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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.50 3α-hydroxysteroid 3-dehydrogenase (Si-specific)
*EC 1.1.1.168 2-dehydropantolactone reductase (Re-specific)
*EC 1.1.1.213 3α-hydroxysteroid 3-dehydrogenase (Re-specific)
*EC 1.1.1.214 2-dehydropantolactone reductase (Si-specific)
*EC 1.1.1.266 dTDP-4-dehydro-6-deoxyglucose reductase
EC 1.1.1.354 farnesol dehydrogenase (NAD+)
EC 1.1.1.355 2′-dehydrokanamycin reductase
EC 1.1.1.356 GDP-L-colitose synthase
EC 1.1.1.357 3α-hydroxysteroid 3-dehydrogenase
EC 1.1.1.358 2-dehydropantolactone reductase
EC 1.1.1.359 aldose 1-dehydrogenase [NAD(P)+]
EC 1.1.1.360 glucose/galactose 1-dehydrogenase
EC 1.1.5.9 glucose 1-dehydrogenase (FAD, quinone)
EC 1.1.99.10 transferred
*EC 1.1.99.38 2-deoxy-scyllo-inosamine dehydrogenase (AdoMet-dependent)
EC 1.2.1.87 propanal dehydrogenase (CoA-propanoylating)
EC 1.2.1.88 L-glutamate γ-semialdehyde dehydrogenase
*EC 1.2.7.1 pyruvate synthase
EC 1.2.7.2 deleted
*EC 1.3.1.10 enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific)
*EC 1.3.1.39 enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific)
EC 1.3.1.102 2-alkenal reductase (NADP+)
EC 1.3.1.103 2-haloacrylate reductase
EC 1.5.1.12 transferred
*EC 1.6.1.1 NAD(P)+ transhydrogenase (Si-specific)
*EC 1.6.1.2 NAD(P)+ transhydrogenase (Re/Si-specific)
EC 1.6.1.3 NAD(P)+ transhydrogenase
EC 1.8.1.18 NAD(P)H sulfur oxidoreductase (CoA-dependent)
EC 1.10.3.13 caldariellaquinol oxidase (H+-transporting)
*EC 1.13.11.2 catechol 2,3-dioxygenase
EC 1.13.11.75 all-trans-8′-apo-β-carotenal 15,15′-oxygenase
EC 1.14.11.38 verruculogen synthase
EC 1.14.11.39 L-asparagine hydroxylase
EC 1.14.11.40 enduracididine β-hydroxylase
EC 1.14.11.41 L-arginine hydroxylase
EC 1.14.13.177 fumitremorgin C monooxygenase
EC 1.14.13.178 methylxanthine N1-demethylase
EC 1.14.13.179 methylxanthine N3-demethylase
EC 1.14.20.3 (5R)-carbapenem-3-carboxylate synthase
EC 1.14.21.10 fumitremorgin C synthase
EC 1.14.99.41 transferred
EC 2.1.1.273 benzoate O-methyltransferase
EC 2.1.1.274 salicylate 1-O-methyltransferase
EC 2.1.1.275 gibberellin A9 O-methyltransferase
EC 2.1.1.276 gibberellin A4 carboxyl methyltransferase
EC 2.1.1.277 anthranilate O-methyltransferase
EC 2.1.1.278 indole-3-acetate O-methyltransferase
EC 2.1.1.279 trans-anol O-methyltransferase
EC 2.1.1.280 selenocysteine Se-methyltransferase
EC 2.1.1.281 phenylpyruvate C3-methyltransferase
EC 2.1.1.282 tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase
EC 2.1.1.283 emodin O-methyltransferase
EC 2.1.1.284 8-demethylnovobiocic acid C8-methyltransferase
EC 2.1.1.285 demethyldecarbamoylnovobiocin O-methyltransferase
EC 2.1.1.286 25S rRNA (adenine2142-N1)-methyltransferase
EC 2.1.1.287 25S rRNA (adenine645-N1)-methyltransferase
EC 2.1.3.12 decarbamoylnovobiocin carbamoyltransferase
EC 2.3.1.224 acetyl-CoA-benzylalcohol acetyltransferase
EC 2.3.1.225 protein S-acyltransferase
EC 2.3.1.226 carboxymethylproline synthase
*EC 2.4.1.1 glycogen phosphorylase
EC 2.4.1.301 2′-deamino-2′-hydroxyneamine 1-α-D-kanosaminyltransferase
EC 2.4.1.302 L-demethylnoviosyl transferase
EC 2.4.1.303 UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol β-1,3-galactosyltransferase
EC 2.4.1.304 UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol β-1,4-galactosyltransferase
EC 2.4.1.305 UDP-Glc:α-D-GlcNAc-glucosaminyl-diphosphoundecaprenol β-1,3-glucosyltransferase
EC 2.4.1.306 UDP-GalNAc:α-D-GalNAc-diphosphoundecaprenol α-1,3-N-acetylgalactosaminyltransferase
EC 2.4.1.307 UDP-Gal:α-D-GalNAc-1,3-α-D-GalNAc-diphosphoundecaprenol β-1,3-galactosyltransferase
EC 2.4.1.308 GDP-Fuc:β-D-Gal-1,3-α-D-GalNAc-1,3-α-GalNAc-diphosphoundecaprenol α-1,2-fucosyltransferase
EC 2.4.1.309 UDP-Gal:α-L-Fuc-1,2-β-Gal-1,3-α-GalNAc-1,3-α-GalNAc-diphosphoundecaprenol α-1,3-galactosyltransferase
EC 2.4.2.23 transferred
*EC 2.5.1.79 thermospermine synthase
EC 2.5.1.108 2-(3-amino-3-carboxypropyl)histidine synthase
EC 2.5.1.109 brevianamide F prenyltransferase (deoxybrevianamide E-forming)
EC 2.5.1.110 12α,13α-dihydroxyfumitremorgin C prenyltransferase
EC 2.6.1.102 GDP-perosamine synthase
EC 2.6.99.3 O-ureido-L-serine synthase
EC 2.7.7.86 cyclic GMP-AMP synthase
EC 2.7.7.87 L-threonylcarbamoyladenylate synthase
*EC 2.7.8.38 archaetidylserine synthase
EC 2.7.8.39 archaetidylinositol phosphate synthase
EC 2.7.8.40 UDP-N-acetylgalactosamine-undecaprenyl-phosphate N-acetylgalactosaminephosphotransferase
EC 3.1.3.90 maltose 6′-phosphate phosphatase
*EC 3.2.1.88 non-reducing end β-L-arabinopyranosidase
EC 3.5.3.25 Nω-hydroxy-L-arginine amidinohydrolase
*EC 3.6.1.5 apyrase
*EC 3.6.1.62 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] hydrolase
*EC 3.6.3.4 Cu2+-exporting ATPase
EC 3.6.3.54 Cu+-exporting ATPase
EC 4.1.2.52 4-hydroxy-2-oxoheptanedioate aldolase
EC 4.1.2.53 2-keto-3-deoxy-L-rhamnonate aldolase
EC 4.1.3.43 4-hydroxy-2-oxohexanoate aldolase
*EC 4.1.99.5 aldehyde oxygenase (deformylating)
EC 4.1.99.20 3-amino-4-hydroxybenzoate synthase
*EC 4.2.1.105 2-hydroxyisoflavanone dehydratase
EC 5.1.1.19 O-ureido-serine racemase
EC 5.4.2.1 transferred
EC 5.4.2.11 phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
EC 5.4.2.12 phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
EC 6.3.1.15 8-demethylnovobiocic acid synthase
EC 6.3.3.5 O-ureido-D-serine cyclo-ligase
EC 6.3.4.23 formate—phosphoribosylaminoimidazolecarboxamide ligase


*EC 1.1.1.50
Accepted name: 3α-hydroxysteroid 3-dehydrogenase (Si-specific)
Reaction: a 3α-hydroxysteroid + NAD(P)+ = a 3-oxosteroid + NAD(P)H + H+
Other name(s): hydroxyprostaglandin dehydrogenase; 3α-hydroxysteroid oxidoreductase; sterognost 3α; 3α-hydroxysteroid dehydrogenase (B-specific); 3α-hydroxysteroid 3-dehydrogenase (B-specific); 3α-hydroxysteroid:NAD(P)+ 3-oxidoreductase (B-specific)
Systematic name: 3α-hydroxysteroid:NAD(P)+ 3-oxidoreductase (Si-specific)
Comments: The enzyme acts on androsterone and other 3α-hydroxysteroids and on 9-, 11- and 15-hydroxyprostaglandin. Si-specific with respect to NAD+ or NADP+. cf. EC 1.1.1.213, 3α-hydroxysteroid 3-dehydrogenase (Re-specific).
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, CAS registry number: 9028-56-2
References:
1.  Jarabak, J. and Talalay, P. Stereospecificity of hydrogen transfer by pyridine nucleotide-linked hydroxysteroid hydrogenase. J. Biol. Chem. 235 (1960) 2147–2151. [PMID: 14406805]
2.  Kochakian, C.D., Carroll, B.R. and Uhri, B. Comparisons of the oxidation of C19-hydroxysteroids by guinea pig liver homogenates. J. Biol. Chem. 224 (1957) 811–818. [PMID: 13405910]
3.  Marcus, P.I. and Talalay, P. Induction and purification of α- and β-hydroxysteroid dehydrogenases. J. Biol. Chem. 218 (1956) 661–674. [PMID: 13295221]
4.  Penning, T.M. and Sharp, R.B. Prostaglandin dehydrogenase activity of purified rat liver 3α-hydroxysteroid dehydrogenase. Biochem. Biophys. Res. Commun. 148 (1987) 646–652. [PMID: 3479982]
[EC 1.1.1.50 created 1961, modified 1986, modified 1990, modified 2012, modified 2013]
 
 
*EC 1.1.1.168
Accepted name: 2-dehydropantolactone reductase (Re-specific)
Reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+
Other name(s): 2-oxopantoyl lactone reductase; ketopantoyl lactone reductase; 2-ketopantoyl lactone reductase; 2-dehydropantoyl-lactone reductase (A-specific); (R)-pantolactone:NADP+ oxidoreductase (A-specific); 2-dehydropantolactone reductase (A-specific)
Systematic name: (R)-pantolactone:NADP+ oxidoreductase (Re-specific)
Comments: The yeast enzyme differs from that from Escherichia coli [EC 1.1.1.214 2-dehydropantolactone reductase (Si-specific)], which is specific for the Si-face of NADP+, and in receptor requirements from EC 1.1.99.26 3-hydroxycyclohexanone dehydrogenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37211-75-9
References:
1.  King, H.L., Jr., Dyar, R.E. and Wilken, D.R. Ketopantoyl lactone and ketopantoic acid reductases. Characterization of the reactions and purification of two forms of ketopantoyl lactone reductase. J. Biol. Chem. 247 (1972) 4689–4695. [PMID: 4603075]
2.  Wilken, D.R., King, H.L., Jr. and Dyar, R.E. Ketopantoic acid and ketopantoyl lactone reductases. Stereospecificity of transfer of hydrogen from reduced nicotinamide adenine dinucleotide phosphate. J. Biol. Chem. 250 (1975) 2311–2314. [PMID: 234966]
[EC 1.1.1.168 created 1976, modified 1986, modified 1999]
 
 
*EC 1.1.1.213
Accepted name: 3α-hydroxysteroid 3-dehydrogenase (Re-specific)
Reaction: a 3α-hydroxysteroid + NAD(P)+ = a 3-oxosteroid + NAD(P)H + H+
Other name(s): 3α-hydroxysteroid dehydrogenase; 3α-hydroxysteroid:NAD(P)+ 3-oxidoreductase (A-specific); 3α-hydroxysteroid 3-dehydrogenase (A-specific)
Systematic name: 3α-hydroxysteroid:NAD(P)+ 3-oxidoreductase (Re-specific)
Comments: The enzyme acts on multiple 3α-hydroxysteroids. Re-specific with respect to NAD+ or NADP+ [cf. EC 1.1.1.50, 3α-hydroxysteroid 3-dehydrogenase (Si-specific)]. Enzymes whose stereo-specificity with respect to NAD+ or NADP+ is not known are described by EC 1.1.1.357, 3α-hydroxysteroid 3-dehydrogenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9028-56-2
References:
1.  Björkhem, I. and Danielsson, H. Stereochemistry of hydrogen transfer from pyridine nucleotides catalyzed by Δ4-3-oxosteroid 5-β-reductase and 3-α-hydroxysteroid dehydrogenase from rat liver. Eur. J. Biochem. 12 (1970) 80–84. [PMID: 4392180]
2.  Tomkins, G.M. A mammalian 3α-hydroxysteroid dehydrogenase. J. Biol. Chem. 218 (1956) 437–447. [PMID: 13278351]
[EC 1.1.1.213 created 1986, modified 2012]
 
 
*EC 1.1.1.214
Accepted name: 2-dehydropantolactone reductase (Si-specific)
Reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+
Other name(s): 2-oxopantoyl lactone reductase; 2-ketopantoyl lactone reductase; ketopantoyl lactone reductase; 2-dehydropantoyl-lactone reductase (B-specific); (R)-pantolactone:NADP+ oxidoreductase (B-specific); 2-dehydropantolactone reductase (B-specific)
Systematic name: (R)-pantolactone:NADP+ oxidoreductase (Si-specific)
Comments: The Escherichia coli enzyme differs from that from yeast [EC 1.1.1.168 2-dehydropantolactone reductase (Re-specific)], which is specific for the Re-face of NADP+, and in receptor requirements from EC 1.1.99.26 3-hydroxycyclohexanone dehydrogenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37211-75-9
References:
1.  Wilken, D.R., King, H.L., Jr. and Dyar, R.E. Ketopantoic acid and ketopantoyl lactone reductases. Stereospecificity of transfer of hydrogen from reduced nicotinamide adenine dinucleotide phosphate. J. Biol. Chem. 250 (1975) 2311–2314. [PMID: 234966]
[EC 1.1.1.214 created 1986, modified 1999, modified 2013]
 
 
*EC 1.1.1.266
Accepted name: dTDP-4-dehydro-6-deoxyglucose reductase
Reaction: dTDP-α-D-fucopyranose + NAD(P)+ = dTDP-4-dehydro-6-deoxy-α-D-glucose + NAD(P)H + H+
For diagram of dTDP-6-deoxyhexose biosynthesis, click here
Glossary: dTDP-4-dehydro-6-deoxy-α-D-glucose = dTDP-6-deoxy-α-D-xylo-hexopyranos-4-ulose = thymidine 5′-[3-(6-deoxy--D-xylo-hexopyranosyl-4-ulose) diphosphate]
Other name(s): dTDP-4-keto-6-deoxyglucose reductase; dTDP-D-fucose:NADP+ oxidoreductase; Fcf1; dTDP-6-deoxy-D-xylo-hex-4-ulopyranose reductase
Systematic name: dTDP-α-D-fucopyranose:NAD(P)+ oxidoreductase
Comments: The enzymes from the Gram-negative bacteria Aggregatibacter actinomycetemcomitans and Escherichia coli O52 are involved in activation of fucose for incorporation into capsular polysaccharide O-antigens [1,3]. The enzyme from the Gram-positive bacterium Anoxybacillus tepidamans (Geobacillus tepidamans) is involved in activation of fucose for incorporation into the organism’s S-layer [2]. The enzyme from Escherichia coli O52 has a higher catalytic efficiency with NADH than with NADPH [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yoshida, Y., Nakano, Y., Nezu, T., Yamashita, Y. and Koga, T. A novel NDP-6-deoxyhexosyl-4-ulose reductase in the pathway for the synthesis of thymidine diphosphate-D-fucose. J. Biol. Chem. 274 (1999) 16933–16939. [PMID: 10358040]
2.  Zayni, S., Steiner, K., Pfostl, A., Hofinger, A., Kosma, P., Schaffer, C. and Messner, P. The dTDP-4-dehydro-6-deoxyglucose reductase encoding fcd gene is part of the surface layer glycoprotein glycosylation gene cluster of Geobacillus tepidamans GS5-97T. Glycobiology 17 (2007) 433–443. [PMID: 17202151]
3.  Wang, Q., Ding, P., Perepelov, A.V., Xu, Y., Wang, Y., Knirel, Y.A., Wang, L. and Feng, L. Characterization of the dTDP-D-fucofuranose biosynthetic pathway in Escherichia coli O52. Mol. Microbiol. 70 (2008) 1358–1367. [PMID: 19019146]
[EC 1.1.1.266 created 2001, modified 2013]
 
 
EC 1.1.1.354
Accepted name: farnesol dehydrogenase (NAD+)
Reaction: (2E,6E)-farnesol + NAD+ = (2E,6E)-farnesal + NADH + H+
For diagram of juvenile hormone biosynthesis, click here
Other name(s): NAD+-farnesol dehydrogenase
Systematic name: (2E,6E)-farnesol:NAD+ 1-oxidoreductase
Comments: The enzyme from the prune mite Carpoglyphus lactis also acts on geraniol with greater activity [cf. EC 1.1.1.347, geraniol dehydrogenase (NAD+)]. Unlike EC 1.1.1.216, farnesol dehydrogenase (NADP+), this enzyme cannot use NADP+ as cofactor.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Noge, K., Kato, M., Mori, N., Kataoka, M., Tanaka, C., Yamasue, Y., Nishida, R. and Kuwahara, Y. Geraniol dehydrogenase, the key enzyme in biosynthesis of the alarm pheromone, from the astigmatid mite Carpoglyphus lactis (Acari: Carpoglyphidae). FEBS J. 275 (2008) 2807–2817. [PMID: 18422649]
[EC 1.1.1.354 created 2013]
 
 
EC 1.1.1.355
Accepted name: 2′-dehydrokanamycin reductase
Reaction: kanamycin A + NADP+ = 2′-dehydrokanamycin A + NADPH + H+
For diagram of kanamycin A biosynthesis, click here
Glossary: kanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-(6-amino-6-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
2′-dehydrokanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-[(6-amino-6-deoxy-α-D-arabino-hexopyranosyl-2-ulose)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
Other name(s): kanK (gene name, ambiguous)
Systematic name: kanamycin A:NADP+ oxidoreductase
Comments: Found in the bacterium Streptomyces kanamyceticus where it is involved in the conversion of kanamycin B to kanamycin A.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sucipto, H., Kudo, F. and Eguchi, T. The last step of kanamycin biosynthesis: unique deamination reaction catalyzed by the α-ketoglutarate-dependent nonheme iron dioxygenase KanJ and the NADPH-dependent reductase KanK. Angew. Chem. Int. Ed. Engl. 51 (2012) 3428–3431. [PMID: 22374809]
[EC 1.1.1.355 created 2013]
 
 
EC 1.1.1.356
Accepted name: GDP-L-colitose synthase
Reaction: GDP-β-L-colitose + NAD(P)+ = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + NAD(P)H + H+
For diagram of GDP-colitose biosynthesis, click here
Glossary: L-colitose = 3,6-dideoxy-L-xylo-hexopyranose
GDP-4-dehydro-3,6-dideoxy-α-D-mannose = GDP-3,6-dideoxy-α-D-threo-hexopyranos-4-ulose
Other name(s): ColC
Systematic name: GDP-β-L-colitose:NAD(P)+ 4-oxidoreductase (5-epimerizing)
Comments: The enzyme is involved in biosynthesis of L-colitose, a 3,6-dideoxyhexose found in the O-antigen of Gram-negative lipopolysaccharides, where it catalyses the reaction in the reverse direction. The enzyme also performs the NAD(P)H-dependent epimerisation at C-5 of the sugar. The enzyme from Yersinia pseudotuberculosis is Si-specific with respect to NAD(P)H [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Alam, J., Beyer, N. and Liu, H.W. Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC). Biochemistry 43 (2004) 16450–16460. [PMID: 15610039]
[EC 1.1.1.356 created 2013]
 
 
EC 1.1.1.357
Accepted name: 3α-hydroxysteroid 3-dehydrogenase
Reaction: a 3α-hydroxysteroid + NAD(P)+ = a 3-oxosteroid + NAD(P)H + H+
Other name(s): 3α-hydroxysteroid dehydrogenase; AKR1C4 (gene name); AKR1C2 (gene name); hsdA (gene name)
Systematic name: 3α-hydroxysteroid:NAD(P)+ 3-oxidoreductase
Comments: The enzyme acts on multiple 3α-hydroxysteroids, such as androsterone and 5 α-dihydrotestosterone. The mammalian enzymes are involved in inactivation of steroid hormones, while the bacterial enzymes are involved in steroid degradation. This entry stands for enzymes whose stereo-specificity with respect to NAD+ or NADP+ is not known. [cf. EC 1.1.1.50, 3α-hydroxysteroid 3-dehydrogenase (Si-specific) and EC 1.1.1.213, 3α-hydroxysteroid 3-dehydrogenase (Re-specific)].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Deyashiki, Y., Ogasawara, A., Nakayama, T., Nakanishi, M., Miyabe, Y., Sato, K. and Hara, A. Molecular cloning of two human liver 3 α-hydroxysteroid/dihydrodiol dehydrogenase isoenzymes that are identical with chlordecone reductase and bile-acid binder. Biochem. J. 299 (1994) 545–552. [PMID: 8172617]
2.  Khanna, M., Qin, K.N., Wang, R.W. and Cheng, K.C. Substrate specificity, gene structure, and tissue-specific distribution of multiple human 3 α-hydroxysteroid dehydrogenases. J. Biol. Chem. 270 (1995) 20162–20168. [PMID: 7650035]
3.  Oppermann, U.C. and Maser, E. Characterization of a 3 α-hydroxysteroid dehydrogenase/carbonyl reductase from the gram-negative bacterium Comamonas testosteroni. Eur. J. Biochem. 241 (1996) 744–749. [PMID: 8944761]
4.  Mobus, E. and Maser, E. Molecular cloning, overexpression, and characterization of steroid-inducible 3α-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni. A novel member of the short-chain dehydrogenase/reductase superfamily. J. Biol. Chem. 273 (1998) 30888–30896. [PMID: 9812981]
5.  Nahoum, V., Gangloff, A., Legrand, P., Zhu, D.W., Cantin, L., Zhorov, B.S., Luu-The, V., Labrie, F., Breton, R. and Lin, S.X. Structure of the human 3α-hydroxysteroid dehydrogenase type 3 in complex with testosterone and NADP at 1.25-Å resolution. J. Biol. Chem. 276 (2001) 42091–42098. [PMID: 11514561]
[EC 1.1.1.357 created 2013]
 
 
EC 1.1.1.358
Accepted name: 2-dehydropantolactone reductase
Reaction: (R)-pantolactone + NADP+ = 2-dehydropantolactone + NADPH + H+
Other name(s): 2-oxopantoyl lactone reductase; 2-ketopantoyl lactone reductase; ketopantoyl lactone reductase; 2-dehydropantoyl-lactone reductase
Systematic name: (R)-pantolactone:NADP+ oxidoreductase
Comments: The enzyme participates in an alternative pathway for biosynthesis of (R)-pantothenate (vitamin B5). This entry covers enzymes whose stereo specificity for NADP+ is not known. cf. EC 1.1.1.168 2-dehydropantolactone reductase (Re-specific) and EC 1.1.1.214, 2-dehydropantolactone reductase (Si-specific).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hata, H., Shimizu, S., Hattori, S. and Yamada, H. Ketopantoyl-lactone reductase from Candida parapsilosis: purification and characterization as a conjugated polyketone reductase. Biochim. Biophys. Acta 990 (1989) 175–181. [PMID: 2644973]
[EC 1.1.1.358 created 2013]
 
 
EC 1.1.1.359
Accepted name: aldose 1-dehydrogenase [NAD(P)+]
Reaction: an aldopyranose + NAD(P)+ = an aldono-1,5-lactone + NAD(P)H + H+
Systematic name: an aldopyranose:NAD(P)+ 1-oxidoreductase
Comments: The enzyme from the archaeon Sulfolobus solfataricus shows broad specificity towards aldoses (D-glucose, D-galactose, D-xylose, L-arabinose, 6-deoxy-D-glucose, D-fucose) and can utilize NAD+ and NADP+ with similar catalytic efficiency. It is involved in aldose catabolism via the branched variant of the Entner-Doudoroff pathway.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Giardina, P., de Biasi, M.G., de Rosa, M., Gambacorta, A. and Buonocore, V. Glucose dehydrogenase from the thermoacidophilic archaebacterium Sulfolobus solfataricus. Biochem. J. 239 (1986) 517–522. [PMID: 3827812]
2.  Smith, L.D., Budgen, N., Bungard, S.J., Danson, M.J. and Hough, D.W. Purification and characterization of glucose dehydrogenase from the thermoacidophilic archaebacterium Thermoplasma acidophilum. Biochem. J. 261 (1989) 973–977. [PMID: 2803257]
3.  Lamble, H.J., Heyer, N.I., Bull, S.D., Hough, D.W. and Danson, M.J. Metabolic pathway promiscuity in the archaeon Sulfolobus solfataricus revealed by studies on glucose dehydrogenase and 2-keto-3-deoxygluconate aldolase. J. Biol. Chem. 278 (2003) 34066–34072. [PMID: 12824170]
4.  Theodossis, A., Milburn, C.C., Heyer, N.I., Lamble, H.J., Hough, D.W., Danson, M.J. and Taylor, G.L. Preliminary crystallographic studies of glucose dehydrogenase from the promiscuous Entner-Doudoroff pathway in the hyperthermophilic archaeon Sulfolobus solfataricus. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61 (2005) 112–115. [PMID: 16508107]
5.  Milburn, C.C., Lamble, H.J., Theodossis, A., Bull, S.D., Hough, D.W., Danson, M.J. and Taylor, G.L. The structural basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus. J. Biol. Chem. 281 (2006) 14796–14804. [PMID: 16556607]
6.  Haferkamp, P., Kutschki, S., Treichel, J., Hemeda, H., Sewczyk, K., Hoffmann, D., Zaparty, M. and Siebers, B. An additional glucose dehydrogenase from Sulfolobus solfataricus: fine-tuning of sugar degradation. Biochem. Soc. Trans. 39 (2011) 77–81. [PMID: 21265750]
[EC 1.1.1.359 created 2013]
 
 
EC 1.1.1.360
Accepted name: glucose/galactose 1-dehydrogenase
Reaction: (1) D-glucopyranose + NADP+ = D-glucono-1,5-lactone + NADPH + H+
(2) D-galactopyranose + NADP+ = D-galactono-1,5-lactone + NADPH + H+
For diagram of the Entner-Doudoroff Pathway, click here
Other name(s): GdhA; dual-specific glucose/galactose dehydrogenase; glucose (galactose) dehydrogenase; glucose/galactose dehydrogenase
Systematic name: D-glucose/D-galactose 1-dehydrogenase (NADPH)
Comments: A zinc protein. The enzyme from the archaeon Picrophilus torridus is involved in glucose and galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway. It shows 20-fold higher activity with NADP+ compared to NAD+. The oxidation of D-glucose and D-galactose is catalysed at a comparable rate (cf. EC 1.1.1.119, glucose 1-dehydrogenase (NADP+) and EC 1.1.1.120, galactose 1-dehydrogenase (NADP+)).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Angelov, A., Futterer, O., Valerius, O., Braus, G.H. and Liebl, W. Properties of the recombinant glucose/galactose dehydrogenase from the extreme thermoacidophile, Picrophilus torridus. FEBS J. 272 (2005) 1054–1062. [PMID: 15691337]
2.  Milburn, C.C., Lamble, H.J., Theodossis, A., Bull, S.D., Hough, D.W., Danson, M.J. and Taylor, G.L. The structural basis of substrate promiscuity in glucose dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus. J. Biol. Chem. 281 (2006) 14796–14804. [PMID: 16556607]
[EC 1.1.1.360 created 2013]
 
 
EC 1.1.5.9
Accepted name: glucose 1-dehydrogenase (FAD, quinone)
Reaction: D-glucose + a quinone = D-glucono-1,5-lactone + a quinol
Other name(s): glucose dehydrogenase (Aspergillus); FAD-dependent glucose dehydrogenase; D-glucose:(acceptor) 1-oxidoreductase; glucose dehydrogenase (acceptor); gdh (gene name)
Systematic name: D-glucose:quinone 1-oxidoreductase
Comments: A glycoprotein containing one mole of FAD per mole of enzyme. 2,6-Dichloroindophenol can act as acceptor. cf. EC 1.1.5.2, quinoprotein glucose dehydrogenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37250-84-3
References:
1.  Bak, T.-G. Studies on glucose dehydrogenase of Aspergillus oryzae. II. Purification and physical and chemical properties. Biochim. Biophys. Acta 139 (1967) 277–293. [PMID: 6034674]
2.  Cavener, D.R. and MacIntyre, R.J. Biphasic expression and function of glucose dehydrogenase in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 80 (1983) 6286–6288. [PMID: 6413974]
3.  Lovallo, N. and Cox-Foster, D.L. Alteration in FAD-glucose dehydrogenase activity and hemocyte behavior contribute to initial disruption of Manduca sexta immune response to Cotesia congregata parasitoids. J Insect Physiol 45 (1999) 1037–1048. [PMID: 12770264]
4.  Inose, K., Fujikawa, M., Yamazaki, T., Kojima, K. and Sode, K. Cloning and expression of the gene encoding catalytic subunit of thermostable glucose dehydrogenase from Burkholderia cepacia in Escherichia coli. Biochim. Biophys. Acta 1645 (2003) 133–138. [PMID: 12573242]
5.  Sygmund, C., Klausberger, M., Felice, A.K. and Ludwig, R. Reduction of quinones and phenoxy radicals by extracellular glucose dehydrogenase from Glomerella cingulata suggests a role in plant pathogenicity. Microbiology 157 (2011) 3203–3212. [PMID: 21903757]
6.  Sygmund, C., Staudigl, P., Klausberger, M., Pinotsis, N., Djinovic-Carugo, K., Gorton, L., Haltrich, D. and Ludwig, R. Heterologous overexpression of Glomerella cingulata FAD-dependent glucose dehydrogenase in Escherichia coli and Pichia pastoris. Microb. Cell Fact. 10:106 (2011). [PMID: 22151971]
[EC 1.1.5.9 created 1972 as 1.1.99.10, modified 1976, transferred 2013 to EC 1.1.5.9]
 
 
EC 1.1.99.10
Transferred entry: glucose dehydrogenase (acceptor). Now EC 1.1.5.9, glucose 1-dehydrogenase (FAD, quinone)
[EC 1.1.99.10 created 1972, modified 1976, deleted 2013]
 
 
*EC 1.1.99.38
Accepted name: 2-deoxy-scyllo-inosamine dehydrogenase (AdoMet-dependent)
Reaction: 2-deoxy-scyllo-inosamine + S-adenosyl-L-methionine = 3-amino-2,3-dideoxy-scyllo-inosose + 5′-deoxyadenosine + L-methionine
For diagram of paromamine biosynthesis, click here
Other name(s): btrN (gene name); 2-deoxy-scyllo-inosamine dehydrogenase (SAM-dependent)
Systematic name: 2-deoxy-scyllo-inosamine:S-adenosyl-L-methionine 1-oxidoreductase
Comments: Involved in the biosynthetic pathway of the aminoglycoside antibiotics of the butirosin family. The enzyme from Bacillus circulans was shown to be a radical S-adenosyl-L-methionine (SAM) enzyme. cf. EC 1.1.1.329, 2-deoxy-scyllo-inosamine dehydrogenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yokoyama, K., Numakura, M., Kudo, F., Ohmori, D. and Eguchi, T. Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. J. Am. Chem. Soc. 129 (2007) 15147–15155. [PMID: 18001019]
2.  Yokoyama, K., Ohmori, D., Kudo, F. and Eguchi, T. Mechanistic study on the reaction of a radical SAM dehydrogenase BtrN by electron paramagnetic resonance spectroscopy. Biochemistry 47 (2008) 8950–8960. [PMID: 18672902]
[EC 1.1.99.38 created 2012, modified 2013]
 
 
EC 1.2.1.87
Accepted name: propanal dehydrogenase (CoA-propanoylating)
Reaction: propanal + CoA + NAD+ = propanoyl-CoA + NADH + H+
Other name(s): BphJ
Systematic name: propanal:NAD+ oxidoreductase (CoA-propanoylating)
Comments: The enzyme forms a bifunctional complex with EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase, with a tight channel connecting the two subunits [1,2,3]. Also acts, more slowly, on glycolaldehyde and butanal. In Pseudomonas species the enzyme forms a bifunctional complex with EC 4.1.3.39, 4-hydroxy-2-oxovalerate aldolase. The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). NADP+ can replace NAD+ with a much slower rate [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Baker, P., Pan, D., Carere, J., Rossi, A., Wang, W. and Seah, S.Y.K. Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway. Biochemistry 48 (2009) 6551–6558. [PMID: 19476337]
2.  Carere, J., Baker, P. and Seah, S.Y.K. Investigating the molecular determinants for substrate channeling in BphI-BphJ, an aldolase-dehydrogenase complex from the polychlorinated biphenyls degradation pathway. Biochemistry 50 (2011) 8407–8416. [PMID: 21838275]
3.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [PMID: 22316175]
[EC 1.2.1.87 created 2013]
 
 
EC 1.2.1.88
Accepted name: L-glutamate γ-semialdehyde dehydrogenase
Reaction: L-glutamate 5-semialdehyde + NAD+ + H2O = L-glutamate + NADH + H+
For diagram of reaction, click here
Glossary: L-glutamate 5-semialdehyde = L-glutamate γ-semialdehyde = (S)-2-amino-5-oxopentanoate
Other name(s): 1-pyrroline-5-carboxylate dehydrogenase; Δ1-pyrroline-5-carboxylate dehydrogenase; 1-pyrroline dehydrogenase; pyrroline-5-carboxylate dehydrogenase; pyrroline-5-carboxylic acid dehydrogenase; L-pyrroline-5-carboxylate-NAD+ oxidoreductase; 1-pyrroline-5-carboxylate:NAD+ oxidoreductase; Δ1-pyrroline-5-carboxylic acid dehydrogenase
Systematic name: L-glutamate γ-semialdehyde:NAD+ oxidoreductase
Comments: This enzyme catalyses the irreversible oxidation of glutamate-γ-semialdehyde to glutamate as part of the proline degradation pathway. (S)-1-pyrroline-5-carboxylate, the product of the first enzyme of the pathway (EC 1.5.5.2, proline dehydrogenase) is in spontaneous equilibrium with its tautomer L-glutamate γ-semialdehyde. In many bacterial species, both activities are carried out by a single bifunctional enzyme [3,4].The enzyme can also oxidize other 1-pyrrolines, e.g. 3-hydroxy-1-pyrroline-5-carboxylate is converted into 4-hydroxyglutamate and (R)-1-pyrroline-5-carboxylate is converted into D-glutamate. NADP+ can also act as acceptor, but with lower activity [5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9054-82-4
References:
1.  Adams, E. and Goldstone, A. Hydroxyproline metabolism. IV. Enzymatic synthesis of γ-hydroxyglutamate from Δ1-pyrroline-3-hydroxy-5-carboxylate. J. Biol. Chem. 235 (1960) 3504–3512. [PMID: 13681370]
2.  Strecker, H.J. The interconversion of glutamic acid and proline. III. Δ1-Pyrroline-5-carboxylic acid dehydrogenase. J. Biol. Chem. 235 (1960) 3218–3223.
3.  Forlani, G., Scainelli, D. and Nielsen, E. Δ1-Pyrroline-5-carboxylate dehydrogenase from cultured cells of potato (purification and properties). Plant Physiol. 113 (1997) 1413–1418. [PMID: 12223682]
4.  Brown, E.D. and Wood, J.M. Redesigned purification yields a fully functional PutA protein dimer from Escherichia coli. J. Biol. Chem. 267 (1992) 13086–13092. [PMID: 1618807]
5.  Inagaki, E., Ohshima, N., Sakamoto, K., Babayeva, N.D., Kato, H., Yokoyama, S. and Tahirov, T.H. New insights into the binding mode of coenzymes: structure of Thermus thermophilus Δ1-pyrroline-5-carboxylate dehydrogenase complexed with NADP+. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63 (2007) 462–465. [PMID: 17554163]
[EC 1.2.1.88 created 1972 as 1.5.1.12, modified 2008, transferred 2013 to EC 1.2.1.88]
 
 
*EC 1.2.7.1
Accepted name: pyruvate synthase
Reaction: pyruvate + CoA + 2 oxidized ferredoxin = acetyl-CoA + CO2 + 2 reduced ferredoxin + 2 H+
For diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Other name(s): pyruvate oxidoreductase; pyruvate synthetase; pyruvate:ferredoxin oxidoreductase; pyruvic-ferredoxin oxidoreductase; 2-oxobutyrate synthase; α-ketobutyrate-ferredoxin oxidoreductase; 2-ketobutyrate synthase; α-ketobutyrate synthase; 2-oxobutyrate-ferredoxin oxidoreductase; 2-oxobutanoate:ferredoxin 2-oxidoreductase (CoA-propionylating); 2-oxobutanoate:ferredoxin 2-oxidoreductase (CoA-propanoylating)
Systematic name: pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
Comments: Contains thiamine diphosphate and [4Fe-4S] clusters. The enzyme also decarboxylates 2-oxobutyrate with lower efficiency, but shows no activity with 2-oxoglutarate. This enzyme is a member of the 2-oxoacid oxidoreductases, a family of enzymes that oxidatively decarboxylate different 2-oxoacids to form their CoA derivatives, and are differentiated based on their substrate specificity. For examples of other members of this family, see EC 1.2.7.3, 2-oxoglutarate synthase and EC 1.2.7.7, 3-methyl-2-oxobutanoate dehydrogenase (ferredoxin).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9082-51-3
References:
1.  Evans, M.C.W. and Buchanan, B.B. Photoreduction of ferredoxin and its use in carbon dioxide fixation by a subcellular system from a photosynthetic bacterium. Proc. Natl. Acad. Sci. USA 53 (1965) 1420–1425. [PMID: 5217644]
2.  Gehring, U. and Arnon, D.I. Purification and properties of α-ketoglutarate synthase from a photosynthetic bacterium. J. Biol. Chem. 247 (1972) 6963–6969. [PMID: 4628267]
3.  Uyeda, K. and Rabinowitz, J.C. Pyruvate-ferredoxin oxidoreductase. 3. Purification and properties of the enzyme. J. Biol. Chem. 246 (1971) 3111–3119. [PMID: 5574389]
4.  Uyeda, K. and Rabinowitz, J.C. Pyruvate-ferredoxin oxidoreductase. IV. Studies on the reaction mechanism. J. Biol. Chem. 246 (1971) 3120–3125. [PMID: 4324891]
5.  Charon, M.-H., Volbeda, A., Chabriere, E., Pieulle, L. and Fontecilla-Camps, J.C. Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase. Curr. Opin. Struct. Biol. 9 (1999) 663–669. [PMID: 10607667]
[EC 1.2.7.1 created 1972, modified 2003, modified 2013]
 
 
EC 1.2.7.2
Deleted entry: 2-oxobutyrate synthase. Now included with EC 1.2.7.1, pyruvate synthase.
[EC 1.2.7.2 created 1972, deleted 2013]
 
 
*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 1.3.1.39
Accepted name: enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific)
Reaction: an acyl-[acyl-carrier protein] + NADP+ = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH + H+
Other name(s): acyl-ACP dehydrogenase; enoyl-[acyl carrier protein] (reduced nicotinamide adenine dinucleotide phosphate) reductase; NADPH 2-enoyl Co A reductase; enoyl-ACp reductase; enoyl-[acyl-carrier-protein] reductase (NADPH2, A-specific); acyl-[acyl-carrier-protein]:NADP+ oxidoreductase (A-specific); enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific); acyl-[acyl-carrier protein]:NADP+ oxidoreductase (A-specific)
Systematic name: acyl-[acyl-carrier protein]:NADP+ oxidoreductase (Re-specific)
Comments: This enzyme completes each cycle of fatty acid elongation by catalysing the stereospecific reduction of the double bond at position 2 of a growing fatty acid chain, while linked to an acyl-carrier protein. It is one of the activities of EC 2.3.1.85, animal fatty-acid synthase. The mammalian enzyme is Re-specific with respect to NADP+. cf. EC 1.3.1.10, enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific) and EC 1.3.1.104, enoyl-[acyl-carrier-protein] reductase (NADPH).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Dugan, R.E., Slakey, L.L. and Porter, L.W. Stereospecificity of the transfer of hydrogen from reduced nicotinamide adenine dinucleotide phosphate to the acyl chain in the dehydrogenase-catalyzed reactions of fatty acid synthesis. J. Biol. Chem. 245 (1970) 6312–6316. [PMID: 4394955]
2.  Carlisle-Moore, L., Gordon, C.R., Machutta, C.A., Miller, W.T. and Tonge, P.J. Substrate recognition by the human fatty-acid synthase. J. Biol. Chem. 280 (2005) 42612–42618. [PMID: 16215233]
[EC 1.3.1.39 created 1986, modified 2013]
 
 
EC 1.3.1.102
Accepted name: 2-alkenal reductase (NADP+)
Reaction: an n-alkanal + NADP+ = an alk-2-enal + NADPH + H+
Other name(s): NADPH-dependent alkenal/one oxidoreductase; NADPH:2-alkenal α,β-hydrogenase
Systematic name: n-alkanal:NADP+ 2-oxidoreductase
Comments: Shows highest activity with 1-nitrocyclohexene but also has significant activity with 2-methylpentenal and trans-cinnamaldehyde [3]. Involved in the detoxication of α,β-unsaturated aldehydes and ketones. Has very low activity with NAD as reductant (cf. EC 1.3.1.74, 2-alkenal reductase [NAD(P)+]).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hirata, T., Tamura, Y., Yokobatake, N., Shimoda, K. and Ashida, Y. A 38 kDa allylic alcohol dehydrogenase from the cultured cells of Nicotiana tabacum. Phytochemistry 55 (2000) 297–303. [PMID: 11117876]
2.  Matsushima, A., Sato, Y., Otsuka, M., Watanabe, T., Yamamoto, H. and Hirata, T. An enone reductase from Nicotiana tabacum: cDNA cloning, expression in Escherichia coli, and reduction of enones with the recombinant proteins. Bioorg. Chem. 36 (2008) 23–28. [PMID: 17945329]
3.  Mansell, D.J., Toogood, H.S., Waller, J., Hughes, J.M.X., Levy, C.W., Gardiner, J.M., and Scrutton, N.S. Biocatalytic asymmetric alkene reduction: crystal structure and characterization of a double bond reductase from Nicotiana tabacum. ACS Catal. 3 (2013) 370–379.
[EC 1.3.1.102 created 2013]
 
 
EC 1.3.1.103
Accepted name: 2-haloacrylate reductase
Reaction: (S)-2-chloropropanoate + NADP+ = 2-chloroacrylate + NADPH + H+
Other name(s): CAA43 (gene name)
Systematic name: (S)-2-chloropropanoate:NADP+ oxidoreductase
Comments: The enzyme acts in the degradation pathway of unsaturated organohalogen compounds by the bacterium Burkholderia sp. WS.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kurata, A., Kurihara, T., Kamachi, H. and Esaki, N. 2-Haloacrylate reductase, a novel enzyme of the medium chain dehydrogenase/reductase superfamily that catalyzes the reduction of a carbon-carbon double bond of unsaturated organohalogen compounds. J. Biol. Chem. 280 (2005) 20286–20291. [PMID: 15781461]
[EC 1.3.1.103 created 2013]
 
 
EC 1.5.1.12
Transferred entry: 1-pyrroline-5-carboxylate dehydrogenase. Now EC 1.2.1.88, L-glutamate γ-semialdehyde dehydrogenase.
[EC 1.5.1.12 created 1972, modified 2008, deleted 2013]
 
 
*EC 1.6.1.1
Accepted name: NAD(P)+ transhydrogenase (Si-specific)
Reaction: NADPH + NAD+ = NADP+ + NADH
Other name(s): pyridine nucleotide transhydrogenase; transhydrogenase; NAD(P)+ transhydrogenase; nicotinamide adenine dinucleotide (phosphate) transhydrogenase; NAD+ transhydrogenase; NADH transhydrogenase; nicotinamide nucleotide transhydrogenase; NADPH-NAD+ transhydrogenase; pyridine nucleotide transferase; NADPH-NAD+ oxidoreductase; NADH-NADP+-transhydrogenase; NADPH:NAD+ transhydrogenase; H+-Thase; non-energy-linked transhydrogenase; NADPH:NAD+ oxidoreductase (B-specific); NAD(P)+ transhydrogenase (B-specific)
Systematic name: NADPH:NAD+ oxidoreductase (Si-specific)
Comments: The enzyme from Azotobacter vinelandii is a flavoprotein (FAD). It is Si-specific with respect to both NAD+ and NADP+. Also acts on deamino coenzymes [cf. EC 1.6.1.2 NAD(P)+ transhydrogenase (Re/Si-specific)].
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, CAS registry number: 9014-18-0
References:
1.  Humphrey, G.F. The distribution and properties of transhydrogenase from animal tissues. Biochem. J. 65 (1957) 546–550. [PMID: 13412660]
2.  You, K.-S. Stereospecificity for nicotinamide nucleotides in enzymatic and chemical hydride transfer reactions. CRC Crit. Rev. Biochem. 17 (1985) 313–451. [PMID: 3157549]
[EC 1.6.1.1 created 1961, modified 1986, modified 2013]
 
 
*EC 1.6.1.2
Accepted name: NAD(P)+ transhydrogenase (Re/Si-specific)
Reaction: NADPH + NAD+ = NADP+ + NADH
Other name(s): pyridine nucleotide transhydrogenase; transhydrogenase; NAD(P)+ transhydrogenase; nicotinamide adenine dinucleotide (phosphate) transhydrogenase; NAD+ transhydrogenase; NADH transhydrogenase; nicotinamide nucleotide transhydrogenase; NADPH-NAD+ transhydrogenase; pyridine nucleotide transferase; NADPH-NAD+ oxidoreductase; NADH-NADP+-transhydrogenase; NADPH:NAD+ transhydrogenase; H+-Thase; energy-linked transhydrogenase; NAD(P) transhydrogenase (AB-specific); NAD(P)+ transhydrogenase (AB-specific); NADPH:NAD+ oxidoreductase (AB-specific)
Systematic name: NADPH:NAD+ oxidoreductase (Re/Si-specific)
Comments: The enzyme from heart mitochondria is Re-specific with respect to NAD+ and Si-specific with respect to NADP+ [cf. EC 1.6.1.1 NAD(P)+ transhydrogenase (Si-specific)].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9014-18-0, 9072-60-0
References:
1.  Fisher, R.R. and Earle, S.R. Membrane-bound pyridine dinucleotide transhydrogenases. In: Everse, J., Anderson, B. and You, K. (Eds), The Pyridine Nucleotide Coenzymes, The Pyridine Nucleotide Coenzymes, New York, 1982, pp. 279–324.
2.  You, K.-S. Stereospecificity for nicotinamide nucleotides in enzymatic and chemical hydride transfer reactions. CRC Crit. Rev. Biochem. 17 (1985) 313–451. [PMID: 3157549]
[EC 1.6.1.2 created 1986, modified 2013]
 
 
EC 1.6.1.3
Accepted name: NAD(P)+ transhydrogenase
Reaction: NADPH + NAD+ = NADP+ + NADH
Other name(s): pyridine nucleotide transhydrogenase; transhydrogenase (ambiguous); nicotinamide adenine dinucleotide (phosphate) transhydrogenase (ambiguous); NAD+ transhydrogenase (ambiguous); NADH transhydrogenase (misleading); nicotinamide nucleotide transhydrogenase (ambiguous); NADPH-NAD+ transhydrogenase (ambiguous); pyridine nucleotide transferase (ambiguous); NADPH-NAD+ oxidoreductase (ambiguous); NADH-NADP+-transhydrogenase (ambiguous); NADPH:NAD+ transhydrogenase; H+-Thase (ambiguous); non-energy-linked transhydrogenase (ambiguous)
Systematic name: NADPH:NAD+ oxidoreductase
Comments: The enzyme catalyses the NADPH-driven reduction of NAD+. This entry stands for enzymes whose stereo-specificity with respect to NADPH is not known. [cf. EC 1.6.1.1, NAD(P)+ transhydrogenase (Si-specific) and EC 1.6.1.2 NAD(P)+ transhydrogenase (Re/Si-specific)].
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG
References:
1.  Keister D.L., San Pietro A., Stolzenbach F.E. Pyridine nucleotide transhydrogenase from spinach. I. Purification and properties. J. Biol. Chem. 235 (1960) 2989–2996. [PMID: 13752224]
[EC 1.6.1.3 created 2013]
 
 
EC 1.8.1.18
Accepted name: NAD(P)H sulfur oxidoreductase (CoA-dependent)
Reaction: hydrogen sulfide + NAD(P)+ = sulfur + NAD(P)H + H+
Other name(s): NADPH NSR; S0 reductase; coenzyme A-dependent NADPH sulfur oxidoreductase
Systematic name: hydrogen sulfide:NAD(P)+ oxidoreductase (CoA-dependent)
Comments: This FAD-dependent enzyme, characterized from the archaeon Pyrococcus furiosus, is responsible for NAD(P)H-linked sulfur reduction. The activity with NADH is about half of that with NADPH. The reaction is dependent on CoA, although the nature of this dependency is not well understood.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Schut, G.J., Bridger, S.L. and Adams, M.W. Insights into the metabolism of elemental sulfur by the hyperthermophilic archaeon Pyrococcus furiosus: characterization of a coenzyme A- dependent NAD(P)H sulfur oxidoreductase. J. Bacteriol. 189 (2007) 4431–4441. [PMID: 17449625]
2.  Bridger, S.L., Clarkson, S.M., Stirrett, K., DeBarry, M.B., Lipscomb, G.L., Schut, G.J., Westpheling, J., Scott, R.A. and Adams, M.W. Deletion strains reveal metabolic roles for key elemental sulfur-responsive proteins in Pyrococcus furiosus. J. Bacteriol. 193 (2011) 6498–6504. [PMID: 21965560]
3.  Harris, D.R., Ward, D.E., Feasel, J.M., Lancaster, K.M., Murphy, R.D., Mallet, T.C. and Crane, E.J., 3rd. Discovery and characterization of a coenzyme A disulfide reductase from Pyrococcus horikoshii. Implications for this disulfide metabolism of anaerobic hyperthermophiles. FEBS J. 272 (2005) 1189–1200. [PMID: 15720393]
[EC 1.8.1.18 created 2013]
 
 
EC 1.10.3.13
Accepted name: caldariellaquinol oxidase (H+-transporting)
Reaction: 2 caldariellaquinol + O2 + n H+[side 1] = 2 caldariellaquinone + 2 H2O + n H+[side 2]
Glossary: caldariellaquinol = 6-(3,7,11,15,19,23-hexamethyltetracosyl)-5-(methylsulfanyl)-1-benzothiophene-4,7-diol
Other name(s): SoxABCD quinol oxidase; SoxABCD complex; quinol oxidase SoxABCD; SoxM supercomplex; aa3-type quinol oxidase; aa3 quinol oxidase; cytochrome aa3; terminal quinol oxidase; terminal quinol:oxygen oxidoreductase; caldariella quinol:dioxygen oxidoreductase; cytochrome aa3-type oxidase ; caldariellaquinol:O2 oxidoreductase (H+-transporting)
Systematic name: caldariellaquinol:oxygen oxidoreductase (H+-transporting)
Comments: A copper-containing cytochrome. The enzyme from thermophilic archaea is part of the terminal oxidase and catalyses the reduction of O2 to water, accompanied by the extrusion of protons across the cytoplasmic membrane.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Gleissner, M., Kaiser, U., Antonopoulos, E. and Schafer, G. The archaeal SoxABCD complex is a proton pump in Sulfolobus acidocaldarius. J. Biol. Chem. 272 (1997) 8417–8426. [PMID: 9079667]
2.  Purschke, W.G., Schmidt, C.L., Petersen, A. and Schafer, G. The terminal quinol oxidase of the hyperthermophilic archaeon Acidianus ambivalens exhibits a novel subunit structure and gene organization. J. Bacteriol. 179 (1997) 1344–1353. [PMID: 9023221]
3.  Gilderson, G., Aagaard, A., Gomes, C.M., Adelroth, P., Teixeira, M. and Brzezinski, P. Kinetics of electron and proton transfer during O2 reduction in cytochrome aa3 from A. ambivalens: an enzyme lacking Glu(I-286). Biochim. Biophys. Acta 1503 (2001) 261–270. [PMID: 11115638]
4.  Komorowski, L., Verheyen, W. and Schafer, G. The archaeal respiratory supercomplex SoxM from S. acidocaldarius combines features of quinole and cytochrome c oxidases. Biol. Chem. 383 (2002) 1791–1799. [PMID: 12530544]
5.  Muller, F.H., Bandeiras, T.M., Urich, T., Teixeira, M., Gomes, C.M. and Kletzin, A. Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol. Microbiol. 53 (2004) 1147–1160. [PMID: 15306018]
6.  Bandeiras, T.M., Pereira, M.M., Teixeira, M., Moenne-Loccoz, P. and Blackburn, N.J. Structure and coordination of CuB in the Acidianus ambivalens aa3 quinol oxidase heme-copper center. J. Biol. Inorg. Chem. 10 (2005) 625–635. [PMID: 16163550]
[EC 1.10.3.13 created 2013]
 
 
*EC 1.13.11.2
Accepted name: catechol 2,3-dioxygenase
Reaction: catechol + O2 = 2-hydroxymuconate-6-semialdehyde
For diagram of catechol catabolism (meta ring cleavage), click here
Glossary: 2-hydroxymuconate-6-semialdehyde = (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate
Other name(s): 2,3-pyrocatechase; catechol 2,3-oxygenase; catechol oxygenase; metapyrocatechase; pyrocatechol 2,3-dioxygenase; xylE (gene name); catechol:oxygen 2,3-oxidoreductase (decyclizing)
Systematic name: catechol:oxygen 2,3-oxidoreductase (ring-opening)
Comments: Requires FeII. The enzyme initiates the meta-cleavage pathway of catechol degradation.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD, CAS registry number: 9029-46-3
References:
1.  Hayaishi, O. Direct oxygenation by O2, oxygenases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 8, Academic Press, New York, 1963, pp. 353–371.
2.  Kojima, Y., Itada, N. and Hayaishi, O. Metapyrocatechase: a new catechol-cleaving enzyme. J. Biol. Chem. 236 (1961) 2223–2228. [PMID: 13757654]
3.  Nozaki, M., Kagamiyama, H. and Hayaishi, O. Metapyrocatechase. I. Purification, crystallization and some properties. Biochem. Z. 338 (1963) 582–590. [PMID: 14087325]
4.  Nakai, C., Hori, K., Kagamiyama, H., Nakazawa, T. and Nozaki, M. Purification, subunit structure, and partial amino acid sequence of metapyrocatechase. J. Biol. Chem. 258 (1983) 2916–2922. [PMID: 6826545]
5.  Junker, F., Field, J.A., Bangerter, F., Ramsteiner, K., Kohler, H.-P., Joannou, C.L., Mason, J.R., Leisinger, T. and Cook, A.M. Oxygenation and spontaneous deamination of 2-aminobenzenesulphonic acid in Alcaligenes sp. strain O-1 with subsequent meta ring cleavage and spontaneous desulphonation to 2-hydroxymuconic acid. Biochem. J. 300 (1994) 429–436. [PMID: 8002948]
6.  Junker, F., Leisinger, T. and Cook, A.M. 3-Sulphocatechol 2,3-dioxygenase and other dioxygenases (EC 1.13.11.2 and EC 1.14.12.-) in the degradative pathways of 2-aminobenzenesulphonic, benzenesulphonic and 4-toluenesulphonic acids in Alcaligenes sp. strain O-1. Microbiology 140 (1994) 1713–1722. [PMID: 8075807]
[EC 1.13.11.2 created 1965 as EC 1.13.1.2, transferred 1972 to EC 1.13.11.2, modified 1999, modified 2013]
 
 
EC 1.13.11.75
Accepted name: all-trans-8′-apo-β-carotenal 15,15′-oxygenase
Reaction: all-trans-8′-apo-β-carotenal + O2 = all-trans-retinal + (2E,4E,6E)-2,6-dimethylocta-2,4,6-trienedial
For diagram of 8′-apo-β-carotenal metabolites, click here
Other name(s): Diox1; ACO; 8′-apo-β-carotenal 15,15′-oxygenase
Systematic name: all-trans-8′-apo-β-carotenal:oxygen 15,15′-oxidoreductase (bond-cleaving)
Comments: Contains an Fe2+-4His arrangement. The enzyme is involved in retinal biosynthesis in bacteria [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ruch, S., Beyer, P., Ernst, H. and Al-Babili, S. Retinal biosynthesis in Eubacteria: in vitro characterization of a novel carotenoid oxygenase from Synechocystis sp. PCC 6803. Mol. Microbiol. 55 (2005) 1015–1024. [PMID: 15686550]
2.  Kloer, D.P., Ruch, S., Al-Babili, S., Beyer, P. and Schulz, G.E. The structure of a retinal-forming carotenoid oxygenase. Science 308 (2005) 267–269. [PMID: 15821095]
[EC 1.13.11.75 created 2010 as EC 1.14.99.41, transferred 2013 to EC 1.13.11.75]
 
 
EC 1.14.11.38
Accepted name: verruculogen synthase
Reaction: fumitremorgin B + 2-oxoglutarate + 2 O2 + reduced acceptor = verruculogen + succinate + CO2 + H2O + acceptor
For diagram of fumitremorgin alkaloid biosynthesis (part 2), click here
Glossary: fumitremorgin B = (5aR,6S,12S,14aS)-5a,6-dihydroxy-9-methoxy-11-(3-methylbut-2-en-1-yl)-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1′′,2′′:4′,5′]pyrazino[1′,2′:1,6]pyrido[3,4-b]indole-5,14-dione
verruculogen = (5R,10S,10aR,14aS,15bS)-10,10a-dihydroxy-6-methoxy-2,2-dimethyl-5-(2-methylprop-1-en-1-yl)-1,10,10a,14,14a,15b-hexahydro-12H-3,4-dioxa-5a,11a,15a-triazacycloocta[1,2,3-lm]indeno[5,6-b]fluorene-11,15(2H,13H)-dione
Other name(s): fmtF (gene name); FmtOx1
Systematic name: fumitremorgin B,2-oxoglutarate:oxygen oxidoreductase (verruculogen-forming)
Comments: Requires Fe2+ and ascorbate. Found in the fungus Aspergillus fumigatus. Both atoms of a dioxygen molecule are incorporated into verruculogen [1,2]. Involved in the biosynthetic pathways of several indole alkaloids such as fumitremorgin A.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Steffan, N., Grundmann, A., Afiyatullov, S., Ruan, H. and Li, S.M. FtmOx1, a non-heme Fe(II) and α-ketoglutarate-dependent dioxygenase, catalyses the endoperoxide formation of verruculogen in Aspergillus fumigatus. Org. Biomol. Chem. 7 (2009) 4082–4087. [PMID: 19763315]
2.  Kato, N., Suzuki, H., Takagi, H., Uramoto, M., Takahashi, S. and Osada, H. Gene disruption and biochemical characterization of verruculogen synthase of Aspergillus fumigatus. ChemBioChem. 12 (2011) 711–714. [PMID: 21404415]
[EC 1.14.11.38 created 2013]
 
 
EC 1.14.11.39
Accepted name: L-asparagine hydroxylase
Reaction: L-asparagine + 2-oxoglutarate + O2 = (2S,3S)-3-hydroxyasparagine + succinate + CO2
Other name(s): L-asparagine 3-hydroxylase; AsnO
Systematic name: L-asparagine,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
Comments: Requires Fe2+. The enzyme is only able to hydroxylate free L-asparagine. It is not active toward D-asparagine. The β-hydroxylated asparagine produced is incorporated at position 9 of the calcium-dependent antibiotic (CDA), an 11-residue non-ribosomally synthesized acidic lipopeptide lactone.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Strieker, M., Kopp, F., Mahlert, C., Essen, L.O. and Marahiel, M.A. Mechanistic and structural basis of stereospecific Cβ-hydroxylation in calcium-dependent antibiotic, a daptomycin-type lipopeptide. ACS Chem. Biol. 2 (2007) 187–196. [PMID: 17373765]
[EC 1.14.11.39 created 2013]
 
 
EC 1.14.11.40
Accepted name: enduracididine β-hydroxylase
Reaction: L-enduracididine + 2-oxoglutarate + O2 = (3S)-3-hydroxy-L-enduracididine + succinate + CO2
Glossary: L-enduracididine = 3-[(4R)-2-iminoimidazolidin-4-yl]-L-alanine = 2-amino-3-[(2S)-iminoimidazolin-4-yl]propanoic acid
(3S)-3-hydroxy-L-enduracididine = (2S,3R)-2-amino-3-hydroxy-3-[(S)-2-iminoimidazolidin-4-yl]propanoic acid = (3R)-3-[(4S)-2-iminoimidazolidin-4-yl]-L-serine
Other name(s): MppO; L-enduracididine,2-oxoglutarate:O2 oxidoreductase (3-hydroxylating)
Systematic name: L-enduracididine,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
Comments: Fe2+-dependent enzyme. The enzyme is involved in biosynthesis of the nonproteinogenic amino acid β-hydroxyenduracididine, a component of the mannopeptimycins (cyclic glycopeptide antibiotic), produced by Streptomyces hygroscopicus NRRL 30439.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Haltli, B., Tan, Y., Magarvey, N.A., Wagenaar, M., Yin, X., Greenstein, M., Hucul, J.A. and Zabriskie, T.M. Investigating β-hydroxyenduracididine formation in the biosynthesis of the mannopeptimycins. Chem. Biol. 12 (2005) 1163–1168. [PMID: 16298295]
2.  Magarvey, N.A., Haltli, B., He, M., Greenstein, M. and Hucul, J.A. Biosynthetic pathway for mannopeptimycins, lipoglycopeptide antibiotics active against drug-resistant gram-positive pathogens. Antimicrob. Agents Chemother. 50 (2006) 2167–2177. [PMID: 16723579]
[EC 1.14.11.40 created 2013]
 
 
EC 1.14.11.41
Accepted name: L-arginine hydroxylase
Reaction: L-arginine + 2-oxoglutarate + O2 = (3S)-3-hydroxy-L-arginine + succinate + CO2
Other name(s): VioC (ambiguous); L-arginine,2-oxoglutarate:O2 oxidoreductase (3-hydroxylating)
Systematic name: L-arginine,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
Comments: Fe2+-dependent enzyme. The enzyme is involved in the biosynthesis of the cyclic pentapeptide antibiotic viomycin. It differs from EC 1.14.11.34, 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming), because it does not form guanidine and (S)-1-pyrroline-5-carboxylate from 3-hydroxy-L-arginine.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ju, J., Ozanick, S.G., Shen, B. and Thomas, M.G. Conversion of (2S)-arginine to (2S,3R)-capreomycidine by VioC and VioD from the viomycin biosynthetic pathway of Streptomyces sp. strain ATCC11861. ChemBioChem. 5 (2004) 1281–1285. [PMID: 15368582]
2.  Helmetag, V., Samel, S.A., Thomas, M.G., Marahiel, M.A. and Essen, L.O. Structural basis for the erythro-stereospecificity of the L-arginine oxygenase VioC in viomycin biosynthesis. FEBS J. 276 (2009) 3669–3682. [PMID: 19490124]
[EC 1.14.11.41 created 2013]
 
 
EC 1.14.13.177
Accepted name: fumitremorgin C monooxygenase
Reaction: fumitremorgin C + 2 NADPH + 2 H+ + 2 O2 = 12α,13α-dihydroxyfumitremorgin C + 2 NADP+ + 2 H2O
For diagram of fumitremorgin alkaloid biosynthesis (part 2), click here
Glossary: fumitremorgin C = (5aS,12S,14aS)-9-methoxy-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1′′,2′′:4′,5′]pyrazino[1′,2′:1,6]pyrido[3,4-b]indole-5,14-dione
12α,13α-dihydroxyfumitremorgin = (5aR,6S,12S,14aS)-5a,6-dihydroxy-9-methoxy-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1′′,2′′:4′,5′]pyrazino[1′,2′:1,6]pyrido[3,4-b]indole-5,14-dione
Other name(s): ftmG (gene name)
Systematic name: fumitremorgin C,NADPH:oxygen oxidoreductase (12α,13α-dihydroxyfumitremorgin C-forming)
Comments: A heme-thiolate protein (P-450). Involved in the biosynthetic pathway of the indole alkaloid verruculogen.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kato, N., Suzuki, H., Takagi, H., Asami, Y., Kakeya, H., Uramoto, M., Usui, T., Takahashi, S., Sugimoto, Y. and Osada, H. Identification of cytochrome P450s required for fumitremorgin biosynthesis in Aspergillus fumigatus. ChemBioChem. 10 (2009) 920–928. [PMID: 19226505]
[EC 1.14.13.177 created 2013]
 
 
EC 1.14.13.178
Accepted name: methylxanthine N1-demethylase
Reaction: (1) caffeine + O2 + NAD(P)H + H+ = theobromine + NAD(P)+ + H2O + formaldehyde
(2) theophylline + O2 + NAD(P)H + H+ = 3-methylxanthine + NAD(P)+ + H2O + formaldehyde
(3) paraxanthine + O2 + NAD(P)H + H+ = 7-methylxanthine + NAD(P)+ + H2O + formaldehyde
Glossary: caffeine = 1,3,7-trimethylxanthine
theobromine = 3,7-dimethylxanthine
theophylline = 1,3-dimethylxanthine
paraxanthine = 1,7-dimethylxanthine
Other name(s): ndmA (gene name)
Systematic name: caffeine:oxygen oxidoreductase (N1-demethylating)
Comments: A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida shares an NAD(P)H-FMN reductase subunit with EC 1.14.13.179, methylxanthine N3-demethylase, and has a 5-fold higher activity with NADH than with NADPH [2]. Also demethylate 1-methylxantine with lower efficiency. Forms part of the degradation pathway of methylxanthines.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Summers, R.M., Louie, T.M., Yu, C.L. and Subramanian, M. Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source. Microbiology 157 (2011) 583–592. [PMID: 20966097]
2.  Summers, R.M., Louie, T.M., Yu, C.L., Gakhar, L., Louie, K.C. and Subramanian, M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J. Bacteriol. 194 (2012) 2041–2049. [PMID: 22328667]
[EC 1.14.13.178 created 2013]
 
 
EC 1.14.13.179
Accepted name: methylxanthine N3-demethylase
Reaction: (1) theobromine + O2 + NAD(P)H + H+ = 7-methylxanthine + NAD(P)+ + H2O + formaldehyde
(2) 3-methylxanthine + O2 + NAD(P)H + H+ = xanthine + NAD(P)+ + H2O + formaldehyde
Glossary: theobromine = 3,7-dimethylxanthine
Other name(s): ndmB (gene name)
Systematic name: theobromine:oxygen oxidoreductase (N3-demethylating)
Comments: A non-heme iron oxygenase. The enzyme from the bacterium Pseudomonas putida shares an NAD(P)H-FMN reductase subunit with EC 1.14.13.178, methylxanthine N1-demethylase, and has higher activity with NADH than with NADPH [1]. Also demethylates caffeine and theophylline with lower efficiency. Forms part of the degradation pathway of methylxanthines.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Summers, R.M., Louie, T.M., Yu, C.L. and Subramanian, M. Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source. Microbiology 157 (2011) 583–592. [PMID: 20966097]
2.  Summers, R.M., Louie, T.M., Yu, C.L., Gakhar, L., Louie, K.C. and Subramanian, M. Novel, highly specific N-demethylases enable bacteria to live on caffeine and related purine alkaloids. J. Bacteriol. 194 (2012) 2041–2049. [PMID: 22328667]
[EC 1.14.13.179 created 2013]
 
 
EC 1.14.20.3
Accepted name: (5R)-carbapenem-3-carboxylate synthase
Reaction: (3S,5S)-carbapenam-3-carboxylate + 2-oxoglutarate + O2 = (5R)-carbapen-2-em-3-carboxylate + succinate + CO2 + H2O
Glossary: (3S,5S)-carbapenam-3-carboxylate = (2S,5S)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylate
(5R)-carbapen-2-em-3-carboxylate = (5R)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylate
Other name(s): carC (gene name)
Systematic name: (3S,5S)-carbapenam-3-carboxylate,2-oxoglutarate:oxygen oxidoreductase (dehydrating)
Comments: Requires Fe2+. The enzyme is involved in the biosynthesis of the carbapenem β-lactam antibiotic (5R)-carbapen-2-em-3-carboxylate in the bacterium Pectobacterium carotovorum. It catalyses a stereoinversion at C-5 and introduces a double bond between C-2 and C-3.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Clifton, I.J., Doan, L.X., Sleeman, M.C., Topf, M., Suzuki, H., Wilmouth, R.C. and Schofield, C.J. Crystal structure of carbapenem synthase (CarC). J. Biol. Chem. 278 (2003) 20843–20850. [PMID: 12611886]
2.  Stapon, A., Li, R. and Townsend, C.A. Carbapenem biosynthesis: confirmation of stereochemical assignments and the role of CarC in the ring stereoinversion process from L-proline. J. Am. Chem. Soc. 125 (2003) 8486–8493. [PMID: 12848554]
3.  Sleeman, M.C., Smith, P., Kellam, B., Chhabra, S.R., Bycroft, B.W. and Schofield, C.J. Biosynthesis of carbapenem antibiotics: new carbapenam substrates for carbapenem synthase (CarC). ChemBioChem. 5 (2004) 879–882. [PMID: 15174175]
[EC 1.14.20.3 created 2013]
 
 
EC 1.14.21.10
Accepted name: fumitremorgin C synthase
Reaction: tryprostatin A + NADPH + H+ + O2 = fumitremorgin C + NADP+ + 2 H2O
For diagram of fumitremorgin alkaloid biosynthesis (part 1), click here
Glossary: tryprostatin A = (3S,8aS)-3-{[6-methoxy-2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
fumitremorgin C = (5aS,12S,14aS)-9-methoxy-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1′′,2′′:4′,5′]pyrazino[1′,2′:1,6]pyrido[3,4-b]indole-5,14-dione
Other name(s): ftmE (gene name)
Systematic name: tryprostatin A,NADPH:oxygen oxidoreductase
Comments: A heme-thiolate protein (P-450). The protein from the fungus Aspergillus fumigatus also has activity with tryprostatin B forming demethoxyfumitremorgin C. Involved in the biosynthetic pathways of several indole alkaloids such as fumitremorgins and verruculogen.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kato, N., Suzuki, H., Takagi, H., Asami, Y., Kakeya, H., Uramoto, M., Usui, T., Takahashi, S., Sugimoto, Y. and Osada, H. Identification of cytochrome P450s required for fumitremorgin biosynthesis in Aspergillus fumigatus. ChemBioChem. 10 (2009) 920–928. [PMID: 19226505]
[EC 1.14.21.10 created 2013]
 
 
EC 1.14.99.41
Transferred entry: all-trans-8′-apo-β-carotenal 15,15′-oxygenase. Now EC 1.13.11.75, all-trans-8′-apo-β-carotenal 15,15′-oxygenase
[EC 1.14.99.41 created 2010, deleted 2013]
 
 
EC 2.1.1.273
Accepted name: benzoate O-methyltransferase
Reaction: S-adenosyl-L-methionine + benzoate = S-adenosyl-L-homocysteine + methyl benzoate
Other name(s): BAMT; S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase
Systematic name: S-adenosyl-L-methionine:benzoate O-methyltransferase
Comments: While the enzyme from the plant Zea mays is specific for benzoate [6], the enzymes from Arabidopsis species and Clarkia breweri also catalyse the reaction of EC 2.1.1.274, salicylate 1-O-methyltransferase [1,5]. In snapdragon (Antirrhinum majus) two isoforms are found, one specific for benzoate [2,3] and one that is also active towards salicylate [4]. The volatile product is an important scent compound in some flowering species [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ross, J.R., Nam, K.H., D'Auria, J.C. and Pichersky, E. S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme involved in floral scent production and plant defense, represents a new class of plant methyltransferases. Arch. Biochem. Biophys. 367 (1999) 9–16. [PMID: 10375393]
2.  Dudareva, N., Murfitt, L.M., Mann, C.J., Gorenstein, N., Kolosova, N., Kish, C.M., Bonham, C. and Wood, K. Developmental regulation of methyl benzoate biosynthesis and emission in snapdragon flowers. Plant Cell 12 (2000) 949–961. [PMID: 10852939]
3.  Murfitt, L.M., Kolosova, N., Mann, C.J. and Dudareva, N. Purification and characterization of S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase, the enzyme responsible for biosynthesis of the volatile ester methyl benzoate in flowers of Antirrhinum majus. Arch. Biochem. Biophys. 382 (2000) 145–151. [PMID: 11051108]
4.  Negre, F., Kolosova, N., Knoll, J., Kish, C.M. and Dudareva, N. Novel S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme responsible for biosynthesis of methyl salicylate and methyl benzoate, is not involved in floral scent production in snapdragon flowers. Arch. Biochem. Biophys. 406 (2002) 261–270. [PMID: 12361714]
5.  Chen, F., D'Auria, J.C., Tholl, D., Ross, J.R., Gershenzon, J., Noel, J.P. and Pichersky, E. An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. Plant J. 36 (2003) 577–588. [PMID: 14617060]
6.  Köllner, T.G., Lenk, C., Zhao, N., Seidl-Adams, I., Gershenzon, J., Chen, F. and Degenhardt, J. Herbivore-induced SABATH methyltransferases of maize that methylate anthranilic acid using s-adenosyl-L-methionine. Plant Physiol. 153 (2010) 1795–1807. [PMID: 20519632]
[EC 2.1.1.273 created 2013]
 
 
EC 2.1.1.274
Accepted name: salicylate 1-O-methyltransferase
Reaction: S-adenosyl-L-methionine + salicylate = S-adenosyl-L-homocysteine + methyl salicylate
Glossary: methyl salicylate = methyl 2-hydroxybenzoate
Other name(s): SAMT; S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase; salicylate carboxymethyltransferase
Systematic name: S-adenosyl-L-methionine:salicylate 1-O-methyltransferase
Comments: The enzyme, which is found in flowering plants, also has the activity of EC 2.1.1.273, benzoate O-methyltransferase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ross, J.R., Nam, K.H., D'Auria, J.C. and Pichersky, E. S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme involved in floral scent production and plant defense, represents a new class of plant methyltransferases. Arch. Biochem. Biophys. 367 (1999) 9–16. [PMID: 10375393]
2.  Negre, F., Kolosova, N., Knoll, J., Kish, C.M. and Dudareva, N. Novel S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme responsible for biosynthesis of methyl salicylate and methyl benzoate, is not involved in floral scent production in snapdragon flowers. Arch. Biochem. Biophys. 406 (2002) 261–270. [PMID: 12361714]
3.  Chen, F., D'Auria, J.C., Tholl, D., Ross, J.R., Gershenzon, J., Noel, J.P. and Pichersky, E. An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. Plant J. 36 (2003) 577–588. [PMID: 14617060]
4.  Zubieta, C., Ross, J.R., Koscheski, P., Yang, Y., Pichersky, E. and Noel, J.P. Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell 15 (2003) 1704–1716. [PMID: 12897246]
[EC 2.1.1.274 created 2013]
 
 
EC 2.1.1.275
Accepted name: gibberellin A9 O-methyltransferase
Reaction: S-adenosyl-L-methionine + gibberellin A9 = S-adenosyl-L-homocysteine + methyl gibberellin A9
Glossary: gibberellin A9 = (1R,4aR,4bR,7R,9aR,10S,10aR)-1-methyl-8-methylene-13-oxododecahydro-4a,1-(epoxymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid
methyl gibberellin A9 = methyl (1R,4aR,4bR,7R,9aR,10S,10aR)-1-methyl-8-methylene-13-oxododecahydro-4a,1-(epoxymethano)-7,9a-methanobenzo[a]azulene-10-carboxylate
Other name(s): GAMT1
Systematic name: S-adenosyl-L-methionine:gibberellin A9 O-methyltransferase
Comments: The enzyme also methylates gibberellins A20 (95%), A3 (80%), A4 (69%) and A34 (46%) with significant activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Varbanova, M., Yamaguchi, S., Yang, Y., McKelvey, K., Hanada, A., Borochov, R., Yu, F., Jikumaru, Y., Ross, J., Cortes, D., Ma, C.J., Noel, J.P., Mander, L., Shulaev, V., Kamiya, Y., Rodermel, S., Weiss, D. and Pichersky, E. Methylation of gibberellins by Arabidopsis GAMT1 and GAMT2. Plant Cell 19 (2007) 32–45. [PMID: 17220201]
[EC 2.1.1.275 created 2013]
 
 
EC 2.1.1.276
Accepted name: gibberellin A4 carboxyl methyltransferase
Reaction: S-adenosyl-L-methionine + gibberellin A4 = S-adenosyl-L-homocysteine + methyl gibberellin A4
Glossary: gibberellin A4 = (1S,2S,4aR,4bR,7R,9aR,10S,10aR)-2-hydroxy-1-methyl-8-methylidene-13-oxododecahydro-4a,1-(epoxymethano)-7,9a-methanobenzo[a]azulene-10-carboxylic acid
methyl gibberellin A4 = methyl (1S,2S,4aR,4bR,7R,9aR,10S,10aR)-2-hydroxy-1-methyl-8-methylene-13-oxododecahydro-4a,1-(epoxymethano)-7,9a-methanobenzo[a]azulene-10-carboxylate
Other name(s): GAMT2; gibberellin A4 O-methyltransferase
Systematic name: S-adenosyl-L-methionine:gibberellin A4 O-methyltransferase
Comments: The enzyme also methylates gibberellins A34 (80%), A9 (60%), and A3 (45%) with significant activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Varbanova, M., Yamaguchi, S., Yang, Y., McKelvey, K., Hanada, A., Borochov, R., Yu, F., Jikumaru, Y., Ross, J., Cortes, D., Ma, C.J., Noel, J.P., Mander, L., Shulaev, V., Kamiya, Y., Rodermel, S., Weiss, D. and Pichersky, E. Methylation of gibberellins by Arabidopsis GAMT1 and GAMT2. Plant Cell 19 (2007) 32–45. [PMID: 17220201]
[EC 2.1.1.276 created 2013]
 
 
EC 2.1.1.277
Accepted name: anthranilate O-methyltransferase
Reaction: S-adenosyl-L-methionine + anthranilate = S-adenosyl-L-homocysteine + O-methyl anthranilate
Other name(s): AAMT
Systematic name: S-adenosyl-L-methionine:anthranilate O-methyltransferase
Comments: In the plant maize (Zea mays), the isoforms AAMT1 and AAMT2 are specific for anthranilate while AAMT3 also has the activity of EC 2.1.1.273, benzoate methyltransferase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Köllner, T.G., Lenk, C., Zhao, N., Seidl-Adams, I., Gershenzon, J., Chen, F. and Degenhardt, J. Herbivore-induced SABATH methyltransferases of maize that methylate anthranilic acid using s-adenosyl-L-methionine. Plant Physiol. 153 (2010) 1795–1807. [PMID: 20519632]
[EC 2.1.1.277 created 2013]
 
 
EC 2.1.1.278
Accepted name: indole-3-acetate O-methyltransferase
Reaction: S-adenosyl-L-methionine + (indol-3-yl)acetate = S-adenosyl-L-homocysteine + methyl (indol-3-yl)acetate
Other name(s): IAA carboxylmethyltransferase; IAMT
Systematic name: S-adenosyl-L-methionine:(indol-3-yl)acetate O-methyltransferase
Comments: Binds Mg2+. The enzyme is found in plants and is important for regulation of the plant hormone (indol-3-yl)acetate. The product, methyl (indol-3-yl)acetate is inactive as hormone [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zubieta, C., Ross, J.R., Koscheski, P., Yang, Y., Pichersky, E. and Noel, J.P. Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell 15 (2003) 1704–1716. [PMID: 12897246]
2.  Li, L., Hou, X., Tsuge, T., Ding, M., Aoyama, T., Oka, A., Gu, H., Zhao, Y. and Qu, L.J. The possible action mechanisms of indole-3-acetic acid methyl ester in Arabidopsis. Plant Cell Rep. 27 (2008) 575–584. [PMID: 17926040]
3.  Zhao, N., Ferrer, J.L., Ross, J., Guan, J., Yang, Y., Pichersky, E., Noel, J.P. and Chen, F. Structural, biochemical, and phylogenetic analyses suggest that indole-3-acetic acid methyltransferase is an evolutionarily ancient member of the SABATH family. Plant Physiol. 146 (2008) 455–467. [PMID: 18162595]
[EC 2.1.1.278 created 2013]
 
 
EC 2.1.1.279
Accepted name: trans-anol O-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + trans-anol = S-adenosyl-L-homocysteine + trans-anethole
(2) S-adenosyl-L-methionine + isoeugenol = S-adenosyl-L-homocysteine + isomethyleugenol
Glossary: trans-anol = 4-[(1E)-prop-1-en-1-yl]phenol
trans-anethole = 1-methoxy-4-[(1E)-prop-1-en-1-yl]benzene
Other name(s): AIMT1; S-adenosyl-L-methionine:t-anol/isoeugenol O-methyltransferase; t-anol O-methyltransferase
Systematic name: S-adenosyl-L-methionine:trans-anol O-methyltransferase
Comments: The enzyme from anise (Pimpinella anisum) is highly specific for substrates in which the double bond in the propenyl side chain is located between C7 and C8, and, in contrast to EC 2.1.1.146, (iso)eugenol O-methyltransferase, does not have activity with eugenol or chavicol.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Koeduka, T., Baiga, T.J., Noel, J.P. and Pichersky, E. Biosynthesis of t-anethole in anise: characterization of t-anol/isoeugenol synthase and an O-methyltransferase specific for a C7-C8 propenyl side chain. Plant Physiol. 149 (2009) 384–394. [PMID: 18987218]
[EC 2.1.1.279 created 2013]
 
 
EC 2.1.1.280
Accepted name: selenocysteine Se-methyltransferase
Reaction: S-methyl-L-methionine + L-selenocysteine = L-methionine + Se-methyl-L-selenocysteine
Other name(s): SMT
Systematic name: S-methyl-L-methionine:L-selenocysteine Se-methyltransferase
Comments: The enzyme uses S-adenosyl-L-methionine as methyl donor less actively than S-methyl-L-methionine. The enzyme from broccoli (Brassica oleracea var. italica) also has the activity of EC 2.1.1.10, homocysteine S-methyltransferase [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Neuhierl, B. and Bock, A. On the mechanism of selenium tolerance in selenium-accumulating plants. Purification and characterization of a specific selenocysteine methyltransferase from cultured cells of Astragalus bisculatus. Eur. J. Biochem. 239 (1996) 235–238. [PMID: 8706715]
2.  Neuhierl, B., Thanbichler, M., Lottspeich, F. and Bock, A. A family of S-methylmethionine-dependent thiol/selenol methyltransferases. Role in selenium tolerance and evolutionary relation. J. Biol. Chem. 274 (1999) 5407–5414. [PMID: 10026151]
3.  Lyi, S.M., Heller, L.I., Rutzke, M., Welch, R.M., Kochian, L.V. and Li, L. Molecular and biochemical characterization of the selenocysteine Se-methyltransferase gene and Se-methylselenocysteine synthesis in broccoli. Plant Physiol. 138 (2005) 409–420. [PMID: 15863700]
4.  Lyi, S.M., Zhou, X., Kochian, L.V. and Li, L. Biochemical and molecular characterization of the homocysteine S-methyltransferase from broccoli (Brassica oleracea var. italica). Phytochemistry 68 (2007) 1112–1119. [PMID: 17391716]
[EC 2.1.1.280 created 2013]
 
 
EC 2.1.1.281
Accepted name: phenylpyruvate C3-methyltransferase
Reaction: S-adenosyl-L-methionine + 3-phenylpyruvate = S-adenosyl-L-homocysteine + (3S)-2-oxo-3-phenylbutanoate
Glossary: 3-phenylpyruvate = 2-oxo-3-phenylpropanoate
(3S)-2-oxo-3-phenylbutanoate = (3S)-β-methyl-phenylpyruvate
Other name(s): phenylpyruvate Cβ-methyltransferase; phenylpyruvate methyltransferase; mppJ (gene name)
Systematic name: S-adenosyl-L-methionine:2-oxo-3-phenylpropanoate C3-methyltransferase
Comments: The enzyme from the bacterium Streptomyces hygroscopicus NRRL3085 is involved in synthesis of the nonproteinogenic amino acid (2S,3S)-β-methyl-phenylalanine, a building block of the antibiotic mannopeptimycin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Huang, Y.T., Lyu, S.Y., Chuang, P.H., Hsu, N.S., Li, Y.S., Chan, H.C., Huang, C.J., Liu, Y.C., Wu, C.J., Yang, W.B. and Li, T.L. In vitro characterization of enzymes involved in the synthesis of nonproteinogenic residue (2S,3S)-β-methylphenylalanine in glycopeptide antibiotic mannopeptimycin. Chembiochem 10 (2009) 2480–2487. [PMID: 19731276]
[EC 2.1.1.281 created 2013]
 
 
EC 2.1.1.282
Accepted name: tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe = S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW3 (gene name); tRNA-yW synthesizing enzyme-3
Systematic name: S-adenosyl-L-methionine:tRNAPhe 7-[(3S)-(3-amino-3-carboxypropyl)-4-demethylwyosine-N4]-methyltransferase
Comments: The enzyme is involved in the biosynthesis of hypermodified tricyclic bases found at position 37 of certain tRNAs. These modifications are important for translational reading-frame maintenance. The enzyme is found in all eukaryotes and in some archaea, but not in bacteria. The eukaryotic enzyme is involved in the biosynthesis of wybutosine.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [PMID: 16642040]
[EC 2.1.1.282 created 2013, modified 2014]
 
 
EC 2.1.1.283
Accepted name: emodin O-methyltransferase
Reaction: S-adenosyl-L-methionine + emodin = S-adenosyl-L-homocysteine + questin
Glossary: emodin = 1,3,8-trihydroxy-6-methyl-9,10-anthraquinone
questin = 1,6-dihydroxy-8-methoxy-3-methyl-9,10-anthraquinone
Other name(s): EOMT
Systematic name: S-adenosyl-L-methionine:emodin 8-O-methyltransferase
Comments: The enzyme is involved in biosynthesis of the seco-anthraquinone (+)-geodin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Chen, Z.G., Fujii, I., Ebizuka, Y. and Sankawa, U. Emodin O-methyltransferase from Aspergillus terreus. Arch. Microbiol. 158 (1992) 29–34. [PMID: 1444712]
[EC 2.1.1.283 created 2013]
 
 
EC 2.1.1.284
Accepted name: 8-demethylnovobiocic acid C8-methyltransferase
Reaction: S-adenosyl-L-methionine + 8-demethylnovobiocic acid = S-adenosyl-L-homocysteine + novobiocic acid
For diagram of novobiocin biosynthesis, click here
Glossary: novobiocic acid = N-(2,7-dihydroxy-8-methyl-4-oxochromen-3-yl)-4-hydroxy-3-(3-methylbut-2-enyl) benzamide
Other name(s): NovO
Systematic name: S-adenosyl-L-methionine:8-demethylnovobiocic acid C8-methyltransferase
Comments: The enzyme is involved in the biosynthesis of the aminocoumarin antibiotic novobiocin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Pacholec, M., Tao, J. and Walsh, C.T. CouO and NovO: C-methyltransferases for tailoring the aminocoumarin scaffold in coumermycin and novobiocin antibiotic biosynthesis. Biochemistry 44 (2005) 14969–14976. [PMID: 16274243]
[EC 2.1.1.284 created 2013]
 
 
EC 2.1.1.285
Accepted name: demethyldecarbamoylnovobiocin O-methyltransferase
Reaction: S-adenosyl-L-methionine + demethyldecarbamoylnovobiocin = S-adenosyl-L-homocysteine + decarbamoylnovobiocin
For diagram of novobiocin biosynthesis, click here
Glossary: demethyldecarbamoylnovobiocin = N-{7-[(6-deoxy-5-methyl-β-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamide
decarbamoylnovobiocin = N-{7-[(6-deoxy-5-methyl-4-O-methyl-β-D-gulopyranosyl)oxy]4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methyl-2-buten-1-yl)benzamide
Other name(s): NovP
Systematic name: S-adenosyl-L-methionine:demethyldecarbamoylnovobiocin 4′′-O-methyltransferase
Comments: The enzyme is involved in the biosynthesis of the aminocoumarin antibiotic novobiocin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Freel Meyers, C.L., Oberthur, M., Xu, H., Heide, L., Kahne, D. and Walsh, C.T. Characterization of NovP and NovN: completion of novobiocin biosynthesis by sequential tailoring of the noviosyl ring. Angew. Chem. Int. Ed. Engl. 43 (2004) 67–70. [PMID: 14694473]
2.  Gomez Garcia, I., Stevenson, C.E., Uson, I., Freel Meyers, C.L., Walsh, C.T. and Lawson, D.M. The crystal structure of the novobiocin biosynthetic enzyme NovP: the first representative structure for the TylF O-methyltransferase superfamily. J. Mol. Biol. 395 (2010) 390–407. [PMID: 19857499]
[EC 2.1.1.285 created 2013]
 
 
EC 2.1.1.286
Accepted name: 25S rRNA (adenine2142-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine2142 in 25S rRNA = S-adenosyl-L-homocysteine + N1-methyladenine2142 in 25S rRNA
Other name(s): BMT2 (gene name); 25S rRNA m1A2142 methyltransferase
Systematic name: S-adenosyl-L-methionine:25S rRNA (adenine2142-N1)-methyltransferase
Comments: In the yeast Saccharomyces cerevisiae this methylation is important for resistance towards hydrogen peroxide and the antibiotic anisomycin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sharma, S., Watzinger, P., Kotter, P. and Entian, K.D. Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res. 41 (2013) 5428–5443. [PMID: 23558746]
[EC 2.1.1.286 created 2013]
 
 
EC 2.1.1.287
Accepted name: 25S rRNA (adenine645-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine645 in 25S rRNA = S-adenosyl-L-homocysteine + N1-methyladenine645 in 25S rRNA
Other name(s): 25S rRNA m1A645 methyltransferase; Rrp8
Systematic name: S-adenosyl-L-methionine:25S rRNA (adenine645-N1)-methyltransferase
Comments: The enzyme is found in eukaryotes. The adenine position refers to rRNA in the yeast Saccharomyces cerevisiae, in which the enzyme is important for ribosome biogenesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Peifer, C., Sharma, S., Watzinger, P., Lamberth, S., Kotter, P. and Entian, K.D. Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res. 41 (2013) 1151–1163. [PMID: 23180764]
[EC 2.1.1.287 created 2013]
 
 
EC 2.1.3.12
Accepted name: decarbamoylnovobiocin carbamoyltransferase
Reaction: carbamoyl phosphate + decarbamoylnovobiocin = phosphate + novobiocin
For diagram of novobiocin biosynthesis, click here
Glossary: decarbamoylnovobiocin = N-{7-[(6-deoxy-5-methyl-4-O-methyl-β-D-gulopyranosyl)oxy]4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methyl-2-buten-1-yl)benzamide
Other name(s): novN (gene name)
Systematic name: carbamoyl phosphate:decarbamoylnovobiocin 3′′-O-carbamoyltransferase
Comments: The enzyme catalyses the last step in the biosynthesis of the aminocoumarin antibiotic novobiocin. The reaction is activated by ATP [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Freel Meyers, C.L., Oberthur, M., Xu, H., Heide, L., Kahne, D. and Walsh, C.T. Characterization of NovP and NovN: completion of novobiocin biosynthesis by sequential tailoring of the noviosyl ring. Angew. Chem. Int. Ed. Engl. 43 (2004) 67–70. [PMID: 14694473]
2.  Gomez Garcia, I., Freel Meyers, C.L., Walsh, C.T. and Lawson, D.M. Crystallization and preliminary X-ray analysis of the O-carbamoyltransferase NovN from the novobiocin-biosynthetic cluster of Streptomyces spheroides. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 1000–1002. [PMID: 18997325]
[EC 2.1.3.12 created 2013]
 
 
EC 2.3.1.224
Accepted name: acetyl-CoA-benzylalcohol acetyltransferase
Reaction: (1) acetyl-CoA + benzyl alcohol = CoA + benzyl acetate
(2) acetyl-CoA + cinnamyl alcohol = CoA + cinnamyl acetate
Other name(s): BEAT
Systematic name: acetyl-CoA:benzylalcohol O-acetyltransferase
Comments: The enzyme is found in flowers like Clarkia breweri, where it is important for floral scent production. Unlike EC 2.3.1.84, alcohol O-acetyltransferase, this enzyme is active with alcohols that contain a benzyl ring.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Dudareva, N., D'Auria, J.C., Nam, K.H., Raguso, R.A. and Pichersky, E. Acetyl-CoA:benzylalcohol acetyltransferase - an enzyme involved in floral scent production in Clarkia breweri. Plant J. 14 (1998) 297–304. [PMID: 9628024]
[EC 2.3.1.224 created 2013]
 
 
EC 2.3.1.225
Accepted name: protein S-acyltransferase
Reaction: palmitoyl-CoA + [protein]-L-cysteine = [protein]-S-palmitoyl-L-cysteine + CoA
Other name(s): DHHC palmitoyl transferase; S-protein acyltransferase; G-protein palmitoyltransferase
Systematic name: palmitoyl-CoA:[protein]-L-cysteine S-palmitoyltransferase
Comments: The enzyme catalyses the posttranslational protein palmitoylation that plays a role in protein-membrane interactions, protein trafficking, and enzyme activity. Palmitoylation increases the hydrophobicity of proteins or protein domains and contributes to their membrane association.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Dunphy, J.T., Greentree, W.K., Manahan, C.L. and Linder, M.E. G-protein palmitoyltransferase activity is enriched in plasma membranes. J. Biol. Chem. 271 (1996) 7154–7159. [PMID: 8636152]
2.  Veit, M., Dietrich, L.E. and Ungermann, C. Biochemical characterization of the vacuolar palmitoyl acyltransferase. FEBS Lett. 540 (2003) 101–105. [PMID: 12681491]
3.  Batistic, O. Genomics and localization of the Arabidopsis DHHC-cysteine-rich domain S-acyltransferase protein family. Plant Physiol. 160 (2012) 1597–1612. [PMID: 22968831]
4.  Jennings, B.C. and Linder, M.E. DHHC protein S-acyltransferases use similar ping-pong kinetic mechanisms but display different acyl-CoA specificities. J. Biol. Chem. 287 (2012) 7236–7245. [PMID: 22247542]
5.  Zhou, L.Z., Li, S., Feng, Q.N., Zhang, Y.L., Zhao, X., Zeng, Y.L., Wang, H., Jiang, L. and Zhang, Y. Protein S-acyl transferase10 is critical for development and salt tolerance in Arabidopsis. Plant Cell 25 (2013) 1093–1107. [PMID: 23482856]
[EC 2.3.1.225 created 2013]
 
 
EC 2.3.1.226
Accepted name: carboxymethylproline synthase
Reaction: malonyl-CoA + (S)-1-pyrroline-5-carboxylate + H2O = CoA + (2S,5S)-5-carboxymethylproline + CO2
Other name(s): CarB (ambiguous)
Systematic name: malonyl-CoA:(S)-1-pyrroline-5-carboxylate malonyltransferase (cyclizing)
Comments: The enzyme is involved in the biosynthesis of the carbapenem β-lactam antibiotic (5R)-carbapen-2-em-3-carboxylate in the bacterium Pectobacterium carotovorum.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sleeman, M.C. and Schofield, C.J. Carboxymethylproline synthase (CarB), an unusual carbon-carbon bond-forming enzyme of the crotonase superfamily involved in carbapenem biosynthesis. J. Biol. Chem. 279 (2004) 6730–6736. [PMID: 14625287]
2.  Gerratana, B., Arnett, S.O., Stapon, A. and Townsend, C.A. Carboxymethylproline synthase from Pectobacterium carotorova: a multifaceted member of the crotonase superfamily. Biochemistry 43 (2004) 15936–15945. [PMID: 15595850]
3.  Sorensen, J.L., Sleeman, M.C. and Schofield, C.J. Synthesis of deuterium labelled L- and D-glutamate semialdehydes and their evaluation as substrates for carboxymethylproline synthase (CarB)—implications for carbapenem biosynthesis. Chem. Commun. (Camb.) (2005) 1155–1157. [PMID: 15726176]
4.  Sleeman, M.C., Sorensen, J.L., Batchelar, E.T., McDonough, M.A. and Schofield, C.J. Structural and mechanistic studies on carboxymethylproline synthase (CarB), a unique member of the crotonase superfamily catalyzing the first step in carbapenem biosynthesis. J. Biol. Chem. 280 (2005) 34956–34965. [PMID: 16096274]
5.  Batchelar, E.T., Hamed, R.B., Ducho, C., Claridge, T.D., Edelmann, M.J., Kessler, B. and Schofield, C.J. Thioester hydrolysis and C-C bond formation by carboxymethylproline synthase from the crotonase superfamily. Angew. Chem. Int. Ed. Engl. 47 (2008) 9322–9325. [PMID: 18972478]
6.  Hamed, R.B., Gomez-Castellanos, J.R., Thalhammer, A., Harding, D., Ducho, C., Claridge, T.D. and Schofield, C.J. Stereoselective C-C bond formation catalysed by engineered carboxymethylproline synthases. Nat. Chem. 3 (2011) 365–371. [PMID: 21505494]
[EC 2.3.1.226 created 2013]
 
 
*EC 2.4.1.1
Accepted name: glycogen phosphorylase
Reaction: [(1→4)-α-D-glucosyl]n + phosphate = [(1→4)-α-D-glucosyl]n-1 + α-D-glucose 1-phosphate
For diagram of glycogen, click here
Other name(s): muscle phosphorylase a and b; amylophosphorylase; polyphosphorylase; amylopectin phosphorylase; glucan phosphorylase; α-glucan phosphorylase; 1,4-α-glucan phosphorylase; glucosan phosphorylase; granulose phosphorylase; maltodextrin phosphorylase; muscle phosphorylase; myophosphorylase; potato phosphorylase; starch phosphorylase; 1,4-α-D-glucan:phosphate α-D-glucosyltransferase; phosphorylase (ambiguous)
Systematic name: (1→4)-α-D-glucan:phosphate α-D-glucosyltransferase
Comments: This entry covers several enzymes from different sources that act in vivo on different forms of (1→4)-α-D-glucans. Some of these enzymes catalyse the first step in the degradation of large branched glycan polymers - the phosphorolytic cleavage of α-1,4-glucosidic bonds from the non-reducing ends of linear poly(1→4)-α-D-glucosyl chains within the polymers. The enzyme stops when it reaches the fourth residue away from an α-1,6 branching point, leaving a highly branched core known as a limit dextrin. The accepted name of the enzyme should be modified for each specific instance by substituting "glycogen" with the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, etc.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9035-74-9
References:
1.  Hanes, C.S. The breakdown and synthesis of starch by an enzyme from pea seeds. Proc. R. Soc. Lond. B Biol. Sci. 128 (1940) 421–450.
2.  Green, A.A. and Cori, G.T. Crystalline muscle phosphorylase. I. Preparation, properties, and molecular weight. J. Biol. Chem. 151 (1943) 21–29.
3.  Baum, H. and Gilbert, G.A. A simple method for the preparation of crystalline potato phosphorylase and Q-enzyme. Nature 171 (1953) 983–984. [PMID: 13063502]
4.  Cowgill, R.W. Lobster muscle phosphorylase: purfication and properties. J. Biol. Chem. 234 (1959) 3146–3153. [PMID: 13812491]
5.  Chen, G.S. and Segel, I.H. Purification and properties of glycogen phosphorylase from Escherichia coli. Arch. Biochem. Biophys. 127 (1968) 175–186. [PMID: 4878695]
6.  Fischer, E.H., Pocker, A. and Saari, J.C. The structure, function and control of glycogen phosphorylase. In: Campbell, P.N. and Greville, G.D. (Eds), Essays in Biochemistry, vol. 6, Academic Press, London and New York, 1970, pp. 23–68.
[EC 2.4.1.1 created 1961, modified 2013]
 
 
EC 2.4.1.301
Accepted name: 2′-deamino-2′-hydroxyneamine 1-α-D-kanosaminyltransferase
Reaction: (1) UDP-α-D-kanosamine + 2′-deamino-2′-hydroxyneamine = UDP + kanamycin A
(2) UDP-α-D-kanosamine + neamine = UDP + kanamycin B
(3) UDP-α-D-kanosamine + paromamine = UDP + kanamycin C
(4) UDP-α-D-kanosamine + 2′-deamino-2′-hydroxyparomamine = UDP + kanamycin X
For diagram of kanamycin A biosynthesis, click here
Glossary: neamine = (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-α-D-glucopyranoside
paromamine = (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2-amino-2-deoxy-α-D-glucopyranoside
UDP-α-D-kanosamine = uridine 5′-[3-(3-amino-3-deoxy-α-D-glucopyranosyl) diphosphate]
kanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-(6-amino-6-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
kanamycin B = (1R,2S,3S,4R,6S)-4,6-diamino-3-(3-amino-3-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-α-D-glucopyranoside
kanamycin C = (1R,2S,3S,4R,6S)-4,6-diamino-3-(3-amino-3-deoxy-α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 2-amino-2-deoxy-α-D-glucopyranoside
kanamycin X = (1S,2R,3R,4S,6R)-4,6-diamino-3-(α-D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
Other name(s): kanE (gene name); kanM2 (gene name)
Systematic name: UDP-α-D-kanosamine:2′-deamino-2′-hydroxyneamine 1-α-D-kanosaminyltransferase
Comments: Involved in the biosynthetic pathway of kanamycins. The enzyme characterized from the bacterium Streptomyces kanamyceticus can also accept UDP-α-D-glucose with lower efficiency [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kudo, F., Sucipto, H. and Eguchi, T. Enzymatic activity of a glycosyltransferase KanM2 encoded in the kanamycin biosynthetic gene cluster. J. Antibiot. (Tokyo) 62 (2009) 707–710. [PMID: 19911031]
2.  Park, J.W., Park, S.R., Nepal, K.K., Han, A.R., Ban, Y.H., Yoo, Y.J., Kim, E.J., Kim, E.M., Kim, D., Sohng, J.K. and Yoon, Y.J. Discovery of parallel pathways of kanamycin biosynthesis allows antibiotic manipulation. Nat. Chem. Biol. 7 (2011) 843–852. [PMID: 21983602]
[EC 2.4.1.301 created 2013]
 
 
EC 2.4.1.302
Accepted name: L-demethylnoviosyl transferase
Reaction: dTDP-4-O-demethyl-β-L-noviose + novobiocic acid = dTDP + demethyldecarbamoyl novobiocin
For diagram of novobiocin biosynthesis, click here
Glossary: novobiocic acid = N-(2,7-dihydroxy-8-methyl-4-oxo-4H-chromen-3-yl)-4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamide
dTDP-4-O-demethyl-β-L-noviose = dTDP-6-deoxy-5-methyl-β-L-altropyranose = dTDP-(2S,3R,4R,5R)-6,6-dimethyltetrahydro-2H-pyran-2,3,4,5-tetraol
demethyldecarbamoyl novobiocin = N-{7-[(6-deoxy-5-methyl-β-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-chromen-3-yl}-4-hydroxy-3-(3-methylbut-2-en-1-yl)benzamide
Other name(s): novM (gene name); dTDP-β-L-noviose:novobiocic acid 7-O-noviosyltransferase; L-noviosyl transferase
Systematic name: dTDP-4-O-demethyl-β-L-noviose:novobiocic acid 7-O-[4-O-demethyl-L-noviosyl]transferase
Comments: The enzyme is involved in the biosynthesis of the aminocoumarin antibiotic, novobiocin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Freel Meyers, C.L., Oberthur, M., Anderson, J.W., Kahne, D. and Walsh, C.T. Initial characterization of novobiocic acid noviosyl transferase activity of NovM in biosynthesis of the antibiotic novobiocin. Biochemistry 42 (2003) 4179–4189. [PMID: 12680772]
2.  Albermann, C., Soriano, A., Jiang, J., Vollmer, H., Biggins, J.B., Barton, W.A., Lesniak, J., Nikolov, D.B. and Thorson, J.S. Substrate specificity of NovM: implications for novobiocin biosynthesis and glycorandomization. Org. Lett. 5 (2003) 933–936. [PMID: 12633109]
[EC 2.4.1.302 created 2013, modified 2016]
 
 
EC 2.4.1.303
Accepted name: UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol β-1,3-galactosyltransferase
Reaction: UDP-α-D-galactose + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + β-D-Gal-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): WbbD; WbbD β3Gal-transferase; UDP-Gal:GlcNAc-R β1,3-galactosyltransferase; UDP-Gal:GlcNAcα-pyrophosphate-R β1,3-galactosyltransferase; UDP-Gal:GlcNAc-R galactosyltransferase
Systematic name: UDP-α-D-galactose:N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol 3-β-galactosyltransferase (configuration-inverting)
Comments: The enzyme is involved in the the biosynthesis of the O-antigen repeating unit of Escherichia coli O7:K1 (VW187). Requires Mn2+. cf. EC 2.4.1.343, UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol α-1,3-galactosyltransferase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Riley, J.G., Menggad, M., Montoya-Peleaz, P.J., Szarek, W.A., Marolda, C.L., Valvano, M.A., Schutzbach, J.S. and Brockhausen, I. The wbbD gene of E. coli strain VW187 (O7:K1) encodes a UDP-Gal: GlcNAcα-pyrophosphate-R β1,3-galactosyltransferase involved in the biosynthesis of O7-specific lipopolysaccharide. Glycobiology 15 (2005) 605–613. [PMID: 15625181]
2.  Brockhausen, I., Riley, J.G., Joynt, M., Yang, X. and Szarek, W.A. Acceptor substrate specificity of UDP-Gal: GlcNAc-R β1,3-galactosyltransferase (WbbD) from Escherichia coli O7:K1. Glycoconj. J. 25 (2008) 663–673. [PMID: 18536883]
[EC 2.4.1.303 created 2013, modified 2017]
 
 
EC 2.4.1.304
Accepted name: UDP-Gal:α-D-GlcNAc-diphosphoundecaprenol β-1,4-galactosyltransferase
Reaction: UDP-α-D-galactose + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + β-D-Gal-(1→4)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): WfeD; UDP-Gal:GlcNAc-R 1,4-Gal-transferase; UDP-Gal:GlcNAc-pyrophosphate-lipid β-1,4-galactosyltransferase
Systematic name: UDP-α-D-galactose:N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol β-1,4-galactosyltransferase
Comments: The enzyme is involved in the the biosynthesis of the O-polysaccharide repeating unit of the bacterium Shigella boydii B14. The activity is stimulated by Mn2+ or to a lesser extent by Mg2+, Ca2+, Ni2+ or Pb2+.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Xu, C., Liu, B., Hu, B., Han, Y., Feng, L., Allingham, J.S., Szarek, W.A., Wang, L. and Brockhausen, I. Biochemical characterization of UDP-Gal:GlcNAc-pyrophosphate-lipid β-1,4-Galactosyltransferase WfeD, a new enzyme from Shigella boydii type 14 that catalyzes the second step in O-antigen repeating-unit synthesis. J. Bacteriol. 193 (2011) 449–459. [PMID: 21057010]
[EC 2.4.1.304 created 2013]
 
 
EC 2.4.1.305
Accepted name: UDP-Glc:α-D-GlcNAc-glucosaminyl-diphosphoundecaprenol β-1,3-glucosyltransferase
Reaction: UDP-α-D-glucose + N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + β-D-Glc-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): WfaP; WfgD; UDP-Glc:GlcNAc-pyrophosphate-lipid β-1,3-glucosyltransferase; UDP-Glc:GlcNAc-diphosphate-lipid β-1,3-glucosyltransferase
Systematic name: UDP-α-D-glucose:N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol β-1,3-glucosyltransferase
Comments: The enzyme is involved in the the biosynthesis of the O-polysaccharide repeating unit of the bacterium Escherichia coli serotype O56 and serotype O152.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Brockhausen, I., Hu, B., Liu, B., Lau, K., Szarek, W.A., Wang, L. and Feng, L. Characterization of two β-1,3-glucosyltransferases from Escherichia coli serotypes O56 and O152. J. Bacteriol. 190 (2008) 4922–4932. [PMID: 18487334]
[EC 2.4.1.305 created 2013]
 
 
EC 2.4.1.306
Accepted name: UDP-GalNAc:α-D-GalNAc-diphosphoundecaprenol α-1,3-N-acetylgalactosaminyltransferase
Reaction: UDP-N-acetyl-α-D-galactosamine + N-acetyl-α-D-galactosaminyl-diphospho-ditrans,octacis-undecaprenol = UDP + α-D-GalNAc-(1→3)-α-D-GalNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): WbnH
Systematic name: UDP-N-acetyl-α-D-galactosamine:N-acetyl-α-D-galactosaminyl-diphospho-ditrans,octacis-undecaprenol α-1,3-N-acetyl-D-galactosyltransferase
Comments: The enzyme is involved in the the biosynthesis of the O-polysaccharide repeating unit of Escherichia coli serotype O86.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yi, W., Yao, Q., Zhang, Y., Motari, E., Lin, S. and Wang, P.G. The wbnH gene of Escherichia coli O86:H2 encodes an α-1,3-N-acetylgalactosaminyl transferase involved in the O-repeating unit biosynthesis. Biochem. Biophys. Res. Commun. 344 (2006) 631–639. [PMID: 16630548]
[EC 2.4.1.306 created 2013]
 
 
EC 2.4.1.307
Deleted entry: UDP-Gal:α-D-GalNAc-1,3-α-D-GalNAc-diphosphoundecaprenol β-1,3-galactosyltransferase. Now included in EC 2.4.1.122, glycoprotein-N-acetylgalactosamine β-1,3-galactosyltransferase
[EC 2.4.1.307 created 2013, deleted 2016]
 
 
EC 2.4.1.308
Accepted name: GDP-Fuc:β-D-Gal-1,3-α-D-GalNAc-1,3-α-GalNAc-diphosphoundecaprenol α-1,2-fucosyltransferase
Reaction: GDP-β-L-fucose + β-D-Gal-(1→3)-α-D-GalNAc-(1→3)-α-D-GalNAc-diphospho-ditrans,octacis-undecaprenol = GDP + α-L-Fuc-(1→2)-β-D-Gal-(1→3)-α-D-GalNAc-(1→3)-α-D-GalNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): WbnK
Systematic name: GDP-β-L-fucose:β-D-Gal-(1→3)-α-D-GalNAc-(1→3)-α-D-GalNAc-diphospho-ditrans,octacis-undecaprenol α-1,2-fucosyltransferase
Comments: The enzyme is involved in the biosynthesis of the O-polysaccharide repeating unit of the bacterium Escherichia coli serotype O86.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yi, W., Shao, J., Zhu, L., Li, M., Singh, M., Lu, Y., Lin, S., Li, H., Ryu, K., Shen, J., Guo, H., Yao, Q., Bush, C.A. and Wang, P.G. Escherichia coli O86 O-antigen biosynthetic gene cluster and stepwise enzymatic synthesis of human blood group B antigen tetrasaccharide. J. Am. Chem. Soc. 127 (2005) 2040–2041. [PMID: 15713070]
2.  Woodward, R., Yi, W., Li, L., Zhao, G., Eguchi, H., Sridhar, P.R., Guo, H., Song, J.K., Motari, E., Cai, L., Kelleher, P., Liu, X., Han, W., Zhang, W., Ding, Y., Li, M. and Wang, P.G. In vitro bacterial polysaccharide biosynthesis: defining the functions of Wzy and Wzz. Nat. Chem. Biol. 6 (2010) 418–423. [PMID: 20418877]
[EC 2.4.1.308 created 2013]
 
 
EC 2.4.1.309
Accepted name: UDP-Gal:α-L-Fuc-1,2-β-Gal-1,3-α-GalNAc-1,3-α-GalNAc-diphosphoundecaprenol α-1,3-galactosyltransferase
Reaction: UDP-α-D-galactose + α-L-Fuc-(1→2)-β-D-Gal-(1→3)-α-D-GalNAc-(1→3)-α-D-GalNAc-diphospho-ditrans,octacis-undecaprenol = UDP + α-D-Gal-(1→3)-(α-L-Fuc-(1→2))-β-D-Gal-(1→3)-α-D-GalNAc-(1→3)-α-D-GalNAc-diphospho-ditrans,octacis-undecaprenol
Other name(s): WbnI
Systematic name: UDP-α-D-galactose:α-L-Fuc-(1→2)-β-D-Gal-(1→3)-α-D-GalNAc-(1→3)-α-D-GalNAc-diphospho-ditrans,octacis-undecaprenol α-1,3-galactosyltransferase
Comments: The enzyme is involved in the the biosynthesis of the O-polysaccharide repeating unit of the bacterium Escherichia coli serotype O86.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yi, W., Shao, J., Zhu, L., Li, M., Singh, M., Lu, Y., Lin, S., Li, H., Ryu, K., Shen, J., Guo, H., Yao, Q., Bush, C.A. and Wang, P.G. Escherichia coli O86 O-antigen biosynthetic gene cluster and stepwise enzymatic synthesis of human blood group B antigen tetrasaccharide. J. Am. Chem. Soc. 127 (2005) 2040–2041. [PMID: 15713070]
2.  Yi, W., Zhu, L., Guo, H., Li, M., Li, J. and Wang, P.G. Formation of a new O-polysaccharide in Escherichia coli O86 via disruption of a glycosyltransferase gene involved in O-unit assembly. Carbohydr. Res. 341 (2006) 2254–2260. [PMID: 16839526]
3.  Woodward, R., Yi, W., Li, L., Zhao, G., Eguchi, H., Sridhar, P.R., Guo, H., Song, J.K., Motari, E., Cai, L., Kelleher, P., Liu, X., Han, W., Zhang, W., Ding, Y., Li, M. and Wang, P.G. In vitro bacterial polysaccharide biosynthesis: defining the functions of Wzy and Wzz. Nat. Chem. Biol. 6 (2010) 418–423. [PMID: 20418877]
[EC 2.4.1.309 created 2013]
 
 
EC 2.4.2.23
Transferred entry: deoxyuridine phosphorylase. This activity has been shown to be catalysed by EC 2.4.2.2, pyrimidine-nucleoside phosphorylase, EC 2.4.2.3, uridine phosphorylase, and EC 2.4.2.4, thymidine phosphorylase.
[EC 2.4.2.23 created 1972, deleted 2013]
 
 
*EC 2.5.1.79
Accepted name: thermospermine synthase
Reaction: S-adenosyl 3-(methylthio)propylamine + spermidine = S-methyl-5′-thioadenosine + thermospermine + H+
Glossary: thermospermine = N1-[3-(3-aminopropylamino)propyl]butane-1,4-diamine
S-adenosyl 3-(methylthio)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): TSPMS; ACL5; SAC51
Systematic name: S-adenosyl 3-(methylthio)propylamine:spermidine 3-aminopropyltransferase (thermospermine synthesizing)
Comments: This enzyme is crucial for the proper functioning of xylem vessel elements in the vascular tissues of plants [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Romer, P., Faltermeier, A., Mertins, V., Gedrange, T., Mai, R. and Proff, P. Investigations about N-aminopropyl transferases probably involved in biomineralization. J. Physiol. Pharmacol. 59 Suppl 5 (2008) 27–37. [PMID: 19075322]
2.  Knott, J.M., Romer, P. and Sumper, M. Putative spermine synthases from Thalassiosira pseudonana and Arabidopsis thaliana synthesize thermospermine rather than spermine. FEBS Lett. 581 (2007) 3081–3086. [PMID: 17560575]
3.  Muniz, L., Minguet, E.G., Singh, S.K., Pesquet, E., Vera-Sirera, F., Moreau-Courtois, C.L., Carbonell, J., Blazquez, M.A. and Tuominen, H. ACAULIS5 controls Arabidopsis xylem specification through the prevention of premature cell death. Development 135 (2008) 2573–2582. [PMID: 18599510]
[EC 2.5.1.79 created 2010, modified 2013]
 
 
EC 2.5.1.108
Accepted name: 2-(3-amino-3-carboxypropyl)histidine synthase
Reaction: S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2] = S-methyl-5′-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Other name(s): Dph2
Systematic name: S-adenosyl-L-methionine:L-histidine-[translation elongation factor 2] 2-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: A [4Fe-4S] enzyme that modifies a histidine residue of the translation elongation factor 2 (EF2) via a 3-amino-3-carboxypropyl radical. The enzyme is present in archae and eukaryotes but not in eubacteria. The enzyme is a member of the ’AdoMet radical’ (radical SAM) family and generates the 3-amino-3-carboxypropyl radical by an uncanonical clevage of S-adenosyl-L-methionine. The relevant histidine of EF2 is His715 in mammals, His699 in yeast and His600 in Pyrococcus horikoshii. Part of diphthamide biosynthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Liu, S., Milne, G.T., Kuremsky, J.G., Fink, G.R. and Leppla, S.H. Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Mol. Cell Biol. 24 (2004) 9487–9497. [PMID: 15485916]
2.  Zhang, Y., Zhu, X., Torelli, A.T., Lee, M., Dzikovski, B., Koralewski, R.M., Wang, E., Freed, J., Krebs, C., Ealick, S.E. and Lin, H. Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature 465 (2010) 891–896. [PMID: 20559380]
3.  Zhu, X., Dzikovski, B., Su, X., Torelli, A.T., Zhang, Y., Ealick, S.E., Freed, J.H. and Lin, H. Mechanistic understanding of Pyrococcus horikoshii Dph2, a [4Fe-4S] enzyme required for diphthamide biosynthesis. Mol. Biosyst. 7 (2011) 74–81. [PMID: 20931132]
4.  Dong, M., Horitani, M., Dzikovski, B., Pandelia, M.E., Krebs, C., Freed, J.H., Hoffman, B.M. and Lin, H. Organometallic complex formed by an unconventional radical S-adenosylmethionine enzyme. J. Am. Chem. Soc. 138 (2016) 9755–9758. [PMID: 27465315]
[EC 2.5.1.108 created 2013]
 
 
EC 2.5.1.109
Accepted name: brevianamide F prenyltransferase (deoxybrevianamide E-forming)
Reaction: dimethylallyl diphosphate + brevianamide F = diphosphate + deoxybrevianamide E
For diagram of fumitremorgin alkaloid biosynthesis (part 1), click here
Glossary: brevianamide F = (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
deoxybrevianamide E = (3S,8aS)-3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-octahydropyrrolo[1,2-a]piperazine-1,4-dione
Other name(s): NotF; BrePT; brevianamide F reverse prenyltransferase
Systematic name: dimethylallyl-diphosphate:brevianamide-F tert-dimethylallyl-C-2-transferase
Comments: The enzyme from the fungus Aspergilus sp. MF297-2 is specific for brevianamide F [1], while the enzyme from Aspergillus versicolor accepts a broad range of trytophan-containing cyclic dipeptides [2]. Involved in the biosynthetic pathways of several indole alkaloids such as paraherquamides and malbrancheamides.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ding, Y., de Wet, J.R., Cavalcoli, J., Li, S., Greshock, T.J., Miller, K.A., Finefield, J.M., Sunderhaus, J.D., McAfoos, T.J., Tsukamoto, S., Williams, R.M. and Sherman, D.H. Genome-based characterization of two prenylation steps in the assembly of the stephacidin and notoamide anticancer agents in a marine-derived Aspergillus sp. J. Am. Chem. Soc. 132 (2010) 12733–12740. [PMID: 20722388]
2.  Yin, S., Yu, X., Wang, Q., Liu, X.Q. and Li, S.M. Identification of a brevianamide F reverse prenyltransferase BrePT from Aspergillus versicolor with a broad substrate specificity towards tryptophan-containing cyclic dipeptides. Appl. Microbiol. Biotechnol. 97 (2013) 1649–1660. [PMID: 22660767]
[EC 2.5.1.109 created 2013]
 
 
EC 2.5.1.110
Accepted name: 12α,13α-dihydroxyfumitremorgin C prenyltransferase
Reaction: dimethylallyl diphosphate + 12α,13α-dihydroxyfumitremorgin C = diphosphate + fumitremorgin B
For diagram of fumitremorgin alkaloid biosynthesis (part 2), click here
Glossary: 12α,13α-dihydroxyfumitremorgin = (5aR,6S,12S,14aS)-5a,6-dihydroxy-9-methoxy-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1′′,2′′:4′,5′]pyrazino[1′,2′:1,6]pyrido[3,4-b]indole-5,14-dione
fumitremorgin B = (5aR,6S,12S,14aS)-5a,6-dihydroxy-9-methoxy-11-(3-methylbut-2-en-1-yl)-12-(2-methylprop-1-en-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1′′,2′′:4′,5′]pyrazino[1′,2′:1,6]pyrido[3,4-b]indole-5,14-dione
Other name(s): ftmH (gene name); FtmPT2
Systematic name: dimethylallyl-diphosphate:12α,13α-dihydroxyfumitremorgin C dimethylallyl-N-1-transferase
Comments: The enzyme from the fungus Aspergillus fumigatus also shows some activity with fumitremorgin C. Involved in the biosynthetic pathways of several indole alkaloids such as fumitremorgins and verruculogen.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Grundmann, A., Kuznetsova, T., Afiyatullov, S.Sh and Li, S.M. FtmPT2, an N-prenyltransferase from Aspergillus fumigatus, catalyses the last step in the biosynthesis of fumitremorgin B. ChemBioChem. 9 (2008) 2059–2063. [PMID: 18683158]
[EC 2.5.1.110 created 2013]
 
 
EC 2.6.1.102
Accepted name: GDP-perosamine synthase
Reaction: GDP-α-D-perosamine + 2-oxoglutarate = GDP-4-dehydro-α-D-rhamnose + L-glutamate
Glossary: GDP-α-D-perosamine = GDP-4-amino-4,6-dideoxy-α-D-mannose
GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose
Other name(s): RfbE; GDP-4-keto-6-deoxy-D-mannose-4-aminotransferase; GDP-perosamine synthetase; PerA; GDP-4-amino-4,6-dideoxy-α-D-mannose:2-oxoglutarate aminotransferase
Systematic name: GDP-α-D-perosamine:2-oxoglutarate aminotransferase
Comments: A pyridoxal 5′-phosphate enzyme. D-Perosamine is one of several dideoxy sugars found in the O-specific polysaccharide of the lipopolysaccharide component of the outer membrane of Gram-negative bacteria. The enzyme catalyses the final step in GDP-α-D-perosamine synthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Albermann, C. and Piepersberg, W. Expression and identification of the RfbE protein from Vibrio cholerae O1 and its use for the enzymatic synthesis of GDP-D-perosamine. Glycobiology 11 (2001) 655–661. [PMID: 11479276]
2.  Zhao, G., Liu, J., Liu, X., Chen, M., Zhang, H. and Wang, P.G. Cloning and characterization of GDP-perosamine synthetase (Per) from Escherichia coli O157:H7 and synthesis of GDP-perosamine in vitro. Biochem. Biophys. Res. Commun. 363 (2007) 525–530. [PMID: 17888872]
3.  Albermann, C. and Beuttler, H. Identification of the GDP-N-acetyl-d-perosamine producing enzymes from Escherichia coli O157:H7. FEBS Lett. 582 (2008) 479–484. [PMID: 18201574]
4.  Cook, P.D., Carney, A.E. and Holden, H.M. Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase. Biochemistry 47 (2008) 10685–10693. [PMID: 18795799]
[EC 2.6.1.102 created 2013]
 
 
EC 2.6.99.3
Accepted name: O-ureido-L-serine synthase
Reaction: O-acetyl-L-serine + hydroxyurea = O-ureido-L-serine + acetate
Glossary: O-ureido-L-serine = (2S)-2-amino-3-[(carbamoylamino)oxy]propanoate
O-acetyl-L-serine = O3-acetyl-L-serine = (2S)-3-acetyloxy-2-aminopropanoic acid
Other name(s): dcsD (gene name)
Systematic name: O-acetyl-L-serine:hydroxyurea 2-amino-2-carboxyethyltransferase
Comments: The enzyme participates in the biosynthetic pathway of D-cycloserine, an antibiotic substance produced by several Streptomyces species. Also catalyses EC 2.5.1.47, cysteine synthase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kumagai, T., Koyama, Y., Oda, K., Noda, M., Matoba, Y. and Sugiyama, M. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob. Agents Chemother. 54 (2010) 1132–1139. [PMID: 20086163]
2.  Uda, N., Matoba, Y., Kumagai, T., Oda, K., Noda, M. and Sugiyama, M. Establishment of an in vitro D-cycloserine-synthesizing system by using O-ureido-L-serine synthase and D-cycloserine synthetase found in the biosynthetic pathway. Antimicrob. Agents Chemother. 57 (2013) 2603–2612. [PMID: 23529730]
[EC 2.6.99.3 created 2013]
 
 
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 2.7.7.87
Accepted name: L-threonylcarbamoyladenylate synthase
Reaction: L-threonine + ATP + HCO3- = L-threonylcarbamoyladenylate + diphosphate + H2O
For diagram of N6-L-Threonylcarbamoyladenosine37 modified tRNA biosynthesis, click here
Other name(s): yrdC (gene name); Sua5; ywlC (gene name); ATP:L-threonyl,bicarbonate adenylyltransferase
Systematic name: ATP:L-threonyl,HCO3- adenylyltransferase
Comments: The enzyme is involved in the synthesis of N6-threonylcarbamoyladenosine37 in tRNAs, with the anticodon NNU, i.e. tRNAIle, tRNAThr, tRNAAsn, tRNALys, tRNASer and tRNAArg [6].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  El Yacoubi, B., Lyons, B., Cruz, Y., Reddy, R., Nordin, B., Agnelli, F., Williamson, J.R., Schimmel, P., Swairjo, M.A. and de Crecy-Lagard, V. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res. 37 (2009) 2894–2909. [PMID: 19287007]
2.  Harris, K.A., Jones, V., Bilbille, Y., Swairjo, M.A. and Agris, P.F. YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase. RNA 17 (2011) 1678–1687. [PMID: 21775474]
3.  Kuratani, M., Kasai, T., Akasaka, R., Higashijima, K., Terada, T., Kigawa, T., Shinkai, A., Bessho, Y. and Yokoyama, S. Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP. Proteins 79 (2011) 2065–2075. [PMID: 21538543]
4.  Lauhon, C.T. Mechanism of N6-threonylcarbamoyladenonsine (t6A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 51 (2012) 8950–8963. [PMID: 23072323]
5.  Deutsch, C., El Yacoubi, B., de Crecy-Lagard, V. and Iwata-Reuyl, D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J. Biol. Chem. 287 (2012) 13666–13673. [PMID: 22378793]
6.  Perrochia, L., Crozat, E., Hecker, A., Zhang, W., Bareille, J., Collinet, B., van Tilbeurgh, H., Forterre, P. and Basta, T. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res. 41 (2013) 1953–1964. [PMID: 23258706]
7.  Wan, L.C.K., Mao, D.Y.L., Neculai, D., Strecker, J., Chiovitti, D., Kurinov, I., Poda, G., Thevakumaran, N., Yuan, F., Szilard, R.K., Lissina, E., Nislow, C., Caudy, A.A., Durocher, D. and Sicheri, F. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res. 41 (2013) 6332–6346. [PMID: 23620299]
[EC 2.7.7.87 created 2013]
 
 
*EC 2.7.8.38
Accepted name: archaetidylserine synthase
Reaction: (1) CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol + L-serine = CMP + 2,3-bis-(O-geranylgeranyl)-sn-glycero-1-phospho-L-serine
(2) CDP-2,3-bis-(O-phytanyl)-sn-glycerol + L-serine = CMP + 2,3-bis-(O-phytanyl)-sn-glycero-1-phospho-L-serine
For diagram of archaetidylserine biosynthesis, click here
Glossary: CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol = CDP-unsaturated archaeol
2,3-bis-(O-geranylgeranyl)-sn-glycero-1-phospho-L-serine = unsaturated archaetidylserine
CDP-2,3-bis-(O-phytanyl)-sn-glycerol = CDP archaeol
2,3-bis-(O-phytanyl)-sn-glycero-1-phospho-L-serine = archaetidylserine
Systematic name: CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol:L-serine 2,3-bis-(O-geranylgeranyl)-sn-glycerol phosphotransferase
Comments: Requires Mn2+. Isolated from the archaeon Methanothermobacter thermautotrophicus.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Morii, H. and Koga, Y. CDP-2,3-di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase) in the methanogenic archaeon Methanothermobacter thermautotrophicus. J. Bacteriol. 185 (2003) 1181–1189. [PMID: 12562787]
[EC 2.7.8.38 created 2013, modified 2013]
 
 
EC 2.7.8.39
Accepted name: archaetidylinositol phosphate synthase
Reaction: CDP-2,3-bis-(O-phytanyl)-sn-glycerol + 1L-myo-inositol 1-phosphate = CMP + 1-archaetidyl-1D-myo-inositol 3-phosphate
Glossary: 1L-myo-inositol 1-phosphate = 1D-myo-inositol 3-phosphate
CDP-2,3-bis-(O-phytanyl)-sn-glycerol = CDP-2,3-di-(O-phytanyl)-sn-glycerol = CDP-archaeol
1-archaetidyl-1D-myo-inositol 3-phosphate = archaetidyl-myo-inositol 1-phosphate
Other name(s): AIP synthase
Systematic name: CDP-2,3-bis-(O-phytanyl)-sn-glycerol:1L-myo-inositol 1-phosphate 1-sn-archaetidyltransferase
Comments: Requires Mg2+ or Mn2+ for activity. The enzyme is involved in biosynthesis of archaetidyl-myo-inositol, a compound essential for glycolipid biosynthesis in archaea.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Morii, H., Kiyonari, S., Ishino, Y. and Koga, Y. A novel biosynthetic pathway of archaetidyl-myo-inositol via archaetidyl-myo-inositol phosphate from CDP-archaeol and D-glucose 6-phosphate in methanoarchaeon Methanothermobacter thermautotrophicus cells. J. Biol. Chem. 284 (2009) 30766–30774. [PMID: 19740749]
[EC 2.7.8.39 created 2013]
 
 
EC 2.7.8.40
Accepted name: UDP-N-acetylgalactosamine-undecaprenyl-phosphate N-acetylgalactosaminephosphotransferase
Reaction: UDP-N-acetyl-α-D-galactosamine + ditrans,octacis-undecaprenyl phosphate = UMP + N-acetyl-α-D-galactosaminyl-diphospho-ditrans,octacis-undecaprenol
Other name(s): WecP; UDP-GalNAc:polyprenol-P GalNAc-1-P transferase; UDP-GalNAc:undecaprenyl-phosphate GalNAc-1-phosphate transferase
Systematic name: UDP-N-acetyl-α-D-galactosamine:ditrans,octacis-undecaprenyl phosphate N-acetyl-D-galactosaminephosphotransferase
Comments: The enzyme catalyses a step in the assembly of the repeating-unit of the O-antigen of the Gram-negative bacterium Aeromonas hydrophila AH-3. The enzyme shows no activity with UDP-N-acetyl-α-D-glucosamine (cf. EC 2.7.8.33, UDP-N-acetylglucosamine-undecaprenyl-phosphate N-acetylglucosaminephosphotransferase).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Merino, S., Jimenez, N., Molero, R., Bouamama, L., Regue, M. and Tomas, J.M. A UDP-HexNAc:polyprenol-P GalNAc-1-P transferase (WecP) representing a new subgroup of the enzyme family. J. Bacteriol. 193 (2011) 1943–1952. [PMID: 21335454]
[EC 2.7.8.40 created 2013]
 
 
EC 3.1.3.90
Accepted name: maltose 6′-phosphate phosphatase
Reaction: maltose 6′-phosphate + H2O = maltose + phosphate
Other name(s): maltose 6′-P phosphatase; mapP (gene name)
Systematic name: maltose 6′-phosphate phosphohydrolase
Comments: The enzyme from the bacterium Enterococcus faecalis also has activity with the sucrose isomer turanose 6′-phosphate (α-D-glucopyranosyl-(1→3)-D-fructose 6-phosphate).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Mokhtari, A., Blancato, V.S., Repizo, G.D., Henry, C., Pikis, A., Bourand, A., de Fatima Alvarez, M., Immel, S., Mechakra-Maza, A., Hartke, A., Thompson, J., Magni, C. and Deutscher, J. Enterococcus faecalis utilizes maltose by connecting two incompatible metabolic routes via a novel maltose 6′-phosphate phosphatase (MapP). Mol. Microbiol. 88 (2013) 234–253. [PMID: 23490043]
[EC 3.1.3.90 created 2013]
 
 
*EC 3.2.1.88
Accepted name: non-reducing end β-L-arabinopyranosidase
Reaction: Removal of a terminal β-L-arabinopyranose residue from the non-reducing end of its substrate.
Other name(s): vicianosidase; β-L-arabinosidase (ambiguous); β-L-arabinoside arabinohydrolase (ambiguous)
Systematic name: β-L-arabinopyranoside non-reducing end β-L-arabinopyranosidase
Comments: The enzyme, which was characterized from dormant seeds of the plant Cajanus cajan (pigeon pea), has been shown to remove the terminal non-reducing β-L-arabinopyranoside residue from the artificial substrate p-nitrophenyl-β-L-arabinopyranose [1]. In the presence of methanol the enzyme demonstrates transglycosylase activity, transferring the arabinose moiety to methanol while retaining the anomeric configuration, generating 1-O-methyl-β-L-arabinopyranose [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 39361-63-2
References:
1.  Dey, P.M. β-L-Arabinosidase from Cajanus indicus: a new enzyme. Biochim. Biophys. Acta 302 (1973) 393–398. [PMID: 4699248]
2.  Dey, P. M. Further characterization of β-L-arabinosidase from Cajanus indicus. Biochim. Biophys. Acta 746 (1983) 8–13.
[EC 3.2.1.88 created 1976, modified 2013]
 
 
EC 3.5.3.25
Accepted name: Nω-hydroxy-L-arginine amidinohydrolase
Reaction: Nω-hydroxy-L-arginine + H2O = L-ornithine + hydroxyurea
Other name(s): dcsB (gene name)
Systematic name: Nω-hydroxy-L-arginine amidinohydrolase
Comments: The enzyme participates in the biosynthetic pathway of D-cycloserine, an antibiotic substance produced by several Streptomyces species.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kumagai, T., Koyama, Y., Oda, K., Noda, M., Matoba, Y. and Sugiyama, M. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob. Agents Chemother. 54 (2010) 1132–1139. [PMID: 20086163]
2.  Kumagai, T., Takagi, K., Koyama, Y., Matoba, Y., Oda, K., Noda, M. and Sugiyama, M. Heme protein and hydroxyarginase necessary for biosynthesis of D-cycloserine. Antimicrob. Agents Chemother. 56 (2012) 3682–3689. [PMID: 22547619]
[EC 3.5.3.25 created 2013]
 
 
*EC 3.6.1.5
Accepted name: apyrase
Reaction: a nucleoside 5′-triphosphate + 2 H2O = a nucleoside 5′-phosphate + 2 phosphate (overall reaction)
(1a) a nucleoside 5′-triphosphate + H2O = a nucleoside 5′-diphosphate + phosphate
(1b) a nucleoside 5′-diphosphate + H2O = a nucleoside 5′-phosphate + phosphate
Other name(s): ATP-diphosphatase; adenosine diphosphatase; ADPase; ATP diphosphohydrolase [ambiguous]
Systematic name: nucleoside triphosphate phosphohydrolase (nucleoside monophosphoate-forming)
Comments: Apyrases are active against both di- and triphosphate nucleotides (NDPs and NTPs) and hydrolyse NTPs to nucleotide monophosphates (NMPs) in two distinct successive phosphate-releasing steps, with NDPs as intermediates. They differ from ATPases, which specifically hydrolyse ATP, by hydrolysing both ATP and ADP. The eukaryotic enzymes requires Ca2+, but Mg2+ can substitute. Most of the ecto-ATPases that occur on the cell surface and hydrolyse extracellular nucleotides belong to this enzyme family.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9000-95-7
References:
1.  Krishnan, P.S. Apyrase, pyrophosphatase and metaphosphatase of Penicillium chrysogenum. Arch. Biochem. Biophys. 37 (1952) 224–234. [PMID: 14953432]
2.  Liébecq, C., Lallemand, A. and Degueldre-Guillaume, M.-J. [Partial purification and properties of potato apyrase.] Bull. Soc. Chim. Biol. 45 (1963) 573–594. [PMID: 13930517] (in French)
3.  Chen, Y.R., Datta, N. and Roux, S.J. Purification and partial characterization of a calmodulin-stimulated nucleoside triphosphatase from pea nuclei. J. Biol. Chem. 262 (1987) 10689–10694. [PMID: 3038893]
4.  Christoforidis, S., Papamarcaki, T., Galaris, D., Kellner, R. and Tsolas, O. Purification and properties of human placental ATP diphosphohydrolase. Eur. J. Biochem. 234 (1995) 66–74. [PMID: 8529670]
5.  Wang, T.F. and Guidotti, G. CD39 is an ecto-(Ca2+,Mg2+)-apyrase. J. Biol. Chem. 271 (1996) 9898–9901. [PMID: 8626624]
6.  Gao, X.D., Kaigorodov, V. and Jigami, Y. YND1, a homologue of GDA1, encodes membrane-bound apyrase required for Golgi N- and O-glycosylation in Saccharomyces cerevisiae. J. Biol. Chem. 274 (1999) 21450–21456. [PMID: 10409709]
7.  Xu, W., Jones, C.R., Dunn, C.A. and Bessman, M.J. Gene ytkD of Bacillus subtilis encodes an atypical nucleoside triphosphatase member of the Nudix hydrolase superfamily. J. Bacteriol. 186 (2004) 8380–8384. [PMID: 15576788]
[EC 3.6.1.5 created 1961, modified 1976, modified 2000, modified 2013]
 
 
*EC 3.6.1.62
Accepted name: 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] hydrolase
Reaction: a 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] + H2O = N7-methylguanosine 5′-diphosphate + a 5′-phospho-[mRNA]
Glossary: N7-methylguanosine 5′-diphosphate = m7GDP
Other name(s): Dcp2; NUDT16; D10 protein; D9 protein; D10 decapping enzyme; decapping enzyme; m7GpppN-mRNA hydrolase; m7GpppN-mRNA m7GDP phosphohydrolase
Systematic name: 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] N7-methylguanosine-5′-diphosphate phosphohydrolase
Comments: Decapping of mRNA is a critical step in eukaryotic mRNA turnover. The enzyme is unable to cleave a free cap structure (m7GpppG) [3]. The enzyme from Vaccinia virus is synergistically activated in the presence of Mg2+ and Mn2+ [5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Xu, J., Yang, J.Y., Niu, Q.W. and Chua, N.H. Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell 18 (2006) 3386–3398. [PMID: 17158604]
2.  Lu, G., Zhang, J., Li, Y., Li, Z., Zhang, N., Xu, X., Wang, T., Guan, Z., Gao, G.F. and Yan, J. hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA. Protein Cell 2 (2011) 64–73. [PMID: 21337011]
3.  van Dijk, E., Cougot, N., Meyer, S., Babajko, S., Wahle, E. and Seraphin, B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 21 (2002) 6915–6924. [PMID: 12486012]
4.  Parrish, S., Resch, W. and Moss, B. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression. Proc. Natl. Acad. Sci. USA 104 (2007) 2139–2144. [PMID: 17283339]
5.  Souliere, M.F., Perreault, J.P. and Bisaillon, M. Characterization of the vaccinia virus D10 decapping enzyme provides evidence for a two-metal-ion mechanism. Biochem. J. 420 (2009) 27–35. [PMID: 19210265]
6.  Parrish, S. and Moss, B. Characterization of a second vaccinia virus mRNA-decapping enzyme conserved in poxviruses. J. Virol. 81 (2007) 12973–12978. [PMID: 17881455]
7.  Song, M.G., Li, Y. and Kiledjian, M. Multiple mRNA decapping enzymes in mammalian cells. Mol. Cell 40 (2010) 423–432. [PMID: 21070968]
[EC 3.6.1.62 created 2012, modified 2013]
 
 
*EC 3.6.3.4
Accepted name: Cu2+-exporting ATPase
Reaction: ATP + H2O + Cu2+[side 1] = ADP + phosphate + Cu2+[side 2]
Other name(s): CopB
Systematic name: ATP phosphohydrolase (Cu2+-exporting)
Comments: A P-type ATPase that undergoes covalent phosphorylation during the transport cycle. The enzyme from the termophilic bacterium Archaeoglobus fulgidus is involved in copper extrusion from the cell [1,2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Mana-Capelli, S., Mandal, A.K. and Arguello, J.M. Archaeoglobus fulgidus CopB is a thermophilic Cu2+-ATPase: functional role of its histidine-rich-N-terminal metal binding domain. J. Biol. Chem. 278 (2003) 40534–40541. [PMID: 12876283]
2.  Jayakanthan, S., Roberts, S.A., Weichsel, A., Arguello, J.M. and McEvoy, M.M. Conformations of the apo-, substrate-bound and phosphate-bound ATP-binding domain of the Cu(II) ATPase CopB illustrate coupling of domain movement to the catalytic cycle. Biosci Rep 32 (2012) 443–453. [PMID: 22663904]
[EC 3.6.3.4 created 2000, modified 2013]
 
 
EC 3.6.3.54
Accepted name: Cu+-exporting ATPase
Reaction: ATP + H2O + Cu+[side 1] = ADP + phosphate + Cu+[side 2]
Other name(s): CopA; ATP7A; ATP7B
Systematic name: ATP phosphohydrolase (Cu+-exporting)
Comments: A P-type ATPase that undergoes covalent phosphorylation during the transport cycle. This enzyme transports Cu+ or Ag+, and cannot transport the divalent ions, contrary to EC 3.6.3.4, Cu2+-exporting ATPase, which mainly transports the divalent copper ion.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Fan, B. and Rosen, B.P. Biochemical characterization of CopA, the Escherichia coli Cu(I)-translocating P-type ATPase. J. Biol. Chem. 277 (2002) 46987–46992. [PMID: 12351646]
2.  Banci, L., Bertini, I., Ciofi-Baffoni, S., D'Onofrio, M., Gonnelli, L., Marhuenda-Egea, F.C. and Ruiz-Duenas, F.J. Solution structure of the N-terminal domain of a potential copper-translocating P-type ATPase from Bacillus subtilis in the apo and Cu(I) loaded states. J. Mol. Biol. 317 (2002) 415–429. [PMID: 11922674]
3.  Mandal, A.K. and Arguello, J.M. Functional roles of metal binding domains of the Archaeoglobus fulgidus Cu+-ATPase CopA. Biochemistry 42 (2003) 11040–11047. [PMID: 12974640]
4.  Gonzalez-Guerrero, M. and Arguello, J.M. Mechanism of Cu+-transporting ATPases: soluble Cu+ chaperones directly transfer Cu+ to transmembrane transport sites. Proc. Natl. Acad. Sci. USA 105 (2008) 5992–5997. [PMID: 18417453]
5.  Lewis, D., Pilankatta, R., Inesi, G., Bartolommei, G., Moncelli, M.R. and Tadini-Buoninsegni, F. Distinctive features of catalytic and transport mechanisms in mammalian sarco-endoplasmic reticulum Ca2+ ATPase (SERCA) and Cu+ (ATP7A/B) ATPases. J. Biol. Chem. 287 (2012) 32717–32727. [PMID: 22854969]
6.  Tadini-Buoninsegni, F., Bartolommei, G., Moncelli, M.R., Pilankatta, R., Lewis, D. and Inesi, G. ATP dependent charge movement in ATP7B Cu+-ATPase is demonstrated by pre-steady state electrical measurements. FEBS Lett. 584 (2010) 4619–4622. [PMID: 20965182]
7.  Mattle, D., Sitsel, O., Autzen, H.E., Meloni, G., Gourdon, P. and Nissen, P. On allosteric modulation of P-type Cu+-ATPases. J. Mol. Biol. 425 (2013) 2299–2308. [PMID: 23500486]
[EC 3.6.3.54 created 2013]
 
 
EC 4.1.2.52
Accepted name: 4-hydroxy-2-oxoheptanedioate aldolase
Reaction: 4-hydroxy-2-oxoheptanedioate = pyruvate + succinate semialdehyde
Other name(s): 2,4-dihydroxyhept-2-enedioate aldolase; HHED aldolase; 4-hydroxy-2-ketoheptanedioate aldolase; HKHD aldolase; HpcH; HpaI; 4-hydroxy-2-oxoheptanedioate succinate semialdehyde lyase (pyruvate-forming)
Systematic name: 4-hydroxy-2-oxoheptanedioate succinate-semialdehyde-lyase (pyruvate-forming)
Comments: Requires Co2+ or Mn2+ for activity. The enzyme is also able to catalyse the aldol cleavage of 4-hydroxy-2-oxopentanoate and 4-hydroxy-2-oxohexanoate, and can use 2-oxobutanoate as carbonyl donor, with lower efficiency. In the reverse direction, is able to condense a range of aldehyde acceptors with pyruvate. The enzyme from the bacterium Escherichia coli produces a racemic mixture of (4R)- and (4S)-hydroxy-2-oxoheptanedioate [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Wang, W. and Seah, S.Y. Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI. Biochemistry 44 (2005) 9447–9455. [PMID: 15996099]
2.  Rea, D., Fulop, V., Bugg, T.D. and Roper, D.I. Structure and mechanism of HpcH: a metal ion dependent class II aldolase from the homoprotocatechuate degradation pathway of Escherichia coli. J. Mol. Biol. 373 (2007) 866–876. [PMID: 17881002]
3.  Wang, W. and Seah, S.Y. The role of a conserved histidine residue in a pyruvate-specific class II aldolase. FEBS Lett. 582 (2008) 3385–3388. [PMID: 18775708]
4.  Wang, W., Baker, P. and Seah, S.Y.K. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 49 (2010) 3774–3782. [PMID: 20364820]
[EC 4.1.2.52 created 2013]
 
 
EC 4.1.2.53
Accepted name: 2-keto-3-deoxy-L-rhamnonate aldolase
Reaction: 2-dehydro-3-deoxy-L-rhamnonate = pyruvate + (S)-lactaldehyde
For diagram of L-Rhamnose metabolism, click here
Glossary: 2-dehydro-3-deoxy-L-rhamnonate = 3,6-dideoxy-L-erythro-hex-2-ulosonate
Other name(s): KDR aldolase; 2-dehydro-3-deoxyrhamnonate aldolase; 2-keto-3-deoxy acid sugar aldolase; YfaU; 2-dehydro-3-deoxy-L-rhamnonate (S)-lactaldehyde lyase (pyruvate-forming); 2-dehydro-3-deoxy-L-rhamnonate (R)-lactaldehyde lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-L-rhamnonate (S)-lactaldehyde-lyase (pyruvate-forming)
Comments: Requires Mg2+ for activity. The enzyme can also use 2-oxo-3-deoxy-L-mannonate, 2-oxo-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) as substrates [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Rakus, J.F., Fedorov, A.A., Fedorov, E.V., Glasner, M.E., Hubbard, B.K., Delli, J.D., Babbitt, P.C., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry 47 (2008) 9944–9954. [PMID: 18754693]
2.  Rea, D., Hovington, R., Rakus, J.F., Gerlt, J.A., Fulop, V., Bugg, T.D. and Roper, D.I. Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12. Biochemistry 47 (2008) 9955–9965. [PMID: 18754683]
[EC 4.1.2.53 created 2013]
 
 
EC 4.1.3.43
Accepted name: 4-hydroxy-2-oxohexanoate aldolase
Reaction: (S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate
Other name(s): BphI
Systematic name: (S)-4-hydroxy-2-oxohexanoate pyruvate-lyase (propanal-forming)
Comments: Requires Mn2+ for maximal activity [1,2]. The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.39, 4-hydroxy-2-oxovalerate aldolase [1,2,6]. The enzyme forms a bifunctional complex with EC 1.2.1.87, propanal dehydrogenase (CoA-propanoylating), with a tight channel connecting the two subunits [3,4,6].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Baker, P., Pan, D., Carere, J., Rossi, A., Wang, W. and Seah, S.Y.K. Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway. Biochemistry 48 (2009) 6551–6558. [PMID: 19476337]
2.  Wang, W., Baker, P. and Seah, S.Y.K. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 49 (2010) 3774–3782. [PMID: 20364820]
3.  Baker, P., Carere, J. and Seah, S.Y.K. Probing the molecular basis of substrate specificity, stereospecificity, and catalysis in the class II pyruvate aldolase, BphI. Biochemistry 50 (2011) 3559–3569. [PMID: 21425833]
4.  Carere, J., Baker, P. and Seah, S.Y.K. Investigating the molecular determinants for substrate channeling in BphI-BphJ, an aldolase-dehydrogenase complex from the polychlorinated biphenyls degradation pathway. Biochemistry 50 (2011) 8407–8416. [PMID: 21838275]
5.  Baker, P. and Seah, S.Y.K. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J. Am. Chem. Soc. 134 (2012) 507–513. [PMID: 22081904]
6.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [PMID: 22316175]
[EC 4.1.3.43 created 2013]
 
 
*EC 4.1.99.5
Accepted name: aldehyde oxygenase (deformylating)
Reaction: a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
Glossary: a long-chain aldehyde = an aldehyde derived from a fatty acid with an aliphatic chain of 13-22 carbons.
Other name(s): decarbonylase; aldehyde decarbonylase; octadecanal decarbonylase; octadecanal alkane-lyase
Systematic name: a long-chain aldehyde alkane-lyase
Comments: Contains a diiron center. Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 is only active in vitro in the presence of ferredoxin, ferredoxin reductase and NADPH, and produces mostly C15 and C17 alkanes [2,3]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents [1]. The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 94185-90-7
References:
1.  Cheesbrough, T.M. and, K olattukudy, P.E. Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. Proc. Natl. Acad. Sci. USA 81 (1984) 6613–6617. [PMID: 6593720]
2.  Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. Microbial biosynthesis of alkanes. Science 329 (2010) 559–562. [PMID: 20671186]
3.  Warui, D.M., Li, N., Nørgaard, H., Krebs, C., Bollinger, J.M. and Booker, S.J. Detection of formate, rather than carbon monoxide, as the stoichiometric coproduct in conversion of fatty aldehydes to alkanes by a cyanobacterial aldehyde decarbonylase. J. Am. Chem. Soc. 133 (2011) 3316–3319. [PMID: 21341652]
4.  Li, N., Chang, W.C., Warui, D.M., Booker, S.J., Krebs, C. and Bollinger, J.M., Jr. Evidence for only oxygenative cleavage of aldehydes to alk(a/e)nes and formate by cyanobacterial aldehyde decarbonylases. Biochemistry 51 (2012) 7908–7916. [PMID: 22947199]
[EC 4.1.99.5 created 1989, modified 2011, modified 2013]
 
 
EC 4.1.99.20
Accepted name: 3-amino-4-hydroxybenzoate synthase
Reaction: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate = 3-amino-4-hydroxybenzoate + phosphate + 2 H2O
For diagram of grixazone biosynthesis, click here
Other name(s): 3,4-AHBA synthase; griH (gene name)
Systematic name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate hydro-lyase (cyclizing, 3-amino-4-hydroxybenzoate-forming)
Comments: Requires Mn2+ for maximum activity. The reaction is suggested to take place in several steps. Schiff base formation, double bond migration and dephosphorylation followed by ring opening and closing to form a pyrrolidine ring, and finally dehydration to form the product 3-amino-4-hydroxybenzoate. In the bacterium Streptomyces griseus the enzyme is involved in biosynthesis of grixazone, a yellow pigment that contains a phenoxazinone chromophore.
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]
[EC 4.1.99.20 created 2013, modified 2016]
 
 
*EC 4.2.1.105
Accepted name: 2-hydroxyisoflavanone dehydratase
Reaction: (1) 2,4′,7-trihydroxyisoflavanone = daidzein + H2O
(2) 2,4′,5,7-tetrahydroxyisoflavanone = genistein + H2O
For diagram of biochanin A biosynthesis, click here and for diagram of daidzein biosynthesis, click here
Glossary: daidzein = 4′,7-dihydroxyisoflavone
genistein = 4′,5,7-dihydroxyisoflavone
Other name(s): 2,7,4′-trihydroxyisoflavanone hydro-lyase; 2,7,4′-trihydroxyisoflavanone hydro-lyase (daidzein-forming)
Systematic name: 2,4′,7-trihydroxyisoflavanone hydro-lyase (daidzein-forming)
Comments: Catalyses the final step in the formation of the isoflavonoid skeleton. The reaction also occurs spontaneously.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 166800-10-8
References:
1.  Hakamatsuka, T., Mori, K., Ishida, S., Ebizuka, Y and Sankawa, U. Purification of 2-hydroxyisoflavanone dehydratase from the cell cultures of Pueraria lobata. Phytochemistry 49 (1998) 497–505.
[EC 4.2.1.105 created 2004, modified 2013]
 
 
EC 5.1.1.19
Accepted name: O-ureido-serine racemase
Reaction: O-ureido-L-serine = O-ureido-D-serine
Glossary: O-ureido-L-serine = (2S)-2-amino-3-[(carbamoylamino)oxy]propanoate
O-ureido-D-serine = (2R)-2-amino-3-[(carbamoylamino)oxy]propanoate
Other name(s): dcsC (gene name)
Systematic name: (2S)-2-amino-3-[(carbamoylamino)oxy]propanoate 2-epimerase
Comments: The enzyme employs a two-base mechanism, with a thiolate-thiol pair in the active site. It participates in the biosynthetic pathway of D-cycloserine, an antibiotic substance produced by several Streptomyces species.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kumagai, T., Koyama, Y., Oda, K., Noda, M., Matoba, Y. and Sugiyama, M. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob. Agents Chemother. 54 (2010) 1132–1139. [PMID: 20086163]
2.  Dietrich, D., van Belkum, M.J. and Vederas, J.C. Characterization of DcsC, a PLP-independent racemase involved in the biosynthesis of D-cycloserine. Org. Biomol. Chem. 10 (2012) 2248–2254. [PMID: 22307920]
[EC 5.1.1.19 created 2013]
 
 
EC 5.4.2.1
Transferred entry: phosphoglycerate mutase. Now recognized as two separate enzymes EC 5.4.2.11, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) and EC 5.4.2.12, phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
[EC 5.4.2.1 created 1961 (EC 2.7.5.3 created 1961, incorporated 1984), deleted 2013]
 
 
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 5.4.2.12
Accepted name: phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): cofactor independent phosphoglycerate mutase; 2,3-diphosphoglycerate-independent phosphoglycerate mutase; phosphoglycerate phosphomutase (ambiguous); phosphoglyceromutase (ambiguous); monophosphoglycerate mutase (ambiguous); monophosphoglyceromutase (ambiguous); GriP mutase (ambiguous); PGA mutase (ambiguous); iPGM; iPGAM; PGAM-i
Systematic name: D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-independent)
Comments: The enzymes from higher plants, algae, fungi, nematodes, sponges, coelenterates, myriapods, arachnids, echinoderms, archaea and some bacteria (particularly Gram-positive) have maximum activity in the absence of 2,3-bisphospho-D-glycerate. cf. EC 5.4.2.11 phosphoglycerate mutase (2,3-diphosphoglycerate-dependent). The enzyme contains two Mn2+ (or in some species two Co2+ ions). The reaction involves a phosphotransferase reaction to serine followed by transfer back to the glycerate at the other position. Both metal ions are involved in the reaction.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Jedrzejas, M.J., Chander, M., Setlow, P. and Krishnasamy, G. Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate. J. Biol. Chem. 275 (2000) 23146–23153. [PMID: 10764795]
2.  Rigden, D.J., Lamani, E., Mello, L.V., Littlejohn, J.E. and Jedrzejas, M.J. Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J. Mol. Biol. 328 (2003) 909–920. [PMID: 12729763]
3.  Zhang, Y., Foster, J.M., Kumar, S., Fougere, M. and Carlow, C.K. Cofactor-independent phosphoglycerate mutase has an essential role in Caenorhabditis elegans and is conserved in parasitic nematodes. J. Biol. Chem. 279 (2004) 37185–37190. [PMID: 15234973]
4.  Nukui, M., Mello, L.V., Littlejohn, J.E., Setlow, B., Setlow, P., Kim, K., Leighton, T. and Jedrzejas, M.J. Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species. Biophys J 92 (2007) 977–988. [PMID: 17085493]
5.  Nowicki, M.W., Kuaprasert, B., McNae, I.W., Morgan, H.P., Harding, M.M., Michels, P.A., Fothergill-Gilmore, L.A. and Walkinshaw, M.D. Crystal structures of Leishmania mexicana phosphoglycerate mutase suggest a one-metal mechanism and a new enzyme subclass. J. Mol. Biol. 394 (2009) 535–543. [PMID: 19781556]
6.  Mercaldi, G.F., Pereira, H.M., Cordeiro, A.T., Michels, P.A. and Thiemann, O.H. Structural role of the active-site metal in the conformation of Trypanosoma brucei phosphoglycerate mutase. FEBS J. 279 (2012) 2012–2021. [PMID: 22458781]
[EC 5.4.2.12 created 2013]
 
 
EC 6.3.1.15
Accepted name: 8-demethylnovobiocic acid synthase
Reaction: ATP + 3-dimethylallyl-4-hydroxybenzoate + 3-amino-4,7-dihydroxycoumarin = AMP + diphosphate + 8-demethylnovobiocic acid
For diagram of novobiocin biosynthesis, click here
Glossary: 8-demethylnovobiocic acid = N-(2,7-dihydroxy-4-oxochromen-3-yl)-4-hydroxy-3-(3-methylbut-2-enyl)benzamide
Other name(s): novL (gene name); novobiocin ligase; novobiocic acid synthetase (misleading); 8-desmethyl-novobiocic acid synthetase; 8-demethylnovobiocic acid synthetase
Systematic name: 3-dimethylallyl-4-hydroxybenzoate:3-amino-4,7-dihydroxycoumarin ligase (AMP-forming)
Comments: The enzyme is involved in the biosynthesis of the aminocoumarin antibiotic novobiocin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Steffensky, M., Li, S.M. and Heide, L. Cloning, overexpression, and purification of novobiocic acid synthetase from Streptomyces spheroides NCIMB 11891. J. Biol. Chem. 275 (2000) 21754–21760. [PMID: 10801869]
2.  Pi, N., Meyers, C.L., Pacholec, M., Walsh, C.T. and Leary, J.A. Mass spectrometric characterization of a three-enzyme tandem reaction for assembly and modification of the novobiocin skeleton. Proc. Natl. Acad. Sci. USA 101 (2004) 10036–10041. [PMID: 15218104]
3.  Pacholec, M., Tao, J. and Walsh, C.T. CouO and NovO: C-methyltransferases for tailoring the aminocoumarin scaffold in coumermycin and novobiocin antibiotic biosynthesis. Biochemistry 44 (2005) 14969–14976. [PMID: 16274243]
[EC 6.3.1.15 created 2013]
 
 
EC 6.3.3.5
Accepted name: O-ureido-D-serine cyclo-ligase
Reaction: O-ureido-D-serine + ATP + H2O = D-cycloserine + CO2 + NH3 + ADP + phosphate
Glossary: O-ureido-D-serine = (2R)-2-amino-3-[(carbamoylamino)oxy]propanoate
Other name(s): dcsG (gene name)
Systematic name: O-ureido-D-serine cyclo-ligase (D-cycloserine-forming)
Comments: The enzyme participates in the biosynthetic pathway of D-cycloserine, an antibiotic substance produced by several Streptomyces species.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kumagai, T., Koyama, Y., Oda, K., Noda, M., Matoba, Y. and Sugiyama, M. Molecular cloning and heterologous expression of a biosynthetic gene cluster for the antitubercular agent D-cycloserine produced by Streptomyces lavendulae. Antimicrob. Agents Chemother. 54 (2010) 1132–1139. [PMID: 20086163]
2.  Uda, N., Matoba, Y., Kumagai, T., Oda, K., Noda, M. and Sugiyama, M. Establishment of an in vitro D-cycloserine-synthesizing system by using O-ureido-L-serine synthase and D-cycloserine synthetase found in the biosynthetic pathway. Antimicrob. Agents Chemother. 57 (2013) 2603–2612. [PMID: 23529730]
[EC 6.3.3.5 created 2013]
 
 
EC 6.3.4.23
Accepted name: formate—phosphoribosylaminoimidazolecarboxamide ligase
Reaction: ATP + formate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide = ADP + phosphate + 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Other name(s): 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase; 5-formaminoimidazole-4-carboxamide-1-β-D-ribofuranosyl 5′-monophosphate synthetase; purP (gene name)
Systematic name: formate:5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide ligase (ADP-forming)
Comments: This archaeal enzyme, characterized from the methanogen Methanocaldococcus jannaschii, catalyses a step in the synthesis of purine nucleotides. It differs from the orthologous bacterial/eukaryotic enzymes, which utilize 10-formyltetrahydrofolate rather than formate and ATP. cf. EC 2.1.2.3, phosphoribosylaminoimidazolecarboxamide formyltransferase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9032-03-5
References:
1.  Ownby, K., Xu, H. and White, R.H. A Methanocaldococcus jannaschii archaeal signature gene encodes for a 5-formaminoimidazole-4-carboxamide-1-β-D-ribofuranosyl 5′-monophosphate synthetase. A new enzyme in purine biosynthesis. J. Biol. Chem. 280 (2005) 10881–10887. [PMID: 15623504]
2.  Zhang, Y., White, R.H. and Ealick, S.E. Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Biochemistry 47 (2008) 205–217. [PMID: 18069798]
[EC 6.3.4.23 created 2013]
 
 


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