of recombinant (S)-2-hydroxypropylphosphonic acid epoxidase from Streptomyces wedmorensis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61 (2005) 534–536. [PMID: 16511089]
7.  Wang, C., Chang, W.C., Guo, Y., Huang, H., Peck, S.C., Pandelia, M.E., Lin, G.M., Liu, H.W., Krebs, C. and Bollinger, J.M., Jr. Evidence that the fosfomycin-producing epoxidase, HppE, is a non-heme-iron peroxidase. Science 342 (2013) 991–995. [PMID: 24114783]
[EC 1.11.1.23 created 2011 as EC 1.14.19.7, transferred 2014 to EC 1.11.1.23]
 
 
EC 1.11.2.5
Accepted name: 3-methyl-L-tyrosine peroxygenase
Reaction: 3-methyl-L-tyrosine + H2O2 = 3-hydroxy-5-methyl-L-tyrosine + H2O
For diagram of saframycin biosynthesis, click here
Other name(s): SfmD; SacD; 3-methyltyrosine peroxidase; 3-methyl-L-tyrosine peroxidase
Systematic name: 3-methyl-L-tyrosine:hydrogen-peroxide oxidoreductase (3-hydroxy-5-methyl-L-tyrosine-forming)
Comments: The heme-containing peroxygenase from the bacterium Streptomyces lavendulae is involved in biosynthesis of saframycin A, a potent antitumor antibiotic that belongs to the tetrahydroisoquinoline family.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Tang, M.C., Fu, C.Y. and Tang, G.L. Characterization of SfmD as a heme peroxidase that catalyzes the regioselective hydroxylation of 3-methyltyrosine to 3-hydroxy-5-methyltyrosine in saframycin A biosynthesis. J. Biol. Chem. 287 (2012) 5112–5121. [PMID: 22187429]
[EC 1.11.2.5 created 2014]
 
 
EC 1.13.11.78
Accepted name: 2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming)
Reaction: (2-amino-1-hydroxyethyl)phosphonate + O2 = glycine + phosphate
Other name(s): phnZ (gene name)
Systematic name: 2-amino-1-hydroxyethylphosphonate:oxygen 1-oxidoreductase (glycine-forming)
Comments: Requires Fe2+. The enzyme, characterized from a marine bacterium, is involved in a 2-aminoethylphosphonate degradation pathway.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  McSorley, F.R., Wyatt, P.B., Martinez, A., DeLong, E.F., Hove-Jensen, B. and Zechel, D.L. PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a carbon-phosphorus bond. J. Am. Chem. Soc. 134 (2012) 8364–8367. [PMID: 22564006]
2.  Worsdorfer, B., Lingaraju, M., Yennawar, N.H., Boal, A.K., Krebs, C., Bollinger, J.M., Jr. and Pandelia, M.E. Organophosphonate-degrading PhnZ reveals an emerging family of HD domain mixed-valent diiron oxygenases. Proc. Natl. Acad. Sci. USA 110 (2013) 18874–18879. [PMID: 24198335]
[EC 1.13.11.78 created 2014]
 
 
EC 1.13.11.79
Accepted name: 5,6-dimethylbenzimidazole synthase
Reaction: FMNH2 + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + other product(s)
For diagram of FAD biosynthesis, click here
Other name(s): BluB
Systematic name: FMNH2 oxidoreductase (5,6-dimethylbenzimidazole-forming)
Comments: The enzyme catalyses a complex oxygen-dependent conversion of reduced flavin mononucleotide to form 5,6-dimethylbenzimidazole, the lower ligand of vitamin B12. This conversion involves many sequential steps in two distinct stages, and an alloxan intermediate that acts as a proton donor, a proton acceptor, and a hydride acceptor [4]. The C-2 of 5,6-dimethylbenzimidazole is derived from C-1′ of the ribityl group of FMNH2 and 2-H from the ribityl 1′-pro-S hydrogen. While D-erythrose 4-phosphate has been shown to be one of the byproducts, the nature of the other product(s) has not been verified yet.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Gray, M.J. and Escalante-Semerena, J.C. Single-enzyme conversion of FMNH2 to 5,6-dimethylbenzimidazole, the lower ligand of B12. Proc. Natl. Acad. Sci. USA 104 (2007) 2921–2926. [PMID: 17301238]
2.  Ealick, S.E. and Begley, T.P. Biochemistry: molecular cannibalism. Nature 446 (2007) 387–388. [PMID: 17377573]
3.  Taga, M.E., Larsen, N.A., Howard-Jones, A.R., Walsh, C.T. and Walker, G.C. BluB cannibalizes flavin to form the lower ligand of vitamin B12. Nature 446:449 (2007). [PMID: 17377583]
4.  Wang, X.L. and Quan, J.M. Intermediate-assisted multifunctional catalysis in the conversion of flavin to 5,6-dimethylbenzimidazole by BluB: a density functional theory study. J. Am. Chem. Soc. 133 (2011) 4079–4091. [PMID: 21344938]
[EC 1.13.11.79 created 2010 as EC 1.14.99.40, transferred 2014 to EC 1.13.11.79]
 
 
EC 1.14.11.45
Accepted name: L-isoleucine 4-hydroxylase
Reaction: L-isoleucine + 2-oxoglutarate + O2 = (4S)-4-hydroxy-L-isoleucine + succinate + CO2
Glossary: (4S)-4-hydroxy-L-isoleucine = (2S,3R,4S)-2-amino-4-hydroxy-3-methylpentanoate
Other name(s): ido (gene name)
Systematic name: L-isoleucine,2-oxoglutarate:oxygen oxidoreductase (4-hydroxylating)
Comments: The enzyme, characterized from the bacterium Bacillus thuringiensis, can also catalyse the hydroxylation of L-leucine, L-norvaline, L-norleucine, and L-allo-isoleucine, as well as the sulfoxidation of L-methionine, L-ethionine, S-methyl-L-cysteine, S-ethyl-L-cysteine, and S-allyl-L-cysteine.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kodera, T., Smirnov, S.V., Samsonova, N.N., Kozlov, Y.I., Koyama, R., Hibi, M., Ogawa, J., Yokozeki, K. and Shimizu, S. A novel L-isoleucine hydroxylating enzyme, L-isoleucine dioxygenase from Bacillus thuringiensis, produces (2S,3R,4S)-4-hydroxyisoleucine. Biochem. Biophys. Res. Commun. 390 (2009) 506–510. [PMID: 19850012]
2.  Hibi, M., Kawashima, T., Kodera, T., Smirnov, S.V., Sokolov, P.M., Sugiyama, M., Shimizu, S., Yokozeki, K. and Ogawa, J. Characterization of Bacillus thuringiensis L-isoleucine dioxygenase for production of useful amino acids. Appl. Environ. Microbiol. 77 (2011) 6926–6930. [PMID: 21821743]
3.  Hibi, M., Kawashima, T., Yajima, H., Smirnov, S.V., Kodera, T., Sugiyama, M., Shimizu, S., Yokozeki, K., and Ogawa, J. Enzymatic synthesis of chiral amino acid sulfoxides by Fe(II)/α ketoglutarate-dependent dioxygenase. Tetrahedron Asym 24 (2013) 990–994.
[EC 1.14.11.45 created 2014]
 
 
EC 1.14.11.46
Accepted name: 2-aminoethylphosphonate dioxygenase
Reaction: (2-aminoethyl)phosphonate + 2-oxoglutarate + O2 = (2-amino-1-hydroxyethyl)phosphonate + succinate + CO2
Other name(s): phnY (gene name)
Systematic name: (2-aminoethyl)phosphonate,2-oxoglutarate:oxygen oxidoreductase (1-hydroxylating)
Comments: Requires Fe2+ and ascorbate. The enzyme, characterized from an uncultured marine bacterium, is involved in a (2-aminoethyl)phosphonate degradation pathway.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  McSorley, F.R., Wyatt, P.B., Martinez, A., DeLong, E.F., Hove-Jensen, B. and Zechel, D.L. PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a carbon-phosphorus bond. J. Am. Chem. Soc. 134 (2012) 8364–8367. [PMID: 22564006]
[EC 1.14.11.46 created 2014]
 
 
EC 1.14.13.189
Accepted name: 5-methyl-1-naphthoate 3-hydroxylase
Reaction: 5-methyl-1-naphthoate + NADPH + H+ + O2 = 3-hydroxy-5-methyl-1-naphthoate + NADP+ + H2O
For diagram of the azinomycin biosynthesis (part of pathway), click here
Other name(s): AziB1
Systematic name: 5-methyl-1-naphthoate,NADPH:oxygen oxidoreductase (3-hydroxylating)
Comments: The enzyme from the bacterium Streptomyces sahachiroi is involved in the biosynthesis of 3-methoxy-5-methyl-1-naphthoate, a component of of the the antitumor antibiotic azinomycin B.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ding, W., Deng, W., Tang, M., Zhang, Q., Tang, G., Bi, Y. and Liu, W. Biosynthesis of 3-methoxy-5-methyl naphthoic acid and its incorporation into the antitumor antibiotic azinomycin B. Mol. Biosyst. 6 (2010) 1071–1081. [PMID: 20485749]
[EC 1.14.13.189 created 2014]
 
 
EC 1.14.13.190
Accepted name: ferruginol synthase
Reaction: abieta-8,11,13-triene + NADPH + H+ + O2 = ferruginol + NADP+ + H2O
For diagram of abietane diterpenoids biosynthesis, click here
Glossary: ferruginol = abieta-8,11,13-trien-12-ol
Other name(s): miltiradiene oxidase (incorrect); CYP76AH1; miltiradiene,NADPH:oxygen oxidoreductase (ferruginol forming) (incorrect)
Systematic name: miltiradiene,NADPH:oxygen oxidoreductase (ferruginol-forming)
Comments: The enzyme is found in some members of the Lamiaceae (mint family). The enzyme from Rosmarinus officinalis (rosemary) is involved in biosynthesis of carnosic acid, while the enzyme from the Chinese medicinal herb Salvia miltiorrhiza is involved in the biosynthesis of the tanshinones, abietane-type norditerpenoid naphthoquinones that are the main lipophilic bioactive components found in the plant.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Guo, J., Zhou, Y.J., Hillwig, M.L., Shen, Y., Yang, L., Wang, Y., Zhang, X., Liu, W., Peters, R.J., Chen, X., Zhao, Z.K. and Huang, L. CYP76AH1 catalyzes turnover of miltiradiene in tanshinones biosynthesis and enables heterologous production of ferruginol in yeasts. Proc. Natl. Acad. Sci. USA 110 (2013) 12108–12113. [PMID: 23812755]
2.  Zi, J. and Peters, R.J. Characterization of CYP76AH4 clarifies phenolic diterpenoid biosynthesis in the Lamiaceae. Org. Biomol. Chem. 11 (2013) 7650–7652. [PMID: 24108414]
3.  Bozic, D., Papaefthimiou, D., Bruckner, K., de Vos, R.C., Tsoleridis, C.A., Katsarou, D., Papanikolaou, A., Pateraki, I., Chatzopoulou, F.M., Dimitriadou, E., Kostas, S., Manzano, D., Scheler, U., Ferrer, A., Tissier, A., Makris, A.M., Kampranis, S.C. and Kanellis, A.K. Towards elucidating carnosic acid biosynthesis in Lamiaceae: functional characterization of the three first steps of the pathway in Salvia fruticosa and Rosmarinus officinalis. PLoS One 10:e0124106 (2015). [PMID: 26020634]
[EC 1.14.13.190 created 2014, modified 2015]
 
 
EC 1.14.13.191
Accepted name: ent-sandaracopimaradiene 3-hydroxylase
Reaction: ent-sandaracopimaradiene + NADPH + H+ + O2 = ent-sandaracopimaradien-3β-ol + NADP+ + H2O
For diagram of oryzalexins biosynthesis, click here
Glossary: ent-sandaracopimaradiene = ent-13α-pimara-8(14),15-diene = (4aR,4bR,7S,10aR)-7-ethenyl-1,1,4a,7-tetramethyl-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthrene
Other name(s): CYP701A; OsKOL4
Systematic name: ent-sandaracopimaradiene,NADPH:oxygen oxidoreductase (ent-sandaracopimaradien-3β-ol forming)
Comments: A heme-thiolate protein (cytochrome P-450). Isolated from Oryza sativa (rice). Participates in the pathway for the biosynthesis of oryzalexins, a group of related phytoalexins produced by rice.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Wang, Q., Hillwig, M.L., Wu, Y. and Peters, R.J. CYP701A8: a rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiol. 158 (2012) 1418–1425. [PMID: 22247270]
2.  Wu, Y., Wang, Q., Hillwig, M.L. and Peters, R.J. Picking sides: distinct roles for CYP76M6 and CYP76M8 in rice oryzalexin biosynthesis. Biochem. J. 454 (2013) 209–216. [PMID: 23795884]
[EC 1.14.13.191 created 2014]
 
 
EC 1.14.13.192
Accepted name: oryzalexin E synthase
Reaction: ent-sandaracopimaradien-3β-ol + NADPH + H+ + O2 = oryzalexin E + NADP+ + H2O
For diagram of oryzalexins biosynthesis, click here
Glossary: oryzalexin E = ent-sandaracopimaradiene-3β,9α-diol = (3R,4aR,4bS,7S,10aR)-7-ethenyl-1,1,4a,7-tetramethyl-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthren-2,4b-diol
ent-sandaracopimaradien-3β-ol = (3R,4aR,4bR,7S,10aS)-7-ethenyl-1,1,4a,7-tetramethyl-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthren-2-ol
Other name(s): CYP76M6
Systematic name: ent-sandaracopimaradien-3β-ol,NADPH:oxygen oxidoreductase (oryzalexin E forming)
Comments: A heme-thiolate protein (cytochrome P-450). Isolated from Oryza sativa (rice). Oryzalexin E is a phytoalexin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Wu, Y., Wang, Q., Hillwig, M.L. and Peters, R.J. Picking sides: distinct roles for CYP76M6 and CYP76M8 in rice oryzalexin biosynthesis. Biochem. J. 454 (2013) 209–216. [PMID: 23795884]
[EC 1.14.13.192 created 2014]
 
 
EC 1.14.13.193
Accepted name: oryzalexin D synthase
Reaction: ent-sandaracopimaradien-3β-ol + NADPH + H+ + O2 = oryzalexin D + NADP+ + H2O
For diagram of oryzalexins biosynthesis, click here
Glossary: oryzalexin D = ent-sandaracopimaradiene-3β,7α-diol = (3R,4aR,4bS,7S,9S,10aS)-7-ethenyl-1,1,4a,7-tetramethyl-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthren-2,9-diol
ent-sandaracopimaradien-3β-ol = (3R,4aR,4bR,7S,10aS)-7-ethenyl-1,1,4a,7-tetramethyl-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthren-2-ol
Other name(s): CYP76M8
Systematic name: ent-sandaracopimaradien-3β-ol,NADPH:oxygen oxidoreductase (oryzalexin D forming)
Comments: A heme-thiolate protein (cytochrome P-450). Isolated from Oryza sativa (rice). Oryzalexin D is a phytoalexin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Wu, Y., Wang, Q., Hillwig, M.L. and Peters, R.J. Picking sides: distinct roles for CYP76M6 and CYP76M8 in rice oryzalexin biosynthesis. Biochem. J. 454 (2013) 209–216. [PMID: 23795884]
[EC 1.14.13.193 created 2014]
 
 
EC 1.14.13.194
Accepted name: phylloquinone ω-hydroxylase
Reaction: phylloquinone + NADPH + H+ + O2 = ω-hydroxyphylloquinone + NADP+ + H2O
Other name(s): vitamin K1 ω-hydroxylase; CYP4F2; CYP4F11
Systematic name: phylloquinone,NADPH:oxygen oxidoreductase (ω-hydroxyphylloquinone forming)
Comments: A heme-thiolate protein (cytochrome P-450). Isolated from human tissue. The enzyme will also act on menaquinone-4. Prolonged action of CYP4F2, but not CYP4F11, on the ω hydroxyl group oxidizes it to the corresponding carboxylic acid. CYP4F2 also oxidizes leukotriene B4; see EC 1.14.13.30, leukotriene-B4 20-monooxygenase [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Jin, R., Koop, D.R., Raucy, J.L. and Lasker, J.M. Role of human CYP4F2 in hepatic catabolism of the proinflammatory agent leukotriene B4. Arch. Biochem. Biophys. 359 (1998) 89–98. [PMID: 9799565]
2.  Tang, Z., Salamanca-Pinzon, S.G., Wu, Z.L., Xiao, Y. and Guengerich, F.P. Human cytochrome P450 4F11: heterologous expression in bacteria, purification, and characterization of catalytic function. Arch. Biochem. Biophys. 494 (2010) 86–93. [PMID: 19932081]
3.  Edson, K.Z., Prasad, B., Unadkat, J.D., Suhara, Y., Okano, T., Guengerich, F.P. and Rettie, A.E. Cytochrome P450-dependent catabolism of vitamin K: ω-hydroxylation catalyzed by human CYP4F2 and CYP4F11. Biochemistry 52 (2013) 8276–8285. [PMID: 24138531]
[EC 1.14.13.194 created 2014]
 
 
EC 1.14.14.15
Accepted name: (3S)-3-amino-3-(3-chloro-4-hydroxyphenyl)propanoyl-[peptidyl-carrier protein SgcC2] monooxygenase
Reaction: (3S)-3-amino-3-(3-chloro-4-hydroxyphenyl)propanoyl-[peptidyl-carrier protein SgcC2] + FADH2 + O2 = (3S)-3-amino-3-(3-chloro-4,5-dihydroxyphenyl)propanoyl-[peptidyl-carrier protein SgcC2] + FAD + H2O
Other name(s): SgcC
Systematic name: (3S)-3-amino-3-(3-chloro-4-hydroxyphenyl)propanoyl-[peptidyl-carrier protein SgcC2],FADH2:oxygen oxidoreductase (5-hydroxylating)
Comments: The enzyme from the bacterium Streptomyces globisporus is involved in the biosynthesis of the (S)-3-chloro-5-hydroxy-β-tyrosine moiety prior to incorporation into the chromoprotein antitumor antibiotic C-1027.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lin, S., Van Lanen, S.G. and Shen, B. Characterization of the two-component, FAD-dependent monooxygenase SgcC that requires carrier protein-tethered substrates for the biosynthesis of the enediyne antitumor antibiotic C-1027. J. Am. Chem. Soc. 130 (2008) 6616–6623. [PMID: 18426211]
[EC 1.14.14.15 created 2014]
 
 
EC 1.14.16.7
Accepted name: phenylalanine 3-monooxygenase
Reaction: L-phenylalanine + tetrahydrobiopterin + O2 = 3-hydroxy-L-phenylalanine + 4a-hydroxytetrahydrobiopterin
Glossary: 3-hydroxy-L-phenylalanine = meta-L-tyrosine = 3-(3-hydroxyphenyl)-L-alanine
Other name(s): PacX; phenylalanine 3-hydroxylase
Systematic name: L-phenylalanine,tetrahydrobiopterin:oxygen oxidoreductase (3-hydroxylating)
Comments: The enzyme from the bacterium Streptomyces coeruleorubidus forms 3-hydroxy-L-phenylalanine (i.e. m-L-tyrosine), which is one of the building blocks in the biosynthesis of the uridyl peptide antibiotics pacidamycins.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zhang, W., Ames, B.D. and Walsh, C.T. Identification of phenylalanine 3-hydroxylase for meta-tyrosine biosynthesis. Biochemistry 50 (2011) 5401–5403. [PMID: 21615132]
[EC 1.14.16.7 created 2014]
 
 
EC 1.14.19.7
Transferred entry: (S)-2-hydroxypropylphosphonic acid epoxidase. Now EC 1.11.1.23, (S)-2-hydroxypropylphosphonic acid epoxidase.
[EC 1.14.19.7 created 2011, deleted 2014]
 
 
EC 1.14.99.40
Transferred entry: 5,6-dimethylbenzimidazole synthase. Now EC 1.13.11.79, 5,6-dimethylbenzimidazole synthase
[EC 1.14.99.40 created 2010, deleted 2014]
 
 
EC 1.16.3.2
Accepted name: bacterial non-heme ferritin
Reaction: 4 Fe(II) + O2 + 6 H2O = 4 [FeO(OH)] + 8 H+ (overall reaction)
(1a) 2 Fe(II) + O2 + 4 H2O = 2 [FeO(OH)] + 4 H+ + H2O2
(1b) 2 Fe(II) + H2O2 + 2 H2O = 2 [FeO(OH)] + 4 H+
Glossary: [FeO(OH)] = iron(III) oxide-hydroxide
Other name(s): FtnA; HuHF
Systematic name: Fe(II):oxygen oxidoreductase ([FeO(OH)]core-producing)
Comments: Ferritins are intracellular iron-storage and detoxification proteins found in all kingdoms of life. They are formed from two subunits that co-assemble in various ratios to form a spherical protein shell. Thousands of mineralized iron atoms are stored within the core of the structure. The product of dioxygen reduction by the bacterial non-heme ferritin is hydrogen peroxide, which is consumed in a subsequent reaction.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hudson, A.J., Andrews, S.C., Hawkins, C., Williams, J.M., Izuhara, M., Meldrum, F.C., Mann, S., Harrison, P.M. and Guest, J.R. Overproduction, purification and characterization of the Escherichia coli ferritin. Eur. J. Biochem. 218 (1993) 985–995. [PMID: 8281950]
2.  Stillman, T.J., Hempstead, P.D., Artymiuk, P.J., Andrews, S.C., Hudson, A.J., Treffry, A., Guest, J.R. and Harrison, P.M. The high-resolution X-ray crystallographic structure of the ferritin (EcFtnA) of Escherichia coli; comparison with human H ferritin (HuHF) and the structures of the Fe3+ and Zn2+ derivatives. J. Mol. Biol. 307 (2001) 587–603. [PMID: 11254384]
3.  Bou-Abdallah, F., Yang, H., Awomolo, A., Cooper, B., Woodhall, M.R., Andrews, S.C. and Chasteen, N.D. Functionality of the three-site ferroxidase center of Escherichia coli bacterial ferritin (EcFtnA). Biochemistry 53 (2014) 483–495. [PMID: 24380371]
[EC 1.16.3.2 created 2014]
 
 
EC 2.1.1.301
Accepted name: cypemycin N-terminal methyltransferase
Reaction: 2 S-adenosyl-L-methionine + N-terminal L-alanine-[cypemycin] = 2 S-adenosyl-L-homocysteine + N-terminal N,N-dimethyl-L-alanine-[cypemycin]
Other name(s): CypM
Systematic name: S-adenosyl-L-methionine:N-terminal L-alanine-[cypemycin] N-methyltransferase
Comments: The enzyme, isolated from the bacterium Streptomyces sp. OH-4156, can methylate a variety of linear oligopeptides, cyclic peptides such as nisin and haloduracin, and the ε-amino group of lysine [2]. Cypemycin is a peptide antibiotic, a member of the linaridins, a class of posttranslationally modified ribosomally synthesized peptides.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Claesen, J. and Bibb, M. Genome mining and genetic analysis of cypemycin biosynthesis reveal an unusual class of posttranslationally modified peptides. Proc. Natl. Acad. Sci. USA 107 (2010) 16297–16302. [PMID: 20805503]
2.  Zhang, Q. and van der Donk, W.A. Catalytic promiscuity of a bacterial α-N-methyltransferase. FEBS Lett. 586 (2012) 3391–3397. [PMID: 22841713]
[EC 2.1.1.301 created 2014]
 
 
EC 2.1.1.302
Accepted name: 3-hydroxy-5-methyl-1-naphthoate 3-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3-hydroxy-5-methyl-1-naphthoate = S-adenosyl-L-homocysteine + 3-methoxy-5-methyl-1-naphthoate
For diagram of the azinomycin biosynthesis (part of pathway), click here
Other name(s): AziB2
Systematic name: S-adenosyl-L-methionine:3-hydroxy-5-methyl-1-naphthoate 3-O-methyltransferase
Comments: The enzyme from the bacterium Streptomyces sahachiroi is involved in the biosynthesis of 3-methoxy-5-methyl-1-naphthoate, a component of of the the antitumor antibiotic azinomycin B.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ding, W., Deng, W., Tang, M., Zhang, Q., Tang, G., Bi, Y. and Liu, W. Biosynthesis of 3-methoxy-5-methyl naphthoic acid and its incorporation into the antitumor antibiotic azinomycin B. Mol. Biosyst. 6 (2010) 1071–1081. [PMID: 20485749]
[EC 2.1.1.302 created 2014]
 
 
EC 2.1.1.303
Accepted name: 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 2,7-dihydroxy-5-methyl-1-naphthoate = S-adenosyl-L-homocysteine + 2-hydroxy-7-methoxy-5-methyl-1-naphthoate
For diagram of neocarzinostatin biosynthesis, click here
Other name(s): NcsB1; neocarzinostatin O-methyltransferase
Systematic name: S-adenosyl-L-methionine:2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase
Comments: The enzyme from the bacterium Streptomyces carzinostaticus is involved in the biosynthesis of 2-hydroxy-7-methoxy-5-methyl-1-naphthoate. This compound is part of the enediyne chromophore of the antitumor antibiotic neocarzinostatin. In vivo the enzyme catalyses the regiospecific methylation at the 7-hydroxy group of its native substrate 2,7-dihydroxy-5-methyl-1-naphthoate. In vitro it also recognizes other dihydroxynaphthoic acids and catalyses their regiospecific O-methylation.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Luo, Y., Lin, S., Zhang, J., Cooke, H.A., Bruner, S.D. and Shen, B. Regiospecific O-methylation of naphthoic acids catalyzed by NcsB1, an O-methyltransferase involved in the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin. J. Biol. Chem. 283 (2008) 14694–14702. [PMID: 18387946]
2.  Cooke, H.A., Guenther, E.L., Luo, Y., Shen, B. and Bruner, S.D. Molecular basis of substrate promiscuity for the SAM-dependent O-methyltransferase NcsB1, involved in the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin. Biochemistry 48 (2009) 9590–9598. [PMID: 19702337]
[EC 2.1.1.303 created 2014]
 
 
EC 2.1.1.304
Accepted name: L-tyrosine C3-methyltransferase
Reaction: S-adenosyl-L-methionine + L-tyrosine = S-adenosyl-L-homocysteine + 3-methyl-L-tyrosine
For diagram of saframycin biosynthesis, click here
Other name(s): SfmM2; SacF
Systematic name: S-adenosyl-L-methionine:L-tyrosine C3-methyltransferase
Comments: The enzyme from the bacterium Streptomyces lavendulae is involved in biosynthesis of saframycin A, a potent antitumor antibiotic that belongs to the tetrahydroisoquinoline family.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Tang, M.C., Fu, C.Y. and Tang, G.L. Characterization of SfmD as a heme peroxidase that catalyzes the regioselective hydroxylation of 3-methyltyrosine to 3-hydroxy-5-methyltyrosine in saframycin A biosynthesis. J. Biol. Chem. 287 (2012) 5112–5121. [PMID: 22187429]
[EC 2.1.1.304 created 2014]
 
 
EC 2.1.1.305
Accepted name: 8-demethyl-8-α-L-rhamnosyltetracenomycin-C 2′-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 8-demethyl-8-α-L-rhamnosyltetracenomycin C = S-adenosyl-L-homocysteine + 8-demethyl-8-(2-O-methyl-α-L-rhamnosyl)tetracenomycin C
For diagram of elloramycin biosynthesis, click here
Glossary: 8-demethyl-8-α-L-rhamnosyltetracenomycin C = methyl (6aR,7S,10aR)-6a,7,10a,12-tetrahydroxy-8-methoxy-1-methyl-6,10,11-trioxo-3-α-L-rhamnosyloxy-6,6a,7,10,10a,11-hexahydrotetracene-2-carboxylate
Other name(s): ElmMI
Systematic name: S-adenosyl-L-methionine:8-demethyl-8-α-L-rhamnosyltetracenomycin-C 2′-O-methyltransferase
Comments: The enzyme from the bacterium Streptomyces olivaceus is involved in the biosynthesis of the polyketide elloramycin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Patallo, E.P., Blanco, G., Fischer, C., Brana, A.F., Rohr, J., Mendez, C. and Salas, J.A. Deoxysugar methylation during biosynthesis of the antitumor polyketide elloramycin by Streptomyces olivaceus. Characterization of three methyltransferase genes. J. Biol. Chem. 276 (2001) 18765–18774. [PMID: 11376004]
[EC 2.1.1.305 created 2014]
 
 
EC 2.1.1.306
Accepted name: 8-demethyl-8-(2-methoxy-α-L-rhamnosyl)tetracenomycin-C 3′-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 8-demethyl-8-(2-O-methyl-α-L-rhamnosyl)tetracenomycin C = S-adenosyl-L-homocysteine + 8-demethyl-8-(2,3-di-O-methyl-α-L-rhamnosyl)tetracenomycin C
For diagram of elloramycin biosynthesis, click here
Glossary: 8-demethyl-8-α-L-rhamnosyltetracenomycin C = methyl (6aR,7S,10aR)-6a,7,10a,12-tetrahydroxy-8-methoxy-1-methyl-6,10,11-trioxo-3-α-L-rhamnosyloxy-6,6a,7,10,10a,11-hexahydrotetracene-2-carboxylate
Other name(s): ElmMII
Systematic name: S-adenosyl-L-methionine:8-demethyl-8-(2-methoxy-α-L-rhamnosyl)tetracenomycin-C 3′-O-methyltransferase
Comments: The enzyme from the bacterium Streptomyces olivaceus is involved in the biosynthesis of the polyketide elloramycin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Patallo, E.P., Blanco, G., Fischer, C., Brana, A.F., Rohr, J., Mendez, C. and Salas, J.A. Deoxysugar methylation during biosynthesis of the antitumor polyketide elloramycin by Streptomyces olivaceus. Characterization of three methyltransferase genes. J. Biol. Chem. 276 (2001) 18765–18774. [PMID: 11376004]
[EC 2.1.1.306 created 2014]
 
 
EC 2.1.1.307
Accepted name: 8-demethyl-8-(2,3-dimethoxy-α-L-rhamnosyl)tetracenomycin-C 4′-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 8-demethyl-8-(2,3-di-O-methyl-α-L-rhamnosyl)tetracenomycin C = S-adenosyl-L-homocysteine + 8-demethyl-8-(2,3,4-tri-O-methyl-α-L-rhamnosyl)tetracenomycin C
For diagram of elloramycin biosynthesis, click here
Glossary: 8-demethyl-8-α-L-rhamnosyltetracenomycin C = methyl (6aR,7S,10aR)-6a,7,10a,12-tetrahydroxy-8-methoxy-1-methyl-6,10,11-trioxo-3-α-L-rhamnosyloxy-6,6a,7,10,10a,11-hexahydrotetracene-2-carboxylate
Other name(s): ElmMIII
Systematic name: S-adenosyl-L-methionine:8-demethyl-8-(2,3-di-O-methoxy-α-L-rhamnosyl)tetracenomycin-C 4′-O-methyltransferase
Comments: The enzyme from the bacterium Streptomyces olivaceus is involved in the biosynthesis of the polyketide elloramycin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Patallo, E.P., Blanco, G., Fischer, C., Brana, A.F., Rohr, J., Mendez, C. and Salas, J.A. Deoxysugar methylation during biosynthesis of the antitumor polyketide elloramycin by Streptomyces olivaceus. Characterization of three methyltransferase genes. J. Biol. Chem. 276 (2001) 18765–18774. [PMID: 11376004]
[EC 2.1.1.307 created 2014]
 
 
EC 2.1.3.13
Deleted entry: ATP carbamoyltransferase. The enzyme has been replaced by EC 6.1.2.2, nebramycin 5′ synthase.
[EC 2.1.3.13 created 2013, deleted 2014]
 
 
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 2.3.1.233
Accepted name: 1,3,6,8-tetrahydroxynaphthalene synthase
Reaction: 5 malonyl-CoA = 1,3,6,8-tetrahydroxynaphthalene + 5 CoA + 5 CO2 + H2O
For diagram of polyketides biosynthesis, click here
Other name(s): PKS1; THNS; SCO1206; RppA
Systematic name: malonyl-CoA C-acyl transferase (1,3,6,8-tetrahydroxynaphthalene forming)
Comments: Isolated from the fungus Colletotrichum lagenarium [1], and the bacteria Streptomyces coelicolor [2,3] and Streptomyces peucetius [4]. It only uses malonyl-CoA, without invovement of acetyl-CoA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Fujii, I., Mori, Y., Watanabe, A., Kubo, Y., Tsuji, G. and Ebizuka, Y. Enzymatic synthesis of 1,3,6,8-tetrahydroxynaphthalene solely from malonyl coenzyme A by a fungal iterative type I polyketide synthase PKS1. Biochemistry 39 (2000) 8853–8858. [PMID: 10913297]
2.  Izumikawa, M., Shipley, P.R., Hopke, J.N., O'Hare, T., Xiang, L., Noel, J.P. and Moore, B.S. Expression and characterization of the type III polyketide synthase 1,3,6,8-tetrahydroxynaphthalene synthase from Streptomyces coelicolor A3(2). J Ind Microbiol Biotechnol 30 (2003) 510–515. [PMID: 12905073]
3.  Austin, M.B., Izumikawa, M., Bowman, M.E., Udwary, D.W., Ferrer, J.L., Moore, B.S. and Noel, J.P. Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates. J. Biol. Chem. 279 (2004) 45162–45174. [PMID: 15265863]
4.  Ghimire, G.P., Oh, T.J., Liou, K. and Sohng, J.K. Identification of a cryptic type III polyketide synthase (1,3,6,8-tetrahydroxynaphthalene synthase) from Streptomyces peucetius ATCC 27952. Mol. Cells 26 (2008) 362–367. [PMID: 18612244]
[EC 2.3.1.233 created 2014]
 
 
*EC 2.4.1.208
Accepted name: diglucosyl diacylglycerol synthase (1,2-linking)
Reaction: UDP-α-D-glucose + 1,2-diacyl-3-O-(α-D-glucopyranosyl)-sn-glycerol = 1,2-diacyl-3-O-[α-D-glucopyranosyl-(1→2)-O-α-D-glucopyranosyl]-sn-glycerol + UDP
Other name(s): monoglucosyl diacylglycerol (1→2) glucosyltransferase; MGlcDAG (1→2) glucosyltransferase; DGlcDAG synthase (ambiguous); UDP-glucose:1,2-diacyl-3-O-(α-D-glucopyranosyl)-sn-glycerol (1→2) glucosyltransferase; diglucosyl diacylglycerol synthase
Systematic name: UDP-α-D-glucose:1,2-diacyl-3-O-(α-D-glucopyranosyl)-sn-glycerol 2-glucosyltransferase
Comments: The enzyme from Acholeplasma laidlawii requires Mg2+.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 168680-19-1
References:
1.  Karlsson, O.P., Rytomaa, M., Dahlqvist, A., Kinnunen, P.K., Wieslander, A. Correlation between bilayer lipid dynamics and activity of the diglucosyldiacylglycerol synthase from Acholeplasma laidlawii membranes. Biochemistry 35 (1996) 10094–10102. [PMID: 8756472]
[EC 2.4.1.208 created 1999, modified 2014]
 
 
EC 2.4.1.325
Accepted name: TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase
Reaction: dTDP-4-acetamido-4,6-dideoxy-α-D-galactose + N-acetyl-β-D-mannosaminouronyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = dTDP + 4-acetamido-4,6-dideoxy-α-D-galactosyl-(1→4)-N-acetyl-β-D-mannosaminouronyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Glossary: dTDP-4-acetamido-4,6-dideoxy-α-D-galactose = dTDP-N-acetyl-α-D-fucosamine
a lipid II = an undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl peptide; the peptide element refers to L-alanyl-D-γ-glutamyl-L-lysyl/meso-2,6-diaminopimelyl-D-alanyl-D-alanine or a modified version thereof = an undecaprenyldiphospho-4-O-(N-acetyl-β-D-glucosaminyl)-3-O-peptidyl-α-N-acetylmuramate; the peptide element refers to L-alanyl-D-γ-glutamyl-L-lysyl/meso-2,6-diaminopimelyl-D-alanyl-D-alanine or a modified version thereof
lipid III = N-acetyl-β-D-fucosyl-(1→4)-N-acetyl-β-D-mannosaminouronyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): TDP-Fuc4NAc:lipid II Fuc4NAc-transferase; TDP-Fuc4NAc:lipid II Fuc4NAc transferase; wecF (gene name)
Systematic name: dTDP-N-acetyl-α-D-fucose:N-acetyl-β-D-mannosaminouronyl-(1→4)-N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol N-acetylfucosaminyltransferase
Comments: Involved in the enterobacterial common antigen (ECA) biosynthesis in the bacterium Escherichia coli. The trisaccharide of the product (lipid III) is the repeat unit of ECA.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Rahman, A., Barr, K. and Rick, P.D. Identification of the structural gene for the TDP-Fuc4NAc:lipid II Fuc4NAc transferase involved in synthesis of enterobacterial common antigen in Escherichia coli K-12. J. Bacteriol. 183 (2001) 6509–6516. [PMID: 11673418]
[EC 2.4.1.325 created 2014]
 
 
EC 2.4.1.326
Accepted name: aklavinone 7-L-rhodosaminyltransferase
Reaction: dTDP-β-L-rhodosamine + aklavinone = dTDP + aclacinomycin T
For diagram of aklavinone biosynthesis, click here
Glossary: dTDP-β-L-rhodosamine = dTDP-2,3,6-trideoxy-3-dimethylamino-β-L-lyxo-hexose
aklavinone = methyl (1R,2R,4S)-2-ethyl-2,4,5,7-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate
aclacinomycin T = 7-O-(α-L-rhodosaminyl)aklavinone
Other name(s): AknS/AknT; aklavinone 7-β-L-rhodosaminyltransferase; dTDP-β-L-rhodosamine:aklavinone 7-α-L-rhodosaminyltransferase
Systematic name: dTDP-β-L-rhodosamine:aklavinone 7-α-L-rhodosaminyltransferase (configuration-inverting)
Comments: Isolated from the bacterium Streptomyces galilaeus. Forms a complex with its accessory protein AknT, and has very low activity in its absence. The enzyme can also use dTDP-2-deoxy-β-L-fucose. Involved in the biosynthesis of other aclacinomycins.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lu, W., Leimkuhler, C., Gatto, G.J., Jr., Kruger, R.G., Oberthur, M., Kahne, D. and Walsh, C.T. AknT is an activating protein for the glycosyltransferase AknS in L-aminodeoxysugar transfer to the aglycone of aclacinomycin A. Chem. Biol. 12 (2005) 527–534. [PMID: 15911373]
2.  Leimkuhler, C., Fridman, M., Lupoli, T., Walker, S., Walsh, C.T. and Kahne, D. Characterization of rhodosaminyl transfer by the AknS/AknT glycosylation complex and its use in reconstituting the biosynthetic pathway of aclacinomycin A. J. Am. Chem. Soc. 129 (2007) 10546–10550. [PMID: 17685523]
[EC 2.4.1.326 created 2014, modified 2015]
 
 
EC 2.4.1.327
Accepted name: aclacinomycin-T 2-deoxy-L-fucose transferase
Reaction: dTDP-2-deoxy-β-L-fucose + aclacinomycin T = dTDP + aclacinomycin S
For diagram of aclacinomycin A and Y biosynthesis, click here
Glossary: idarubicin = (7S,9S)-9-acetyl-7-(3-amino-2,3,6-trideoxy-β-L-lyxo-hexosyloxy)-6,9,11-trihydroxy-7,8,9,10-tetrahydrotetracene-5,12-dione
aclacinomycin S = 7-O-(2-deoxy-α-L-fucosyl-(1→4)-rhodosaminyl)aklavinone
aclacinomycin T = 7-O-(α-L-rhodosaminyl)aklavinone
Other name(s): AknK
Systematic name: dTDP-2-deoxy-β-L-fucose:7-(α-L-rhodosaminyl)aklavinone 2-deoxy-α-L-fucosyltransferase
Comments: The enzyme, isolated from the bacterium Streptomyces galilaeus, is involved in the biosynthesis of other aclacinomycins. Also acts on idarubicin. It will slowly add a second 2-deoxy-L-fucose unit to aclacinomycin S in vitro.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lu, W., Leimkuhler, C., Oberthur, M., Kahne, D. and Walsh, C.T. AknK is an L-2-deoxyfucosyltransferase in the biosynthesis of the anthracycline aclacinomycin A. Biochemistry 43 (2004) 4548–4558. [PMID: 15078101]
[EC 2.4.1.327 created 2014]
 
 
EC 2.4.1.328
Accepted name: erythronolide mycarosyltransferase
Reaction: dTDP-β-L-mycarose + erythronolide B = dTDP + 3-α-L-mycarosylerythronolide B
For diagram of erythromycin biosynthesis, click here
Glossary: dTDP-β-L-mycarose = dTDP-2,6-dideoxy-3-C-methyl-β-L-ribo-hexose
L-mycarose = 2,6-dideoxy-3-C-methyl-L-ribo-hexose
Other name(s): EryBV
Systematic name: dTDP-β-L-mycarose:erythronolide B L-mycarosyltransferase
Comments: Isolated from the bacterium Saccharopolyspora erythraea. The enzyme is involved in the biosynthesis of the antibiotic erythromycin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zhang, C., Fu, Q., Albermann, C., Li, L. and Thorson, J.S. The in vitro characterization of the erythronolide mycarosyltransferase EryBV and its utility in macrolide diversification. Chembiochem 8 (2007) 385–390. [PMID: 17262863]
[EC 2.4.1.328 created 2014]
 
 
EC 2.5.1.121
Accepted name: 5,10-dihydrophenazine-1-carboxylate 9-dimethylallyltransferase
Reaction: dimethylallyl diphosphate + 5,10-dihydrophenazine-1-carboxylate = diphosphate + 9-(dimethylallyl)-5,10-dihydrophenazine-1-carboxylate
Glossary: 9-(dimethylallyl)-5,10-dihydrophenazine-1-carboxylate = 9-(3-methylbut-2-en-1-yl)-5,10-dihydrophenazine-1-carboxylate
Other name(s): PpzP; dihydrophenazine-1-carboxylate dimethylallyltransferase; 5,10-dihydrophenazine 1-carboxylate dimethylallyltransferase
Systematic name: dimethylallyl diphosphate:5,10-dihydrophenazine-1-carboxylate 9-dimethylallyltransferase
Comments: The enzyme is involved in the biosynthesis of prenylated phenazines by the bacterium Streptomyces anulatus. It is specific for both dimethylallyl diphosphate and 5,10-dihydrophenazine-1-carboxylate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Saleh, O., Gust, B., Boll, B., Fiedler, H.P. and Heide, L. Aromatic prenylation in phenazine biosynthesis: dihydrophenazine-1-carboxylate dimethylallyltransferase from Streptomyces anulatus. J. Biol. Chem. 284 (2009) 14439–14447. [PMID: 19339241]
[EC 2.5.1.121 created 2014]
 
 
EC 2.5.1.122
Accepted name: 4-O-dimethylallyl-L-tyrosine synthase
Reaction: dimethylallyl diphosphate + L-tyrosine = diphosphate + 4-O-dimethylallyl-L-tyrosine
Other name(s): SirD
Systematic name: dimethylallyl diphosphate:L-tyrosine 4-O-dimethylallyltransferase
Comments: The enzyme is involved in biosynthesis of the phytotoxin sirodesmin PL by the phytopathogenic ascomycete Leptosphaeria maculans.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kremer, A. and Li, S.M. A tyrosine O-prenyltransferase catalyses the first pathway-specific step in the biosynthesis of sirodesmin PL. Microbiology 156 (2010) 278–286. [PMID: 19762440]
2.  Zou, H.X., Xie, X., Zheng, X.D. and Li, S.M. The tyrosine O-prenyltransferase SirD catalyzes O-, N-, and C-prenylations. Appl. Microbiol. Biotechnol. 89 (2011) 1443–1451. [PMID: 21038099]
[EC 2.5.1.122 created 2014]
 
 
EC 2.5.1.123
Accepted name: flaviolin linalyltransferase
Reaction: geranyl diphosphate + flaviolin = 3-linalylflaviolin + diphosphate
For diagram of flaviolin metabolism, click here
Glossary: flaviolin = 2,5,7-trihydroxynaphthalene-1,4-dione
3-linalylflaviolin = 2,5,7-trihydroxy-3-(3,7-dimethylocta-1,6-dien-3-yl)naphthalene-1,4-dione
Other name(s): Fnq26
Systematic name: geranyl-diphosphate:flaviolin 3-linalyltransferase
Comments: Does not require Mg2+ or any other metal ions. Isolated from the bacterium Streptomyces cinnamonensis. In vitro the enzyme also forms traces of 3-geranylflaviolin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Haagen, Y., Unsold, I., Westrich, L., Gust, B., Richard, S.B., Noel, J.P. and Heide, L. A soluble, magnesium-independent prenyltransferase catalyzes reverse and regular C-prenylations and O-prenylations of aromatic substrates. FEBS Lett. 581 (2007) 2889–2893. [PMID: 17543953]
[EC 2.5.1.123 created 2014]
 
 
EC 2.7.1.183
Accepted name: glycoprotein-mannosyl O6-kinase
Reaction: ATP + O3-[N-acetyl-β-D-galactosaminyl-(1→3)-N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl/L-seryl-[protein] = ADP + O3-[N-acetyl-β-D-galactosaminyl-(1→3)-N-acetyl-β-D-glucosaminyl-(1→4)-α-D-(6-phospho)mannosyl]-L-threonyl/L-seryl-[protein]
For diagram of glycoprotein biosynthesis, click here
Other name(s): SGK196; protein O-mannose kinase
Systematic name: ATP:O3-[N-acetyl-β-D-galactosaminyl-(1→3)-N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl/L-seryl-[protein] 6-phosphotransferase
Comments: In humans this phosphorylated trisaccharide is attached to an L-threonine residue of α-dystroglycan, an extracellular peripheral glycoprotein that acts as a receptor for extracellular matrix proteins containing laminin-G domains, and is important for its activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yoshida-Moriguchi, T., Willer, T., Anderson, M.E., Venzke, D., Whyte, T., Muntoni, F., Lee, H., Nelson, S.F., Yu, L. and Campbell, K.P. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science 341 (2013) 896–899. [PMID: 23929950]
[EC 2.7.1.183 created 2014]
 
 
EC 2.7.1.184
Accepted name: sulfofructose kinase
Reaction: ATP + 6-deoxy-6-sulfo-D-fructose = ADP + 6-deoxy-6-sulfo-D-fructose 1-phosphate
For diagram of sulphoglycolysis of sulfoquinovose, click here
Other name(s): yihV (gene name)
Systematic name: ATP:6-deoxy-6-sulfo-D-fructose 1-phosphotransferase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114–117. [PMID: 24463506]
[EC 2.7.1.184 created 2014]
 
 
*EC 2.7.7.86
Accepted name: cyclic GMP-AMP synthase
Reaction: ATP + GTP = 2 diphosphate + cyclic Gp(2′-5′)Ap(3′-5′) (overall reaction)
(1a) ATP + GTP = pppGp(2′-5′)A + diphosphate
(1b) pppGp(2′-5′)A = cyclic Gp(2′-5′)Ap(3′-5′) + diphosphate
Glossary: cyclic Gp(2′-5′)Ap(3′-5′) = cyclo[(3′→5′)-guanylyl-(2′→5′)-adenylyl]
Other name(s): cGAMP synthase; cGAS
Systematic name: ATP:GTP adenylyltransferase (cyclizing)
Comments: Cyclic Gp(2′-5′)Ap(3′-5′) is a signalling molecule in mammalian cells that triggers the production of type I interferons and other cytokines.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sun, L., Wu, J., Du, F., Chen, X. and Chen, Z.J. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 339 (2013) 786–791. [PMID: 23258413]
2.  Ablasser, A., Goldeck, M., Cavlar, T., Deimling, T., Witte, G., Rohl, I., Hopfner, K.P., Ludwig, J. and Hornung, V. cGAS produces a 2′-5′-linked cyclic dinucleotide second messenger that activates STING. Nature 498 (2013) 380–384. [PMID: 23722158]
[EC 2.7.7.86 created 2013, modified 2014]
 
 
EC 2.8.2.37
Accepted name: trehalose 2-sulfotransferase
Reaction: 3′-phosphoadenylyl sulfate + α,α-trehalose = adenosine 3′,5′-bisphosphate + 2-O-sulfo-α,α-trehalose
Glossary: 2-O-sulfo-α,α-trehalose = trehalose 2-sulfate = α-D-glucopyranosyl 2-O-sulfo-α-D-glucopyranoside
Other name(s): Stf0 sulfotransferase
Systematic name: 3′-phosphoadenylyl-sulfate:α,α-trehalose 2-sulfotransferase
Comments: The sulfation of trehalose in the bacterium Mycobacterium tuberculosis is required for the biosynthesis of sulfolipid-1.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Mougous, J.D., Petzold, C.J., Senaratne, R.H., Lee, D.H., Akey, D.L., Lin, F.L., Munchel, S.E., Pratt, M.R., Riley, L.W., Leary, J.A., Berger, J.M. and Bertozzi, C.R. Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis. Nat. Struct. Mol. Biol. 11 (2004) 721–729. [PMID: 15258569]
2.  Pi, N., Hoang, M.B., Gao, H., Mougous, J.D., Bertozzi, C.R. and Leary, J.A. Kinetic measurements and mechanism determination of Stf0 sulfotransferase using mass spectrometry. Anal. Biochem. 341 (2005) 94–104. [PMID: 15866533]
[EC 2.8.2.37 created 2014]
 
 
EC 3.1.1.96
Accepted name: D-aminoacyl-tRNA deacylase
Reaction: a D-aminoacyl-tRNA + H2O = a D-amino acid + tRNA
Other name(s): Dtd2; D-Tyr-tRNA(Tyr) deacylase; D-Tyr-tRNATyr deacylase; D-tyrosyl-tRNATyr aminoacylhydrolase; dtdA (gene name)
Systematic name: D-aminoacyl-tRNA aminoacylhydrolase
Comments: The enzyme from Escherichia coli can cleave D-tyrosyl-tRNATyr, D-aspartyl-tRNAAsp and D-tryptophanyl-tRNATrp [1]. Whereas the enzyme from the archaeon Pyrococcus abyssi is a zinc protein, the enzyme from Escherichia coli does not carry any zinc [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Soutourina, J., Plateau, P. and Blanquet, S. Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells. J. Biol. Chem. 275 (2000) 32535–32542. [PMID: 10918062]
2.  Ferri-Fioni, M.L., Schmitt, E., Soutourina, J., Plateau, P., Mechulam, Y. and Blanquet, S. Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases. J. Biol. Chem. 276 (2001) 47285–47290. [PMID: 11568181]
3.  Ferri-Fioni, M.L., Fromant, M., Bouin, A.P., Aubard, C., Lazennec, C., Plateau, P. and Blanquet, S. Identification in archaea of a novel D-Tyr-tRNATyr deacylase. J. Biol. Chem. 281 (2006) 27575–27585. [PMID: 16844682]
4.  Wydau, S., Ferri-Fioni, M.L., Blanquet, S. and Plateau, P. GEK1, a gene product of Arabidopsis thaliana involved in ethanol tolerance, is a D-aminoacyl-tRNA deacylase. Nucleic Acids Res. 35 (2007) 930–938. [PMID: 17251192]
[EC 3.1.1.96 created 2014]
 
 
EC 3.1.4.57
Accepted name: phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase
Reaction: (1) 5-phospho-α-D-ribose 1,2-cyclic phosphate + H2O = D-ribofuranose 2,5-bisphosphate
(2) D-ribofuranose 2,5-bisphosphate + H2O = D-ribofuranose 5-phosphate + phosphate
Other name(s): cyclic phosphate dihydrolase; phnPP (gene name)
Systematic name: 5-phospho-α-D-ribose 1,2-cyclic phosphate 1,2-diphosphophosphohydrolase
Comments: The enzyme, characterized from the bacterium Eggerthella lenta, is involed in degradation of methylphosphonate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ghodge, S.V., Cummings, J.A., Williams, H.J. and Raushel, F.M. Discovery of a cyclic phosphodiesterase that catalyzes the sequential hydrolysis of both ester bonds to phosphorus. J. Am. Chem. Soc. 135 (2013) 16360–16363. [PMID: 24147537]
[EC 3.1.4.57 created 2014]
 
 
EC 3.1.12 Exodeoxyribonucleases producing 3′-phosphomonoesters
 
EC 3.1.12.1
Accepted name: 5′ to 3′ exodeoxyribonuclease (nucleoside 3′-phosphate-forming)
Reaction: exonucleolytic cleavage in the 5′- to 3′-direction to yield nucleoside 3′-phosphates
Other name(s): Cas4; 5′ to 3′ single stranded DNA exonuclease
Comments: Preference for single-stranded DNA. The enzyme from the archaeon Sulfolobus solfataricus contains a [4Fe-4S] cluster and requires a divalent metal cation, such as Mg2+ or Mn2+, for activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zhang, J., Kasciukovic, T. and White, M.F. The CRISPR associated protein Cas4 Is a 5′ to 3′ DNA exonuclease with an iron-sulfur cluster. PLoS One 7:e47232 (2012). [PMID: 23056615]
2.  Lemak, S., Beloglazova, N., Nocek, B., Skarina, T., Flick, R., Brown, G., Popovic, A., Joachimiak, A., Savchenko, A. and Yakunin, A.F. Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus. J. Am. Chem. Soc. 135 (2013) 17476–17487. [PMID: 24171432]
[EC 3.1.12.1 created 2014]
 
 
*EC 3.5.1.46
Accepted name: 6-aminohexanoate-oligomer exohydrolase
Reaction: (1) [N-(6-aminohexanoyl)]n + H2O = [N-(6-aminohexanoyl)]n-1 + 6-aminohexanoate
(2) N-(6-aminohexanoyl)-6-aminohexanoate + H2O = 2 6-aminohexanoate
Other name(s): 6-aminohexanoate-dimer hydrolase; nylB (gene name); 6-aminohexanoic acid oligomer hydrolase (ambiguous); N-(6-aminohexanoyl)-6-aminohexanoate amidohydrolase; nylon-6 hydrolase (ambiguous)
Systematic name: N-(6-aminohexanoyl)-6-aminohexanoate exoamidohydrolase
Comments: The enzyme is involved in degradation of nylon-6 oligomers. It degrades linear oligomers of 6-aminohexanoate with a degree of polymerization of 2–20 by exo-type cleavage, removing residues sequentially from the N-terminus. Activity decreases with the increase of the polymerization number of the oligomer. cf. EC 3.5.1.117, 6-aminohexanoate-oligomer endohydrolase and EC 3.5.2.12, 6-aminohexanoate-cyclic-dimer hydrolase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 75216-15-8
References:
1.  Kinoshita, S., Terada, T., Taniguchi, T., Takeney, Y., Masuda, S., Matsunaga, N. and Okada, H. Purification and characterization of 6-aminohexanoic-acid-oligomer hydrolase of Flavobacterium sp. KI72. Eur. J. Biochem. 116 (1981) 547–551. [PMID: 7262074]
[EC 3.5.1.46 created 1983, modified 2014]
 
 
EC 3.5.1.117
Accepted name: 6-aminohexanoate-oligomer endohydrolase
Reaction: [N-(6-aminohexanoyl)]n + H2O = [N-(6-aminohexanoyl)]n-x + [N-(6-aminohexanoyl)]x
Other name(s): endo-type 6-aminohexanoate oligomer hydrolase; Ahx endo-type-oligomer hydrolase; 6-aminohexanoate oligomer hydrolase; Ahx-oligomer hydrolase; nylon hydrolase; nylon-oligomer hydrolase; NylC; nylon-6 hydrolase (ambiguous)
Systematic name: 6-aminohexanoate oligomer endoamidohydrolase
Comments: The enzyme is involved in degradation of nylon-6 oligomers. It degrades linear or cyclic oligomers of poly(6-aminohexanoate) with a degree of polymerization greater than three (n > 3) by endo-type cleavage, to oligomers of a length of two or more (2 ≤ x < n). It shows negligible activity with N-(6-aminohexanoyl)-6-aminohexanoate (cf. EC 3.5.1.46, 6-aminohexanoate-oligomer exo hydrolase) or with 1,8-diazacyclotetradecane-2,9-dione (cf. EC 3.5.2.12, 6-aminohexanoate-cyclic-dimer hydrolase).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kakudo, S., Negoro, S., Urabe, I. and Okada, H. Nylon oligomer degradation gene, nylC, on plasmid pOAD2 from a Flavobacterium strain encodes endo-type 6-aminohexanoate oligomer hydrolase: purification and characterization of the nylC gene product. Appl. Environ. Microbiol. 59 (1993) 3978–3980. [PMID: 8285701]
2.  Yasuhira, K., Tanaka, Y., Shibata, H., Kawashima, Y., Ohara, A., Kato, D., Takeo, M. and Negoro, S. 6-Aminohexanoate oligomer hydrolases from the alkalophilic bacteria Agromyces sp. strain KY5R and Kocuria sp. strain KY2. Appl. Environ. Microbiol. 73 (2007) 7099–7102. [PMID: 17827307]
3.  Negoro, S., Shibata, N., Tanaka, Y., Yasuhira, K., Shibata, H., Hashimoto, H., Lee, Y.H., Oshima, S., Santa, R., Oshima, S., Mochiji, K., Goto, Y., Ikegami, T., Nagai, K., Kato, D., Takeo, M. and Higuchi, Y. Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis. J. Biol. Chem. 287 (2012) 5079–5090. [PMID: 22187439]
[EC 3.5.1.117 created 2014]
 
 
*EC 3.5.4.17
Accepted name: adenosine-phosphate deaminase
Reaction: (1) AMP + H2O = IMP + NH3
(2) ADP + H2O = IDP + NH3
(3) ATP + H2O = ITP + NH3
Glossary: IMP = inosine 5′-phosphate
AMP = adenosine 5′-phosphate
Other name(s): adenylate deaminase; adenine nucleotide deaminase; adenosine (phosphate) deaminase
Systematic name: adenosine-phosphate aminohydrolase
Comments: Acts on AMP, ADP, ATP, NAD+ and adenosine, in decreasing order of activity. The bacterial enzyme can also accept the deoxy derivatives. cf. EC 3.5.4.6, AMP deaminase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37289-20-6
References:
1.  Su, J.-C., Li, C.-C. and Ting, C.C. A new adenylate deaminase from red marine alga Porphyra crispata. Biochemistry 5 (1966) 536–543. [PMID: 5940938]
2.  Yates, M.G. A non-specific adenine nucleotide deaminase from Desulfovibrio desulfuricans. Biochim. Biophys. Acta 171 (1969) 299–310. [PMID: 5773435]
[EC 3.5.4.17 created 1972, modified 1980, modified 2014]
 
 
*EC 3.5.99.7
Accepted name: 1-aminocyclopropane-1-carboxylate deaminase
Reaction: 1-aminocyclopropane-1-carboxylate + H2O = 2-oxobutanoate + NH3 (overall reaction)
(1a) 1-aminocyclopropane-1-carboxylate = 2-aminobut-2-enoate
(1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous)
(1c) 2-iminobutanoate + H2O = 2-oxobutanoate + NH3 (spontaneous)
Other name(s): 1-aminocyclopropane-1-carboxylate endolyase (deaminating); ACC deaminase; 1-aminocyclopropane carboxylic acid deaminase
Systematic name: 1-aminocyclopropane-1-carboxylate aminohydrolase (isomerizing)
Comments: A pyridoxal 5′-phosphate enzyme. The enzyme, found in certain soil bacteria and fungi, catalyses the ring opening of 1-aminocyclopropane-1-carboxylate, the immediate precursor to ethylene, an important plant hormone that regulates fruit ripening and other processes. The enzyme releases an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. The enzyme has been used to make fruit ripening dependent on externally added ethylene, as it removes the substrate for endogenous ethylene formation.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 69553-48-6
References:
1.  Honma, M. and Shimomura, T. Metabolism of 1-aminocyclopropane-1-carboxylic acid. Agric. Biol. Chem. 42 (1978) 1825–1831.
2.  Yao, M., Ose, T., Sugimoto, H., Horiuchi, A., Nakagawa, A., Wakatsuki, S., Yokoi, D., Murakami, T., Honma, M. and Tanaka, I. Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus. J. Biol. Chem. 275 (2000) 34557–34565. [PMID: 10938279]
3.  Thibodeaux, C.J. and Liu, H.W. Mechanistic studies of 1-aminocyclopropane-1-carboxylate deaminase: characterization of an unusual pyridoxal 5′-phosphate-dependent reaction. Biochemistry 50 (2011) 1950–1962. [PMID: 21244019]
[EC 3.5.99.7 created 1981 as EC 4.1.99.4, transferred 2002 to EC 3.5.99.7, modified 2014]
 
 
EC 3.13.1.4
Accepted name: 3-sulfinopropanoyl-CoA desulfinase
Reaction: 3-sulfinopropanoyl-CoA + H2O = propanoyl-CoA + sulfite
Other name(s): 3SP-CoA desulfinase; AcdDPN7; 3-sulfinopropionyl-CoA desulfinase
Systematic name: 3-sulfinopropanoyl-CoA sulfinohydrolase
Comments: The enzyme from the β-proteobacterium Advenella mimigardefordensis contains one non-covalently bound FAD per subunit.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Schurmann, M., Deters, A., Wubbeler, J.H. and Steinbuchel, A. A novel 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis strain DPN7T acting as a key enzyme during catabolism of 3,3′-dithiodipropionic acid is a member of the acyl-CoA dehydrogenase superfamily. J. Bacteriol. 195 (2013) 1538–1551. [PMID: 23354747]
2.  Schurmann, M., Demming, R.M., Krewing, M., Rose, J., Wubbeler, J.H. and Steinbuchel, A. Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. J. Bacteriol. 196 (2014) 882–893. [PMID: 24317404]
[EC 3.13.1.4 created 2014]
 
 
EC 4.1.1.98
Accepted name: 4-hydroxy-3-polyprenylbenzoate decarboxylase
Reaction: a 4-hydroxy-3-polyprenylbenzoate = a 2-polyprenylphenol + CO2
For diagram of ubiquinol biosynthesis, click here
Other name(s): ubiD (gene name); 4-hydroxy-3-solanesylbenzoate decarboxylase; 3-octaprenyl-4-hydroxybenzoate decarboxylase
Systematic name: 4-hydroxy-3-polyprenylbenzoate carboxy-lyase
Comments: The enzyme catalyses a step in prokaryotic ubiquinone biosynthesis, as well as in plastoquinone biosynthesis in cyanobacteria. The enzyme can accept substrates with different polyprenyl tail lengths in vitro, but uses a specific length in vivo, which is determined by the polyprenyl diphosphate synthase that exists in the specific organism. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Leppik, R.A., Young, I.G. and Gibson, F. Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase. Biochim. Biophys. Acta 436 (1976) 800–810. [PMID: 782527]
2.  Gulmezian, M., Hyman, K.R., Marbois, B.N., Clarke, C.F. and Javor, G.T. The role of UbiX in Escherichia coli coenzyme Q biosynthesis. Arch. Biochem. Biophys. 467 (2007) 144–153. [PMID: 17889824]
3.  Pfaff, C., Glindemann, N., Gruber, J., Frentzen, M. and Sadre, R. Chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate decarboxylase are required for plastoquinone biosynthesis in the cyanobacterium Synechocystis sp. PCC6803. J. Biol. Chem. 289 (2014) 2675–2686. [PMID: 24337576]
4.  Lin, F., Ferguson, K.L., Boyer, D.R., Lin, X.N. and Marsh, E.N. Isofunctional enzymes PAD1 and UbiX catalyze formation of a novel cofactor required by ferulic acid decarboxylase and 4-hydroxy-3-polyprenylbenzoic acid decarboxylase. ACS Chem. Biol. 10 (2015) 1137–1144. [PMID: 25647642]
5.  Payne, K.A., White, M.D., Fisher, K., Khara, B., Bailey, S.S., Parker, D., Rattray, N.J., Trivedi, D.K., Goodacre, R., Beveridge, R., Barran, P., Rigby, S.E., Scrutton, N.S., Hay, S. and Leys, D. New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature 522 (2015) 497–501. [PMID: 26083754]
[EC 4.1.1.98 created 2014, modified 2015]
 
 
EC 4.1.2.57
Accepted name: sulfofructosephosphate aldolase
Reaction: 6-deoxy-6-sulfo-D-fructose 1-phosphate = glycerone phosphate + 2-hydroxy-3-oxopropane-1-sulfonate
For diagram of sulphoglycolysis of sulfoquinovose, click here
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
2-hydroxy-3-oxopropane-1-sulfonate = 3-sulfolactaldehyde
Other name(s): yihT (gene name)
Systematic name: 6-deoxy-6-sulfofructose-1-phosphate 2-hydroxy-3-oxopropane-1-sulfonate-lyase (glycerone-phosphate-forming)
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114–117. [PMID: 24463506]
[EC 4.1.2.57 created 2014]
 
 
*EC 4.2.1.134
Accepted name: very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase
Reaction: a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain trans-2,3-dehydroacyl-CoA + H2O
Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.
Other name(s): PHS1 (gene name); PAS2 (gene name)
Systematic name: very-long-chain (3R)-3-hydroxyacyl-CoA hydro-lyase
Comments: This is the third 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. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Bach, L., Michaelson, L.V., Haslam, R., Bellec, Y., Gissot, L., Marion, J., Da Costa, M., Boutin, J.P., Miquel, M., Tellier, F., Domergue, F., Markham, J.E., Beaudoin, F., Napier, J.A. and Faure, J.D. The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO2 is essential and limiting for plant development. Proc. Natl. Acad. Sci. USA 105 (2008) 14727–14731. [PMID: 18799749]
2.  Kihara, A., Sakuraba, H., Ikeda, M., Denpoh, A. and Igarashi, Y. Membrane topology and essential amino acid residues of Phs1, a 3-hydroxyacyl-CoA dehydratase involved in very long-chain fatty acid elongation. J. Biol. Chem. 283 (2008) 11199–11209. [PMID: 18272525]
[EC 4.2.1.134 created 2012, modified 2014]
 
 
EC 4.2.1.152
Accepted name: hydroperoxy icosatetraenoate dehydratase
Reaction: a hydroperoxyicosatetraenoate = an oxoicosatetraenoate + H2O
Glossary: (12R)-HPETE = (5Z,8Z,10E,12R,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
(12S)-HPETE = (5Z,8Z,10E,12S,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
12-KETE = 12-oxo-ETE = (5Z,8Z,10E,14Z)-12-oxoicosa-5,8,10,14-tetraenoate
(8R)-HPETE = (5Z,8R,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate
(15R)-HPETE = (5Z,8Z,11Z,13E,15R)-15-hydroperoxyicosa-5,8,11,13-tetraenoate
Other name(s): epidermal lipoxygenase-3 (ambiguous); eLOX3 (ambiguous)
Systematic name: hydroperoxyicosatetraenoate hydro-lyase (oxoicosatetraenoate-forming)
Comments: Binds Fe2+. The mammalian enzymes accept a range of hydroperoxyicosatetraenoates (HPETE). The human enzyme has highest activity with (12R)-HPETE, followed by (12S)-HPETE and (15R)-HPETE with much lower efficiency. The murine enzyme has highest activity with (8R)-HPETE followed by (8S)-HPETE. All HPETE isoforms are converted to the corresponding oxoicosatetraenoate forms (KETE) [2]. The enzymes also catalyse the reaction of EC 5.4.4.7, hydroperoxy icosatetraenoate isomerase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yu, Z., Schneider, C., Boeglin, W.E., Marnett, L.J. and Brash, A.R. The lipoxygenase gene ALOXE3 implicated in skin differentiation encodes a hydroperoxide isomerase. Proc. Natl. Acad. Sci. USA 100 (2003) 9162–9167. [PMID: 12881489]
2.  Yu, Z., Schneider, C., Boeglin, W.E. and Brash, A.R. Human and mouse eLOX3 have distinct substrate specificities: implications for their linkage with lipoxygenases in skin. Arch. Biochem. Biophys. 455 (2006) 188–196. [PMID: 17045234]
3.  Zheng, Y. and Brash, A.R. Dioxygenase activity of epidermal lipoxygenase-3 unveiled: typical and atypical features of its catalytic activity with natural and synthetic polyunsaturated fatty acids. J. Biol. Chem. 285 (2010) 39866–39875. [PMID: 20921226]
[EC 4.2.1.152 created 2014]
 
 
EC 4.2.1.153
Accepted name: 3-methylfumaryl-CoA hydratase
Reaction: (S)-citramalyl-CoA = 3-methylfumaryl-CoA + H2O
For diagram of the 3-hydroxypropanoate cycle, click here
Glossary: (S)-citramalyl-CoA = (3S)-3-carboxy-3-hydroxybutanoyl-CoA
3-methylfumaryl-CoA = (E)-3-carboxybut-2-enoyl-CoA
Other name(s): Meh; mesaconyl-C4-CoA hydratase; mesaconyl-coenzyme A hydratase (ambiguous)
Systematic name: (S)-citramalyl-CoA hydro-lyase (3-methylfumaryl-CoA-forming)
Comments: The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zarzycki, J., Brecht, V., Muller, M. and Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. USA 106 (2009) 21317–21322. [PMID: 19955419]
[EC 4.2.1.153 created 2014]
 
 
EC 4.2.1.154
Accepted name: tetracenomycin F2 cyclase
Reaction: tetracenomycin F2 = tetracenomycin F1 + H2O
For diagram of tetracenomycin biosynthesis, click here
Glossary: tetracenomycin F1 = 3,8,10,12-tetrahydroxy-1-methyl-11-oxo-6,11-dihydro-2-tetracenecarboxylate = 6,11-dihydro-3,8,10,12-tetrahydroxy-1-methyl-11-oxonaphthacene-2-carboxylate
tetracenomycin F2 = (3E)-4-(3-acetyl-4,5,7-trihydroxy-10-oxo-9,10-dihydroanthracen-2-yl)-3-hydroxybut-3-enoate
Other name(s): tcmI (gene name)
Systematic name: tetracenomycin F2 hydro-lyase (tetracenomycin-F1-forming)
Comments: The enzyme is involved in biosynthesis of the anthracycline antibiotic tetracenomycin C by the bacterium Streptomyces glaucescens.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Shen, B. and Hutchinson, C.R. Tetracenomycin F2 cyclase: intramolecular aldol condensation in the biosynthesis of tetracenomycin C in Streptomyces glaucescens. Biochemistry 32 (1993) 11149–11154. [PMID: 8218177]
2.  Thompson, T.B., Katayama, K., Watanabe, K., Hutchinson, C.R. and Rayment, I. Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase. J. Biol. Chem. 279 (2004) 37956–37963. [PMID: 15231835]
[EC 4.2.1.154 created 2014]
 
 
EC 4.2.3.145
Accepted name: ophiobolin F synthase
Reaction: (2E,6E,10E,14E)-geranylfarnesyl diphosphate + H2O = ophiobolin F + diphosphate
For diagram of biosynthesis of diterpenoids from ent-copalyl diphosphate, click here and for diagram of sesterterpenoids biosynthesis, click here
Systematic name: (2E,6E,10E,14E)-geranylfarnesyl-diphosphate diphosphate-lyase (cyclizing, ophiobolin-F-forming)
Comments: Isolated from the fungus Aspergillus clavatus. The product is a sesterterpenoid (C25 terpenoid).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Chiba, R., Minami, A., Gomi, K. and Oikawa, H. Identification of ophiobolin F synthase by a genome mining approach: a sesterterpene synthase from Aspergillus clavatus. Org. Lett. 15 (2013) 594–597. [PMID: 23324037]
[EC 4.2.3.145 created 2014]
 
 
EC 4.2.3.146
Accepted name: cyclooctat-9-en-7-ol synthase
Reaction: geranylgeranyl diphosphate + H2O = cyclooctat-9-en-7-ol + diphosphate
For diagram of biosynthesis of fusicoccane diterpenoids, click here
Glossary: cyclooctat-9-en-7-ol = (1S,3aS,4R,7S,9aS,10aS)-1,4,9a-trimethyl-7-(propan-2-yl)-1,2,3,3a,4,5,7,8,9,9a,10,10a-dodecahydrodicyclopenta[a,d][8]annulen-4-ol
Other name(s): cetB2
Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (cyclooctat-9-en-7-ol-forming)
Comments: Requires Mg2+. Isolated from the bacterium Streptomyces melanosporofaciens, where it is part of the biosynthesis of cyclooctatin, a potent inhibitor of lysophospholipase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kim, S.Y., Zhao, P., Igarashi, M., Sawa, R., Tomita, T., Nishiyama, M. and Kuzuyama, T. Cloning and heterologous expression of the cyclooctatin biosynthetic gene cluster afford a diterpene cyclase and two P450 hydroxylases. Chem. Biol. 16 (2009) 736–743. [PMID: 19635410]
2.  Zhang, X., Shang, G., Gu, L. and Shen, Y. Crystallization and preliminary X-ray diffraction analysis of the diterpene cyclooctatin synthase (CYC) from Streptomyces sp. LZ35. Acta Crystallogr. F Struct. Biol. Commun. 70 (2014) 366–369. [PMID: 24598929]
[EC 4.2.3.146 created 2014]
 
 
EC 5.1.3.29
Accepted name: L-fucose mutarotase
Reaction: α-L-fucopyranose = β-L-fucopyranose
Other name(s): FucU; fucose mutarotase; FucM
Systematic name: L-fucose 1-epimerase
Comments: This enzyme shows no 1-epimerase activity with D-glucose, L-rhamnose and D-fucose (cf. EC 5.1.3.3, aldose 1-epimerase) [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ryu, K.S., Kim, C., Kim, I., Yoo, S., Choi, B.S. and Park, C. NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration. J. Biol. Chem. 279 (2004) 25544–25548. [PMID: 15060078]
2.  Park, D., Ryu, K.S., Choi, D., Kwak, J. and Park, C. Characterization and role of fucose mutarotase in mammalian cells. Glycobiology 17 (2007) 955–962. [PMID: 17602138]
[EC 5.1.3.29 created 2014]
 
 
EC 5.3.1.31
Accepted name: sulfoquinovose isomerase
Reaction: sulfoquinovose = 6-deoxy-6-sulfo-D-fructose
For diagram of sulphoglycolysis of sulfoquinovose, click here
Glossary: sulfoquinovose = 6-deoxy-6-sulfo-D-glucopyranose
Other name(s): yihS (gene name)
Systematic name: 6-deoxy-6-sulfo-D-glucopyranose aldose-ketose-isomerase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114–117. [PMID: 24463506]
[EC 5.3.1.31 created 2014]
 
 
*EC 5.4.2.11
Accepted name: phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate (overall reaction)
(1a) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 2/3-phospho-D-glycerate
(1b) [enzyme]-Nτ-phospho-L-histidine + 2-phospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
(1c) [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Nτ-phospho-L-histidine + 3-phospho-D-glycerate
(1d) [enzyme]-Nτ-phospho-L-histidine + 2/3-bisphospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
For diagram of the Entner-Doudoroff pathway, click here
Glossary: 2/3-phospho-D-glycerate = 2-phospho-D-glycerate or 3-phospho-D-glycerate
Other name(s): glycerate phosphomutase (diphosphoglycerate cofactor); 2,3-diphosphoglycerate dependent phosphoglycerate mutase; cofactor dependent phosphoglycerate mutase; phosphoglycerate phosphomutase (ambiguous); phosphoglyceromutase (ambiguous); monophosphoglycerate mutase (ambiguous); monophosphoglyceromutase (ambiguous); GriP mutase (ambiguous); PGA mutase (ambiguous); MPGM; PGAM; PGAM-d; PGM; dPGM
Systematic name: D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-dependent)
Comments: The enzymes from vertebrates, platyhelminths, mollusks, annelids, crustaceans, insects, algae, fungi, yeast and some bacteria (particularly Gram-negative) require 2,3-bisphospho-D-glycerate as a cofactor. The enzyme is activated by 2,3-bisphospho-D-glycerate by transferring a phosphate to histidine (His10 in man and Escherichia coli, His8 in Saccharomyces cerevisiae). This phosphate can be transferred to the free OH of 2-phospho-D-glycerate, followed by transfer of the phosphate already on the phosphoglycerate back to the histidine. cf. EC 5.4.2.12 phosphoglycerate mutase. The enzyme has no requirement for metal ions. This enzyme also catalyse, slowly, the reactions of EC 5.4.2.4 bisphosphoglycerate mutase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Grisolia, S. Phosphoglyceric acid mutase. Methods Enzymol. 5 (1962) 236–242.
2.  Ray, W.J., Jr. and Peck, E.J., Jr. Phosphomutases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 6, 1972, pp. 407–477.
3.  Rose, Z.B. The enzymology of 2,3-bisphosphoglycerate. Adv. Enzymol. Relat. Areas Mol. Biol. 51 (1980) 211–253. [PMID: 6255773]
4.  Rigden, D.J., Walter, R.A., Phillips, S.E. and Fothergill-Gilmore, L.A. Sulphate ions observed in the 2.12 Å structure of a new crystal form of S. cerevisiae phosphoglycerate mutase provide insights into understanding the catalytic mechanism. J. Mol. Biol. 286 (1999) 1507–1517. [PMID: 10064712]
5.  Bond, C.S., White, M.F. and Hunter, W.N. High resolution structure of the phosphohistidine-activated form of Escherichia coli cofactor-dependent phosphoglycerate mutase. J. Biol. Chem. 276 (2001) 3247–3253. [PMID: 11038361]
6.  Rigden, D.J., Mello, L.V., Setlow, P. and Jedrzejas, M.J. Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from Bacillus stearothermophilus with broad specificity phosphatase activity. J. Mol. Biol. 315 (2002) 1129–1143. [PMID: 11827481]
7.  Rigden, D.J., Littlejohn, J.E., Henderson, K. and Jedrzejas, M.J. Structures of phosphate and trivanadate complexes of Bacillus stearothermophilus phosphatase PhoE: structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily. J. Mol. Biol. 325 (2003) 411–420. [PMID: 12498792]
[EC 5.4.2.11 created 1961 as EC 5.4.2.1 (EC 2.7.5.3 created 1961, incorporated 1984) transferred 2013 to 5.4.2.11, modified 2014]
 
 
EC 5.4.4.7
Accepted name: hydroperoxy icosatetraenoate isomerase
Reaction: a hydroperoxyicosatetraenoate = a hydroxyepoxyicosatrienoate
Glossary: (12R)-HPETE = (5Z,8Z,10E,12R,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
(8S)-HPETE = (5Z,8S,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate
Other name(s): epidermal lipoxygenase-3 (ambiguous); eLOX3 (ambiguous)
Systematic name: hydroperoxyicosatetraenoate hydroxymutase
Comments: Binds Fe2+. The enzyme from mammals accepts a range of hydroperoxyicosatetraenoates producing one or several different hydroxyepoxyicosatrienoates. The human enzyme has highest activity with (12R)-HPETE producing (5Z,8R,9E,11R,12R,14Z)-8-hydroxy-11,12-epoxyicosa-5,9,14-trienoate, followed by (12S)-HPETE producing (5Z,8Z,10R,11S,12S,14Z)-10-hydroxy-11,12-epoxyicosa-5,8,14-trienoate and (5Z,8R,9E,11S,12S,14Z)-8-hydroxy-11,12-epoxyicosa-5,9,14-trienoate [1]. The mouse enzyme has highest activity with (8S)-HPETE, producing (5Z,8S,9S,10R,11Z,14Z)-10-hydroxy-8,9-epoxyicosa-5,11,14-trienoate [2]. The enzymes also have the activity of EC 4.2.1.152, hydroperoxy icosatetraenoate dehydratase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yu, Z., Schneider, C., Boeglin, W.E., Marnett, L.J. and Brash, A.R. The lipoxygenase gene ALOXE3 implicated in skin differentiation encodes a hydroperoxide isomerase. Proc. Natl. Acad. Sci. USA 100 (2003) 9162–9167. [PMID: 12881489]
2.  Yu, Z., Schneider, C., Boeglin, W.E. and Brash, A.R. Human and mouse eLOX3 have distinct substrate specificities: implications for their linkage with lipoxygenases in skin. Arch. Biochem. Biophys. 455 (2006) 188–196. [PMID: 17045234]
3.  Zheng, Y. and Brash, A.R. Dioxygenase activity of epidermal lipoxygenase-3 unveiled: typical and atypical features of its catalytic activity with natural and synthetic polyunsaturated fatty acids. J. Biol. Chem. 285 (2010) 39866–39875. [PMID: 20921226]
[EC 5.4.4.7 created 2014]
 
 
*EC 5.5.1.23
Accepted name: aklanonic acid methyl ester cyclase
Reaction: aklaviketone = methyl aklanonate
For diagram of aklavinone biosynthesis, click here
Glossary: aklaviketone = methyl (1R,2R)-2-ethyl-2,5,7-trihydroxy-4,6,11-trioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate
methyl aklanonate = methyl [4,5-dihydroxy-9,10-dioxo-3-(3-oxopentanoyl)-9,10-dihydroanthracen-2-yl]acetate
Other name(s): dauD (gene name); aknH (gene name); dnrD (gene name); methyl aklanonate cyclase; methyl aklanonate-aklaviketone isomerase (cyclizing); aklaviketone lyase (decyclizing)
Systematic name: aklaviketone lyase (ring-opening)
Comments: The enzyme is involved in the biosynthesis of aklaviketone, an intermediate in the biosynthetic pathways leading to formation of several anthracycline antibiotics, including aclacinomycin, daunorubicin and doxorubicin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Dickens, M.L., Ye, J. and Strohl, W.R. Analysis of clustered genes encoding both early and late steps in daunomycin biosynthesis by Streptomyces sp. strain C5. J. Bacteriol. 177 (1995) 536–543. [PMID: 7836284]
2.  Kendrew, S.G., Katayama, K., Deutsch, E., Madduri, K. and Hutchinson, C.R. DnrD cyclase involved in the biosynthesis of doxorubicin: purification and characterization of the recombinant enzyme. Biochemistry 38 (1999) 4794–4799. [PMID: 10200167]
3.  Kallio, P., Sultana, A., Niemi, J., Mantsala, P. and Schneider, G. Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity. J. Mol. Biol. 357 (2006) 210–220. [PMID: 16414075]
[EC 5.5.1.23 created 2013, modified 2014]
 
 
EC 6.1.2.2
Accepted name: nebramycin 5′ synthase
Reaction: (1) tobramycin + carbamoyl phosphate + ATP + H2O = nebramycin 5′ + AMP + diphosphate + phosphate (overall reaction)
(1a) carbamoyl phosphate + ATP + H2O = diphosphate + O-carbamoyladenylate + phosphate
(1b) O-carbamoyladenylate + tobramycin = AMP + nebramycin 5′
(2) kanamycin A + carbamoyl phosphate + ATP + H2O = 6′′-O-carbamoylkanamycin A + AMP + diphosphate + phosphate (overall reaction)
(2a) carbamoyl phosphate + ATP + H2O = diphosphate + O-carbamoyladenylate + phosphate
(2b) O-carbamoyladenylate + kanamycin A = AMP + 6′′-O-carbamoylkanamycin A
For diagram of kanamycin A biosynthesis, click here
Glossary: tobramycin = (1S,2S,3R,4S,6R)-4,6-diamino-3-(2,6-diamino-2,3,6-trideoxy-α-D-ribo-hexopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
nebramycin 5′ = (1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-α-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-6-O-carbamoyl-3-deoxy-α-D-glucopyranoside
kanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-(6-amino-6-deoxy--D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy--D-glucopyranoside
6′′-O-carbamoylkanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-[(6-amino-6-deoxy-α-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-6-O-carbamoyl-3-deoxy-α-D-glucopyranoside
Other name(s): tobramycin carbamoyltransferase; TobZ
Systematic name: tobramycin:carbamoyl phosphate ligase (AMP,phosphate-forming)
Comments: Requires Fe(III). The enzyme from the bacterium Streptoalloteichus tenebrarius catalyses the activation of carbamoyl phosphate to O-carbamoyladenylate and the subsequent carbamoylation of kanamycin and tobramycin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Parthier, C., Gorlich, S., Jaenecke, F., Breithaupt, C., Brauer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Bottcher, C., Scheel, D. and Stubbs, M.T. The O-carbamoyltransferase TobZ catalyzes an ancient enzymatic reaction. Angew. Chem. Int. Ed. Engl. 51 (2012) 4046–4052. [PMID: 22383337]
[EC 6.1.2.2 created 2014]
 
 
EC 6.2.1.41
Accepted name: 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate—CoA ligase
Reaction: ATP + 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + CoA = AMP + diphosphate + 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoyl-CoA
For diagram of cholesterol catabolism, click here
Glossary: 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate = HIP
Other name(s): fadD3 (gene name); HIP—CoA ligase
Systematic name: 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from actinobacterium Mycobacterium tuberculosis, catalyses a step in the degradation of cholesterol and cholate. The enzyme is very specific for its substrate, and requires that the side chain at C17 is completely removed.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
References:
1.  Horinouchi, M., Hayashi, T., Koshino, H. and Kudo, T. ORF18-disrupted mutant of Comamonas testosteroni TA441 accumulates significant amounts of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid and its derivatives after incubation with steroids. J. Steroid Biochem. Mol. Biol. 101 (2006) 78–84. [PMID: 16891113]
2.  Casabon, I., Crowe, A.M., Liu, J. and Eltis, L.D. FadD3 is an acyl-CoA synthetase that initiates catabolism of cholesterol rings C and D in actinobacteria. Mol. Microbiol. 87 (2013) 269–283. [PMID: 23146019]
[EC 6.2.1.41 created 2014]
 
 
EC 6.2.1.42
Accepted name: 3-oxocholest-4-en-26-oate—CoA ligase
Reaction: ATP + (25S)-3-oxocholest-4-en-26-oate + CoA = AMP + diphosphate + (25S)-3-oxocholest-4-en-26-oyl-CoA
For diagram of cholic acid biosynthesis (sidechain), click here
Other name(s): fadD19 (gene name)
Systematic name: (25S)-3-oxocholest-4-en-26-oate:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from actinobacterium Mycobacterium tuberculosis, catalyses a step in the degradation of cholesterol. It is responsible for the activation of the C8 side chain. 3β-hydroxycholest-5-en-26-oate can also be used as substrate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
References:
1.  Wilbrink, M.H., Petrusma, M., Dijkhuizen, L. and van der Geize, R. FadD19 of Rhodococcus rhodochrous DSM43269, a steroid-coenzyme A ligase essential for degradation of C-24 branched sterol side chains. Appl. Environ. Microbiol. 77 (2011) 4455–4464. [PMID: 21602385]
2.  Casabon, I., Swain, K., Crowe, A.M., Eltis, L.D. and Mohn, W.W. Actinobacterial acyl coenzyme a synthetases involved in steroid side-chain catabolism. J. Bacteriol. 196 (2014) 579–587. [PMID: 24244004]
[EC 6.2.1.42 created 2014]
 
 
EC 6.2.1.43
Accepted name: 2-hydroxy-7-methoxy-5-methyl-1-naphthoate—CoA ligase
Reaction: ATP + 2-hydroxy-7-methoxy-5-methyl-1-naphthoate + CoA = AMP + diphosphate + 2-hydroxy-7-methoxy-5-methyl-1-naphthoyl-CoA
For diagram of neocarzinostatin biosynthesis, click here
Other name(s): NcsB2
Systematic name: 2-hydroxy-7-methoxy-5-methyl-1-naphthoate:CoA ligase
Comments: The enzyme from the bacterium Streptomyces carzinostaticus is involved in the attachment of the 2-hydroxy-7-methoxy-5-methyl-1-naphthoate moiety of the antibiotic neocarzinostatin. In vitro the enzyme also catalyses the activation of other 1-naphthoic acid analogues, e.g. 2-hydroxy-5-methyl-1-naphthoate or 2,7-dihydroxy-5-methyl-1-naphthoate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Cooke, H.A., Zhang, J., Griffin, M.A., Nonaka, K., Van Lanen, S.G., Shen, B. and Bruner, S.D. Characterization of NcsB2 as a promiscuous naphthoic acid/coenzyme A ligase integral to the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin. J. Am. Chem. Soc. 129 (2007) 7728–7729. [PMID: 17539640]
[EC 6.2.1.43 created 2014]
 
 
*EC 6.3.1.9
Accepted name: trypanothione synthase
Reaction: (1) glutathione + spermidine + ATP = glutathionylspermidine + ADP + phosphate
(2) glutathione + glutathionylspermidine + ATP = N1,N8-bis(glutathionyl)spermidine + ADP + phosphate
For diagram of trypanothione biosynthesis, click here and for diagram of trypanothione biosynthesis, click here
Glossary: N1,N8-bis(glutathionyl)spermidine = trypanothione
Other name(s): glutathionylspermidine:glutathione ligase (ADP-forming)
Systematic name: spermidine/glutathionylspermidine:glutathione ligase (ADP-forming)
Comments: The enzyme, characterized from several trypanosomatids (e.g. Trypanosoma cruzi) catalyses two subsequent reactions, leading to production of trypanothione from glutathione and spermidine. Some trypanosomatids (e.g. Crithidia species and some Leishmania species) also contain an enzyme that only carries out the first reaction (cf. EC 6.3.1.8, glutathionylspermidine synthase). The enzyme is bifunctional, and also catalyses the hydrolysis of glutathionylspermidine and trypanothione (cf. EC 3.5.1.78, glutathionylspermidine amidase).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 130246-69-4
References:
1.  Smith, K., Nadeau, K., Bradley, M., Walsh, C.T., Fairlamb, A.H. Purification of glutathionylspermidine and trypanothione synthase from Crithidia fasciculata. Protein Sci. 1 (1992) 874–883. [PMID: 1304372]
2.  Oza, S.L., Tetaud, E., Ariyanayagam, M.R., Warnon, S.S. and Fairlamb, A.H. A single enzyme catalyses formation of trypanothione from glutathione and spermidine in Trypanosoma cruzi. J. Biol. Chem. 277 (2002) 35853–35861. [PMID: 12121990]
3.  Comini, M., Menge, U., Wissing, J. and Flohe, L. Trypanothione synthesis in crithidia revisited. J. Biol. Chem. 280 (2005) 6850–6860. [PMID: 15537651]
4.  Oza, S.L., Shaw, M.P., Wyllie, S. and Fairlamb, A.H. Trypanothione biosynthesis in Leishmania major. Mol. Biochem. Parasitol. 139 (2005) 107–116. [PMID: 15610825]
5.  Fyfe, P.K., Oza, S.L., Fairlamb, A.H. and Hunter, W.N. Leishmania trypanothione synthetase-amidase structure reveals a basis for regulation of conflicting synthetic and hydrolytic activities. J. Biol. Chem. 283 (2008) 17672–17680. [PMID: 18420578]
[EC 6.3.1.9 created 1999, modified 2014]
 
 
EC 6.3.1.18
Accepted name: γ-glutamylanilide synthase
Reaction: ATP + L-glutamate + aniline = ADP + phosphate + N5-phenyl-L-glutamine
Glossary: γ-glutamylanilide = N5-phenyl-L-glutamine
Other name(s): atdA1 (gene name); tdnQ (gene name); dcaQ (gene name)
Systematic name: L-glutamate:aniline ligase (ADP-forming)
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Acinetobacter sp. YAA, catalyses the first step in the degradation of aniline. It can also accept chlorinated and methylated forms of aniline, preferrably in the o- and p-positions.
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, PDB
References:
1.  Takeo, M., Ohara, A., Sakae, S., Okamoto, Y., Kitamura, C., Kato, D. and Negoro, S. Function of a glutamine synthetase-like protein in bacterial aniline oxidation via γ-glutamylanilide. J. Bacteriol. 195 (2013) 4406–4414. [PMID: 23893114]
[EC 6.3.1.18 created 2014]
 
 


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