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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.246 transferred
*EC 1.1.1.310 (S)-sulfolactate dehydrogenase
EC 1.1.1.347 geraniol dehydrogenase (NAD+)
EC 1.1.1.348 (3R)-2′-hydroxyisoflavanone reductase
EC 1.1.1.349 norsolorinic acid ketoreductase
EC 1.1.1.350 ureidoglycolate dehydrogenase (NAD+)
EC 1.1.1.351 phosphogluconate dehydrogenase [NAD(P)+-dependent, decarboxylating]
EC 1.1.1.352 5′-hydroxyaverantin dehydrogenase
EC 1.1.1.353 versiconal hemiacetal acetate reductase
EC 1.2.99.8 glyceraldehyde dehydrogenase (FAD-containing)
EC 1.3.1.100 chanoclavine-I aldehyde reductase
EC 1.3.1.101 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H]
EC 1.3.3.13 albonoursin synthase
*EC 1.3.7.7 ferredoxin:protochlorophyllide reductase (ATP-dependent)
EC 1.3.7.10 transferred
EC 1.3.99.33 urocanate reductase
EC 1.3.99.34 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor)
EC 1.5.1.47 dihydromethanopterin reductase [NAD(P)+]
EC 1.6.1.2 NAD(P)+ transhydrogenase (Re/Si-specific)
*EC 1.7.1.4 nitrite reductase [NAD(P)H]
EC 1.7.1.15 nitrite reductase (NADH)
EC 1.13.11.74 2-aminophenol 1,6-dioxygenase
EC 1.14.11.37 kanamycin B dioxygenase
EC 1.14.13.86 deleted
*EC 1.14.13.136 2-hydroxyisoflavanone synthase
EC 1.14.13.172 salicylate 5-hydroxylase
EC 1.14.13.173 11-oxo-β-amyrin 30-oxidase
EC 1.14.13.174 averantin hydroxylase
EC 1.14.13.175 aflatoxin B synthase
EC 1.14.13.176 tryprostatin B 6-hydroxylase
EC 1.14.15.13 pulcherriminic acid synthase
EC 1.14.19.8 pentalenolactone synthase
EC 1.14.21.9 mycocyclosin synthase
EC 1.18.1.7 ferredoxin—NAD(P)+ reductase (naphthalene dioxygenase ferredoxin-specific)
EC 1.21.3.9 dichlorochromopyrrolate synthase
*EC 2.1.1.98 diphthine synthase
*EC 2.1.1.110 sterigmatocystin 8-O-methyltransferase
*EC 2.1.1.197 malonyl-[acyl-carrier protein] O-methyltransferase
EC 2.1.1.269 dimethylsulfoniopropionate demethylase
EC 2.1.1.270 (+)-6a-hydroxymaackiain 3-O-methyltransferase
EC 2.1.1.271 cobalt-precorrin-4 methyltransferase
EC 2.1.1.272 cobalt-factor III methyltransferase
*EC 2.3.1.174 3-oxoadipyl-CoA thiolase
*EC 2.3.1.203 UDP-N-acetylbacillosamine N-acetyltransferase
EC 2.3.1.223 3-oxo-5,6-didehydrosuberyl-CoA thiolase
EC 2.3.2.20 cyclo(L-leucyl-L-phenylalanyl) synthase
EC 2.3.2.21 cyclo(L-tyrosyl-L-tyrosyl) synthase
EC 2.3.2.22 cyclo(L-leucyl-L-leucyl) synthase
*EC 2.4.2.2 pyrimidine-nucleoside phosphorylase
EC 2.4.2.11 transferred
EC 2.4.2.23 transferred
*EC 2.4.2.36 NAD+—diphthamide ADP-ribosyltransferase
EC 2.4.2.52 triphosphoribosyl-dephospho-CoA synthase
EC 2.4.2.53 undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
EC 2.4.2.54 β-ribofuranosylphenol 5′-phosphate synthase
EC 2.5.1.104 N1-aminopropylagmatine synthase
EC 2.5.1.105 7,8-dihydropterin-6-yl-methyl-4-(β-D-ribofuranosyl)aminobenzene 5′-phosphate synthase
EC 2.5.1.106 tryprostatin B synthase
EC 2.5.1.107 verruculogen prenyltransferase
*EC 2.6.1.34 UDP-N-acetylbacillosamine transaminase
EC 2.6.1.91 deleted
EC 2.7.1.178 2-dehydro-3-deoxyglucono/galactono-kinase
EC 2.7.1.179 kanosamine kinase
EC 2.7.7.54 deleted
EC 2.7.7.55 deleted
EC 2.7.7.85 diadenylate cyclase
EC 2.7.8.25 transferred
EC 2.7.8.30 transferred
EC 2.8.3.18 succinyl-CoA:acetate CoA-transferase
EC 3.1.1.94 versiconal hemiacetal acetate esterase
EC 3.1.3.89 5′-deoxynucleotidase
EC 3.1.4.56 7,8-dihydroneopterin 2′,3′-cyclic phosphate phosphodiesterase
EC 3.1.6.19 (R)-specific secondary-alkylsulfatase
*EC 3.2.1.10 oligo-1,6-glucosidase
*EC 3.2.1.55 non-reducing end α-L-arabinofuranosidase
EC 3.2.1.185 non-reducing end β-L-arabinofuranosidase
EC 3.3.2.12 oxepin-CoA hydrolase
EC 3.5.3.24 N1-aminopropylagmatine ureohydrolase
*EC 3.5.4.5 cytidine deaminase
EC 3.5.4.14 transferred
EC 3.5.4.37 double-stranded RNA adenine deaminase
EC 3.5.4.38 single-stranded DNA cytosine deaminase
EC 3.5.4.39 GTP cyclohydrolase IV
*EC 3.6.1.59 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] diphosphatase
EC 3.6.1.65 (d)CTP diphosphatase
EC 3.7.1.15 transferred
EC 3.7.1.16 transferred
EC 4.1.2.51 2-dehydro-3-deoxy-D-gluconate aldolase
EC 4.2.1.138 (+)-caryolan-1-ol synthase
EC 4.2.1.139 medicarpin synthase
EC 4.2.1.140 gluconate/galactonate dehydratase
EC 4.2.1.141 2-dehydro-3-deoxy-D-arabinonate dehydratase
EC 4.2.1.142 5′-oxoaverantin cyclase
EC 4.2.1.143 versicolorin B synthase
EC 4.2.1.144 3-amino-5-hydroxybenzoate synthase
EC 4.2.3.143 kunzeaol synthase
EC 4.2.99.22 tuliposide A-converting enzyme
EC 4.3.1.26 transferred
EC 6.3.2.40 cyclopeptine synthase
EC 6.3.4.1 transferred
*EC 6.3.4.2 CTP synthase (glutamine hydrolysing)
EC 6.3.4.21 nicotinate phosphoribosyltransferase
EC 6.3.4.22 tRNAIle2-agmatinylcytidine synthase
*EC 6.3.5.2 GMP synthase (glutamine-hydrolysing)


EC 1.1.1.246
Transferred entry: pterocarpin synthase. This activity is now known to be catalysed by two enzymes, vestitone reductase (EC 1.1.1.348) and medicarpin synthase (EC 4.2.1.139).
[EC 1.1.1.246 created 1992, deleted 2013]
 
 
*EC 1.1.1.310
Accepted name: (S)-sulfolactate dehydrogenase
Reaction: (2S)-3-sulfolactate + NAD+ = 3-sulfopyruvate + NADH + H+
Other name(s): (2S)-3-sulfolactate dehydrogenase; SlcC
Systematic name: (2S)-sulfolactate:NAD+ oxidoreductase
Comments: This enzyme, isolated from the bacterium Chromohalobacter salexigens DSM 3043, acts only on the (S)-enantiomer of 3-sulfolactate. Combined with EC 1.1.1.338, (2R)-3-sulfolactate dehydrogenase (NADP+), it provides a racemase system that converts (2S)-3-sulfolactate to (2R)-3-sulfolactate, which is degraded further by EC 4.4.1.24, (2R)-sulfolactate sulfo-lyase. The enzyme is specific for NAD+.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Denger, K. and Cook, A.M. Racemase activity effected by two dehydrogenases in sulfolactate degradation by Chromohalobacter salexigens: purification of (S)-sulfolactate dehydrogenase. Microbiology 156 (2010) 967–974. [PMID: 20007648]
[EC 1.1.1.310 created 2011, modified 2013]
 
 
EC 1.1.1.347
Accepted name: geraniol dehydrogenase (NAD+)
Reaction: geraniol + NAD+ = geranial + NADH + H+
For diagram of acyclic monoterpenoid biosynthesis, click here
Other name(s): GeDH; geoA (gene name)
Systematic name: geraniol:NAD+ oxidoreductase
Comments: The enzyme from the bacterium Castellaniella defragrans is most active in vitro with perillyl alcohol [2]. The enzyme from the prune mite Carpoglyphus lactis also acts (more slowly) on farnesol but not on nerol [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD
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]
2.  Lüddeke, F., Wülfing, A., Timke, M., Germer, F., Weber, J., Dikfidan, A., Rahnfeld, T., Linder, D., Meyerdierks, A. and Harder, J. Geraniol and geranial dehydrogenases induced in anaerobic monoterpene degradation by Castellaniella defragrans. Appl. Environ. Microbiol. 78 (2012) 2128–2136. [PMID: 22286981]
[EC 1.1.1.347 created 2013]
 
 
*EC 1.1.1.348 – public review until 10 November 2017 [Last modified: 2013-06-11 05:19:58]
Accepted name: (3R)-2′-hydroxyisoflavanone reductase
Reaction: a (4R)-4,2′-dihydroxyisoflavan + NADP+ = a (3R)-2′-hydroxyisoflavanone + NADPH + H+
For diagram of medicarpin and formononetin derivatives biosynthesis, click here
Glossary: (3R)-vestitone = (3R)-2′,7-dihydroxy-4′-methoxyisoflavanone
Other name(s): vestitone reductase; pterocarpin synthase (incorrect); pterocarpan synthase (incorrect)
Systematic name: (3R)-2′-hydroxyisoflavanone:NADP+ 4-oxidoreductase
Comments: This plant enzyme participates in the biosynthesis of the pterocarpan phytoalexins medicarpin, maackiain, and several forms of glyceollin. The ezyme has a strict stereo specificity for the 3R-isoflavanones.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, MetaCyc, CAS registry number: 118477-70-6
References:
1.  Bless, W. and Barz, W. Isolation of pterocarpan synthase, the terminal enzyme of pterocarpan phytoalexin biosynthesis in cell-suspension cultures of Cicer arietinum. FEBS Lett. 235 (1988) 47–50.
2.  Guo, L., Dixon, R.A. and Paiva, N.L. Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2′-dihydroxy-4′-methoxyisoflavanol dehydratase. J. Biol. Chem. 269 (1994) 22372–22378. [PMID: 8071365]
3.  Guo, L., Dixon, R.A. and Paiva, N.L. The ‘pterocarpan synthase’ of alfalfa: association and co-induction of vestitone reductase and 7,2′-dihydroxy-4′-methoxy-isoflavanol (DMI) dehydratase, the two final enzymes in medicarpin biosynthesis. FEBS Lett. 356 (1994) 221–225. [PMID: 7805842]
4.  Guo, L. and Paiva, N.L. Molecular cloning and expression of alfalfa (Medicago sativa L.) vestitone reductase, the penultimate enzyme in medicarpin biosynthesis. Arch. Biochem. Biophys. 320 (1995) 353–360. [PMID: 7625843]
5.  Shao, H., Dixon, R.A. and Wang, X. Crystal structure of vestitone reductase from alfalfa (Medicago sativa L.). J. Mol. Biol. 369 (2007) 265–276. [PMID: 17433362]
[EC 1.1.1.348 created 1992 as EC 1.1.1.246, part transferred 2013 to EC 1.1.1.348]
 
 
EC 1.1.1.349
Accepted name: norsolorinic acid ketoreductase
Reaction: (1′S)-averantin + NADP+ = norsolorinic acid + NADPH + H+
For diagram of aflatoxin biosynthesis (part 1), click here
Glossary: norsolorinic acid = 2-hexanoyl-1,3,6,8-tetrahydroxy-9,10-anthraquinone
(1′S)-averantin = 1,3,6,8-tetrahydroxy-[(1S)-2-hydroxyhexyl]-9,10-anthraquinone
Other name(s): aflD (gene name); nor-1 (gene name)
Systematic name: (1′S)-averantin:NADP+ oxidoreductase
Comments: Involved in the synthesis of aflatoxins in the fungus Aspergillus parasiticus.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yabe, K., Matsuyama, Y., Ando, Y., Nakajima, H. and Hamasaki, T. Stereochemistry during aflatoxin biosynthesis: conversion of norsolorinic acid to averufin. Appl. Environ. Microbiol. 59 (1993) 2486–2492. [PMID: 8368836]
2.  Zhou, R. and Linz, J.E. Enzymatic function of the nor-1 protein in aflatoxin biosynthesis in Aspergillus parasiticus. Appl. Environ. Microbiol. 65 (1999) 5639–5641. [PMID: 10584035]
[EC 1.1.1.349 created 2013]
 
 
EC 1.1.1.350
Accepted name: ureidoglycolate dehydrogenase (NAD+)
Reaction: (S)-ureidoglycolate + NAD+ = N-carbamoyl-2-oxoglycine + NADH + H+
For diagram of AMP catabolism, click here
Systematic name: (S)-ureidoglycolate:NAD+ oxidoreductase
Comments: Involved in catabolism of purines. The enzyme from the bacterium Escherichia coli is specific for NAD+ [2]. cf. EC 1.1.1.154, ureidoglycolate dehydrogenase [NAD(P)+].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Cusa, E., Obradors, N., Baldoma, L., Badia, J. and Aguilar, J. Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli. J. Bacteriol. 181 (1999) 7479–7484. [PMID: 10601204]
2.  Kim, M.I., Shin, I., Cho, S., Lee, J. and Rhee, S. Structural and functional insights into (S)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization. PLoS One 7:e52066 (2012). [PMID: 23284870]
[EC 1.1.1.350 created 2013]
 
 
EC 1.1.1.351
Accepted name: phosphogluconate dehydrogenase [NAD(P)+-dependent, decarboxylating]
Reaction: 6-phospho-D-gluconate + NAD(P)+ = D-ribulose 5-phosphate + CO2 + NAD(P)H + H+
For diagram of the early stages of the pentose-phosphate pathway, click here
Systematic name: 6-phospho-D-gluconate:NAD(P)+ 2-oxidoreductase (decarboxylating)
Comments: The enzyme participates in the oxidative branch of the pentose phosphate pathway, whose main purpose is to produce reducing power and pentose for biosynthetic reactions. Unlike EC 1.1.1.44, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating), it is not specific for NADP+ and can accept both cofactors with similar efficiency. cf. EC 1.1.1.343, phosphogluconate dehydrogenase [NAD+-dependent, decarboxylating].
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, CAS registry number: 9073-95-4
References:
1.  Ben-Bassat, A. and Goldberg, I. Purification and properties of glucose-6-phosphate dehydrogenase (NADP+/NAD+) and 6-phosphogluconate dehydrogenase (NADP+/NAD+) from methanol-grown Pseudomonas C. Biochim. Biophys. Acta 611 (1980) 1–10. [PMID: 7350909]
2.  Stournaras, C., Maurer, P. and Kurz, G. 6-phospho-D-gluconate dehydrogenase from Pseudomonas fluorescens. Properties and subunit structure. Eur. J. Biochem. 130 (1983) 391–396. [PMID: 6402366]
3.  Levy, H.R., Vought, V.E., Yin, X. and Adams, M.J. Identification of an arginine residue in the dual coenzyme-specific glucose-6-phosphate dehydrogenase from Leuconostoc mesenteroides that plays a key role in binding NADP+ but not NAD+. Arch. Biochem. Biophys. 326 (1996) 145–151. [PMID: 8579362]
[EC 1.1.1.351 created 2013]
 
 
EC 1.1.1.352
Accepted name: 5′-hydroxyaverantin dehydrogenase
Reaction: (1) (1′S,5′S)-hydroxyaverantin + NAD+ = 5′-oxoaverantin + NADH + H+
(2) (1′S,5′R)-hydroxyaverantin + NAD+ = 5′-oxoaverantin + NADH + H+
For diagram of aflatoxin biosynthesis (part 1), click here
Glossary: 5′-oxoaverantin = 1,3,6,8-tetrahydroxy-2-[(1S)-1-hydroxy-5-oxohexyl]anthracene-9,10-dione
Other name(s): HAVN dehydrogenase; adhA (gene name)
Systematic name: (1′S,5′S)-hydroxyaverantin:NAD+ oxidoreductase
Comments: Isolated from the aflatoxin-producing mold Aspergillus parasiticus [2]. Involved in aflatoxin biosynthesis. 5′-Oxoaverantin will spontaneously form averufin by intramolecular ketalisation. cf. EC 4.2.1.142, 5′-oxoaverantin cyclase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Chang, P.K., Yu, J., Ehrlich, K.C., Boue, S.M., Montalbano, B.G., Bhatnagar, D. and Cleveland, T.E. adhA in Aspergillus parasiticus is involved in conversion of 5′-hydroxyaverantin to averufin. Appl. Environ. Microbiol. 66 (2000) 4715–4719. [PMID: 11055914]
2.  Sakuno, E., Yabe, K. and Nakajima, H. Involvement of two cytosolic enzymes and a novel intermediate, 5′-oxoaverantin, in the pathway from 5′-hydroxyaverantin to averufin in aflatoxin biosynthesis. Appl. Environ. Microbiol. 69 (2003) 6418–6426. [PMID: 14602595]
[EC 1.1.1.352 created 2013]
 
 
EC 1.1.1.353
Accepted name: versiconal hemiacetal acetate reductase
Reaction: (1) versicolorone + NADP+ = 1′-hydroxyversicolorone + NADPH + H+
(2) versiconol acetate + NADP+ = versiconal hemiacetal acetate + NADPH + H+
(3) versiconol + NADP+ = versiconal + NADPH + H+
For diagram of aflatoxin biosynthesis (part 2), click here
Glossary: 1′-hydroxyversicolorone = (2S,3S)-2,4,6,8-tetrahydroxy-3-(3-oxobutyl)anthra[2,3-b]furan-5,10-dione
versiconal = (2S,3S)-2,4,6,8-tetrahydroxy-3-(2-hydroxyethyl)anthra[2,3-b]furan-5,10-dione
versiconal hemiacetal acetate = 2-[(2S,3S)-2,4,6,8-tetrahydroxy-5,10-dioxo-5,10-dihydroanthra[2,3-b]furan-3-yl]ethyl acetate
versiconol = 1,3,6,8-tetrahydroxy-3-[(2S)-1,4-dihydroxybutan-2-yl]anthracene-5,10-dione
versiconol acetate = (3S)-4-hydroxy-3-[1,3,6,8-tetrahydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl]butyl acetate
versicolorone = 1,3,6,8-tetrahydroxy-2-[(2S)-1-hydroxy-5-oxohexan-2-yl]anthracene-5,10-dione
Other name(s): VHA reductase; VHA reductase I; VHA reductase II; vrdA (gene name)
Systematic name: versiconol-acetate:NADP+ oxidoreductase
Comments: Isolated from the mold Aspergillus parasiticus. Involved in a metabolic grid that leads to aflatoxin biosynthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Matsushima, K., Ando, Y., Hamasaki, T. and Yabe, K. Purification and characterization of two versiconal hemiacetal acetate reductases involved in aflatoxin biosynthesis. Appl. Environ. Microbiol. 60 (1994) 2561–2567. [PMID: 16349333]
2.  Shima, Y., Shiina, M., Shinozawa, T., Ito, Y., Nakajima, H., Adachi, Y. and Yabe, K. Participation in aflatoxin biosynthesis by a reductase enzyme encoded by vrdA gene outside the aflatoxin gene cluster. Fungal Genet. Biol. 46 (2009) 221–231. [PMID: 19211038]
[EC 1.1.1.353 created 2013]
 
 
EC 1.2.99.8
Accepted name: glyceraldehyde dehydrogenase (FAD-containing)
Reaction: D-glyceraldehyde + H2O + acceptor = D-glycerate + reduced acceptor
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): glyceraldehyde oxidoreductase
Systematic name: D-glyceraldehyde:acceptor oxidoreductase (FAD-containing)
Comments: The enzyme from the archaeon Sulfolobus acidocaldarius catalyses the oxidation of D-glyceraldehyde in the nonphosphorylative Entner-Doudoroff pathway. With 2,6-dichlorophenolindophenol as artificial electron acceptor, the enzyme shows a broad substrate range, but is most active with D-glyceraldehyde. It is not known which acceptor is utilized in vivo. The iron-sulfur protein contains FAD and molybdopterin guanine dinucleotide.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kardinahl, S., Schmidt, C.L., Hansen, T., Anemuller, S., Petersen, A. and Schafer, G. The strict molybdate-dependence of glucose-degradation by the thermoacidophile Sulfolobus acidocaldarius reveals the first crenarchaeotic molybdenum containing enzyme—an aldehyde oxidoreductase. Eur. J. Biochem. 260 (1999) 540–548. [PMID: 10095793]
[EC 1.2.99.8 created 2013]
 
 
EC 1.3.1.100
Accepted name: chanoclavine-I aldehyde reductase
Reaction: dihydrochanoclavine-I aldehyde + NADP+ = chanoclavine-I aldehyde + NADPH + H+
For diagram of fumigaclavin alkaloid biosynthesis, click here
Glossary: chanoclavine-I aldehyde = (1E)-2-methyl-3-[(4R,5R)-4-(methylamino)-1,3,4,5-tetrahydrobenz[cd]indol-5-yl]prop-2-enal
Other name(s): FgaOx3; easA (gene name)
Systematic name: chanoclavine-I aldehyde:NAD+ oxidoreductase
Comments: Contains FMN. The enzyme participates in the biosynthesis of fumigaclavine C, an ergot alkaloid produced by some fungi of the Trichocomaceae family. The enzyme catalyses the reduction of chanoclavine-I aldehyde to dihydrochanoclavine-I aldehyde. This hydrolyses spontaneously to form 6,8-dimethyl-6,7-didehydroergoline, which is converted to festuclavine by EC 1.5.1.44, festuclavine dehydrogenase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Coyle, C.M., Cheng, J.Z., O'Connor, S.E. and Panaccione, D.G. An old yellow enzyme gene controls the branch point between Aspergillus fumigatus and Claviceps purpurea ergot alkaloid pathways. Appl. Environ. Microbiol. 76 (2010) 3898–3903. [PMID: 20435769]
2.  Cheng, J.Z., Coyle, C.M., Panaccione, D.G. and O'Connor, S.E. A role for Old Yellow Enzyme in ergot alkaloid biosynthesis. J. Am. Chem. Soc. 132 (2010) 1776–1777. [PMID: 20102147]
3.  Wallwey, C., Matuschek, M., Xie, X.L. and Li, S.M. Ergot alkaloid biosynthesis in Aspergillus fumigatus: Conversion of chanoclavine-I aldehyde to festuclavine by the festuclavine synthase FgaFS in the presence of the old yellow enzyme FgaOx3. Org. Biomol. Chem. 8 (2010) 3500–3508. [PMID: 20526482]
4.  Xie, X., Wallwey, C., Matuschek, M., Steinbach, K. and Li, S.M. Formyl migration product of chanoclavine-I aldehyde in the presence of the old yellow enzyme FgaOx3 from Aspergillus fumigatus: a NMR structure elucidation. Magn. Reson. Chem. 49 (2011) 678–681. [PMID: 21898587]
[EC 1.3.1.100 created 2013]
 
 
EC 1.3.1.101
Accepted name: 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H]
Reaction: 2,3-bis-(O-phytanyl)-sn-glycerol 1-phosphate + 8 NAD(P)+ = 2,3-bis-(O-geranylgeranyl)-sn-glycerol 1-phosphate + 8 NAD(P)H + 8 H+
For diagram of archaetidylserine biosynthesis, click here
Glossary: phytanol = (7R,11R,15R)-3,7,11,15-tetramethylhexadecan-1-ol
Other name(s): digeranylgeranylglycerophospholipid reductase; Ta0516m (gene name); DGGGPL reductase; 2,3-digeranylgeranylglycerophospholipid reductase
Systematic name: 2,3-bis-(O-phytany)l-sn-glycerol 1-phosphate:NAD(P)+ oxidoreductase
Comments: A flavoprotein (FAD). The enzyme from the archaeon Thermoplasma acidophilum is involved in the biosynthesis of membrane lipids. In vivo the reaction occurs in the reverse direction with the formation of 2,3-bis-O-phytanyl-sn-glycerol 1-phosphate. cf. EC 1.3.7.11, 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Nishimura, Y. and Eguchi, T. Biosynthesis of archaeal membrane lipids: digeranylgeranylglycerophospholipid reductase of the thermoacidophilic archaeon Thermoplasma acidophilum. J. Biochem. 139 (2006) 1073–1081. [PMID: 16788058]
2.  Nishimura, Y. and Eguchi, T. Stereochemistry of reduction in digeranylgeranylglycerophospholipid reductase involved in the biosynthesis of archaeal membrane lipids from Thermoplasma acidophilum. Bioorg. Chem. 35 (2007) 276–283. [PMID: 17275067]
3.  Xu, Q., Eguchi, T., Mathews, I.I., Rife, C.L., Chiu, H.J., Farr, C.L., Feuerhelm, J., Jaroszewski, L., Klock, H.E., Knuth, M.W., Miller, M.D., Weekes, D., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids. J. Mol. Biol. 404 (2010) 403–417. [PMID: 20869368]
[EC 1.3.1.101 created 2013]
 
 
EC 1.3.3.13
Accepted name: albonoursin synthase
Reaction: cyclo(L-leucyl-L-phenylalanyl) + 2 O2 = albonoursin + 2 H2O2 (overall reaction)
(1a) cyclo(L-leucyl-L-phenylalanyl) + O2 = cyclo[(Z)-α,β-didehydrophenylalanyl-L-leucyl] + H2O2
(1b) cyclo[(Z)-α,β-didehydrophenylalanyl-L-leucyl] + O2 = albonoursin + H2O2
For diagram of cyclic dipeptide biosynthesis, click here
Glossary: cyclo(L-leucyl-L-phenylalanyl) = (3S,6S)-3-benzyl-6-(2-methylpropyl)piperazine-2,5-dione
cyclo[(Z)-α,β-didehydrophenylalanyl-L-leucyl] = (3Z,6S)-3-benzylidene-6-(2-methylpropyl)piperazine-2,5-dione
albonoursin = (3Z,6Z)-3-benzylidene-6-(2-methylpropylidene)piperazine-2,5-dione
Other name(s): cyclo(dipeptide):oxygen oxidoreductase; cyclic dipeptide oxidase; AlbA
Systematic name: cyclo(L-leucyl-L-phenylalanyl):oxygen oxidoreductase
Comments: A flavoprotein from the bacterium Streptomyces noursei. The enzyme can also oxidize several other cyclo dipeptides, the best being cyclo(L-tryptophyl-L-tryptophyl) and cyclo(L-phenylalanyl-L-phenylalanyl) [1,2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Gondry, M., Lautru, S., Fusai, G., Meunier, G., Menez, A. and Genet, R. Cyclic dipeptide oxidase from Streptomyces noursei. Isolation, purification and partial characterization of a novel, amino acyl α,β-dehydrogenase. Eur. J. Biochem. 268 (2001) 1712–1721. [PMID: 11248691]
2.  Lautru, S., Gondry, M., Genet, R. and Pernodet, J.L. The albonoursin gene cluster of S. noursei. Biosynthesis of diketopiperazine metabolites independent of nonribosomal peptide synthetases. Chem. Biol. 9 (2002) 1355–1364. [PMID: 12498889]
[EC 1.3.3.13 created 2013]
 
 
*EC 1.3.7.7
Accepted name: ferredoxin:protochlorophyllide reductase (ATP-dependent)
Reaction: chlorophyllide a + oxidized ferredoxin + 2 ADP + 2 phosphate = protochlorophyllide a + reduced ferredoxin + 2 ATP + 2 H2O
For diagram of chlorophyll biosynthesis (later stages), click here
Other name(s): light-independent protochlorophyllide reductase
Systematic name: ATP-dependent ferredoxin:protochlorophyllide-a 7,8-oxidoreductase
Comments: Occurs in photosynthetic bacteria, cyanobacteria, green algae and gymnosperms. The enzyme catalyses trans-reduction of the D-ring of protochlorophyllide; the product has the (7S,8S)-configuration. Unlike EC 1.3.1.33 (protochlorophyllide reductase), light is not required. The enzyme contains a [4Fe-4S] cluster, and structurally resembles the Fe protein/MoFe protein complex of nitrogenase (EC 1.18.6.1), which catalyses an ATP-driven reduction.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Fujita, Y., Matsumoto, H., Takahashi, Y. and Matsubara, H. Identification of a nifDK-like gene (ORF467) involved in the biosynthesis of chlorophyll in the cyanobacterium Plectonema boryanum. Plant Cell Physiol. 34 (1993) 305–314. [PMID: 8199775]
2.  Nomata, J., Ogawa, T., Kitashima, M., Inoue, K. and Fujita, Y. NB-protein (BchN-BchB) of dark-operative protochlorophyllide reductase is the catalytic component containing oxygen-tolerant Fe-S clusters. FEBS Lett. 582 (2008) 1346–1350. [PMID: 18358835]
3.  Muraki, N., Nomata, J., Ebata, K., Mizoguchi, T., Shiba, T., Tamiaki, H., Kurisu, G. and Fujita, Y. X-ray crystal structure of the light-independent protochlorophyllide reductase. Nature 465 (2010) 110–114. [PMID: 20400946]
[EC 1.3.7.7 created 2011, modified 2013]
 
 
EC 1.3.7.10
Transferred entry: pentalenolactone synthase. Now EC 1.14.19.8, pentalenolactone synthase
[EC 1.3.7.10 created 2012, deleted 2013]
 
 
EC 1.3.99.33
Accepted name: urocanate reductase
Reaction: dihydrourocanate + acceptor = urocanate + reduced acceptor
For diagram of histidine catabolism, click here
Glossary: urocanate = 3-(1H-imidazol-4-yl)prop-2-enoate
dihydrourocanate = 3-(1H-imidazol-4-yl)propanoate
Other name(s): urdA (gene name)
Systematic name: dihydrourocanate:acceptor oxidoreductase
Comments: The enzyme from the bacterium Shewanella oneidensis MR-1 contains a noncovalently-bound FAD and a covalently-bound FMN. It functions as part of an anaerobic electron transfer chain that utilizes urocanate as the terminal electron acceptor. The activity has been demonstrated with the artificial donor reduced methylviologen.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Bogachev, A.V., Bertsova, Y.V., Bloch, D.A. and Verkhovsky, M.I. Urocanate reductase: identification of a novel anaerobic respiratory pathway in Shewanella oneidensis MR-1. Mol. Microbiol. 86 (2012) 1452–1463. [PMID: 23078170]
[EC 1.3.99.33 created 2013]
 
 
EC 1.3.99.34
Transferred entry: 2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor). Now classified as EC 1.3.7.11, 2,3-bis-O-geranylgeranyl-sn-glycero-phospholipid reductase.
[EC 1.3.99.34 created 2013, deleted 2015]
 
 
EC 1.5.1.47
Accepted name: dihydromethanopterin reductase [NAD(P)+]
Reaction: 5,6,7,8-tetrahydromethanopterin + NAD(P)+ = 7,8-dihydromethanopterin + NAD(P)H + H+
For diagram of methanopterin biosynthesis (part 4), click here
Other name(s): DmrA; H2MPT reductase; 5,6,7,8-tetrahydromethanopterin 5,6-oxidoreductase; dihydromethanopterin reductase
Systematic name: 5,6,7,8-tetrahydromethanopterin:NAD(P)+ 5,6-oxidoreductase
Comments: The enzyme, characterized from the bacterium Methylobacterium extorquens, is involved in biosynthesis of dephospho-tetrahydromethanopterin. The specific activity with NADH is 15% of that with NADPH at the same concentration [1]. It does not reduce 7,8-dihydrofolate (cf. EC 1.5.1.3, dihydrofolate reductase).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Caccamo, M.A., Malone, C.S. and Rasche, M.E. Biochemical characterization of a dihydromethanopterin reductase involved in tetrahydromethanopterin biosynthesis in Methylobacterium extorquens AM1. J. Bacteriol. 186 (2004) 2068–2073. [PMID: 15028691]
[EC 1.5.1.47 created 2013, modified 2014]
 
 
EC 1.6.1.2
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 1.7.1.4
Accepted name: nitrite reductase [NAD(P)H]
Reaction: NH3 + 3 NAD(P)+ + 2 H2O = nitrite + 3 NAD(P)H + 5 H+
Other name(s): nitrite reductase (reduced nicotinamide adenine dinucleotide (phosphate)); assimilatory nitrite reductase (ambiguous); nitrite reductase [NAD(P)H2]; NAD(P)H2:nitrite oxidoreductase; nit-6 (gene name)
Systematic name: ammonia:NAD(P)+ oxidoreductase
Comments: An iron-sulfur flavoprotein (FAD) containing siroheme. The enzymes from the fungi Neurospora crassa [1], Emericella nidulans [2] and Candida nitratophila [4] and the bacterium Aliivibrio fischeri [3] can use either NADPH or NADH as electron donor. cf. EC 1.7.1.15, nitrite reductase (NADH).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9029-29-2
References:
1.  Nicholas, D.J.D., Medina, A. and Jones, O.T.G. A nitrite reductase from Neurospora crassa. Biochim. Biophys. Acta 37 (1960) 468–476.
2.  Pateman, J.A., Rever, B.M. and Cove, D.J. Genetic and biochemical studies of nitrate reduction in Aspergillus nidulans. Biochem. J. 104 (1967) 103–111. [PMID: 4382427]
3.  Prakash, O.M. and Sadana, J.C. Purification, characterization and properties of nitrite reductase of Achromobacter fischeri. Arch. Biochem. Biophys. 148 (1972) 614–632. [PMID: 4401695]
4.  Rivas, J., Guerrero, M. G., Paneque, A. and Losada, M. Characterization of the nitrate-reducing system of the yeast Torulopsis nitratophila. Plant Sci. Lett. 1 (1973) 105–113.
5.  Lafferty, M.A. and Garrett, R.H. Purification and properties of the Neurospora crassa assimilatory nitrite reductase. J. Biol. Chem. 249 (1974) 7555–7567. [PMID: 4154942]
6.  Vega, J.M. and Garrett, R.H. Siroheme: a prosthetic group of the Neurospora crassa assimilatory nitrite reductase. J. Biol. Chem. 250 (1975) 7980–7989. [PMID: 126995]
7.  Greenbaum, P., Prodouz, K.N. and Garrett, R.H. Preparation and some properties of homogeneous Neurospora crassa assimilatory NADPH-nitrite reductase. Biochim. Biophys. Acta 526 (1978) 52–64. [PMID: 150863]
8.  Prodouz, K.N. and Garrett, R.H. Neurospora crassa NAD(P)H-nitrite reductase. Studies on its composition and structure. J. Biol. Chem. 256 (1981) 9711–9717. [PMID: 6457037]
9.  Exley, G.E., Colandene, J.D. and Garrett, R.H. Molecular cloning, characterization, and nucleotide sequence of nit-6, the structural gene for nitrite reductase in Neurospora crassa. J. Bacteriol. 175 (1993) 2379–2392. [PMID: 8096840]
10.  Colandene, J.D. and Garrett, R.H. Functional dissection and site-directed mutagenesis of the structural gene for NAD(P)H-nitrite reductase in Neurospora crassa. J. Biol. Chem. 271 (1996) 24096–24104. [PMID: 8798648]
[EC 1.7.1.4 created 1961 as EC 1.6.6.4, transferred 2002 to EC 1.7.1.4, modified 2013]
 
 
EC 1.7.1.15
Accepted name: nitrite reductase (NADH)
Reaction: NH3 + 3 NAD+ + 2 H2O = nitrite + 3 NADH + 5 H+
Other name(s): nitrite reductase (reduced nicotinamide adenine dinucleotide); NADH-nitrite oxidoreductase; assimilatory nitrite reductase (ambiguous); nirB (gene name); nirD (gene name)
Systematic name: ammonia:NAD+ oxidoreductase
Comments: An iron-sulfur flavoprotein (FAD) containing siroheme. This prokaryotic enzyme is specific for NADH. In addition to catalysing the 6-electron reduction of nitrite to ammonia, the enzyme from Escherichia coli can also catalyse the 2-electron reduction of hydroxylamine to ammonia. cf. EC 1.7.1.4, nitrite reductase [NAD(P)H].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9029-29-2
References:
1.  Vega, J.M., Guerrero, M.G., Leadbetter, E. and Losada, M. Reduced nicotinamide-adenine dinucleotide-nitrite reductase from Azotobacter chroococcum. Biochem. J. 133 (1973) 701–708. [PMID: 4147887]
2.  Jackson, R.H., Cornish-Bowden, A. and Cole, J.A. Prosthetic groups of the NADH-dependent nitrite reductase from Escherichia coli K12. Biochem. J. 193 (1981) 861–867. [PMID: 7030314]
3.  Cammack, R., Jackson, R.H., Cornish-Bowden, A. and Cole, J.A. Electron-spin-resonance studies of the NADH-dependent nitrite reductase from Escherichia coli K12. Biochem. J. 207 (1982) 333–339. [PMID: 6297458]
4.  Harborne, N.R., Griffiths, L., Busby, S.J. and Cole, J.A. Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon. Mol. Microbiol. 6 (1992) 2805–2813. [PMID: 1435259]
[EC 1.7.1.15 created 2013]
 
 
EC 1.13.11.74
Accepted name: 2-aminophenol 1,6-dioxygenase
Reaction: 2-aminophenol + O2 = 2-aminomuconate 6-semialdehyde
Other name(s): amnA (gene name); amnB (gene name); 2-aminophenol:oxygen 1,6-oxidoreductase (decyclizing)
Systematic name: 2-aminophenol:oxygen 1,6-oxidoreductase (ring-opening)
Comments: The enzyme, a member of the nonheme-iron(II)-dependent dioxygenase family, is an extradiol-type dioxygenase that utilizes a non-heme ferrous iron to cleave the aromatic ring at the meta position (relative to the hydroxyl substituent). The enzyme also has some activity with 2-amino-5-methylphenol and 2-amino-4-methylphenol [1]. The enzyme from the bacterium Comamonas testosteroni CNB-1 also has the activity of EC 1.13.11.76, 2-amino-5-chlorophenol 1,6-dioxygenase [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Takenaka, S., Murakami, S., Shinke, R., Hatakeyama, K., Yukawa, H. and Aoki, K. Novel genes encoding 2-aminophenol 1,6-dioxygenase from Pseudomonas species AP-3 growing on 2-aminophenol and catalytic properties of the purified enzyme. J. Biol. Chem. 272 (1997) 14727–14732. [PMID: 9169437]
2.  Wu, J.F., Sun, C.W., Jiang, C.Y., Liu, Z.P. and Liu, S.J. A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1: purification, properties, genetic cloning and expression in Escherichia coli. Arch. Microbiol. 183 (2005) 1–8. [PMID: 15580337]
3.  Li, D.F., Zhang, J.Y., Hou, Y.J., Liu, L., Hu, Y., Liu, S.J., Wang da, C. and Liu, W. Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor. Acta Crystallogr. D Biol. Crystallogr. 69 (2013) 32–43. [PMID: 23275161]
[EC 1.13.11.74 created 2013]
 
 
EC 1.14.11.37
Accepted name: kanamycin B dioxygenase
Reaction: kanamycin B + 2-oxoglutarate + O2 = 2′-dehydrokanamycin A + succinate + NH3 + CO2
For diagram of kanamycin A biosynthesis, click here
Other name(s): kanJ (gene name)
Systematic name: kanamycin-B,2-oxoglutarate:oxygen oxidoreductase (deaminating, 2′-hydroxylating)
Comments: Requires Fe2+ and ascorbate. Found in the bacterium Streptomyces kanamyceticus where it is involved in the conversion of the aminoglycoside antibiotic 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 1.14.11.37 created 2013, modified 2013]
 
 
EC 1.14.13.86
Deleted entry: 2-hydroxyisoflavanone synthase. This enzyme was classified on the basis of an incorrect reaction. The activity is covered by EC 1.14.13.136, 2-hydroxyisoflavanone synthase
[EC 1.14.13.86 created 2004]
 
 
*EC 1.14.13.136
Accepted name: 2-hydroxyisoflavanone synthase
Reaction: (1) liquiritigenin + O2 + NADPH + H+ = 2,4′,7-trihydroxyisoflavanone + H2O + NADP+
(2) (2S)-naringenin + O2 + NADPH + H+ = 2,4′,5,7-tetrahydroxyisoflavanone + H2O + NADP+
For diagram of daidzein biosynthesis, click here
Glossary: liquiritigenin = 4′,7-dihydroxyflavanone
(2S)-naringenin = 4′,5,7-dihydroxyflavanone
2,4′,5,7-tetrahydroxyisoflavanone = 2-hydroxy-2,3-dihydrogenistein
Other name(s): CYP93C; IFS; isoflavonoid synthase
Systematic name: liquiritigenin,NADPH:oxygen oxidoreductase (hydroxylating, aryl migration)
Comments: Requires cytochrome P-450. The reaction involves the migration of the 2-phenyl group of the flavanone to the 3-position of the isoflavanone. The 2-hydroxyl group is derived from the oxygen molecule. EC 4.2.1.105, 2-hydroxyisoflavanone dehydratase, acts on the products with loss of water and formation of genistein and daidzein, respectively.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kochs, G. and Grisebach, H. Enzymic synthesis of isoflavones. Eur. J. Biochem. 155 (1986) 311–318. [PMID: 3956488]
2.  Hashim, M.F., Hakamatsuka, T., Ebizuka, Y. and Sankawa, U. Reaction mechanism of oxidative rearrangement of flavanone in isoflavone biosynthesis. FEBS Lett. 271 (1990) 219–222. [PMID: 2226805]
3.  Steele, C. L., Gijzen, M., Qutob, D. and Dixon, R.A. Molecular characterization of the enzyme catalyzing the aryl migration reaction of isoflavonoid biosynthesis in soybean. Arch. Biochem. Biophys. 367 (1999) 146–150. [PMID: 10375412]
4.  Sawada, Y., Kinoshita, K., Akashi, T., Aoki, T. and Ayabe, S. Key amino acid residues required for aryl migration catalysed by the cytochrome P450 2-hydroxyisoflavanone synthase. Plant J. 31 (2002) 555–564. [PMID: 12207646]
5.  Sawada, Y. and Ayabe, S. Multiple mutagenesis of P450 isoflavonoid synthase reveals a key active-site residue. Biochem. Biophys. Res. Commun. 330 (2005) 907–913. [PMID: 15809082]
[EC 1.14.13.136 created 2011, modified 2013]
 
 
EC 1.14.13.172
Accepted name: salicylate 5-hydroxylase
Reaction: salicylate + NADH + H+ + O2 = 2,5-dihydroxybenzoate + NAD+ + H2O
Glossary: 2,5-dihydroxybenzoate = gentisate
Other name(s): nagG (gene name); nagH (gene name)
Systematic name: salicylate,NADH:oxygen oxidoreductase (5-hydroxylating)
Comments: This enzyme, which was characterized from the bacterium Ralstonia sp. U2, comprises a multicomponent system, containing a reductase that is an iron-sulfur flavoprotein (FAD; EC 1.18.1.7, ferredoxin—NAD(P)+ reductase), an iron-sulfur oxygenase, and ferredoxin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, UM-BBD
References:
1.  Fuenmayor, S.L., Wild, M., Boyes, A.L. and Williams, P.A. A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2. J. Bacteriol. 180 (1998) 2522–2530. [PMID: 9573207]
[EC 1.14.13.172 created 2013]
 
 
EC 1.14.13.173
Accepted name: 11-oxo-β-amyrin 30-oxidase
Reaction: 11-oxo-β-amyrin + 3 O2 + 3 NADPH + 3 H+ = glycyrrhetinate + 3 NADP+ + 4 H2O (overall reaction)
(1a) 11-oxo-β-amyrin + O2 + NADPH + H+ = 30-hydroxy-11-oxo-β-amyrin + NADP+ + H2O
(1b) 30-hydroxy-11-oxo-β-amyrin + O2 + NADPH + H+ = glycyrrhetaldehyde + NADP+ + 2 H2O
(1c) glycyrrhetaldehyde + O2 + NADPH + H+ = glycyrrhetinate + NADP+ + H2O
For diagram of glycyrrhenate biosynthesis, click here
Other name(s): CYP72A; CYP72A154
Systematic name: 11-oxo-β-amyrin,NADPH:oxygen oxidoreductase (30-hydroxylating)
Comments: A heme-thiolate protein (cytochrome P-450). The enzyme is involved in the biosynthesis of the triterpenoid saponin glycyrrhizin in the plant Glycyrrhiza uralensis (licorice). The enzyme from the plant Medicago truncatula can also hydroxylate β-amyrin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Seki, H., Sawai, S., Ohyama, K., Mizutani, M., Ohnishi, T., Sudo, H., Fukushima, E.O., Akashi, T., Aoki, T., Saito, K. and Muranaka, T. Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin. Plant Cell 23 (2011) 4112–4123. [PMID: 22128119]
[EC 1.14.13.173 created 2013]
 
 
EC 1.14.13.174
Accepted name: averantin hydroxylase
Reaction: (1) (1′S)-averantin + NADPH + H+ + O2 = (1′S,5′S)-5′-hydroxyaverantin + NADP+ + H2O
(2) (1′S)-averantin + NADPH + H+ + O2 = (1′S,5′R)-5′-hydroxyaverantin + NADP+ + H2O
For diagram of aflatoxin biosynthesis (part 1), click here
Glossary: averantin = 1,3,6,8-tetrahydroxy-2-[(1S)-1-hydroxyhexyl]anthracene-9,10-dione
Other name(s): AVN hydroxylase; avnA (gene name); (1′S)-averantin,NADPH:O2 oxidoreductase (5′-hydroxylating)
Systematic name: (1′S)-averantin,NADPH:oxygen oxidoreductase (5′-hydroxylating)
Comments: A heme-thiolate (P-450) monooxygenase isolated from Aspergillus parasiticus. There is no reaction with (1′R)-averantin. Involved in aflatoxin biosynthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Yabe, K., Matsuyama, Y., Ando, Y., Nakajima, H. and Hamasaki, T. Stereochemistry during aflatoxin biosynthesis: conversion of norsolorinic acid to averufin. Appl. Environ. Microbiol. 59 (1993) 2486–2492. [PMID: 8368836]
[EC 1.14.13.174 created 2013]
 
 
EC 1.14.13.175
Accepted name: aflatoxin B synthase
Reaction: (1) 8-O-methylsterigmatocystin + 2 NADPH + 2 H+ + 2 O2 = aflatoxin B1 + 2 NADP+ + H2O + methanol + CO2
(2) 8-O-methyldihydrosterigmatocystin + 2 NADPH + 2 H+ + 2 O2 = aflatoxin B2 + 2 NADP+ + H2O + methanol + CO2
For diagram of aflatoxin biosynthesis (part 4), click here
Glossary: aflatoxin B1 = (6aR,9aS)-4-methoxy-2,3,6a,9a-tetrahydrocyclopenta[c]furo[3′,2′:4,5]furo[2,3-h][1]benzopyran-1,11-dione
aflatoxin B2 = (6aR,9aS)-4-methoxy-2,3,6a,8,9,9a-hexahydrocyclopenta[c]furo[3′,2′:4,5]furo[2,3-h][1]benzopyran-1,11-dione
8-O-methylsterigmatocystin = 6,8-dimethoxy-3a,12c-dihydrofuro[3′,2′:4,5]furo[2,3-c]xanthen-7-one
8-O-methyldihydrosterigmatocystin = 6,8-dimethoxy-1,2,3a,12c-tetrahydrofuro[3′,2′:4,5]furo[2,3-c]xanthen-7-one
Other name(s): ordA (gene name); 8-O-methylsterigmatocystin,NADPH:O2 oxidoreductase (aflatoxin-B forming)
Systematic name: 8-O-methylsterigmatocystin,NADPH:oxygen oxidoreductase (aflatoxin-B forming)
Comments: A heme-thiolate (P-450) enzyme. Isolated from the mold Aspergillus parasiticus.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Bhatnagar, D., Cleveland, T.E. and Kingston, D.G. Enzymological evidence for separate pathways for aflatoxin B1 and B2 biosynthesis. Biochemistry 30 (1991) 4343–4350. [PMID: 1902378]
2.  Yu, J., Chang, P.K., Ehrlich, K.C., Cary, J.W., Montalbano, B., Dyer, J.M., Bhatnagar, D. and Cleveland, T.E. Characterization of the critical amino acids of an Aspergillus parasiticus cytochrome P-450 monooxygenase encoded by ordA that is involved in the biosynthesis of aflatoxins B1, G1, B2, and G2. Appl. Environ. Microbiol. 64 (1998) 4834–4841. [PMID: 9835571]
3.  Udwary, D.W., Casillas, L. K. and Townsend, C.A. Synthesis of 11-hydroxyl O-methylsterigmatocystin and the role of a cytochrome P-450 in the final step of aflatoxin biosynthesis. J. Am. Chem. Soc. 124 (2002) 5294–5303. [PMID: 11996570]
[EC 1.14.13.175 created 2013]
 
 
EC 1.14.13.176
Accepted name: tryprostatin B 6-hydroxylase
Reaction: tryprostatin B + NADPH + H+ + O2 = 6-hydroxytryprostatin B + NADP+ + H2O
Glossary: tryprostatin B = (3S,8aS)-3-{[2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
6-hydroxytryprostatin B = (3S,8aS)-3-{[6-hydroxy-2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
Other name(s): ftmC (gene name)
Systematic name: tryprostatin B,NADPH:oxygen oxidoreductase (6-hydroxytryprostatin B-forming)
Comments: A heme-thiolate protein (P-450). Involved in the biosynthetic pathways of several indole alkaloids such as tryprostatins, 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 1.14.13.176 created 2013]
 
 
EC 1.14.15.13
Accepted name: pulcherriminic acid synthase
Reaction: cyclo(L-leucyl-L-leucyl) + 6 reduced ferredoxin + 3 O2 = pulcherriminic acid + 6 oxidized ferredoxin + 4 H2O
For diagram of cyclic dipeptide biosynthesis, click here
Glossary: cyclo(L-leucyl-L-leucyl) = (3S,6S)-3,6-bis(2-methylpropyl)piperazine-2,5-dione
pulcherriminic acid = 2,5-dihydroxy-3,6-bis(2-methylpropyl)pyrazine bis-N-oxide
Other name(s): cyclo-L-leucyl-L-leucyl dipeptide oxidase; CYP134A1; CypX (ambiguous)
Systematic name: cyclo(L-leucyl-L-leucyl),reduced-ferredoxin:oxygen oxidoreductase (N-hydroxylating,aromatizing)
Comments: A heme-thiolate (P-450) enzyme from the bacterium Bacillus subtilis. The order of events during the overall reaction is unknown. Pulcherrimic acid spontaneously forms an iron chelate with Fe(3+) to form the red pigment pulcherrimin [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  MacDonald, J.C. Biosynthesis of pulcherriminic acid. Biochem. J. 96 (1965) 533–538. [PMID: 5837792]
2.  Cryle, M.J., Bell, S.G. and Schlichting, I. Structural and biochemical characterization of the cytochrome P450 CypX (CYP134A1) from Bacillus subtilis: a cyclo-L-leucyl-L-leucyl dipeptide oxidase. Biochemistry 49 (2010) 7282–7296. [PMID: 20690619]
[EC 1.14.15.13 created 2013]
 
 
EC 1.14.19.8
Accepted name: pentalenolactone synthase
Reaction: pentalenolactone F + O2 + 2 reduced ferredoxin + 2 H+ = pentalenolactone + 2 oxidized ferredoxin + 2 H2O
For diagram of pentalenolactone biosynthesis, click here
Glossary: pentalenolactone F = (1R,4aR,6aS,9aR)-8,8-dimethyl-2-oxo-4,4a,6a,8,9-hexahydrospiro[oxirane-2,1-pentaleno[1,6a-c]pyran]-5-carboxylic acid
pentalenolactone = (1R,4aR,6aR,7S,9aS)-7,8-dimethyl-2-oxo-4,4a,6a,7-tetrahydrospiro[oxirane-2,1-pentaleno[1,6a-c]pyran]-5-carboxylic acid
Other name(s): penM (gene name); pntM (gene name)
Systematic name: pentalenolactone-reduced-ferredoxin:oxygen oxidoreductase (pentalenolactone forming)
Comments: A heme-thiolate protein (P-450). Isolated from the bacteria Streptomyces exfoliatus and Streptomyces arenae.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zhu, D., Seo, M.J., Ikeda, H. and Cane, D.E. Genome mining in streptomyces. Discovery of an unprecedented P450-catalyzed oxidative rearrangement that is the final step in the biosynthesis of pentalenolactone. J. Am. Chem. Soc. 133 (2011) 2128–2131. [PMID: 21284395]
[EC 1.14.19.8 created 2012 as EC 1.3.7.10, transferred 2013 to EC 1.14.19.8]
 
 
EC 1.14.21.9
Accepted name: mycocyclosin synthase
Reaction: cyclo(L-tyrosyl-L-tyrosyl) + NADPH + H+ + O2 = mycocyclosin + NADP+ + 2 H2O
Glossary: mycocyclosin = (1S,14S)-6,9-dihydroxy-15,17-diazatetracyclo[12.2.2.13,7.18,12]icosa-3(20),4,6,8(19),9,11-hexaene-16,18-dione
Other name(s): CYP121; rv2276 (gene name)
Systematic name: cyclo(L-tyrosyl-L-tyrosyl),NADPH:oxygen oxidoreductase (diarylbridge-forming)
Comments: A heme-thiolate (P-450) enzyme from the bacterium Mycobacterium tuberculosis catalysing an oxidative reaction that does not incorporate oxygen into the product.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Belin, P., Le Du, M.H., Fielding, A., Lequin, O., Jacquet, M., Charbonnier, J.B., Lecoq, A., Thai, R., Courcon, M., Masson, C., Dugave, C., Genet, R., Pernodet, J.L. and Gondry, M. Identification and structural basis of the reaction catalyzed by CYP121, an essential cytochrome P450 in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 106 (2009) 7426–7431. [PMID: 19416919]
[EC 1.14.21.9 created 2013]
 
 
EC 1.18.1.7
Accepted name: ferredoxin—NAD(P)+ reductase (naphthalene dioxygenase ferredoxin-specific)
Reaction: 2 reduced [2Fe-2S] ferredoxin + NAD(P)+ + H+ = 2 oxidized [2Fe-2S] ferredoxin + NAD(P)H
Glossary: ferredoxin
Other name(s): NADH-ferredoxin(NAP) reductase
Systematic name: ferredoxin:NAD(P)+ oxidoreductase
Comments: The enzyme from the aerobic bacterium Ralstonia sp. U2 donates electrons to both EC 1.14.12.12, naphthalene 1,2-dioxygenase and EC 1.14.13.172, salicylate 5-hydroxylase [1]. The enzyme from Pseudomonas NCIB 9816 is specific for the ferredoxin associated with naphthalene dioxygenase; it contains FAD and a [2Fe-2S] cluster.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Zhou, N.Y., Al-Dulayymi, J., Baird, M.S. and Williams, P.A. Salicylate 5-hydroxylase from Ralstonia sp. strain U2: a monooxygenase with close relationships to and shared electron transport proteins with naphthalene dioxygenase. J. Bacteriol. 184 (2002) 1547–1555. [PMID: 11872705]
2.  Haigler, B.E. and Gibson, D.T. Purification and properties of NADH-ferredoxinNAP reductase, a component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816. J. Bacteriol. 172 (1990) 457–464. [PMID: 2294092]
[EC 1.18.1.7 created 2013]
 
 
EC 1.21.3.9
Transferred entry: dichlorochromopyrrolate synthase, now classified as EC 1.21.98.2, dichlorochromopyrrolate synthase
[EC 1.21.3.9 created 2010 as 4.3.1.26, transferred 2013 to EC 1.21.3.9, deleted 2016]
 
 
*EC 2.1.1.98
Accepted name: diphthine synthase
Reaction: 3 S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = 3 S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2] (overall reaction)
(1a) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2]
(1b) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(methylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2]
(1c) S-adenosyl-L-methionine + 2-[(3S)-3-carboxy-3-(dimethylamino)propyl]-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + diphthine-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Glossary: diphthine = 2-[(3S)-3-carboxy-3-(trimethylamino)propyl]-L-histidine
Other name(s): S-adenosyl-L-methionine:elongation factor 2 methyltransferase (ambiguous); diphthine methyltransferase (ambiguous); S-adenosyl-L-methionine:2-(3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] methyltransferase; Dph5 (ambiguous)
Systematic name: S-adenosyl-L-methionine:2-[(3S)-3-carboxy-3-aminopropyl]-L-histidine-[translation elongation factor 2] methyltransferase (diphthine-[translation elongation factor 2]-forming)
Comments: This archaeal enzyme produces the trimethylated product diphthine, which is converted into diphthamide by EC 6.3.1.14, diphthine—ammonia ligase. Different from the eukaryotic enzyme, which produces diphthine methyl ester (cf. EC 2.1.1.314). In the archaeon Pyrococcus horikoshii the enzyme acts on His600 of elongation factor 2.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 114514-25-9
References:
1.  Zhu, X., Kim, J., Su, X. and Lin, H. Reconstitution of diphthine synthase activity in vitro. Biochemistry 49 (2010) 9649–9657. [PMID: 20873788]
[EC 2.1.1.98 created 1990, modified 2013, modified 2015]
 
 
*EC 2.1.1.110
Accepted name: sterigmatocystin 8-O-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + sterigmatocystin = S-adenosyl-L-homocysteine + 8-O-methylsterigmatocystin
(2) S-adenosyl-L-methionine + dihydrosterigmatocystin = S-adenosyl-L-homocysteine + 8-O-methyldihydrosterigmatocystin
For diagram of sterigmatocystin biosynthesis, click here
Glossary: sterigmatocystin = 3a,12c-dihydro-8-hydroxy-6-methoxyfuro[3′,2′:4,5]furo[2,3-c]xanthen-7-one
dihydrosterigmatocystin = 1,2,3a,12c-tetrahydro-8-hydroxy-6-methoxyfuro[3′,2′:4,5]furo[2,3-c]xanthen-7-one
8-O-methylsterigmatocystin = 6,8-dimethoxy-3a,12c-dihydrofuro[3′,2′:4,5]furo[2,3-c]xanthen-7-one
8-O-methyldihydrosterigmatocystin = 6,8-dimethoxy-1,2,3a,12c-tetrahydrofuro[3′,2′:4,5]furo[2,3-c]xanthen-7-one
Other name(s): sterigmatocystin methyltransferase; O-methyltransferase II; sterigmatocystin 7-O-methyltransferase (incorrect); S-adenosyl-L-methionine:sterigmatocystin 7-O-methyltransferase (incorrect); OmtA
Systematic name: S-adenosyl-L-methionine:sterigmatocystin 8-O-methyltransferase
Comments: Dihydrosterigmatocystin can also act as acceptor. Involved in the biosynthesis of aflatoxins in fungi.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 116958-29-3
References:
1.  Bhatnagar, D., McCormick, S.P., Lee, L.S. and Hill, R.A. Identification of O-methylsterigmatocystin as an aflatoxin B1 and G1 precursor in Aspergillus parasiticus. Appl. Environ. Microbiol. 53 (1987) 1028–1033. [PMID: 3111363]
2.  Yabe, K., Ando, Y., Hashimoto, J. and Hamasaki, T. 2 distinct O-methyltransferases in aflatoxin biosynthesis. Appl. Environ. Microbiol. 55 (1989) 2172–2177. [PMID: 2802602]
3.  Yu, J., Cary, J.W., Bhatnagar, D., Cleveland, T.E., Keller, N.P. and Chu, F.S. Cloning and characterization of a cDNA from Aspergillus parasiticus encoding an O-methyltransferase involved in aflatoxin biosynthesis. Appl. Environ. Microbiol. 59 (1993) 3564–3571. [PMID: 8285664]
4.  Lee, L.W., Chiou, C.H. and Linz, J.E. Function of native OmtA in vivo and expression and distribution of this protein in colonies of Aspergillus parasiticus. Appl. Environ. Microbiol. 68 (2002) 5718–5727. [PMID: 12406770]
[EC 2.1.1.110 created 1992, modified 2005, modified 2013]
 
 
*EC 2.1.1.197
Accepted name: malonyl-[acyl-carrier protein] O-methyltransferase
Reaction: S-adenosyl-L-methionine + malonyl-[acyl-carrier protein] = S-adenosyl-L-homocysteine + malonyl-[acyl-carrier protein] methyl ester
Other name(s): BioC
Systematic name: S-adenosyl-L-methionine:malonyl-[acyl-carrier protein] O-methyltransferase
Comments: Involved in an early step of biotin biosynthesis in Gram-negative bacteria. This enzyme catalyses the transfer of a methyl group to the ω-carboxyl group of malonyl-[acyl-carrier protein] forming a methyl ester. The methyl ester is recognized by the fatty acid synthetic enzymes, which process it via the fatty acid elongation cycle to give pimelyl-[acyl-carrier-protein] methyl ester [5]. While the enzyme can also accept malonyl-CoA, it has a much higher activity with malonyl-[acyl-carrier protein] [6]
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Del Campillo-Campbell, A., Kayajanian, G., Campbell, A. and Adhya, S. Biotin-requiring mutants of Escherichia coli K-12. J. Bacteriol. 94 (1967) 2065–2066. [PMID: 4864413]
2.  Rolfe, B. and Eisenberg, M.A. Genetic and biochemical analysis of the biotin loci of Escherichia coli K-12. J. Bacteriol. 96 (1968) 515–524. [PMID: 4877129]
3.  Otsuka, A.J., Buoncristiani, M.R., Howard, P.K., Flamm, J., Johnson, C., Yamamoto, R., Uchida, K., Cook, C., Ruppert, J. and Matsuzaki, J. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. J. Biol. Chem. 263 (1988) 19577–19585. [PMID: 3058702]
4.  Cleary, P.P. and Campbell, A. Deletion and complementation analysis of biotin gene cluster of Escherichia coli. J. Bacteriol. 112 (1972) 830–839. [PMID: 4563978]
5.  Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. 6 (2010) 682–688. [PMID: 20693992]
6.  Lin, S. and Cronan, J.E. The BioC O-methyltransferase catalyzes methyl esterification of malonyl-acyl carrier protein, an essential step in biotin synthesis. J. Biol. Chem. 287 (2012) 37010–37020. [PMID: 22965231]
[EC 2.1.1.197 created 2010, modified 2013]
 
 
EC 2.1.1.269
Accepted name: dimethylsulfoniopropionate demethylase
Reaction: S,S-dimethyl-β-propiothetin + tetrahydrofolate = 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
For diagram of 3-(dimethylsulfonio)propanoate metabolism, click here
Glossary: S,S-dimethyl-β-propiothetin = 3-(S,S-dimethylsulfonio)propanoate
Other name(s): dmdA (gene name); dimethylsulfoniopropionate-dependent demethylase A
Systematic name: S,S-dimethyl-β-propiothetin:tetrahydrofolate S-methyltransferase
Comments: The enzyme from the marine bacteria Pelagibacter ubique and Ruegeria pomeroyi are specific towards S,S-dimethyl-β-propiothetin. They do not demethylate glycine-betaine [1,2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Jansen, M. and Hansen, T.A. Tetrahydrofolate serves as a methyl acceptor in the demethylation of dimethylsulfoniopropionate in cell extracts of sulfate-reducing bacteria. Arch. Microbiol. 169 (1998) 84–87. [PMID: 9396840]
2.  Reisch, C.R., Moran, M.A. and Whitman, W.B. Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190 (2008) 8018–8024. [PMID: 18849431]
3.  Schuller, D.J., Reisch, C.R., Moran, M.A., Whitman, W.B. and Lanzilotta, W.N. Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagibacter ubique. Protein Sci. 21 (2012) 289–298. [PMID: 22162093]
[EC 2.1.1.269 created 2013]
 
 
EC 2.1.1.270
Accepted name: (+)-6a-hydroxymaackiain 3-O-methyltransferase
Reaction: S-adenosyl-L-methionine + (+)-6a-hydroxymaackiain = S-adenosyl-L-homocysteine + (+)-pisatin
Glossary: (+)-6a-hydroxymaackiain = (6aR,12aR)-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromene-3,6a(12aH)-diol
(+)-pisatin = (6aR,12aR)-3-methoxy-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-6a(12aH)-ol
Other name(s): HM3OMT; HMM2
Systematic name: S-adenosyl-L-methionine:(+)-6a-hydroxymaackiain 3-O-methyltransferase
Comments: The protein from the plant Pisum sativum (garden pea) methylates (+)-6a-hydroxymaackiain at the 3-position. It also methylates 2,7,4′-trihydroxyisoflavanone on the 4′-position (cf. EC 2.1.1.212, 2,7,4-trihydroxyisoflavanone 4-O-methyltransferase) with lower activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Preisig, C.L., Matthews, D.E. and Vanetten, H.D. Purification and characterization of S-adenosyl-L-methionine:6a-hydroxymaackiain 3-O-methyltransferase from Pisum sativum. Plant Physiol. 91 (1989) 559–566. [PMID: 16667069]
2.  Wu, Q., Preisig, C.L. and VanEtten, H.D. Isolation of the cDNAs encoding (+)6a-hydroxymaackiain 3-O-methyltransferase, the terminal step for the synthesis of the phytoalexin pisatin in Pisum sativum. Plant Mol. Biol. 35 (1997) 551–560. [PMID: 9349277]
3.  Liu, C.J., Deavours, B.E., Richard, S.B., Ferrer, J.L., Blount, J.W., Huhman, D., Dixon, R.A. and Noel, J.P. Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. Plant Cell 18 (2006) 3656–3669. [PMID: 17172354]
4.  Akashi, T., VanEtten, H.D., Sawada, Y., Wasmann, C.C., Uchiyama, H. and Ayabe, S. Catalytic specificity of pea O-methyltransferases suggests gene duplication for (+)-pisatin biosynthesis. Phytochemistry 67 (2006) 2525–2530. [PMID: 17067644]
[EC 2.1.1.270 created 2013]
 
 
EC 2.1.1.271
Accepted name: cobalt-precorrin-4 methyltransferase
Reaction: S-adenosyl-L-methionine + cobalt-precorrin-4 = S-adenosyl-L-homocysteine + cobalt-precorrin-5A
For diagram of anaerobic corrin biosynthesis (part 1), click here
Other name(s): CbiF
Systematic name: S-adenosyl-L-methionine:cobalt-precorrin-4 11-methyltransferase
Comments: Part of the anaerobic route to adenosylcobalamin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Raux, E., Schubert, H.L., Woodcock, S.C., Wilson, K.S. and Warren, M.J. Cobalamin (vitamin B12) biosynthesis--cloning, expression and crystallisation of the Bacillus megaterium S-adenosyl-L-methionine-dependent cobalt-precorrin-4 transmethylase CbiF. Eur. J. Biochem. 254 (1998) 341–346. [PMID: 9660189]
2.  Schubert, H.L., Wilson, K.S., Raux, E., Woodcock, S.C. and Warren, M.J. The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase. Nat. Struct. Biol. 5 (1998) 585–592. [PMID: 9665173]
3.  Kajiwara, Y., Santander, P.J., Roessner, C.A., Perez, L.M. and Scott, A.I. Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes. J. Am. Chem. Soc. 128 (2006) 9971–9978. [PMID: 16866557]
[EC 2.1.1.271 created 2013]
 
 
EC 2.1.1.272
Accepted name: cobalt-factor III methyltransferase
Reaction: S-adenosyl-L-methionine + cobalt-factor III + reduced acceptor = S-adenosyl-L-homocysteine + cobalt-precorrin-4 + acceptor
For diagram of anaerobic corrin biosynthesis (part 1), click here
Other name(s): CbiH60 (gene name)
Systematic name: S-adenosyl-L-methionine:cobalt-factor III 17-methyltransferase (ring contracting)
Comments: Isolated from Bacillus megaterium. The enzyme catalyses both methylation at C-17 and ring contraction. Contains a [4Fe-4S] cluster. It can also convert cobalt-precorrin-3 to cobalt-precorrin-4. The reductant may be thioredoxin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Moore, S.J., Biedendieck, R., Lawrence, A.D., Deery, E., Howard, M.J., Rigby, S.E. and Warren, M.J. Characterization of the enzyme CbiH60 involved in anaerobic ring contraction of the cobalamin (vitamin B12) biosynthetic pathway. J. Biol. Chem. 288 (2013) 297–305. [PMID: 23155054]
[EC 2.1.1.272 created 2013]
 
 
*EC 2.3.1.174
Accepted name: 3-oxoadipyl-CoA thiolase
Reaction: succinyl-CoA + acetyl-CoA = CoA + 3-oxoadipyl-CoA
For diagram of aerobic phenylacetate catabolism, click here and for diagram of benzoate metabolism, click here
Systematic name: succinyl-CoA:acetyl-CoA C-succinyltransferase
Comments: The enzyme from the bacterium Escherichia coli also has the activity of EC 2.3.1.223 (3-oxo-5,6-dehydrosuberyl-CoA thiolase).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 403496-07-1
References:
1.  Kaschabek, S.R., Kuhn, B., Müller, D., Schmidt, E. and Reineke, W. Degradation of aromatics and chloroaromatics by Pseudomonas sp. strain B13: purification and characterization of 3-oxoadipate:succinyl-coenzyme A (CoA) transferase and 3-oxoadipyl-CoA thiolase. J. Bacteriol. 184 (2002) 207–215. [PMID: 11741862]
2.  Gobel, M., Kassel-Cati, K., Schmidt, E. and Reineke, W. Degradation of aromatics and chloroaromatics by Pseudomonas sp. strain B13: cloning, characterization, and analysis of sequences encoding 3-oxoadipate:succinyl-coenzyme A (CoA) transferase and 3-oxoadipyl-CoA thiolase. J. Bacteriol. 184 (2002) 216–223. [PMID: 11741863]
3.  Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390–14395. [PMID: 20660314]
[EC 2.3.1.174 created 2005, modified 2013]
 
 
*EC 2.3.1.203
Accepted name: UDP-N-acetylbacillosamine N-acetyltransferase
Reaction: acetyl-CoA + UDP-N-acetylbacillosamine = CoA + UDP-N,N′-diacetylbacillosamine
For diagram of legionaminic acid biosynthesis, click here
Glossary: UDP-N-acetylbacillosamine = UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine
UDP-N,N′-diacetylbacillosamine = UDP-2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose
Other name(s): UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase; pglD (gene name)
Systematic name: acetyl-CoA:UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine N-acetyltransferase
Comments: The product, UDP-N,N′-diacetylbacillosamine, is an intermediate in protein glycosylation pathways in several bacterial species, including N-linked glycosylation of certain L-asparagine residues in Campylobacter species [1,2] and O-linked glycosylation of certain L-serine residues in Neisseria species [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N′-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659–13669. [PMID: 17087520]
2.  Rangarajan, E.S., Ruane, K.M., Sulea, T., Watson, D.C., Proteau, A., Leclerc, S., Cygler, M., Matte, A. and Young, N.M. Structure and active site residues of PglD, an N-acetyltransferase from the bacillosamine synthetic pathway required for N-glycan synthesis in Campylobacter jejuni. Biochemistry 47 (2008) 1827–1836. [PMID: 18198901]
3.  Hartley, M.D., Morrison, M.J., Aas, F.E., Borud, B., Koomey, M. and Imperiali, B. Biochemical characterization of the O-linked glycosylation pathway in Neisseria gonorrhoeae responsible for biosynthesis of protein glycans containing N,N′-diacetylbacillosamine. Biochemistry 50 (2011) 4936–4948. [PMID: 21542610]
[EC 2.3.1.203 created 2012, modified 2013]
 
 
EC 2.3.1.223
Accepted name: 3-oxo-5,6-didehydrosuberyl-CoA thiolase
Reaction: 2,3-didehydroadipoyl-CoA + acetyl-CoA = CoA + 3-oxo-5,6-didehydrosuberoyl-CoA
Glossary: 2,3-didehydroadipoyl-CoA = 5-carboxypent-2-enoyl-CoA
3-oxo-5,6-didehydrosuberoyl-CoA = 7-carboxy-3-oxohept-5-enoyl-CoA
Other name(s): paaJ (gene name)
Systematic name: 2,3-didehydroadipoyl-CoA:acetyl-CoA C-didehydroadipoyltransferase (double bond migration)
Comments: The enzyme acts in the opposite direction. The enzymes from the bacteria Escherichia coli and Pseudomonas sp. Y2 also have the activity of EC 2.3.1.174 (3-oxoadipyl-CoA thiolase).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390–14395. [PMID: 20660314]
[EC 2.3.1.223 created 2013]
 
 
EC 2.3.2.20
Accepted name: cyclo(L-leucyl-L-phenylalanyl) synthase
Reaction: L-leucyl-tRNALeu + L-phenylalanyl-tRNAPhe = tRNALeu + tRNAPhe + cyclo(L-leucyl-L-phenylalanyl)
For diagram of cyclic dipeptide biosynthesis, click here
Glossary: cyclo(L-leucyl-L-phenylalanyl) = (3S,6S)-3-benzyl-6-(2-methylpropyl)piperazine-2,5-dione
Other name(s): AlbC; cFL synthase
Systematic name: L-leucyl-tRNALeu:L-phenylalanyl-tRNAPhe leucyltransferase (cyclizing)
Comments: The reaction proceeds following a ping-pong mechanism forming a covalent intermediate between an active site serine and the L-phenylalanine residue [2]. The protein, found in the bacterium Streptomyces noursei, also forms cyclo(L-phenylalanyl-L-phenylalanyl), cyclo(L-methionyl-L-phenylalanyl), cyclo(L-phenylalanyl-L-tyrosyl) and cyclo(L-methionyl-L-tyrosyl) [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Gondry, M., Sauguet, L., Belin, P., Thai, R., Amouroux, R., Tellier, C., Tuphile, K., Jacquet, M., Braud, S., Courcon, M., Masson, C., Dubois, S., Lautru, S., Lecoq, A., Hashimoto, S., Genet, R. and Pernodet, J.L. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat. Chem. Biol. 5 (2009) 414–420. [PMID: 19430487]
2.  Sauguet, L., Moutiez, M., Li, Y., Belin, P., Seguin, J., Le Du, M.H., Thai, R., Masson, C., Fonvielle, M., Pernodet, J.L., Charbonnier, J.B. and Gondry, M. Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis. Nucleic Acids Res. 39 (2011) 4475–4489. [PMID: 21296757]
[EC 2.3.2.20 created 2013]
 
 
EC 2.3.2.21
Accepted name: cyclo(L-tyrosyl-L-tyrosyl) synthase
Reaction: 2 L-tyrosyl-tRNATyr = 2 tRNATyr + cyclo(L-tyrosyl-L-tyrosyl)
For diagram of cyclic dipeptide biosynthesis, click here
Glossary: cyclo(L-tyrosyl-L-tyrosyl) = (3S,6S)-3,6-bis[(4-hydroxyphenyl)methyl]piperazine-2,5-dione
Other name(s): Rv2275 (gene name); cYY synthase; cyclodityrosine synthase
Systematic name: L-tyrosyl-tRNATyr:L-tyrosyl-tRNATyr tyrosyltransferase (cyclizing)
Comments: The reaction proceeds following a ping-pong mechanism forming a covalent intermediate between an active site serine and the first L-tyrosine residue [2]. The protein, from the bacterium Mycobacterium tuberculosis, also forms small amounts of cyclo(L-tyrosyl-L-phenylalanyl) [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Gondry, M., Sauguet, L., Belin, P., Thai, R., Amouroux, R., Tellier, C., Tuphile, K., Jacquet, M., Braud, S., Courcon, M., Masson, C., Dubois, S., Lautru, S., Lecoq, A., Hashimoto, S., Genet, R. and Pernodet, J.L. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat. Chem. Biol. 5 (2009) 414–420. [PMID: 19430487]
2.  Vetting, M.W., Hegde, S.S. and Blanchard, J.S. The structure and mechanism of the Mycobacterium tuberculosis cyclodityrosine synthetase. Nat. Chem. Biol. 6 (2010) 797–799. [PMID: 20852636]
[EC 2.3.2.21 created 2013]
 
 
EC 2.3.2.22
Accepted name: cyclo(L-leucyl-L-leucyl) synthase
Reaction: 2 L-leucyl-tRNALeu = 2 tRNALeu + cyclo(L-leucyl-L-leucyl)
For diagram of cyclic dipeptide biosynthesis, click here
Glossary: cyclo(L-leucyl-L-leucyl) = (3S,6S)-3,6-bis(2-methylpropyl)piperazine-2,5-dione
Other name(s): YvmC; cLL synthase; cyclodileucine synthase
Systematic name: L-leucyl-tRNALeu:L-leucyl-tRNALeu leucyltransferase (cyclizing)
Comments: The reaction proceeds following a ping-pong mechanism forming a covalent intermediate between an active site serine and the first L-leucine residue [2]. The proteins from bacteria of the genus Bacillus also form small amounts of cyclo(L-phenylalanyl-L-leucyl) and cyclo(L-leucyl-L-methionyl) [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Gondry, M., Sauguet, L., Belin, P., Thai, R., Amouroux, R., Tellier, C., Tuphile, K., Jacquet, M., Braud, S., Courcon, M., Masson, C., Dubois, S., Lautru, S., Lecoq, A., Hashimoto, S., Genet, R. and Pernodet, J.L. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat. Chem. Biol. 5 (2009) 414–420. [PMID: 19430487]
2.  Bonnefond, L., Arai, T., Sakaguchi, Y., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog. Proc. Natl. Acad. Sci. USA 108 (2011) 3912–3917. [PMID: 21325056]
[EC 2.3.2.22 created 2013]
 
 
*EC 2.4.2.2
Accepted name: pyrimidine-nucleoside phosphorylase
Reaction: (1) uridine + phosphate = uracil + α-D-ribose 1-phosphate
(2) thymidine + phosphate = thymine + 2-deoxy-α-D-ribose 1-phosphate
(3) 2′-deoxyuridine + phosphate = uracil + 2-deoxy-α-D-ribose 1-phosphate
Other name(s): Py-NPase; pdp (gene name)
Systematic name: pyrimidine-nucleoside:phosphate (2′-deoxy)-α-D-ribosyltransferase
Comments: Unlike EC 2.4.2.3, uridine phosphorylase, and EC 2.4.2.4, thymidine phosphorylase, this enzyme can accept both the ribonucleoside uridine and the 2′-deoxyribonucleosides 2′-deoxyuridine and thymidine [3]. The reaction is reversible, and the enzyme does not distinguish between α-D-ribose 1-phosphate and 2-deoxy-α-D-ribose 1-phosphate in the synthetic direction.
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, CAS registry number: 9055-35-0
References:
1.  Friedkin, M. and Kalckar, H. Nucleoside phosphorylases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 237–255.
2.  Saunders, P.P., Wilson, B.A. and Saunders, G.F. Purification and comparative properties of a pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus. J. Biol. Chem. 244 (1969) 3691–3697. [PMID: 4978445]
3.  Hamamoto, T., Noguchi, T. and Midorikawa, Y. Purification and characterization of purine nucleoside phosphorylase and pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus TH 6-2. Biosci. Biotechnol. Biochem. 60 (1996) 1179–1180. [PMID: 8782414]
4.  Okuyama, K., Hamamoto, T., Noguchi, T. and Midorikawa, Y. Molecular cloning and expression of the pyrimidine nucleoside phosphorylase gene from Bacillus stearothermophilus TH 6-2. Biosci. Biotechnol. Biochem. 60 (1996) 1655–1659. [PMID: 8987664]
5.  Pugmire, M.J. and Ealick, S.E. The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation. Structure 6 (1998) 1467–1479. [PMID: 9817849]
[EC 2.4.2.2 created 1961]
 
 
EC 2.4.2.11
Transferred entry: nicotinate phosphoribosyltransferase. Now EC 6.3.4.21, nicotinate phosphoribosyltransferase.
[EC 2.4.2.11 created 1961, deleted 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 2.4.2.36
Accepted name: NAD+—diphthamide ADP-ribosyltransferase
Reaction: NAD+ + diphthamide-[translation elongation factor 2] = nicotinamide + N-(ADP-D-ribosyl)diphthamide-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Glossary: diphthamide = 2-[4-amino-4-oxo-3-(trimethylammonio)butyl]-L-histidine
Other name(s): ADP-ribosyltransferase; mono(ADPribosyl)transferase; NAD—diphthamide ADP-ribosyltransferase; NAD+:peptide-diphthamide N-(ADP-D-ribosyl)transferase
Systematic name: NAD+:diphthamide-[translation elongation factor 2] N-(ADP-D-ribosyl)transferase
Comments: Diphtheria toxin and some other bacterial toxins catalyse this reaction, which inactivates translation elongation factor 2 (EF2). The acceptor is diphthamide, a unique modification of a histidine residue in the elongation factor found in archaebacteria and all eukaryotes, but not in eubacteria. cf. EC 2.4.2.31 NAD(P)+—protein-arginine ADP-ribosyltransferase. The relevant histidine of EF2 is His715 in mammals, His699 in yeast and His600 in Pyrococcus horikoshii.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 52933-21-8
References:
1.  Lee, H. and Iglewski, W.J. Cellular ADP-ribosyltransferase with the same mechanism of action as diphtheria toxin and Pseudomonas toxin A. Proc. Natl. Acad. Sci. USA 81 (1984) 2703–2707. [PMID: 6326138]
2.  Ueda, K. and Hayaishi, O. ADP-ribosylation. Annu. Rev. Biochem. 54 (1985) 73–100. [PMID: 3927821]
[EC 2.4.2.36 created 1990, modified 2013]
 
 
EC 2.4.2.52
Accepted name: triphosphoribosyl-dephospho-CoA synthase
Reaction: ATP + 3′-dephospho-CoA = 2′-(5-triphospho-α-D-ribosyl)-3′-dephospho-CoA + adenine
For diagram of holo-citrate-lyase biosynthesis, click here
Other name(s): 2′-(5′′-triphosphoribosyl)-3-dephospho-CoA synthase; ATP:dephospho-CoA 5-triphosphoribosyl transferase; CitG; ATP:dephospho-CoA 5′-triphosphoribosyl transferase; MdcB; ATP:3-dephospho-CoA 5′′-triphosphoribosyltransferase; MadG
Systematic name: ATP:3′-dephospho-CoA 5-triphospho-α-D-ribosyltransferase
Comments: ATP cannot be replaced by GTP, CTP, UTP, ADP or AMP. The reaction involves the formation of a new α (1′′→2′) glycosidic bond between the two ribosyl moieties, with concomitant displacement of the adenine moiety of ATP [1,4]. The 2′-(5-triphosphoribosyl)-3′-dephospho-CoA produced can be transferred by EC 2.7.7.61, citrate lyase holo-[acyl-carrier protein] synthase, to the apo-acyl-carrier protein subunit (γ-subunit) of EC 4.1.3.6, citrate (pro-3S) lyase, thus converting it from an apo-enzyme into a holo-enzyme [1,3]. Alternatively, it can be transferred to the apo-ACP subunit of malonate decarboxylase by the action of EC 2.7.7.66, malonate decarboxylase holo-[acyl-carrier protein] synthase [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 313345-38-9
References:
1.  Schneider, K., Dimroth, P. and Bott, M. Biosynthesis of the prosthetic group of citrate lyase. Biochemistry 39 (2000) 9438–9450. [PMID: 10924139]
2.  Schneider, K., Dimroth, P. and Bott, M. Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group. FEBS Lett. 483 (2000) 165–168. [PMID: 11042274]
3.  Schneider, K., Kästner, C.N., Meyer, M., Wessel, M., Dimroth, P. and Bott, M. Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group. J. Bacteriol. 184 (2002) 2439–2446. [PMID: 11948157]
4.  Hoenke, S., Wild, M.R. and Dimroth, P. Biosynthesis of triphosphoribosyl-dephospho-coenzyme A, the precursor of the prosthetic group of malonate decarboxylase. Biochemistry 39 (2000) 13223–13232. [PMID: 11052675]
[EC 2.4.2.52 created 2002 as EC 2.7.8.25, modified 2008, transferred 2013 to EC 2.4.2.52]
 
 
EC 2.4.2.53
Accepted name: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Reaction: UDP-4-deoxy-4-formamido-β-L-arabinopyranose + ditrans,octacis-undecaprenyl phosphate = UDP + 4-deoxy-4-formamido-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate
For diagram of UDP-4-amino-4-deoxy-β-L-arabinose biosynthesis, click here
Other name(s): undecaprenyl-phosphate Ara4FN transferase; Ara4FN transferase; polymyxin resistance protein PmrF; UDP-4-amino-4-deoxy-α-L-arabinose:ditrans,polycis-undecaprenyl phosphate 4-amino-4-deoxy-α-L-arabinosyltransferase
Systematic name: UDP-4-amino-4-deoxy-α-L-arabinose:ditrans,octacis-undecaprenyl phosphate 4-amino-4-deoxy-α-L-arabinosyltransferase
Comments: The enzyme shows no activity with UDP-4-amino-4-deoxy-β-L-arabinose.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Breazeale, S.D., Ribeiro, A.A. and Raetz, C.R. Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy-L-arabinose. J. Biol. Chem. 277 (2002) 2886–2896. [PMID: 11706007]
2.  Breazeale, S.D., Ribeiro, A.A., McClerren, A.L. and Raetz, C.R.H. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-amino-4-deoxy-L-arabinose. Identification and function of UDP-4-deoxy-4-formamido-L-arabinose. J. Biol. Chem. 280 (2005) 14154–14167. [PMID: 15695810]
[EC 2.4.2.53 created 2010 as EC 2.7.8.30, modified 2011, transferred 2013 to EC 2.4.2.53]
 
 
EC 2.4.2.54
Accepted name: β-ribofuranosylphenol 5′-phosphate synthase
Reaction: 5-phospho-α-D-ribose 1-diphosphate + 4-hydroxybenzoate = 4-(β-D-ribofuranosyl)phenol 5′-phosphate + CO2 + diphosphate
For diagram of methanopterin biosynthesis (part 2), click here
Other name(s): β-RFAP synthase (incorrect); β-RFA-P synthase (incorrect); AF2089 (gene name); MJ1427 (gene name); β-ribofuranosylhydroxybenzene 5′-phosphate synthase; 4-(β-D-ribofuranosyl)aminobenzene 5′-phosphate synthase (incorrect); β-ribofuranosylaminobenzene 5′-phosphate synthase (incorrect); 5-phospho-α-D-ribose 1-diphosphate:4-aminobenzoate 5-phospho-β-D-ribofuranosyltransferase (decarboxylating) (incorrect)
Systematic name: 5-phospho-α-D-ribose-1-diphosphate:4-hydroxybenzoate 5-phospho-β-D-ribofuranosyltransferase (decarboxylating)
Comments: The enzyme is involved in biosynthesis of tetrahydromethanopterin in archaea. It was initially thought to use 4-aminobenzoate as a substrate, but was later shown to utilize 4-hydroxybenzoate [4]. The activity is dependent on Mg2+ or Mn2+ [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Rasche, M.E. and White, R.H. Mechanism for the enzymatic formation of 4-(β-D-ribofuranosyl)aminobenzene 5′-phosphate during the biosynthesis of methanopterin. Biochemistry 37 (1998) 11343–11351. [PMID: 9698382]
2.  Scott, J.W. and Rasche, M.E. Purification, overproduction, and partial characterization of β-RFAP synthase, a key enzyme in the methanopterin biosynthesis pathway. J. Bacteriol. 184 (2002) 4442–4448. [PMID: 12142414]
3.  Dumitru, R.V. and Ragsdale, S.W. Mechanism of 4-(β-D-ribofuranosyl)aminobenzene 5′-phosphate synthase, a key enzyme in the methanopterin biosynthetic pathway. J. Biol. Chem. 279 (2004) 39389–39395. [PMID: 15262968]
4.  White, R.H. The conversion of a phenol to an aniline occurs in the biochemical formation of the 1-(4-aminophenyl)-1-deoxy-D-ribitol moiety in methanopterin. Biochemistry 50 (2011) 6041–6052. [PMID: 21634403]
[EC 2.4.2.54 created 2013, modified 2014, modified 2015]
 
 
EC 2.5.1.104
Accepted name: N1-aminopropylagmatine synthase
Reaction: S-adenosyl 3-(methylthio)propylamine + agmatine = S-methyl-5′-thioadenosine + N1-(3-aminopropyl)agmatine
For diagram of spermidine biosynthesis, click here
Glossary: 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): agmatine/cadaverine aminopropyl transferase; ACAPT; PF0127 (gene name); triamine/agmatine aminopropyltransferase; SpeE; agmatine aminopropyltransferase
Systematic name: S-adenosyl 3-(methylthio)propylamine:agmatine 3-aminopropyltransferase
Comments: The enzyme is involved in the biosynthesis of spermidine from agmatine in some archaea and bacteria. The enzyme from the Gram-negative bacterium Thermus thermophilus accepts agmatine, spermidine and norspermidine with similar catalytic efficiency. The enzymes from the archaea Pyrococcus furiosus and Thermococcus kodakarensis prefer agmatine, but can utilize cadaverine, putrescine and propane-1,3-diamine with much lower catalytic efficiency. cf. EC 2.5.1.16, spermidine synthase, and EC 2.5.1.23, sym-norspermidine synthase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ohnuma, M., Terui, Y., Tamakoshi, M., Mitome, H., Niitsu, M., Samejima, K., Kawashima, E. and Oshima, T. N1-aminopropylagmatine, a new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus. J. Biol. Chem. 280 (2005) 30073–30082. [PMID: 15983049]
2.  Cacciapuoti, G., Porcelli, M., Moretti, M.A., Sorrentino, F., Concilio, L., Zappia, V., Liu, Z.J., Tempel, W., Schubot, F., Rose, J.P., Wang, B.C., Brereton, P.S., Jenney, F.E. and Adams, M.W. The first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 189 (2007) 6057–6067. [PMID: 17545282]
3.  Morimoto, N., Fukuda, W., Nakajima, N., Masuda, T., Terui, Y., Kanai, T., Oshima, T., Imanaka, T. and Fujiwara, S. Dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 192 (2010) 4991–5001. [PMID: 20675472]
4.  Ohnuma, M., Ganbe, T., Terui, Y., Niitsu, M., Sato, T., Tanaka, N., Tamakoshi, M., Samejima, K., Kumasaka, T. and Oshima, T. Crystal structures and enzymatic properties of a triamine/agmatine aminopropyltransferase from Thermus thermophilus. J. Mol. Biol. 408 (2011) 971–986. [PMID: 21458463]
[EC 2.5.1.104 created 2013]
 
 
EC 2.5.1.105
Accepted name: 7,8-dihydropterin-6-yl-methyl-4-(β-D-ribofuranosyl)aminobenzene 5′-phosphate synthase
Reaction: (7,8-dihydropterin-6-yl)methyl diphosphate + 4-(β-D-ribofuranosyl)aniline 5′-phosphate = N-[(7,8-dihydropterin-6-yl)methyl]-4-(β-D-ribofuranosyl)aniline 5′-phosphate + diphosphate
For diagram of methanopterin biosynthesis (part 2), click here
Other name(s): MJ0301 (gene name); dihydropteroate synthase (ambiguous)
Systematic name: (7,8-dihydropterin-6-yl)methyl diphosphate:4-(β-D-ribofuranosyl)aniline 5′-phosphate 6-hydroxymethyl-7,8-dihydropterintransferase
Comments: The enzyme, which has been studied in the archaeon Methanocaldococcus jannaschii, is involved in the biosynthesis of tetrahydromethanopterin.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Xu, H., Aurora, R., Rose, G.D. and White, R.H. Identifying two ancient enzymes in Archaea using predicted secondary structure alignment. Nat. Struct. Biol. 6 (1999) 750–754. [PMID: 10426953]
[EC 2.5.1.105 created 2013]
 
 
EC 2.5.1.106
Accepted name: tryprostatin B synthase
Reaction: dimethylallyl diphosphate + brevianamide F = diphosphate + tryprostatin B
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
tryprostatin B = (3S,8aS)-3-{[2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
Other name(s): ftmPT1 (gene name); brevianamide F prenyltransferase (ambiguous)
Systematic name: dimethylallyl-diphosphate:brevianamide-F dimethylallyl-C-2-transferase
Comments: The enzyme from the fungus Aspergillus fumigatus can also prenylate other tryptophan-containing cyclic dipeptides. Prenylation occurs mainly at C-2 [1], but also at C-3 [2]. Involved in the biosynthetic pathways of several indole alkaloids such as tryprostatins, cyclotryprostatins, spirotryprostatins, fumitremorgins and verruculogen.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Grundmann, A. and Li, S.M. Overproduction, purification and characterization of FtmPT1, a brevianamide F prenyltransferase from Aspergillus fumigatus. Microbiology 151 (2005) 2199–2207. [PMID: 16000710]
2.  Wollinsky, B., Ludwig, L., Xie, X. and Li, S.M. Breaking the regioselectivity of indole prenyltransferases: identification of regular C3-prenylated hexahydropyrrolo[2,3-b]indoles as side products of the regular C2-prenyltransferase FtmPT1. Org. Biomol. Chem. 10 (2012) 9262–9270. [PMID: 23090579]
[EC 2.5.1.106 created 2013]
 
 
EC 2.5.1.107
Accepted name: verruculogen prenyltransferase
Reaction: dimethylallyl diphosphate + verruculogen = diphosphate + fumitremorgin A
For diagram of fumitremorgin alkaloid biosynthesis (part 2), click here
Glossary: 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
fumitremorgin A = (5R,10S,10aR,14aS,15bS)-10a-hydroxy-7-methoxy-2,2-dimethyl-10-[(3-methylbut-2-en-1-yl)oxy]-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(H,13H)-dione
Other name(s): FtmPT3
Systematic name: dimethylallyl-diphosphate:verruculogen dimethylallyl-O-transferase
Comments: Found in a number of fungi. Catalyses the last step in the biosynthetic pathway of the indole alkaloid fumitremorgin A. The enzyme from the fungus Neosartorya fischeri is also active with fumitremorgin B and 12α,13α-dihydroxyfumitremorgin C.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Mundt, K., Wollinsky, B., Ruan, H.L., Zhu, T. and Li, S.M. Identification of the verruculogen prenyltransferase FtmPT3 by a combination of chemical, bioinformatic and biochemical approaches. ChemBioChem. 13 (2012) 2583–2592. [PMID: 23109474]
[EC 2.5.1.107 created 2013]
 
 
*EC 2.6.1.34
Accepted name: UDP-N-acetylbacillosamine transaminase
Reaction: UDP-N-acetylbacillosamine + 2-oxoglutarate = UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose + L-glutamate
For diagram of legionaminic acid biosynthesis, click here
Glossary: UDP-N-acetylbacillosamine = UDP-2-acetamido-4-amino-2,4,6-trideoxy-α-D-glucose = UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine
Other name(s): uridine diphospho-4-amino-2-acetamido-2,4,6-trideoxyglucose aminotransferase; UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine transaminase; UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose transaminase; pglE (gene name); UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose:2-oxoglutarate aminotransferase
Systematic name: UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine:2-oxoglutarate aminotransferase
Comments: A pyridoxal-phosphate protein. The enzyme is involved in biosynthesis of UDP-N,N′-diacetylbacillosamine, an intermediate in protein glycosylation pathways in several bacterial species, including N-linked glycosylation of certain L-asparagine residues in Campylobacter species [2-4] and O-linked glycosylation of certain L-serine residues in Neisseria species [5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 37277-89-7
References:
1.  Distler, J., Kaufman, B. and Roseman, S. Enzymic synthesis of a diamino sugar nucleotide by extracts of type XIV Diplococcus pneumoniae. Arch. Biochem. Biophys. 116 (1966) 466–478. [PMID: 4381351]
2.  Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N′-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659–13669. [PMID: 17087520]
3.  Schoenhofen, I.C., McNally, D.J., Vinogradov, E., Whitfield, D., Young, N.M., Dick, S., Wakarchuk, W.W., Brisson, J.R. and Logan, S.M. Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281 (2006) 723–732. [PMID: 16286454]
4.  Rangarajan, E.S., Ruane, K.M., Sulea, T., Watson, D.C., Proteau, A., Leclerc, S., Cygler, M., Matte, A. and Young, N.M. Structure and active site residues of PglD, an N-acetyltransferase from the bacillosamine synthetic pathway required for N-glycan synthesis in Campylobacter jejuni. Biochemistry 47 (2008) 1827–1836. [PMID: 18198901]
5.  Hartley, M.D., Morrison, M.J., Aas, F.E., Borud, B., Koomey, M. and Imperiali, B. Biochemical characterization of the O-linked glycosylation pathway in Neisseria gonorrhoeae responsible for biosynthesis of protein glycans containing N,N′-diacetylbacillosamine. Biochemistry 50 (2011) 4936–4948. [PMID: 21542610]
[EC 2.6.1.34 created 1972, modified 2013]
 
 
EC 2.6.1.91
Deleted entry: UDP-4-amino-4,6-dideoxy-N-acetyl-α-D-glucosamine transaminase. Identical to EC 2.6.1.34, UDP-N-acetylbacillosamine transaminase.
[EC 2.6.1.91 created 2011, deleted 2013]
 
 
EC 2.7.1.178
Accepted name: 2-dehydro-3-deoxyglucono/galactono-kinase
Reaction: (1) ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 2-dehydro-3-deoxy-6-phospho-D-gluconate
(2) ATP + 2-dehydro-3-deoxy-D-galactonate = ADP + 2-dehydro-3-deoxy-6-phospho-D-galactonate
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): KDG kinase (ambiguous); KDGK (ambiguous); 2-keto-3-deoxy-D-gluconate kinase (ambiguous)
Systematic name: ATP:2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-D-galactonate 6-phosphotransferase
Comments: The enzyme from the archaeon Sulfolobus solfataricus is involved in glucose and galactose catabolism via the branched variant of the Entner-Doudoroff pathway. It phosphorylates 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate with similar catalytic efficiency. cf. EC 2.7.1.45, 2-dehydro-3-deoxygluconokinase and EC 2.7.1.58, 2-dehydro-3-deoxygalactonokinase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lamble, H.J., Theodossis, A., Milburn, C.C., Taylor, G.L., Bull, S.D., Hough, D.W. and Danson, M.J. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett. 579 (2005) 6865–6869. [PMID: 16330030]
2.  Potter, J.A., Kerou, M., Lamble, H.J., Bull, S.D., Hough, D.W., Danson, M.J. and Taylor, G.L. The structure of Sulfolobus solfataricus 2-keto-3-deoxygluconate kinase. Acta Crystallogr. D Biol. Crystallogr. 64 (2008) 1283–1287. [PMID: 19018105]
3.  Kim, S. and Lee, S.B. Characterization of Sulfolobus solfataricus 2-keto-3-deoxy-D-gluconate kinase in the modified Entner-Doudoroff pathway. Biosci. Biotechnol. Biochem. 70 (2006) 1308–1316. [PMID: 16794308]
[EC 2.7.1.178 created 2013]
 
 
EC 2.7.1.179
Accepted name: kanosamine kinase
Reaction: ATP + kanosamine = ADP + kanosamine 6-phosphate
Glossary: kanosamine = 3-amino-3-deoxy-D-glucose
Other name(s): rifN (gene name)
Systematic name: ATP:kanosamine 6-phosphotransferase
Comments: The enzyme from the bacterium Amycolatopsis mediterranei is specific for kanosamine.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Arakawa, K., Muller, R., Mahmud, T., Yu, T.W. and Floss, H.G. Characterization of the early stage aminoshikimate pathway in the formation of 3-amino-5-hydroxybenzoic acid: the RifN protein specifically converts kanosamine into kanosamine 6-phosphate. J. Am. Chem. Soc. 124 (2002) 10644–10645. [PMID: 12207505]
[EC 2.7.1.179 created 2013]
 
 
EC 2.7.7.54
Deleted entry: phenylalanine adenylyltransferase. The activity is part of EC 6.3.2.40, cyclopeptine synthase.
[EC 2.7.7.54 created 1989, deleted 2013]
 
 
EC 2.7.7.55
Deleted entry: anthranilate adenylyltransferase. The activity is part of EC 6.3.2.40, cyclopeptine synthase.
[EC 2.7.7.55 created 1989, deleted 2013]
 
 
EC 2.7.7.85
Accepted name: diadenylate cyclase
Reaction: 2 ATP = 2 diphosphate + cyclic di-3′,5′-adenylate
Glossary: cyclic di-3′,5′-adenylate = c-di-AMP = c-di-adenylate = cyclic-bis(3′→5′) dimeric AMP
Other name(s): cyclic-di-AMP synthase; dacA (gene name); disA (gene name)
Systematic name: ATP:ATP adenylyltransferase (cyclizing)
Comments: Cyclic di-3′,5′-adenylate is a bioactive molecule produced by some bacteria and archaea, which may function as a secondary signalling molecule [1]. The intracellular bacterial pathogen Listeria monocytogenes secretes it into the host’s cytosol, where it triggers a cytosolic pathway of innate immunity [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Witte, G., Hartung, S., Buttner, K. and Hopfner, K.P. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol. Cell 30 (2008) 167–178. [PMID: 18439896]
2.  Woodward, J.J., Iavarone, A.T. and Portnoy, D.A. c-di-AMP secreted by intracellular Listeria monocytogenes activates a host type I interferon response. Science 328 (2010) 1703–1705. [PMID: 20508090]
[EC 2.7.7.85 created 2013]
 
 
EC 2.7.8.25
Transferred entry: triphosphoribosyl-dephospho-CoA synthase. Now EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase
[EC 2.7.8.25 created 2002, modified 2008, deleted 2013]
 
 
EC 2.7.8.30
Transferred entry: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase. Now EC 2.4.2.53, undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
[EC 2.7.8.30 created 2010, modified 2011, deleted 2013]
 
 
EC 2.8.3.18
Accepted name: succinyl-CoA:acetate CoA-transferase
Reaction: succinyl-CoA + acetate = acetyl-CoA + succinate
Other name(s): aarC (gene name); SCACT
Systematic name: succinyl-CoA:acetate CoA-transferase
Comments: In acetic acid bacteria the enzyme, which is highly specific, catalyses the conversion of toxic acetate to acetyl-CoA [2,3]. In the hydrogenosomes of some trichomonads the enzyme catalyses the production of acetate [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Steinbuchel, A. and Muller, M. Anaerobic pyruvate metabolism of Tritrichomonas foetus and Trichomonas vaginalis hydrogenosomes. Mol. Biochem. Parasitol. 20 (1986) 57–65. [PMID: 3090435]
2.  Mullins, E.A., Francois, J.A. and Kappock, T.J. A specialized citric acid cycle requiring succinyl-coenzyme A (CoA):acetate CoA-transferase (AarC) confers acetic acid resistance on the acidophile Acetobacter aceti. J. Bacteriol. 190 (2008) 4933–4940. [PMID: 18502856]
3.  Mullins, E.A. and Kappock, T.J. Crystal structures of Acetobacter aceti succinyl-coenzyme A (CoA):acetate CoA-transferase reveal specificity determinants and illustrate the mechanism used by class I CoA-transferases. Biochemistry 51 (2012) 8422–8434. [PMID: 23030530]
[EC 2.8.3.18 created 2013]
 
 
EC 3.1.1.94
Accepted name: versiconal hemiacetal acetate esterase
Reaction: (1) versiconal hemiacetal acetate + H2O = versiconal + acetate
(2) versiconol acetate + H2O = versiconol + acetate
For diagram of aflatoxin biosynthesis (part 2), click here
Glossary: versiconal = (2S,3S)-2,4,6,8-tetrahydroxy-3-(2-hydroxyethyl)anthra[2,3-b]furan-5,10-dione
versiconal hemiacetal acetate = 2-[(2S,3S)-2,4,6,8-tetrahydroxy-5,10-dioxo-5,10-dihydroanthra[2,3-b]furan-3-yl]ethyl acetate
versiconol = 1,3,6,8-tetrahydroxy-3-[(2S)-1,4-dihydroxybutan-2-yl]anthracene-5,10-dione
versiconol acetate = (3S)-4-hydroxy-3-[1,3,6,8-tetrahydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl]butyl acetate
Other name(s): VHA esterase
Systematic name: versiconal-hemiacetal-acetate O-acetylhydrolase
Comments: Isolated from the mold Aspergillus parasiticus. Involved in a metabolic grid that leads to aflatoxin biosynthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kusumoto, K. and Hsieh, D.P. Purification and characterization of the esterases involved in aflatoxin biosynthesis in Aspergillus parasiticus. Can. J. Microbiol. 42 (1996) 804–810. [PMID: 8776851]
2.  Chang, P.K., Yabe, K. and Yu, J. The Aspergillus parasiticus estA-encoded esterase converts versiconal hemiacetal acetate to versiconal and versiconol acetate to versiconol in aflatoxin biosynthesis. Appl. Environ. Microbiol. 70 (2004) 3593–3599. [PMID: 15184162]
[EC 3.1.1.94 created 2013]
 
 
EC 3.1.3.89
Accepted name: 5′-deoxynucleotidase
Reaction: a 2′-deoxyribonucleoside 5′-monophosphate + H2O = a 2′-deoxyribonucleoside + phosphate
Other name(s): yfbR (gene name)
Systematic name: 2′-deoxyribonucleoside 5′-monophosphate phosphohydrolase
Comments: The enzyme, characterized from the bacterium Escherichia coli, shows strict specificity towards deoxyribonucleoside 5′-monophosphates and does not dephosphorylate 5′-ribonucleotides or ribonucleoside 3′-monophosphates. A divalent metal cation is required for activity, with cobalt providing the highest activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Proudfoot, M., Kuznetsova, E., Brown, G., Rao, N.N., Kitagawa, M., Mori, H., Savchenko, A. and Yakunin, A.F. General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG. J. Biol. Chem. 279 (2004) 54687–54694. [PMID: 15489502]
2.  Zimmerman, M.D., Proudfoot, M., Yakunin, A. and Minor, W. Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5′-deoxyribonucleotidase YfbR from Escherichia coli. J. Mol. Biol. 378 (2008) 215–226. [PMID: 18353368]
[EC 3.1.3.89 created 2013]
 
 
EC 3.1.4.56
Accepted name: 7,8-dihydroneopterin 2′,3′-cyclic phosphate phosphodiesterase
Reaction: (1) 7,8-dihydroneopterin 2′,3′-cyclic phosphate + H2O = 7,8-dihydroneopterin 3′-phosphate
(2) 7,8-dihydroneopterin 2′,3′-cyclic phosphate + H2O = 7,8-dihydroneopterin 2′-phosphate
For diagram of methanopterin biosynthesis (part 1), click here
Glossary: 7,8-dihydroneopterin 2′,3′-cyclic phosphate = 2-amino-6-{(S)-hydroxy[(4R)-2-hydroxy-2-oxido-1,3,2-dioxaphospholan-4-yl]methyl}-7,8-dihydropteridin-4(1H)-one = 2-amino-6-[(1S,2R)-1,2,3-trihydroxypropyl]-7,8-dihydro-4(1H)-pteridinone 1,2-cyclic phosphate
7,8-dihydroeopterin 3′-phosphate = (2R,3S)-3-(2-amino-4-oxo-1,4,7,8-tetrahydropteridin-6-yl)-2,3-dihydroxypropyl phosphate
7,8-dihydroneopterin 2′-phosphate = (1S,2R)-1-(2-amino-4-oxo-1,4,7,8-tetrahydropteridin-6-yl)-1,3-dihydroxypropan-2-yl phosphate
Other name(s): MptB
Systematic name: 7,8-dihydroneopterin 2′,3′-cyclic phosphate 2′/3′-phosphodiesterase
Comments: Contains one zinc atom and one iron atom per subunit of the dodecameric enzyme. It hydrolyses 7,8-dihydroneopterin 2′,3′-cyclic phosphate, a step in tetrahydromethanopterin biosynthesis. In vitro the enzyme forms 7,8-dihydroneopterin 2′-phosphate and 7,8-dihydroneopterin 3′-phosphate at a ratio of 4:1.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Mashhadi, Z., Xu, H. and White, R.H. An Fe2+-dependent cyclic phosphodiesterase catalyzes the hydrolysis of 7,8-dihydro-D-neopterin 2′,3′-cyclic phosphate in methanopterin biosynthesis. Biochemistry 48 (2009) 9384–9392. [PMID: 19746965]
[EC 3.1.4.56 created 2013]
 
 
EC 3.1.6.19
Accepted name: (R)-specific secondary-alkylsulfatase
Reaction: an (R)-secondary-alkyl sulfate + H2O = an (S)-secondary-alcohol + sulfate
Other name(s): S3 secondary alkylsulphohydrolase; Pisa1; secondary alkylsulphohydrolase; (R)-specific sec-alkylsulfatase; sec-alkylsulfatase
Systematic name: (R)-secondary-alkyl sulfate sulfohydrolase [(S)-secondary-alcohol forming]
Comments: The enzyme from Rhodococcus ruber is involved in the biodegradation of alkyl sulfate esters used as detergents and released into the environment. The prefered substrates are linear secondary-alkyl sulfate esters, particularly octan-2-yl, octan-3-yl, and octan-4-yl sulfates [1]. The enzyme from Pseudomonas sp. DSM6611 utilizes a range of secondary-alkyl sulfate esters bearing aromatic, olefinic and acetylenic moieties. Perfect enantioselectivities are obtained for substrates bearing groups of different size adjacent to the sulfate moiety [4]. The enzymic hydrolysis proceeds through inversion of the configuration at the stereogenic carbon atom [1,4]. The enzyme contains a Zn2+ ion [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Pogorevc, M. and Faber, K. Purification and characterization of an inverting stereo- and enantioselective sec-alkylsulfatase from the gram-positive bacterium Rhodococcus ruber DSM 44541. Appl. Environ. Microbiol. 69 (2003) 2810–2815. [PMID: 12732552]
2.  Wallner, S.R., Nestl, B.M. and Faber, K. Highly enantioselective sec-alkyl sulfatase activity of Sulfolobus acidocaldarius DSM 639. Org. Lett. 6 (2004) 5009–5010. [PMID: 15606122]
3.  Knaus, T., Schober, M., Kepplinger, B., Faccinelli, M., Pitzer, J., Faber, K., Macheroux, P. and Wagner, U. Structure and mechanism of an inverting alkylsulfatase from Pseudomonas sp. DSM6611 specific for secondary alkyl sulfates. FEBS J. 279 (2012) 4374–4384. [PMID: 23061549]
4.  Schober, M., Knaus, T., Toesch, M., Macheroux, P., Wagner, U. and Faber, K. The substrate spectrum of the inverting sec-alkylsulfatase Pisa1. Adv. Synth. Catal. 354 (2012) 1737–1742.
[EC 3.1.6.19 created 2013]
 
 
*EC 3.2.1.10
Accepted name: oligo-1,6-glucosidase
Reaction: Hydrolysis of (1→6)-α-D-glucosidic linkages in some oligosaccharides produced from starch and glycogen by EC 3.2.1.1 (α-amylase), and in isomaltose
Other name(s): limit dextrinase (erroneous); isomaltase; sucrase-isomaltase; exo-oligo-1,6-glucosidase; dextrin 6α-glucanohydrolase; α-limit dextrinase; dextrin 6-glucanohydrolase; oligosaccharide α-1,6-glucohydrolase; α-methylglucosidase
Systematic name: oligosaccharide 6-α-glucohydrolase
Comments: This enzyme, like EC 3.2.1.33 (amylo-α-1,6-glucosidase), can release an α-1→6-linked glucose, whereas the shortest chain that can be released by EC 3.2.1.41 (pullulanase), EC 3.2.1.142 (limit dextrinase), and EC 3.2.1.68 (isoamylase) is maltose. It also hydrolyses isomaltulose (palatinose), isomaltotriose and panose, but has no action on glycogen or phosphorylase limit dextrin. The enzyme from intestinal mucosa is a single polypeptide chain that also catalyses the reaction of EC 3.2.1.48 (sucrose α-glucosidase). Differs from EC 3.2.1.33 (amylo-α-1,6-glucosidase) in its preference for short-chain substrates and in its not requiring the 6-glucosylated residue to be at a branch point, i.e. linked at both C-1 and C-4.
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, CAS registry number: 9032-15-9
References:
1.  Hauri, H.-P., Quaroni, A. and Isselbacher, K.J. Biogenesis of intestinal plasma membrane: posttranslational route and cleavage of sucrase-isomaltase. Proc. Natl. Acad. Sci. USA 76 (1979) 5183–5186. [PMID: 291933]
2.  Sjöström, H., Norén, O., Christiansen, L., Wacker, H. and Semenza, G. A fully active, two-active-site, single-chain sucrase-isomaltase from pig small intestine. Implications for the biosynthesis of a mammalian integral stalked membrane protein. J. Biol. Chem. 255 (1980) 11332–11338. [PMID: 7002920]
3.  Rodriguez, I.R., Taravel, F.R. and Whelan, W.J. Characterization and function of pig intestinal sucrase-isomaltase and its separate subunits. Eur. J. Biochem. 143 (1984) 575–582. [PMID: 6479163]
4.  Khan, N.A. and Eaton, N.R. Purification and characterization of maltase and α-methyl glucosidase from yeast. Biochim. Biophys. Acta 146 (1967) 173–180. [PMID: 6060462]
5.  Yamamoto, K., Nakayama, A., Yamamoto, Y. and Tabata, S. Val216 decides the substrate specificity of α-glucosidase in Saccharomyces cerevisiae. Eur. J. Biochem. 271 (2004) 3414–3420. [PMID: 15291818]
[EC 3.2.1.10 created 1961, modified 2000, modified 2013]
 
 
*EC 3.2.1.55
Accepted name: non-reducing end α-L-arabinofuranosidase
Reaction: Hydrolysis of terminal non-reducing α-L-arabinofuranoside residues in α-L-arabinosides.
Other name(s): arabinosidase (ambiguous); α-arabinosidase; α-L-arabinosidase; α-arabinofuranosidase; polysaccharide α-L-arabinofuranosidase; α-L-arabinofuranoside hydrolase; L-arabinosidase (ambiguous); α-L-arabinanase
Systematic name: α-L-arabinofuranoside non-reducing end α-L-arabinofuranosidase
Comments: The enzyme acts on α-L-arabinofuranosides, α-L-arabinans containing (1,3)- and/or (1,5)-linkages, arabinoxylans and arabinogalactans. Some β-galactosidases (EC 3.2.1.23) and β-D-fucosidases (EC 3.2.1.38) also hydrolyse α-L-arabinosides. cf. EC 3.2.1.185, non-reducing end β-L-arabinofuranosidase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9067-74-7
References:
1.  Tagawa, K. and Kaji, A. Preparation of L-arabinose-containing polysaccharides and the action of an α-L-arabinofuranosidase on these polysaccharides. Carbohydr. Res. 11 (1969) 293–301.
2.  Kaji, A. and Tagawa, K. Purification, crystallization and amino acid composition of α-L-arabinofuranosidase from Aspergillus niger. Biochim. Biophys. Acta 207 (1970) 456–464. [PMID: 5452669]
3.  Kaji, A. and Yoshihara, O. Properties of purified α-L-arabinofuranosidase from Corticium rolfsii. Biochim. Biophys. Acta 250 (1971) 367–371. [PMID: 5143344]
4.  Margolles-Clark, E., Tenkanen, M., Nakari-Setala, T. and Penttila, M. Cloning of genes encoding α-L-arabinofuranosidase and β-xylosidase from Trichoderma reesei by expression in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 62 (1996) 3840–3846. [PMID: 8837440]
5.  Inacio, J.M., Correia, I.L. and de Sa-Nogueira, I. Two distinct arabinofuranosidases contribute to arabino-oligosaccharide degradation in Bacillus subtilis. Microbiology 154 (2008) 2719–2729. [PMID: 18757805]
[EC 3.2.1.55 created 1972, modified 1976 (EC 3.2.1.79 created 1972, incorporated 1976), modified 2013]
 
 
EC 3.2.1.185
Accepted name: non-reducing end β-L-arabinofuranosidase
Reaction: β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranose + H2O = 2 β-L-arabinofuranose
Other name(s): HypBA1
Systematic name: β-L-arabinofuranoside non-reducing end β-L-arabinofuranosidase
Comments: The enzyme, which was identified in the bacterium Bifidobacterium longum JCM1217, removes the β-L-arabinofuranose residue from the non-reducing end of multiple substrates, including β-L-arabinofuranosyl-hydroxyproline (Ara-Hyp), Ara2-Hyp, Ara3-Hyp, and β-L-arabinofuranosyl-(1→2)-1-O-methyl-β-L-arabinofuranose. In the presence of 1-alkanols, the enzyme demonstrates transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue. cf. EC 3.2.1.55, non-reducing end α-L-arabinofuranosidase
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Fujita, K., Takashi, Y., Obuchi, E., Kitahara, K. and Suganuma, T. Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 family member. J. Biol. Chem. 286 (2011) 38079–38085. [PMID: 21914802]
[EC 3.2.1.185 created 2013]
 
 
EC 3.3.2.12
Accepted name: oxepin-CoA hydrolase
Reaction: 2-oxepin-2(3H)-ylideneacetyl-CoA + H2O = 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde
For diagram of aerobic phenylacetate catabolism, click here
Glossary: oxepin-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA
Other name(s): paaZ (gene name)
Systematic name: 2-oxepin-2(3H)-ylideneacetyl-CoA hydrolase
Comments: The enzyme from Escherichia coli is a bifunctional fusion protein that also catalyses EC 1.17.1.7, 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase.Combined the two activities result in a two-step conversion of oxepin-CoA to 3-oxo-5,6-dehydrosuberyl-CoA, part of an aerobic phenylacetate degradation pathway [1,3,4]. The enzyme from Escherichia coli also exhibits enoyl-CoA hydratase activity utilizing crotonyl-CoA as a substrate [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ferrandez, A., Minambres, B., Garcia, B., Olivera, E.R., Luengo, J.M., Garcia, J.L. and Diaz, E. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J. Biol. Chem. 273 (1998) 25974–25986. [PMID: 9748275]
2.  Park, S.J. and Lee, S.Y. Identification and characterization of a new enoyl coenzyme A hydratase involved in biosynthesis of medium-chain-length polyhydroxyalkanoates in recombinant Escherichia coli. J. Bacteriol. 185 (2003) 5391–5397. [PMID: 12949091]
3.  Ismail, W., El-Said Mohamed, M., Wanner, B.L., Datsenko, K.A., Eisenreich, W., Rohdich, F., Bacher, A. and Fuchs, G. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli. Eur. J. Biochem. 270 (2003) 3047–3054. [PMID: 12846838]
4.  Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390–14395. [PMID: 20660314]
[EC 3.3.2.12 created 2011 as EC 3.7.1.16, transferred 2013 to EC 3.3.2.12]
 
 
EC 3.5.3.24
Accepted name: N1-aminopropylagmatine ureohydrolase
Reaction: N1-aminopropylagmatine + H2O = spermidine + urea
For diagram of spermidine biosynthesis, click here
Systematic name: N1-aminopropylagmatine amidinohydrolase
Comments: The enzyme, which has been characterized from the hyperthermophilic archaeon Pyrococcus kodakarensis and the thermophilic Gram-negative bacterium Thermus thermophilus, is involved in the biosynthesis of spermidine.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ohnuma, M., Terui, Y., Tamakoshi, M., Mitome, H., Niitsu, M., Samejima, K., Kawashima, E. and Oshima, T. N1-aminopropylagmatine, a new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus. J. Biol. Chem. 280 (2005) 30073–30082. [PMID: 15983049]
2.  Morimoto, N., Fukuda, W., Nakajima, N., Masuda, T., Terui, Y., Kanai, T., Oshima, T., Imanaka, T. and Fujiwara, S. Dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 192 (2010) 4991–5001. [PMID: 20675472]
[EC 3.5.3.24 created 2013]
 
 
*EC 3.5.4.5
Accepted name: cytidine deaminase
Reaction: (1) cytidine + H2O = uridine + NH3
(2) 2′-deoxycytidine + H2O = 2′-deoxyuridine + NH3
Other name(s): cytosine nucleoside deaminase; (deoxy)cytidine deaminase; cdd (gene name); CDA (gene name)
Systematic name: cytidine/2′-deoxycytidine aminohydrolase
Comments: Contains zinc. Catalyses the deamination of cytidine and 2′-deoxycytidine with similar efficiencies. The enzyme, which is widely distributed among organisms, is involved in salvage of both exogenous and endogenous cytidine and 2′-deoxycytidine for UMP synthesis.
Links to other databases: BRENDA, EXPASY, GTD, IUBMB, KEGG, PDB, CAS registry number: 9025-06-3
References:
1.  Roberts, D.W.A. The wheat leaf phosphatases. II. Pathway of hydrolysis of some nucleotides at pH 5.5. J. Biol. Chem. 222 (1956) 259–270. [PMID: 13366999]
2.  Wang, T.P., Sable, H.Z. and Lampen, J.O. Enzymatic deamination of cytosine nucleosides. J. Biol. Chem. 184 (1950) 17–28. [PMID: 15421968]
3.  Song, B.H. and Neuhard, J. Chromosomal location, cloning and nucleotide sequence of the Bacillus subtilis cdd gene encoding cytidine/deoxycytidine deaminase. Mol. Gen. Genet. 216 (1989) 462–468. [PMID: 2526291]
4.  Laliberte, J. and Momparler, R.L. Human cytidine deaminase: purification of enzyme, cloning, and expression of its complementary DNA. Cancer Res. 54 (1994) 5401–5407. [PMID: 7923172]
5.  Vincenzetti, S., Cambi, A., Neuhard, J., Schnorr, K., Grelloni, M. and Vita, A. Cloning, expression, and purification of cytidine deaminase from Arabidopsis thaliana. Protein Expr. Purif. 15 (1999) 8–15. [PMID: 10024464]
[EC 3.5.4.5 created 1961, modified 2013]
 
 
EC 3.5.4.14
Transferred entry: deoxycytidine deaminase. Now included in EC 3.5.4.5, (deoxy)cytidine deaminase
[EC 3.5.4.14 created 1972, transferred 2013 to EC 3.5.4.5., deleted 2013]
 
 
EC 3.5.4.37
Accepted name: double-stranded RNA adenine deaminase
Reaction: adenine in double-stranded RNA + H2O = hypoxanthine in double-stranded RNA + NH3
Other name(s): ADAR; double-stranded RNA adenosine deaminase; dsRAD; dsRNA adenosine deaminase; DRADA1; double-stranded RNA-specific adenosine deaminase
Systematic name: double-stranded RNA adenine aminohydrolase
Comments: This eukaryotic enzyme is involved in RNA editing. It destabilizes double-stranded RNA through conversion of adenosine to inosine. Inositol hexakisphosphate is required for activity [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Hough, R.F. and Bass, B.L. Purification of the Xenopus laevis double-stranded RNA adenosine deaminase. J. Biol. Chem. 269 (1994) 9933–9939. [PMID: 8144588]
2.  O'Connell, M.A., Gerber, A. and Keegan, L.P. Purification of native and recombinant double-stranded RNA-specific adenosine deaminases. Methods 15 (1998) 51–62. [PMID: 9614652]
3.  Wong, S.K., Sato, S. and Lazinski, D.W. Substrate recognition by ADAR1 and ADAR2. RNA 7 (2001) 846–858. [PMID: 11421361]
4.  Macbeth, M.R., Schubert, H.L., Vandemark, A.P., Lingam, A.T., Hill, C.P. and Bass, B.L. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science 309 (2005) 1534–1539. [PMID: 16141067]
[EC 3.5.4.37 created 2013]
 
 
EC 3.5.4.38
Accepted name: single-stranded DNA cytosine deaminase
Reaction: cytosine in single-stranded DNA + H2O = uracil in single-stranded DNA + NH3
Other name(s): AID; activation-induced deaminase; AICDA (gene name); activation-induced cytidine deaminase
Systematic name: single-stranded DNA cytosine aminohydrolase
Comments: The enzyme exclusively catalyses deamination of cytosine in single-stranded DNA. It preferentially deaminates five-nucleotide bubbles. The optimal target consists of a single-stranded NWRCN motif (W = A or T, R = A or G) [2]. The enzyme initiates antibody diversification processes by deaminating immunoglobulin sequences.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sohail, A., Klapacz, J., Samaranayake, M., Ullah, A. and Bhagwat, A.S. Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations. Nucleic Acids Res. 31 (2003) 2990–2994. [PMID: 12799424]
2.  Larijani, M., Petrov, A.P., Kolenchenko, O., Berru, M., Krylov, S.N. and Martin, A. AID associates with single-stranded DNA with high affinity and a long complex half-life in a sequence-independent manner. Mol. Cell Biol. 27 (2007) 20–30. [PMID: 17060445]
3.  Brar, S.S., Sacho, E.J., Tessmer, I., Croteau, D.L., Erie, D.A. and Diaz, M. Activation-induced deaminase, AID, is catalytically active as a monomer on single-stranded DNA. DNA Repair (Amst.) 7 (2008) 77–87. [PMID: 17889624]
4.  Larijani, M. and Martin, A. Single-stranded DNA structure and positional context of the target cytidine determine the enzymatic efficiency of AID. Mol. Cell Biol. 27 (2007) 8038–8048. [PMID: 17893327]
5.  Verma, S., Goldammer, T. and Aitken, R. Cloning and expression of activation induced cytidine deaminase from Bos taurus. Vet. Immunol. Immunopathol. 134 (2010) 151–159. [PMID: 19766322]
[EC 3.5.4.38 created 2013]
 
 
EC 3.5.4.39
Accepted name: GTP cyclohydrolase IV
Reaction: GTP + H2O = 7,8-dihydroneopterin 2′,3′-cyclic phosphate + formate + diphosphate
For diagram of methanopterin biosynthesis (part 1), click here
Glossary: 7,8-dihydroneopterin 2′,3′-cyclic phosphate = 2-amino-6-{(S)-hydroxy[(4R)-2-hydroxy-2-oxido-1,3,2-dioxaphospholan-4-yl]methyl}-7,8-dihydropteridin-4(1H)-one = 2-amino-6-[(1S,2R)-1,2,3-trihydroxypropyl]-7,8-dihydro-4(1H)-pteridinone 1,2-cyclic phosphate
Other name(s): MptA; GTP cyclohydrolase MptA
Systematic name: GTP 7,8-8,9-dihydrolase (cyclizing, formate-releasing, diphosphate-releasing)
Comments: Requires Fe2+. A zinc protein. The enzyme is involved in methanopterin biosynthesis in methanogenic archaea. cf. GTP cyclohydrolase I (EC 3.5.4.16), GTP cyclohydrolase II (EC 3.5.4.25) and GTP cyclohydrolase IIa (EC 3.5.4.29).
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Grochowski, L.L., Xu, H., Leung, K. and White, R.H. Characterization of an Fe2+-dependent archaeal-specific GTP cyclohydrolase, MptA, from Methanocaldococcus jannaschii. Biochemistry 46 (2007) 6658–6667. [PMID: 17497938]
[EC 3.5.4.39 created 2013]
 
 
*EC 3.6.1.59
Accepted name: 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] diphosphatase
Reaction: a 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] + H2O = N7-methylguanosine 5′-phosphate + a 5′-diphospho-[mRNA]
Other name(s): DcpS; m7GpppX pyrophosphatase; m7GpppN m7GMP phosphohydrolase; m7GpppX diphosphatase; m7G5′ppp5’N m7GMP phosphohydrolase
Systematic name: 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] N7-methylguanosine 5′-phosphate phosphohydrolase
Comments: The enzyme removes (decaps) the N7-methylguanosine 5-phosphate cap from an mRNA degraded to a maximal length of 10 nucleotides [3,6]. Decapping is an important process in the control of eukaryotic mRNA degradation. The enzyme functions to clear the cell of cap structure following decay of the RNA body [2]. The nematode enzyme can also decap triply methylated substrates, 5′-(N2,N2,N7-trimethyl 5′-triphosphoguanosine)-[mRNA] [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Malys, N. and McCarthy, J.E. Dcs2, a novel stress-induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies. J. Mol. Biol. 363 (2006) 370–382. [PMID: 16963086]
2.  Liu, S.W., Rajagopal, V., Patel, S.S. and Kiledjian, M. Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme. J. Biol. Chem. 283 (2008) 16427–16436. [PMID: 18441014]
3.  Liu, H., Rodgers, N.D., Jiao, X. and Kiledjian, M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 21 (2002) 4699–4708. [PMID: 12198172]
4.  van Dijk, E., Le Hir, H. and Seraphin, B. DcpS can act in the 5′-3′ mRNA decay pathway in addition to the 3′-5′ pathway. Proc. Natl. Acad. Sci. USA 100 (2003) 12081–12086. [PMID: 14523240]
5.  Chen, N., Walsh, M.A., Liu, Y., Parker, R. and Song, H. Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J. Mol. Biol. 347 (2005) 707–718. [PMID: 15769464]
6.  Cohen, L.S., Mikhli, C., Friedman, C., Jankowska-Anyszka, M., Stepinski, J., Darzynkiewicz, E. and Davis, R.E. Nematode m7GpppG and m3(2,2,7)GpppG decapping: activities in Ascaris embryos and characterization of C. elegans scavenger DcpS. RNA 10 (2004) 1609–1624. [PMID: 15383679]
7.  Wypijewska, A., Bojarska, E., Lukaszewicz, M., Stepinski, J., Jemielity, J., Davis, R.E. and Darzynkiewicz, E. 7-Methylguanosine diphosphate (m7GDP) is not hydrolyzed but strongly bound by decapping scavenger (DcpS) enzymes and potently inhibits their activity. Biochemistry 51 (2012) 8003–8013. [PMID: 22985415]
[EC 3.6.1.59 created 2012, modified 2013]
 
 
EC 3.6.1.65
Accepted name: (d)CTP diphosphatase
Reaction: (1) CTP + H2O = CMP + diphosphate
(2) dCTP + H2O = dCMP + diphosphate
Other name(s): (d)CTP pyrophosphohydrolase; (d)CTP diphosphohydrolase; nudG (gene name)
Systematic name: (deoxy)cytidine 5′-triphosphate diphosphohydrolase
Comments: The enzyme, characterized from the bacterium Escherichia coli, is specific for the pyrimidine nucleotides CTP and dCTP. It also acts on 5-methyl-dCTP, 5-hydroxy-dCTP and 8-hydroxy-dGTP.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  O'Handley, S.F., Dunn, C.A. and Bessman, M.J. Orf135 from Escherichia coli is a Nudix hydrolase specific for CTP, dCTP, and 5-methyl-dCTP. J. Biol. Chem. 276 (2001) 5421–5426. [PMID: 11053429]
2.  Fujikawa, K. and Kasai, H. The oxidized pyrimidine ribonucleotide, 5-hydroxy-CTP, is hydrolyzed efficiently by the Escherichia coli recombinant Orf135 protein. DNA Repair (Amst.) 1 (2002) 571–576. [PMID: 12509230]
3.  Kamiya, H., Iida, E. and Harashima, H. Important amino acids in the phosphohydrolase module of Escherichia coli Orf135. Biochem. Biophys. Res. Commun. 323 (2004) 1063–1068. [PMID: 15381107]
4.  Iida, E., Satou, K., Mishima, M., Kojima, C., Harashima, H. and Kamiya, H. Amino acid residues involved in substrate recognition of the Escherichia coli Orf135 protein. Biochemistry 44 (2005) 5683–5689. [PMID: 15823026]
[EC 3.6.1.65 created 2013]
 
 
EC 3.7.1.15
Transferred entry: (+)-caryolan-1-ol synthase. Now EC 4.2.1.138, (+)-caryolan-1-ol synthase
[EC 3.7.1.15 created 2011, deleted 2013]
 
 
EC 3.7.1.16
Transferred entry: oxepin-CoA hydrolase. Now EC 3.3.2.12, oxepin-CoA hydrolase
[EC 3.7.1.16 created 2011, deleted 2013]
 
 
EC 4.1.2.51
Accepted name: 2-dehydro-3-deoxy-D-gluconate aldolase
Reaction: 2-dehydro-3-deoxy-D-gluconate = pyruvate + D-glyceraldehyde
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): Pto1279 (gene name); KDGA; KDG-specific aldolase
Systematic name: 2-dehydro-3-deoxy-D-gluconate D-glyceraldehyde-lyase (pyruvate-forming)
Comments: The enzyme from the archaeon Picrophilus torridus is involved in D-glucose and D-galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway. In the direction of aldol synthesis the enzyme catalyses the formation of 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate at a similar ratio. It shows no activity with 2-dehydro-3-deoxy-D-gluconate 6-phosphate. cf. EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Reher, M., Fuhrer, T., Bott, M. and Schonheit, P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J. Bacteriol. 192 (2010) 964–974. [PMID: 20023024]
[EC 4.1.2.51 created 2013]
 
 
EC 4.2.1.138
Accepted name: (+)-caryolan-1-ol synthase
Reaction: (+)-β-caryophyllene + H2O = (+)-caryolan-1-ol
For diagram of humulene-based sequiterpenoid biosynthesis, click here
Glossary: (+)-caryolan-1-ol = (1S,2R,5S,8R)-4,4,8-trimethyltricyclo[6.3.1.02,5]dodecan-1-ol
Other name(s): GcoA
Systematic name: (+)-β-caryophyllene hydrolase [cyclizing, (+)-caryolan-1-ol-forming]
Comments: A multifunctional enzyme which also forms (+)-β-caryophyllene from farnesyl diphosphate [EC 4.2.3.89, (+)-β-caryophyllene synthase].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Nakano, C., Horinouchi, S. and Ohnishi, Y. Characterization of a novel sesquiterpene cyclase involved in (+)-caryolan-1-ol biosynthesis in Streptomyces griseus. J. Biol. Chem. 286 (2011) 27980–27987. [PMID: 21693706]
[EC 4.2.1.138 created 2011 as EC 3.7.1.15, transferred 2013 to EC 4.2.1.138]
 
 
EC 4.2.1.139
Accepted name: medicarpin synthase
Reaction: 4′-methoxyisoflavan-2′,4,7-triol = (–)-medicarpin + H2O
For diagram of medicarpin and formononetin derivatives biosynthesis, click here
Glossary: (–)-medicarpin = (6aR,11aR)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol
Other name(s): medicarpan synthase; 7,2′-dihydroxy-4′-methoxyisoflavanol dehydratase; 2′,7-dihydroxy-4′-methoxyisoflavanol dehydratase; DMI dehydratase; DMID
Systematic name: 4′-methoxyisoflavan-2′,4,7-triol hydro-lyase [(–)-medicarpin-forming]
Comments: Isolated from the plant Medicago sativa (alfalfa). Catalyses the final step in the biosynthesis of medicarpin, the main pterocarpan phytoalexin in alfalfa.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Guo, L., Dixon, R.A. and Paiva, N.L. The ‘pterocarpan synthase’ of alfalfa: association and co-induction of vestitone reductase and 7,2′-dihydroxy-4′-methoxy-isoflavanol (DMI) dehydratase, the two final enzymes in medicarpin biosynthesis. FEBS Lett. 356 (1994) 221–225. [PMID: 7805842]
2.  Guo, L., Dixon, R.A. and Paiva, N.L. Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2′-dihydroxy-4′-methoxyisoflavanol dehydratase. J. Biol. Chem. 269 (1994) 22372–22378. [PMID: 8071365]
[EC 4.2.1.139 created 2013]
 
 
EC 4.2.1.140
Accepted name: gluconate/galactonate dehydratase
Reaction: (1) D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O
(2) D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
For diagram of the Entner-Doudoroff pathway, click here
Other name(s): gluconate dehydratase (ambiguous); Sso3198 (gene name); Pto0485 (gene name)
Systematic name: D-gluconate/D-galactonate hydro-lyase
Comments: The enzyme is involved in glucose and galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway in Picrophilus torridus [3] and via the branched variant of the Entner-Doudoroff pathway in Sulfolobus solfataricus [1,2]. In vitro it utilizes D-gluconate with 6-10 fold higher catalytic efficiency than D-galactonate [1,3]. It requires Mg2+ for activity [1,2]. cf. EC 4.2.1.6, galactonate dehydratase, and EC 4.2.1.39, gluconate dehydratase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lamble, H.J., Milburn, C.C., Taylor, G.L., Hough, D.W. and Danson, M.J. Gluconate dehydratase from the promiscuous Entner-Doudoroff pathway in Sulfolobus solfataricus. FEBS Lett. 576 (2004) 133–136. [PMID: 15474024]
2.  Ahmed, H., Ettema, T.J., Tjaden, B., Geerling, A.C., van der Oost, J. and Siebers, B. The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem. J. 390 (2005) 529–540. [PMID: 15869466]
3.  Reher, M., Fuhrer, T., Bott, M. and Schonheit, P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J. Bacteriol. 192 (2010) 964–974. [PMID: 20023024]
[EC 4.2.1.140 created 2013]
 
 
EC 4.2.1.141
Accepted name: 2-dehydro-3-deoxy-D-arabinonate dehydratase
Reaction: 2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate + H2O
Systematic name: 2-dehydro-3-deoxy-D-arabinonate hydro-lyase (2,5-dioxopentanoate-forming)
Comments: The enzyme participates in pentose oxidation pathways that convert pentose sugars to the tricarboxylic acid cycle intermediate 2-oxoglutarate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Brouns, S.J., Walther, J., Snijders, A.P., van de Werken, H.J., Willemen, H.L., Worm, P., de Vos, M.G., Andersson, A., Lundgren, M., Mazon, H.F., van den Heuvel, R.H., Nilsson, P., Salmon, L., de Vos, W.M., Wright, P.C., Bernander, R. and van der Oost, J. Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment. J. Biol. Chem. 281 (2006) 27378–27388. [PMID: 16849334]
2.  Brouns, S.J., Barends, T.R., Worm, P., Akerboom, J., Turnbull, A.P., Salmon, L. and van der Oost, J. Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. J. Mol. Biol. 379 (2008) 357–371. [PMID: 18448118]
3.  Johnsen, U., Dambeck, M., Zaiss, H., Fuhrer, T., Soppa, J., Sauer, U. and Schonheit, P. D-Xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J. Biol. Chem. 284 (2009) 27290–27303. [PMID: 19584053]
[EC 4.2.1.141 created 2013]
 
 
EC 4.2.1.142
Accepted name: 5′-oxoaverantin cyclase
Reaction: 5′-oxoaverantin = (1′S,5′S)-averufin + H2O
For diagram of aflatoxin biosynthesis (part 1), click here
Glossary: 5′-oxoaverantin = 1,3,6,8-tetrahydroxy-2-[(1S)-1-hydroxy-5-oxohexyl]anthracene-9,10-dione
averufin = 7,9,11-trihydroxy-2-methyl-3,4,5,6-tetrahydro-2,6-epoxy-2H-anthra[2,3-b]oxocin-8,13-dione
Other name(s): OAVN cyclase; 5′-oxoaverantin hydro-lyase [(2′S,5′S)-averufin forming]
Systematic name: 5′-oxoaverantin hydro-lyase [(1′S,5′S)-averufin forming]
Comments: Isolated from the aflatoxin-producing mold Aspergillus parasiticus. The enzyme also catalyses the conversion of versiconal to versicolorin B (EC 4.2.1.143, versicolorin B synthase). Involved in aflatoxin biosynthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Sakuno, E., Yabe, K. and Nakajima, H. Involvement of two cytosolic enzymes and a novel intermediate, 5′-oxoaverantin, in the pathway from 5′-hydroxyaverantin to averufin in aflatoxin biosynthesis. Appl. Environ. Microbiol. 69 (2003) 6418–6426. [PMID: 14602595]
2.  Sakuno, E., Wen, Y., Hatabayashi, H., Arai, H., Aoki, C., Yabe, K. and Nakajima, H. Aspergillus parasiticus cyclase catalyzes two dehydration steps in aflatoxin biosynthesis. Appl. Environ. Microbiol. 71 (2005) 2999–3006. [PMID: 15932995]
[EC 4.2.1.142 created 2013]
 
 
EC 4.2.1.143
Accepted name: versicolorin B synthase
Reaction: versiconal = versicolorin B + H2O
For diagram of aflatoxin biosynthesis (part 2), click here
Glossary: versiconal = (2S,3S)-2,4,6,8-tetrahydroxy-3-(2-hydroxyethyl)anthra[2,3-b]furan-5,10-dione
versicolorin B = (3aR,12bS)-8,10,12-trihydroxy-1,2,3a,12b-tetrahydroanthra[2,3-b]furo[3,2-d]furan-6,11-dione
Other name(s): versiconal cyclase; VBS
Systematic name: versiconal hydro-lyase (versicolorin-B forming)
Comments: Isolated from the aflatoxin-producing mold Aspergillus parasiticus. Involved in aflatoxin biosynthesis.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lin, B.K. and Anderson, J.A. Purification and properties of versiconal cyclase from Aspergillus parasiticus. Arch. Biochem. Biophys. 293 (1992) 67–70. [PMID: 1731640]
2.  McGuire, S.M., Silva, J.C., Casillas, E.G. and Townsend, C.A. Purification and characterization of versicolorin B synthase from Aspergillus parasiticus. Catalysis of the stereodifferentiating cyclization in aflatoxin biosynthesis essential to DNA interaction. Biochemistry 35 (1996) 11470–11486. [PMID: 8784203]
3.  Silva, J.C., Minto, R.E., Barry, C.E., 3rd, Holland, K.A. and Townsend, C.A. Isolation and characterization of the versicolorin B synthase gene from Aspergillus parasiticus. Expansion of the aflatoxin b1 biosynthetic gene cluster. J. Biol. Chem. 271 (1996) 13600–13608. [PMID: 8662689]
4.  Silva, J.C. and Townsend, C.A. Heterologous expression, isolation, and characterization of versicolorin B synthase from Aspergillus parasiticus. A key enzyme in the aflatoxin B1 biosynthetic pathway. J. Biol. Chem. 272 (1997) 804–813. [PMID: 8995367]
[EC 4.2.1.143 created 2013]
 
 
EC 4.2.1.144
Accepted name: 3-amino-5-hydroxybenzoate synthase
Reaction: 5-amino-5-deoxy-3-dehydroshikimate = 3-amino-5-hydroxybenzoate + H2O
Other name(s): AHBA synthase; rifK (gene name)
Systematic name: 5-amino-5-deoxy-3-dehydroshikimate hydro-lyase (3-amino-5-hydroxybenzoate-forming)
Comments: A pyridoxal 5′-phosphate enzyme. The enzyme from the bacterium Amycolatopsis mediterranei participates in the pathway for rifamycin B biosynthesis. The enzyme also functions as a transaminase earlier in the pathway, producing UDP-α-D-kanosamine [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kim, C.G., Yu, T.W., Fryhle, C.B., Handa, S. and Floss, H.G. 3-Amino-5-hydroxybenzoic acid synthase, the terminal enzyme in the formation of the precursor of mC7N units in rifamycin and related antibiotics. J. Biol. Chem. 273 (1998) 6030–6040. [PMID: 9497318]
2.  Eads, J.C., Beeby, M., Scapin, G., Yu, T.W. and Floss, H.G. Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase. Biochemistry 38 (1999) 9840–9849. [PMID: 10433690]
3.  Floss, H.G., Yu, T.W. and Arakawa, K. The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review. J. Antibiot. (Tokyo) 64 (2011) 35–44. [PMID: 21081954]
[EC 4.2.1.144 created 2013]
 
 
EC 4.2.3.143
Accepted name: kunzeaol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = kunzeaol + diphosphate
For diagram of germacrene sesquiterpenoid biosynthesis, click here
Glossary: kunzeaol = 6β-hydroxygermacra-1(10),4-diene = (1R,2E,6E,10R)-3,7-dimethyl-10-isopropylcyclodeca-2,6-dienol
Other name(s): TgTPS2 (gene name)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (kunzeaol forming)
Comments: Isolated from the root of the plant Thapsia garganica. The enzyme also produces germacrene D, bicyclogermacrene and traces of other sesquiterpenoids. See EC 4.2.3.77, (+)-germacrene D synthase and EC 4.2.3.100, bicyclogermacrene synthase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Pickel, B., Drew, D.P., Manczak, T., Weitzel, C., Simonsen, H.T. and Ro, D.K. Identification and characterization of a kunzeaol synthase from Thapsia garganica: implications for the biosynthesis of the pharmaceutical thapsigargin. Biochem. J. 448 (2012) 261–271. [PMID: 22938155]
[EC 4.2.3.143 created 2013]
 
 
EC 4.2.99.22
Accepted name: tuliposide A-converting enzyme
Reaction: 6-tuliposide A = tulipalin A + D-glucose
Glossary: 6-tuliposide A = 6-O-(4-hydroxy-2-methylenebutanoyl)-D-glucose
tulipalin A = 2-methylenebutanolactone
Other name(s): tuliposide-converting enzyme; 6-O-(4′-hydroxy-2′-methylenebutyryl)-D-glucose acyltransferase (lactone-forming); TCA; TCEA
Systematic name: 6-tuliposide A D-glucose-lyase (tulipalin A forming)
Comments: Isolated from the plant Tulipa gesneriana (tulip). The reaction is an intramolecular transesterification producing the lactone. The enzyme also has a weak activity with 6-tuliposide B and 6-O-benzoyl-D-glucose.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kato, Y., Shoji, K., Ubukata, M., Shigetomi, K., Sato, Y., Nakajima, N. and Ogita, S. Purification and characterization of a tuliposide-converting enzyme from bulbs of Tulipa gesneriana. Biosci. Biotechnol. Biochem. 73 (2009) 1895–1897. [PMID: 19661715]
2.  Nomura, T., Ogita, S. and Kato, Y. A novel lactone-forming carboxylesterase: molecular identification of a tuliposide A-converting enzyme in tulip. Plant Physiol. 159 (2012) 565–578. [PMID: 22474185]
[EC 4.2.99.22 created 2013]
 
 
EC 4.3.1.26
Transferred entry: chromopyrrolate synthase. Now EC 1.21.3.9, dichlorochromopyrrolate synthase
[EC 4.3.1.26 created 2010, deleted 2013]
 
 
EC 6.3.2.40
Accepted name: cyclopeptine synthase
Reaction: 2 ATP + S-adenosyl-L-methionine + anthranilate + L-phenylalanine = cyclopeptine + 2 AMP + 2 diphosphate + S-adenosyl-L-homocysteine
For diagram of reaction, click here
Glossary: cyclopeptine = (3S)-3-benzyl-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
Systematic name: S-adenosyl-L-methionine:anthranilate:L-phenylalanine ligase (cyclopeptine forming)
Comments: Cyclopeptine synthase is the key enzyme of benzodiazepine alkaloid biosynthesis in the fungus Penicillium cyclopium. The enzyme is a non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lerbs, W. and Luckner, M. Cyclopeptine synthetase activity in surface cultures of Penicillium cyclopium. J. Basic Microbiol. 25 (1985) 387–391. [PMID: 2995633]
2.  Gerlach, M, Schwelle, N., Lerbs, W. and Luckner, M. Enzymatic synthesis of cyclopeptine intermediates in Penicillium cyclopium. Phytochemistry 24 (1985) 1935–1939.
[EC 6.3.2.40 created 2013]
 
 
EC 6.3.4.1
Transferred entry: GMP synthase. Now included in EC 6.3.5.2, GMP synthase (glutamine-hydrolysing)
[EC 6.3.4.1 created 1961, deleted 2013]
 
 
*EC 6.3.4.2
Accepted name: CTP synthase (glutamine hydrolysing)
Reaction: ATP + UTP + L-glutamine = ADP + phosphate + CTP + L-glutamate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) ATP + UTP + NH3 = ADP + phosphate + CTP
Other name(s): UTP—ammonia ligase; cytidine triphosphate synthetase; uridine triphosphate aminase; cytidine 5′-triphosphate synthetase; CTPS (gene name); pyrG (gene name); CTP synthase; UTP:ammonia ligase (ADP-forming)
Systematic name: UTP:L-glutamine amido-ligase (ADP-forming)
Comments: The enzyme contains three functionally distinct sites: an allosteric GTP-binding site, a glutaminase site where glutamine hydrolysis occurs (cf. EC 3.5.1.2, glutaminase), and the active site where CTP synthesis takes place. The reaction proceeds via phosphorylation of UTP by ATP to give an activated intermediate 4-phosphoryl UTP and ADP [4,5]. Ammonia then reacts with this intermediate generating CTP and a phosphate. The enzyme can also use ammonia from the surrounding solution [3,6].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9023-56-7
References:
1.  Lieberman, I. Enzymatic amination of uridine triphosphate to cytidine triphosphate. J. Biol. Chem. 222 (1956) 765–775. [PMID: 13367044]
2.  Long, C.W., Levitzki, A., Houston, L.L and Koshland, D.E., Jr. Subunit structures and interactions of CTP synthetase. Fed. Proc. 28 (1969) 342.
3.  Levitzki, A. and Koshland, D.E., Jr. Ligand-induced dimer-to-tetramer transformation in cytosine triphosphate synthetase. Biochemistry 11 (1972) 247–253. [PMID: 4550560]
4.  von der Saal, W., Anderson, P.M. and Villafranca, J.J. Mechanistic investigations of Escherichia coli cytidine-5′-triphosphate synthetase. Detection of an intermediate by positional isotope exchange experiments. J. Biol. Chem. 260 (1985) 14993–14997. [PMID: 2933396]
5.  Lewis, D.A. and Villafranca, J.J. Investigation of the mechanism of CTP synthetase using rapid quench and isotope partitioning methods. Biochemistry 28 (1989) 8454–8459. [PMID: 2532543]
6.  Wadskov-Hansen, S.L., Willemoes, M., Martinussen, J., Hammer, K., Neuhard, J. and Larsen, S. Cloning and verification of the Lactococcus lactis pyrG gene and characterization of the gene product, CTP synthase. J. Biol. Chem. 276 (2001) 38002–38009. [PMID: 11500486]
[EC 6.3.4.2 created 1961, modified 2013]
 
 
EC 6.3.4.21
Accepted name: nicotinate phosphoribosyltransferase
Reaction: nicotinate + 5-phospho-α-D-ribose 1-diphosphate + ATP + H2O = β-nicotinate D-ribonucleotide + diphosphate + ADP + phosphate
For diagram of NAD+ biosynthesis, click here
Other name(s): niacin ribonucleotidase; nicotinic acid mononucleotide glycohydrolase; nicotinic acid mononucleotide pyrophosphorylase; nicotinic acid phosphoribosyltransferase; nicotinate-nucleotide:diphosphate phospho-α-D-ribosyltransferase
Systematic name: 5-phospho-α-D-ribose 1-diphosphate:nicotinate ligase (ADP, diphosphate-forming)
Comments: The enzyme, which is involved in pyridine nucleotide recycling, can form β-nicotinate D-ribonucleotide and diphosphate from nicotinate and 5-phospho-α-D-ribose 1-diphosphate (PRPP) in the absence of ATP. However, when ATP is available the enzyme is phosphorylated resulting in a much lower Km for nicotinate. The phospho-enzyme is hydrolysed during the transferase reaction, regenerating the low affinity form. The presence of ATP shifts the products/substrates equilibrium from 0.67 to 1100 [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9030-26-6
References:
1.  Imsande, J. Pathway of diphosphopyridine nucleotide biosynthesis in Escherichia coli. J. Biol. Chem. 236 (1961) 1494–1497. [PMID: 13717628]
2.  Imsande, J. and Handler, P. Biosynthesis of diphosphopyridine nucleotide. III. Nicotinic acid mononucleotide pyrophosphorylase. J. Biol. Chem. 236 (1961) 525–530. [PMID: 13717627]
3.  Kosaka, A., Spivey, H.O. and Gholson, R.K. Nicotinate phosphoribosyltransferase of yeast. Purification and properties. J. Biol. Chem. 246 (1971) 3277–3283. [PMID: 4324895]
4.  Vinitsky, A. and Grubmeyer, C. A new paradigm for biochemical energy coupling. Salmonella typhimurium nicotinate phosphoribosyltransferase. J. Biol. Chem. 268 (1993) 26004–26010. [PMID: 7503993]
[EC 6.3.4.21 created 1961 as EC 2.4.2.11, transferred 2013 to EC 6.3.4.21]
 
 
EC 6.3.4.22
Accepted name: tRNAIle2-agmatinylcytidine synthase
Reaction: ATP + agmatine + [tRNAIle2]-cytidine34 + H2O = [tRNAIle2]-2-agmatinylcytidine34 + AMP + 2 phosphate
Other name(s): TiaS; AF2259; tRNAIle-2-agmatinylcytidine synthetase; tRNAIle-agm2C synthetase; tRNAIle-agmatidine synthetase
Systematic name: agmatine:[tRNAIle]-cytidine34 ligase
Comments: The enzyme from the archaeon Archaeoglobus fulgidus modifies the wobble base of the CAU anticodon of the archaeal tRNAIle2 at the oxo group in position 2 of cytidine34. This modification is crucial for accurate decoding of the genetic code. In bacteria EC 6.3.4.19, tRNAIle-lysidine synthase, catalyses the modification of [tRNAIle2]-cytidine34 to [tRNAIle2]-lysidine34 .
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Ikeuchi, Y., Kimura, S., Numata, T., Nakamura, D., Yokogawa, T., Ogata, T., Wada, T., Suzuki, T. and Suzuki, T. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat. Chem. Biol. 6 (2010) 277–282. [PMID: 20139989]
2.  Terasaka, N., Kimura, S., Osawa, T., Numata, T. and Suzuki, T. Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS. Nat. Struct. Mol. Biol. 18 (2011) 1268–1274. [PMID: 22002222]
3.  Osawa, T., Inanaga, H., Kimura, S., Terasaka, N., Suzuki, T. and Numata, T. Crystallization and preliminary X-ray diffraction analysis of an archaeal tRNA-modification enzyme, TiaS, complexed with tRNA(Ile2) and ATP. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 67 (2011) 1414–1416. [PMID: 22102245]
[EC 6.3.4.22 created 2013]
 
 
*EC 6.3.5.2
Accepted name: GMP synthase (glutamine-hydrolysing)
Reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) ATP + XMP + NH3 = AMP + diphosphate + GMP
For diagram of AMP and GMP biosynthesis, click here
Glossary: XMP = xanthosine 5′-phosphate
Other name(s): GMP synthetase (glutamine-hydrolysing); guanylate synthetase (glutamine-hydrolyzing); guanosine monophosphate synthetase (glutamine-hydrolyzing); xanthosine 5′-phosphate amidotransferase; guanosine 5′-monophosphate synthetase
Systematic name: xanthosine-5′-phosphate:L-glutamine amido-ligase (AMP-forming)
Comments: Involved in the de novo biosynthesis of guanosine nucleotides. An N-terminal glutaminase domain binds L-glutamine and generates ammonia, which is transferred by a substrate-protective tunnel to the ATP-pyrophosphatase domain. The enzyme can catalyse the second reaction alone in the presence of ammonia.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 37318-71-1
References:
1.  Lagerkvist, U. Biosynthesis of guanosine 5′-phosphate. II. Amination of xanthosine 5′-phosphate by purified enzyme from pigeon liver. J. Biol. Chem. 233 (1958) 143–149. [PMID: 13563458]
2.  Abrams, R. and Bentley, M. Biosynthesis of nucleic acid purines. III. Guanosine 5′-phosphate formation from xanthosine 5′-phosphate and L-glutamine. Arch. Biochem. Biophys. 79 (1959) 91–110.
3.  Zalkin, H., Argos, P., Narayana, S.V., Tiedeman, A.A. and Smith, J.M. Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase. J. Biol. Chem. 260 (1985) 3350–3354. [PMID: 2982857]
4.  Abbott, J.L., Newell, J.M., Lightcap, C.M., Olanich, M.E., Loughlin, D.T., Weller, M.A., Lam, G., Pollack, S. and Patton, W.A. The effects of removing the GAT domain from E. coli GMP synthetase. Protein J. 25 (2006) 483–491. [PMID: 17103135]
[EC 6.3.5.2 created 1961, modified 2013]
 
 


Data © 2001–2017 IUBMB
Web site © 2005–2017 Andrew McDonald