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, Ron Caspi, Ture Damhus, Shinya Fushinobu, Julia Hauenstein, Antje Jäde, Ingrid Keseler, Masaaki Kotera, Andrew McDonald, Gerry Moss, 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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.262 4-hydroxythreonine-4-phosphate dehydrogenase
EC 1.1.1.289 sorbose reductase
EC 1.1.1.290 4-phosphoerythronate dehydrogenase
EC 1.1.99.19 transferred
*EC 1.2.1.10 acetaldehyde dehydrogenase (acetylating)
EC 1.2.1.71 succinylglutamate-semialdehyde dehydrogenase
EC 1.2.1.72 erythrose-4-phosphate dehydrogenase
EC 1.2.99.1 transferred
*EC 1.3.99.19 quinoline-4-carboxylate 2-oxidoreductase
*EC 1.4.3.5 pyridoxal 5′-phosphate synthase
*EC 1.4.4.2 glycine dehydrogenase (aminomethyl-transferring)
EC 1.7.1.13 preQ1 synthase
*EC 1.8.1.4 dihydrolipoyl dehydrogenase
*EC 1.11.1.14 lignin peroxidase
EC 1.11.1.16 versatile peroxidase
*EC 1.13.11.11 tryptophan 2,3-dioxygenase
*EC 1.13.11.19 cysteamine dioxygenase
EC 1.13.11.42 deleted
EC 1.13.11.52 indoleamine 2,3-dioxygenase
EC 1.13.11.53 acireductone dioxygenase (Ni2+-requiring)
EC 1.13.11.54 acireductone dioxygenase [iron(II)-requiring]
EC 1.13.11.55 sulfur oxygenase/reductase
EC 1.13.12.14 chlorophyllide-a oxygenase
EC 1.14.13.65 deleted
EC 1.14.13.101 senecionine N-oxygenase
*EC 1.14.99.3 heme oxygenase (biliverdin-producing)
EC 1.17.99.4 uracil/thymine dehydrogenase
*EC 2.1.2.10 aminomethyltransferase
*EC 2.3.1.11 thioethanolamine S-acetyltransferase
*EC 2.3.1.38 [acyl-carrier-protein] S-acetyltransferase
*EC 2.3.1.39 [acyl-carrier-protein] S-malonyltransferase
*EC 2.3.1.41 β-ketoacyl-[acyl-carrier-protein] synthase I
*EC 2.3.1.109 arginine N-succinyltransferase
EC 2.3.1.177 3,5-dihydroxybiphenyl synthase
EC 2.3.1.178 diaminobutyrate acetyltransferase
EC 2.3.1.179 β-ketoacyl-[acyl-carrier-protein] synthase II
EC 2.3.1.180 β-ketoacyl-[acyl-carrier-protein] synthase III
EC 2.3.1.181 lipoyl(octanoyl) transferase
*EC 2.4.1.195 N-hydroxythioamide S-β-glucosyltransferase
EC 2.4.1.223 glucuronosyl-galactosyl-proteoglycan 4-α-N-acetylglucosaminyltransferase
EC 2.4.1.243 6G-fructosyltransferase
EC 2.4.1.244 N-acetyl-β-glucosaminyl-glycoprotein 4-β-N-acetylgalactosaminyltransferase
*EC 2.6.1.52 phosphoserine transaminase
*EC 2.6.1.76 diaminobutyrate—2-oxoglutarate transaminase
EC 2.6.1.81 succinylornithine transaminase
EC 2.6.99.2 pyridoxine 5′-phosphate synthase
*EC 2.7.1.151 inositol-polyphosphate multikinase
EC 2.7.1.158 inositol-pentakisphosphate 2-kinase
EC 2.7.1.159 inositol-1,3,4-trisphosphate 5/6-kinase
EC 2.7.4.22 UMP kinase
EC 2.7.7.63 lipoate—protein ligase
*EC 2.8.1.6 biotin synthase
EC 2.8.1.8 lipoyl synthase
EC 3.1.3.76 lipid-phosphate phosphatase
EC 3.1.13.5 ribonuclease D
*EC 3.1.26.3 ribonuclease III
*EC 3.2.1.81 β-agarase
*EC 3.2.1.83 κ-carrageenase
EC 3.2.1.155 xyloglucan-specific endo-processive β-1,4-glucanase
EC 3.2.1.157 ι-carrageenase
EC 3.2.1.158 α-agarase
EC 3.2.1.159 α-neoagaro-oligosaccharide hydrolase
EC 3.2.1.161 β-apiosyl-β-glucosidase
EC 3.3.2.3 transferred
*EC 3.3.2.6 leukotriene-A4 hydrolase
*EC 3.3.2.7 hepoxilin-epoxide hydrolase
EC 3.3.2.9 microsomal epoxide hydrolase
EC 3.3.2.10 soluble epoxide hydrolase
EC 3.3.2.11 cholesterol-5,6-oxide hydrolase
EC 3.4.21.87 transferred
EC 3.4.23.49 omptin
EC 3.5.1.94 γ-glutamyl-γ-aminobutyrate hydrolase
EC 3.5.1.95 N-malonylurea hydrolase
EC 3.5.1.96 succinylglutamate desuccinylase
*EC 3.5.2.1 barbiturase
EC 3.5.3.23 N-succinylarginine dihydrolase
*EC 3.6.3.5 Zn2+-exporting ATPase
*EC 3.6.3.44 xenobiotic-transporting ATPase
EC 3.6.3.45 deleted
*EC 4.1.1.21 phosphoribosylaminoimidazole carboxylase
EC 4.1.1.86 diaminobutyrate decarboxylase
*EC 4.1.2.8 indole-3-glycerol-phosphate lyase
EC 4.1.3.39 4-hydroxy-2-oxovalerate aldolase
*EC 4.2.1.60 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
EC 4.2.1.108 ectoine synthase
*EC 4.2.3.9 aristolochene synthase
EC 4.2.3.22 germacradienol synthase
EC 4.2.3.23 germacrene-A synthase
EC 4.2.3.24 amorpha-4,11-diene synthase
EC 4.2.3.25 S-linalool synthase
EC 4.2.3.26 R-linalool synthase
EC 4.4.1.24 (2R)-sulfolactate sulfo-lyase
EC 4.4.1.25 L-cysteate sulfo-lyase
EC 5.3.3.14 trans-2-decenoyl-[acyl-carrier protein] isomerase
EC 5.4.99.18 5-(carboxyamino)imidazole ribonucleotide mutase
EC 6.2.1.7 cholate—CoA ligase
*EC 6.3.2.6 phosphoribosylaminoimidazolesuccinocarboxamide synthase
*EC 6.3.2.27 aerobactin synthase
EC 6.3.4.18 5-(carboxyamino)imidazole ribonucleotide synthase

*EC 1.1.1.262
Accepted name: 4-hydroxythreonine-4-phosphate dehydrogenase
Reaction: 4-phosphooxy-L-threonine + NAD+ = 3-amino-2-oxopropyl phosphate + CO2 + NADH + H+
For diagram of pyridoxal biosynthesis, click here
Other name(s): NAD+-dependent threonine 4-phosphate dehydrogenase; L-threonine 4-phosphate dehydrogenase; 4-(phosphohydroxy)-L-threonine dehydrogenase; PdxA; 4-(phosphonooxy)-L-threonine:NAD+ oxidoreductase; 4-phosphooxy-L-threonine:NAD+ oxidoreductase
Systematic name: 4-phosphooxy-L-threonine:NAD+ 3-oxidoreductase (decarboxylating)
Comments: The enzyme is part of the biosynthesis pathway of the cofactor pyridoxal 5′-phosphate found in anaerobic bacteria.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 230310-36-8
References:
1.  Cane, D.E., Hsiung, Y., Cornish, J.A., Robinson, J.K and Spenser, I.D. Biosynthesis of vitamine B6: The oxidation of L-threonine 4-phosphate by PdxA. J. Am. Chem. Soc. 120 (1998) 1936–1937.
2.  Laber, B., Maurer, W., Scharf, S., Stepusin, K. and Schmidt, F.S. Vitamin B6 biosynthesis: formation of pyridoxine 5′-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. FEBS Lett. 449 (1999) 45–48. [DOI] [PMID: 10225425]
3.  Sivaraman, J., Li, Y., Banks, J., Cane, D.E., Matte, A. and Cygler, M. Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway. J. Biol. Chem. 278 (2003) 43682–43690. [DOI] [PMID: 12896974]
4.  Banks, J. and Cane, D.E. Biosynthesis of vitamin B6: direct identification of the product of the PdxA-catalyzed oxidation of 4-hydroxy-l-threonine-4-phosphate using electrospray ionization mass spectrometry. Bioorg. Med. Chem. Lett. 14 (2004) 1633–1636. [PMID: 15026039]
[EC 1.1.1.262 created 2000, modified 2006]
 
 
EC 1.1.1.289
Accepted name: sorbose reductase
Reaction: D-glucitol + NADP+ = L-sorbose + NADPH + H+
For diagram of reaction, click here
Glossary: L-sorbose = L-xylo-hex-2-ulose
Other name(s): Sou1p
Systematic name: D-glucitol:NADP+ oxidoreductase
Comments: The reaction occurs predominantly in the reverse direction. This enzyme can also convert D-fructose into D-mannitol, but more slowly. Belongs in the short-chain dehydrogenase family.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 138440-90-1
References:
1.  Greenberg, J.R., Price, N.P., Oliver, R.P., Sherman, F. and Rustchenko, E. Candida albicans SOU1 encodes a sorbose reductase required for L-sorbose utilization. Yeast 22 (2005) 957–969. [DOI] [PMID: 16134116]
2.  Greenberg, J.R., Price, N.P., Oliver, R.P., Sherman, F. and Rustchenko, E. Erratum report: Candida albicans SOU1 encodes a sorbose reductase required for L-sorbose utilization. Yeast 22 (2005) 1171.
3.  Sugisawa, T., Hoshino, T. and Fujiwara, A. Purification and properties of NADPH-linked L-sorbose reductase from Gluconobacter melanogenus N44-1. Agric. Biol. Chem. 55 (1991) 2043–2049.
4.  Shinjoh, M., Tazoe, M. and Hoshino, T. NADPH-dependent L-sorbose reductase is responsible for L-sorbose assimilation in Gluconobacter suboxydans IFO 3291. J. Bacteriol. 184 (2002) 861–863. [DOI] [PMID: 11790761]
[EC 1.1.1.289 created 2006]
 
 
EC 1.1.1.290
Accepted name: 4-phosphoerythronate dehydrogenase
Reaction: 4-phospho-D-erythronate + NAD+ = (3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + NADH + H+
For diagram of pyridoxal biosynthesis, click here
Other name(s): PdxB; PdxB 4PE dehydrogenase; 4-O-phosphoerythronate dehydrogenase; 4PE dehydrogenase; erythronate-4-phosphate dehydrogenase
Systematic name: 4-phospho-D-erythronate:NAD+ 2-oxidoreductase
Comments: This enzyme catalyses a step in a bacterial pathway for the biosynthesis of pyridoxal 5′-phosphate. The enzyme contains a tightly-bound NAD(H) cofactor that is not re-oxidized by free NAD+. In order to re-oxidize the cofactor and restore enzyme activity, the enzyme catalyses the reduction of a 2-oxo acid (such as 2-oxoglutarate, oxaloacetate, or pyruvate) to the respective (R)-hydroxy acid [6]. cf. EC 1.1.1.399, 2-oxoglutarate reductase.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 125858-75-5
References:
1.  Lam, H.M. and Winkler, M.E. Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in Escherichia coli K-12. J. Bacteriol. 172 (1990) 6518–6528. [DOI] [PMID: 2121717]
2.  Pease, A.J., Roa, B.R., Luo, W. and Winkler, M.E. Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12. J. Bacteriol. 184 (2002) 1359–1369. [DOI] [PMID: 11844765]
3.  Zhao, G. and Winkler, M.E. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178 (1996) 232–239. [DOI] [PMID: 8550422]
4.  Grant, G.A. A new family of 2-hydroxyacid dehydrogenases. Biochem. Biophys. Res. Commun. 165 (1989) 1371–1374. [DOI] [PMID: 2692566]
5.  Schoenlein, P.V., Roa, B.B. and Winkler, M.E. Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12. J. Bacteriol. 171 (1989) 6084–6092. [DOI] [PMID: 2681152]
6.  Rudolph, J., Kim, J. and Copley, S.D. Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates. Biochemistry 49 (2010) 9249–9255. [DOI] [PMID: 20831184]
[EC 1.1.1.290 created 2006, modified 2016]
 
 
EC 1.1.99.19
Transferred entry: uracil dehydrogenase. Now EC 1.17.99.4, uracil/thymine dehydrogenase
[EC 1.1.99.19 created 1961 as EC 1.2.99.1, transferred 1984 to EC 1.1.99.19, deleted 2006]
 
 
*EC 1.2.1.10
Accepted name: acetaldehyde dehydrogenase (acetylating)
Reaction: acetaldehyde + CoA + NAD+ = acetyl-CoA + NADH + H+
For diagram of 3-phenylpropanoate catabolism, click here, for diagram of catechol catabolism (meta ring cleavage), click here and for diagram of cinnamate catabolism, click here
Other name(s): aldehyde dehydrogenase (acylating); ADA; acylating acetaldehyde dehyrogenase; DmpF; BphJ
Systematic name: acetaldehyde:NAD+ oxidoreductase (CoA-acetylating)
Comments: Also acts, more slowly, on glycolaldehyde, propanal and butanal. In several bacterial species this enzyme forms a bifunctional complex with EC 4.1.3.39, 4-hydroxy-2-oxovalerate aldolase. The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 1.2.1.87, propanal dehydrogenase (propanoylating). Involved in the meta-cleavage pathway for the degradation of phenols, methylphenols and catechols. NADP+ can replace NAD+ but the rate of reaction is much slower [3].
Links to other databases: BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9028-91-5
References:
1.  Burton, R.M. and Stadtman, E.R. The oxidation of acetaldehyde to acetyl coenzyme A. J. Biol. Chem. 202 (1953) 873–890. [PMID: 13061511]
2.  Smith, L.T. and Kaplan, N.O. Purification, properties, and kinetic mechanism of coenzyme A-linked aldehyde dehydrogenase from Clostridium kluyveri. Arch. Biochem. Biophys. 203 (1980) 663–675. [DOI] [PMID: 7458347]
3.  Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377–385. [DOI] [PMID: 8419288]
4.  Baker, P., Pan, D., Carere, J., Rossi, A., Wang, W. and Seah, S.Y.K. Characterization of an aldolase-dehydrogenase complex that exhibits substrate channeling in the polychlorinated biphenyls degradation pathway. Biochemistry 48 (2009) 6551–6558. [DOI] [PMID: 19476337]
5.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [DOI] [PMID: 22316175]
[EC 1.2.1.10 created 1961, modified 2006, modified 2011]
 
 
EC 1.2.1.71
Accepted name: succinylglutamate-semialdehyde dehydrogenase
Reaction: N-succinyl-L-glutamate 5-semialdehyde + NAD+ + H2O = N-succinyl-L-glutamate + NADH + 2 H+
For diagram of arginine catabolism, click here
Other name(s): succinylglutamic semialdehyde dehydrogenase; N-succinylglutamate 5-semialdehyde dehydrogenase; SGSD; AruD; AstD
Systematic name: N-succinyl-L-glutamate 5-semialdehyde:NAD+ oxidoreductase
Comments: This is the fourth enzyme in the arginine succinyltransferase (AST) pathway for the catabolism of arginine [1]. This pathway converts the carbon skeleton of arginine into glutamate, with the concomitant production of ammonia and conversion of succinyl-CoA into succinate and CoA. The five enzymes involved in this pathway are EC 2.3.1.109 (arginine N-succinyltransferase), EC 3.5.3.23 (N-succinylarginine dihydrolase), EC 2.6.1.11 (acetylornithine transaminase), EC 1.2.1.71 (succinylglutamate-semialdehyde dehydrogenase) and EC 3.5.1.96 (succinylglutamate desuccinylase) [3,6].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Vander Wauven, C., Jann, A., Haas, D., Leisinger, T. and Stalon, V. N2-succinylornithine in ornithine catabolism of Pseudomonas aeruginosa. Arch. Microbiol. 150 (1988) 400–404. [PMID: 3144259]
2.  Vander Wauven, C. and Stalon, V. Occurrence of succinyl derivatives in the catabolism of arginine in Pseudomonas cepacia. J. Bacteriol. 164 (1985) 882–886. [PMID: 2865249]
3.  Tricot, C., Vander Wauven, C., Wattiez, R., Falmagne, P. and Stalon, V. Purification and properties of a succinyltransferase from Pseudomonas aeruginosa specific for both arginine and ornithine. Eur. J. Biochem. 224 (1994) 853–861. [DOI] [PMID: 7523119]
4.  Itoh, Y. Cloning and characterization of the aru genes encoding enzymes of the catabolic arginine succinyltransferase pathway in Pseudomonas aeruginosa. J. Bacteriol. 179 (1997) 7280–7290. [DOI] [PMID: 9393691]
5.  Schneider, B.L., Kiupakis, A.K. and Reitzer, L.J. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180 (1998) 4278–4286. [PMID: 9696779]
6.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 50 (1986) 314–352. [PMID: 3534538]
7.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Erratum report: Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 51 (1987) 178. [PMID: 16350242]
[EC 1.2.1.71 created 2006]
 
 
EC 1.2.1.72
Accepted name: erythrose-4-phosphate dehydrogenase
Reaction: D-erythrose 4-phosphate + NAD+ + H2O = 4-phosphoerythronate + NADH + 2 H+
For diagram of pyridoxal biosynthesis, click here
Other name(s): erythrose 4-phosphate dehydrogenase; E4PDH; GapB; Epd dehydrogenase; E4P dehydrogenase
Systematic name: D-erythrose 4-phosphate:NAD+ oxidoreductase
Comments: This enzyme was originally thought to be a glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12), but this has since been disproved, as glyceraldehyde 3-phosphate is not a substrate [1,2]. Forms part of the pyridoxal-5′-phosphate cofactor biosynthesis pathway in Escherichia coli, along with EC 1.1.1.290 (4-phosphoerythronate dehydrogenase), EC 2.6.1.52 (phosphoserine transaminase), EC 1.1.1.262 (4-hydroxythreonine-4-phosphate dehydrogenase), EC 2.6.99.2 (pyridoxine 5′-phosphate synthase) and EC 1.4.3.5 (pyridoxamine-phosphate oxidase).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 131554-04-6
References:
1.  Zhao, G., Pease, A.J., Bharani, N. and Winkler, M.E. Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5′-phosphate biosynthesis. J. Bacteriol. 177 (1995) 2804–2812. [DOI] [PMID: 7751290]
2.  Boschi-Muller, S., Azza, S., Pollastro, D., Corbier, C. and Branlant, G. Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase. J. Biol. Chem. 272 (1997) 15106–15112. [DOI] [PMID: 9182530]
3.  Yang, Y., Zhao, G., Man, T.K. and Winkler, M.E. Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5′-phosphate coenzyme biosynthesis in Escherichia coli K-12. J. Bacteriol. 180 (1998) 4294–4299. [PMID: 9696782]
[EC 1.2.1.72 created 2006]
 
 
EC 1.2.99.1
Transferred entry: uracil dehydrogenase. Now EC 1.17.99.4, uracil/thymine dehydrogenase
[EC 1.2.99.1 created 1961, deleted 1984]
 
 
*EC 1.3.99.19
Accepted name: quinoline-4-carboxylate 2-oxidoreductase
Reaction: quinoline-4-carboxylate + acceptor + H2O = 2-oxo-1,2-dihydroquinoline-4-carboxylate + reduced acceptor
For diagram of reaction, click here
Other name(s): quinaldic acid 4-oxidoreductase; quinoline-4-carboxylate:acceptor 2-oxidoreductase (hydroxylating)
Systematic name: quinoline-4-carboxylate:acceptor 2-oxidoreductase (hydroxylating)
Comments: A molybdenum—iron—sulfur flavoprotein with molybdopterin cytosine dinucleotide as the molybdenum cofactor. Quinoline, 4-methylquinoline and 4-chloroquinoline can also serve as substrates for the enzyme from Agrobacterium sp. 1B. Iodonitrotetrazolium chloride, thionine, menadione and 2,6-dichlorophenolindophenol can act as electron acceptors.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 175780-18-4
References:
1.  Bauer, G. and Lingens, F. Microbial metabolism of quinoline and related compounds. XV. Quinoline-4-carboxylic acid oxidoreductase from Agrobacterium spec.1B: a molybdenum-containing enzyme. Biol. Chem. Hoppe-Seyler 373 (1992) 699–705. [PMID: 1418685]
[EC 1.3.99.19 created 1999, modified 2006]
 
 
*EC 1.4.3.5
Accepted name: pyridoxal 5′-phosphate synthase
Reaction: (1) pyridoxamine 5′-phosphate + H2O + O2 = pyridoxal 5′-phosphate + NH3 + H2O2
(2) pyridoxine 5′-phosphate + O2 = pyridoxal 5′-phosphate + H2O2
For diagram of pyridoxal biosynthesis, click here
Glossary: pyridoxamine = 4-aminomethyl-3-hydroxy-5-hydroxymethyl-2-methylpyridine
Other name(s): pyridoxamine 5′-phosphate oxidase; pyridoxamine phosphate oxidase; pyridoxine (pyridoxamine)phosphate oxidase; pyridoxine (pyridoxamine) 5′-phosphate oxidase; pyridoxaminephosphate oxidase (EC 1.4.3.5: deaminating); PMP oxidase; pyridoxol-5′-phosphate:oxygen oxidoreductase (deaminating) (incorrect); pyridoxamine-phosphate oxidase; PdxH
Systematic name: pyridoxamine-5′-phosphate:oxygen oxidoreductase (deaminating)
Comments: A flavoprotein (FMN). In Escherichia coli, the cofactor pyridoxal 5′-phosphate is synthesized de novo by a pathway that involves EC 1.2.1.72 (erythrose-4-phosphate dehydrogenase), EC 1.1.1.290 (4-phosphoerythronate dehydrogenase), EC 2.6.1.52 (phosphoserine transaminase), EC 1.1.1.262 (4-hydroxythreonine-4-phosphate dehydrogenase), EC 2.6.99.2 (pyridoxine 5′-phosphate synthase) and EC 1.4.3.5 (with pyridoxine 5′-phosphate as substrate). N4′-Substituted pyridoxamine derivatives are also oxidized in reaction (1) to form pyridoxal 5-phosphate and the corresponding primary amine.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9029-21-4
References:
1.  Choi, J.-D., Bowers-Komro, D.M., Davis, M.D., Edmondson, D.E. and McCormick, D.B. Kinetic properties of pyridoxamine (pyridoxine)-5′-phosphate oxidase from rabbit liver. J. Biol. Chem. 258 (1983) 840–845. [PMID: 6822512]
2.  Wada, H. and Snell, E.E. The enzymatic oxidation of pyridoxine and pyridoxamine phosphates. J. Biol. Chem. 236 (1961) 2089–2095. [PMID: 13782387]
3.  Notheis, C., Drewke, C. and Leistner, E. Purification and characterization of the pyridoxol-5′-phosphate:oxygen oxidoreductase (deaminating) from Escherichia coli. Biochim. Biophys. Acta 1247 (1995) 265–271. [DOI] [PMID: 7696318]
4.  Laber, B., Maurer, W., Scharf, S., Stepusin, K. and Schmidt, F.S. Vitamin B6 biosynthesis: formation of pyridoxine 5′-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. FEBS Lett. 449 (1999) 45–48. [DOI] [PMID: 10225425]
5.  Musayev, F.N., Di Salvo, M.L., Ko, T.P., Schirch, V. and Safo, M.K. Structure and properties of recombinant human pyridoxine 5′-phosphate oxidase. Protein Sci. 12 (2003) 1455–1463. [DOI] [PMID: 12824491]
6.  Safo, M.K., Musayev, F.N. and Schirch, V. Structure of Escherichia coli pyridoxine 5′-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme. Acta Crystallogr. D Biol. Crystallogr. 61 (2005) 599–604. [DOI] [PMID: 15858270]
7.  Zhang, Z. and McCormick, D.B. Uptake and metabolism of N-(4′-pyridoxyl)amines by isolated rat liver cells. Arch. Biochem. Biophys. 294 (1992) 394–397. [DOI] [PMID: 1567194]
[EC 1.4.3.5 created 1961, modified 2006]
 
 
*EC 1.4.4.2
Accepted name: glycine dehydrogenase (aminomethyl-transferring)
Reaction: glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
For diagram of glycine cleavage system, click here
Glossary: dihydrolipoyl group
Other name(s): P-protein; glycine decarboxylase; glycine-cleavage complex; glycine:lipoylprotein oxidoreductase (decarboxylating and acceptor-aminomethylating); protein P1; glycine dehydrogenase (decarboxylating); glycine cleavage system P-protein; glycine-cleavage complex P-protein
Systematic name: glycine:H-protein-lipoyllysine oxidoreductase (decarboxylating, acceptor-amino-methylating)
Comments: A pyridoxal-phosphate protein. A component of the glycine cleavage system, which is composed of four components that only loosely associate: the P protein (EC 1.4.4.2), the T protein (EC 2.1.2.10, aminomethyltransferase), the L protein (EC 1.8.1.4, dihydrolipoyl dehydrogenase) and the lipoyl-bearing H protein [3]. Previously known as glycine synthase.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37259-67-9
References:
1.  Hiraga, K. and Kikuchi, G. The mitochondrial glycine cleavage system. Functional association of glycine decarboxylase and aminomethyl carrier protein. J. Biol. Chem. 255 (1980) 11671–11676. [PMID: 7440563]
2.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
3.  Nesbitt, N.M., Baleanu-Gogonea, C., Cicchillo, R.M., Goodson, K., Iwig, D.F., Broadwater, J.A., Haas, J.A., Fox, B.G. and Booker, S.J. Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase. Protein Expr. Purif. 39 (2005) 269–282. [DOI] [PMID: 15642479]
[EC 1.4.4.2 created 1984, modified 2003, modified 2006, modified 2013]
 
 
EC 1.7.1.13
Accepted name: preQ1 synthase
Reaction: 7-aminomethyl-7-carbaguanine + 2 NADP+ = 7-cyano-7-carbaguanine + 2 NADPH + 2 H+
For diagram of queuine biosynthesis, click here
Glossary: 7-aminomethyl-7-carbaguanine = preQ1 = 7-aminomethyl-7-deazaguanine
7-cyano-7-carbaguanine = preQ0 = 7-cyano-7-deazaguanine
Other name(s): YkvM; QueF; preQ0 reductase; preQ0 oxidoreductase; 7-cyano-7-deazaguanine reductase; queuine synthase (incorrect as queuine is not the product); queuine:NADP+ oxidoreductase (incorrect as queuine is not the product)
Systematic name: 7-aminomethyl-7-carbaguanine:NADP+ oxidoreductase
Comments: The reaction occurs in the reverse direction. This enzyme catalyses one of the early steps in the synthesis of queuosine (Q-tRNA), and is followed by the action of EC 2.4.2.29, tRNA-guanosine34 transglycosylase. Queuosine is found in the wobble position of tRNAGUN in Eukarya and Bacteria [2] and is thought to be involved in translational modulation. The enzyme is not a GTP cyclohydrolase, as was thought previously based on sequence-homology studies.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 1256460-80-6
References:
1.  Van Lanen, S.G., Reader, J.S., Swairjo, M.A., de Crécy-Lagard, V., Lee, B. and Iwata-Reuyl, D. From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc. Natl. Acad. Sci. USA 102 (2005) 4264–4269. [DOI] [PMID: 15767583]
2.  Yokoyama, S., Miyazawa, T., Iitaka, Y., Yamaizumi, Z., Kasai, H. and Nishimura, S. Three-dimensional structure of hyper-modified nucleoside Q located in the wobbling position of tRNA. Nature 282 (1979) 107–109. [PMID: 388227]
3.  Kuchino, Y., Kasai, H., Nihei, K. and Nishimura, S. Biosynthesis of the modified nucleoside Q in transfer RNA. Nucleic Acids Res. 3 (1976) 393–398. [DOI] [PMID: 1257053]
4.  Okada, N., Noguchi, S., Nishimura, S., Ohgi, T., Goto, T., Crain, P.F. and McCloskey, J.A. Structure determination of a nucleoside Q precursor isolated from E. coli tRNA: 7-(aminomethyl)-7-deazaguanosine. Nucleic Acids Res. 5 (1978) 2289–2296. [DOI] [PMID: 353740]
5.  Noguchi, S., Yamaizumi, Z., Ohgi, T., Goto, T., Nishimura, Y., Hirota, Y. and Nishimura, S. Isolation of Q nucleoside precursor present in tRNA of an E. coli mutant and its characterization as 7-(cyano)-7-deazaguanosine. Nucleic Acids Res. 5 (1978) 4215–4223. [DOI] [PMID: 364423]
6.  Swairjo, M.A., Reddy, R.R., Lee, B., Van Lanen, S.G., Brown, S., de Crécy-Lagard, V., Iwata-Reuyl, D. and Schimmel, P. Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme. Acta Crystallogr. F Struct. Biol. Cryst. Commun. 61 (2005) 945–948. [DOI] [PMID: 16511203]
[EC 1.7.1.13 created 2006]
 
 
*EC 1.8.1.4
Accepted name: dihydrolipoyl dehydrogenase
Reaction: protein N6-(dihydrolipoyl)lysine + NAD+ = protein N6-(lipoyl)lysine + NADH + H+
For diagram of glycine cleavage system, click here, for diagram of the citric acid cycle, click here and for diagram of oxo-acid dehydrogenase complexes, click here
Glossary: dihydrolipoyl = (6R)-6,8-disulfanyloctanoyl
For structure of dihydrolipoyl, click here
Other name(s): LDP-Glc; LDP-Val; dehydrolipoate dehydrogenase; diaphorase; dihydrolipoamide dehydrogenase; dihydrolipoamide:NAD+ oxidoreductase; dihydrolipoic dehydrogenase; dihydrothioctic dehydrogenase; lipoamide dehydrogenase (NADH); lipoamide oxidoreductase (NADH); lipoamide reductase; lipoamide reductase (NADH); lipoate dehydrogenase; lipoic acid dehydrogenase; lipoyl dehydrogenase; protein-6-N-(dihydrolipoyl)lysine:NAD+ oxidoreductase
Systematic name: protein-N6-(dihydrolipoyl)lysine:NAD+ oxidoreductase
Comments: A flavoprotein (FAD). A component of the multienzyme 2-oxo-acid dehydrogenase complexes. In the pyruvate dehydrogenase complex, it binds to the core of EC 2.3.1.12, dihydrolipoyllysine-residue acetyltransferase, and catalyses oxidation of its dihydrolipoyl groups. It plays a similar role in the oxoglutarate and 3-methyl-2-oxobutanoate dehydrogenase complexes. Another substrate is the dihydrolipoyl group in the H-protein of the glycine-cleavage system (click here for diagram), in which it acts, together with EC 1.4.4.2, glycine dehydrogenase (decarboxylating), and EC 2.1.2.10, aminomethyltransferase, to break down glycine. It can also use free dihydrolipoate, dihydrolipoamide or dihydrolipoyllysine as substrate. This enzyme was first shown to catalyse the oxidation of NADH by methylene blue; this activity was called diaphorase. The glycine cleavage system is composed of four components that only loosely associate: the P protein (EC 1.4.4.2), the T protein (EC 2.1.2.10), the L protein (EC 1.8.1.4) and the lipoyl-bearing H protein [6].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9001-18-7
References:
1.  Massey, V. Lipoyl dehydrogenase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 275–306.
2.  Massey, V., Gibson, Q.H. and Veeger, C. Intermediates in the catalytic action of lipoyl dehydrogenase (diaphorase). Biochem. J. 77 (1960) 341–351. [PMID: 13767908]
3.  Savage, N. Preparation and properties of highly purified diaphorase. Biochem. J. 67 (1957) 146–155. [PMID: 13471525]
4.  Straub, F.B. Isolation and properties of a flavoprotein from heart muscle tissue. Biochem. J. 33 (1939) 787–792. [PMID: 16746974]
5.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
6.  Nesbitt, N.M., Baleanu-Gogonea, C., Cicchillo, R.M., Goodson, K., Iwig, D.F., Broadwater, J.A., Haas, J.A., Fox, B.G. and Booker, S.J. Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase. Protein Expr. Purif. 39 (2005) 269–282. [DOI] [PMID: 15642479]
[EC 1.8.1.4 created 1961 as EC 1.6.4.3, modified 1976, transferred 1983 to EC 1.8.1.4, modified 2003, modified 2006]
 
 
*EC 1.11.1.14
Accepted name: lignin peroxidase
Reaction: (1) 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol + H2O2 = 3,4-dimethoxybenzaldehyde + 2-methoxyphenol + glycolaldehyde + H2O
(2) 2 (3,4-dimethoxyphenyl)methanol + H2O2 = 2 (3,4-dimethoxyphenyl)methanol radical + 2 H2O
Glossary: veratryl alcohol = (3,4-dimethoxyphenyl)methanol
veratraldehyde = 3,4-dimethoxybenzaldehyde
2-methoxyphenol = guaiacol
Other name(s): diarylpropane oxygenase; ligninase I; diarylpropane peroxidase; LiP; diarylpropane:oxygen,hydrogen-peroxide oxidoreductase (C-C-bond-cleaving); 1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol:hydrogen-peroxide oxidoreductase (incorrect); (3,4-dimethoxyphenyl)methanol:hydrogen-peroxide oxidoreductase
Systematic name: 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol:hydrogen-peroxide oxidoreductase
Comments: A hemoprotein, involved in the oxidative breakdown of lignin by white-rot basidiomycete fungi. The reaction involves an initial oxidation of the heme iron by hydrogen peroxide, forming compound I (FeIV=O radical cation) at the active site. A single one-electron reduction of compound I by an electron derived from a substrate molecule yields compound II (FeIV=O non-radical cation), followed by a second one-electron transfer that returns the enzyme to the ferric oxidation state. The electron transfer events convert the substrate molecule into a transient cation radical intermediate that fragments spontaneously. The enzyme can act on a wide range of aromatic compounds, including methoxybenzenes and nonphenolic β-O-4 linked arylglycerol β-aryl ethers, but cannot act directly on the lignin molecule, which is too large to fit into the active site. However larger lignin molecules can be degraded in the presence of veratryl alcohol. It has been suggested that the free radical that is formed when the enzyme acts on veratryl alcohol can diffuse into the lignified cell wall, where it oxidizes lignin and other organic substrates. In the presence of high concentration of hydrogen peroxide and lack of substrate, the enzyme forms a catalytically inactive form (compound III). This form can be rescued by interaction with two molecules of the free radical products. In the case of veratryl alcohol, such an interaction yields two molecules of veratryl aldehyde.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, PDB, CAS registry number: 93792-13-3
References:
1.  Kersten, P.J., Tien, M., Kalyanaraman, B. and Kirk, T.K. The ligninase of Phanerochaete chrysosporium generates cation radicals from methoxybenzenes. J. Biol. Chem. 260 (1985) 2609–2612. [PMID: 2982828]
2.  Paszczynski, A., Huynh, V.-B. and Crawford, R. Comparison of ligninase-I and peroxidase-M2 from the white-rot fungus Phanerochaete chrysosporium. Arch. Biochem. Biophys. 244 (1986) 750–765. [DOI] [PMID: 3080953]
3.  Harvey, P.J., Schoemaker, H.E. and Palmer, J.M. Veratryl alcohol as a mediator and the role of radical cations in lignin biodegradation by Phanerochaete chrysosporium. FEBS Lett. 195 (1986) 242–246.
4.  Wariishi, H., Marquez, L., Dunford, H.B. and Gold, M.H. Lignin peroxidase compounds II and III. Spectral and kinetic characterization of reactions with peroxides. J. Biol. Chem. 265 (1990) 11137–11142. [PMID: 2162833]
5.  Cai, D.Y. and Tien, M. Characterization of the oxycomplex of lignin peroxidases from Phanerochaete chrysosporium: equilibrium and kinetics studies. Biochemistry 29 (1990) 2085–2091. [PMID: 2328240]
6.  Khindaria, A., Yamazaki, I. and Aust, S.D. Veratryl alcohol oxidation by lignin peroxidase. Biochemistry 34 (1995) 16860–16869. [PMID: 8527462]
7.  Khindaria, A., Yamazaki, I. and Aust, S.D. Stabilization of the veratryl alcohol cation radical by lignin peroxidase. Biochemistry 35 (1996) 6418–6424. [DOI] [PMID: 8639588]
8.  Khindaria, A., Nie, G. and Aust, S.D. Detection and characterization of the lignin peroxidase compound II-veratryl alcohol cation radical complex. Biochemistry 36 (1997) 14181–14185. [DOI] [PMID: 9369491]
9.  Doyle, W.A., Blodig, W., Veitch, N.C., Piontek, K. and Smith, A.T. Two substrate interaction sites in lignin peroxidase revealed by site-directed mutagenesis. Biochemistry 37 (1998) 15097–15105. [DOI] [PMID: 9790672]
10.  Pollegioni, L., Tonin, F. and Rosini, E. Lignin-degrading enzymes. FEBS J. 282 (2015) 1190–1213. [DOI] [PMID: 25649492]
[EC 1.11.1.14 created 1992, modified 2006, modified 2011, modified 2016]
 
 
EC 1.11.1.16
Accepted name: versatile peroxidase
Reaction: (1) 1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol + H2O2 = 4-hydroxy-3-methoxybenzaldehyde + 2-methoxyphenol + glycolaldehyde + H2O
(2) 2 manganese(II) + 2 H+ + H2O2 = 2 manganese(III) + 2 H2O
Glossary: 4-hydroxy-3-methoxybenzaldehyde = vanillin
2-methoxyphenol = guaiacol
Other name(s): VP; hybrid peroxidase; polyvalent peroxidase; reactive-black-5:hydrogen-peroxide oxidoreductase
Systematic name: 1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol:hydrogen-peroxide oxidoreductase
Comments: A hemoprotein. This ligninolytic peroxidase combines the substrate-specificity characteristics of the two other ligninolytic peroxidases, EC 1.11.1.13, manganese peroxidase and EC 1.11.1.14, lignin peroxidase. Unlike these two enzymes, it is also able to oxidize phenols, hydroquinones and both low- and high-redox-potential dyes, due to a hybrid molecular architecture that involves multiple binding sites for substrates [2,4].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 42613-30-9, 114995-15-2
References:
1.  Martínez, M.J., Ruiz-Dueñas, F.J., Guillén, F. and Martínez, A.T. Purification and catalytic properties of two manganese peroxidase isoenzymes from Pleurotus eryngii. Eur. J. Biochem. 237 (1996) 424–432. [DOI] [PMID: 8647081]
2.  Heinfling, A., Ruiz-Dueñas, F.J., Martínez, M.J., Bergbauer, M., Szewzyk, U. and Martínez, A.T. A study on reducing substrates of manganese-oxidizing peroxidases from Pleurotus eryngii and Bjerkandera adusta. FEBS Lett. 428 (1998) 141–146. [DOI] [PMID: 9654123]
3.  Ruiz-Dueñas, F.J., Martínez, M.J. and Martínez, A.T. Molecular characterization of a novel peroxidase isolated from the ligninolytic fungus Pleurotus eryngii. Mol. Microbiol. 31 (1999) 223–235. [DOI] [PMID: 9987124]
4.  Camarero, S., Sarkar, S., Ruiz-Dueñas, F.J., Martínez, M.J. and Martínez, A.T. Description of a versatile peroxidase involved in the natural degradation of lignin that has both manganese peroxidase and lignin peroxidase substrate interaction sites. J. Biol. Chem. 274 (1999) 10324–10330. [DOI] [PMID: 10187820]
5.  Ruiz-Dueñas, F.J., Martínez, M.J. and Martínez, A.T. Heterologous expression of Pleurotus eryngii peroxidase confirms its ability to oxidize Mn2+ and different aromatic substrates. Appl. Environ. Microbiol. 65 (1999) 4705–4707. [PMID: 10508113]
6.  Camarero, S., Ruiz-Dueñas, F.J., Sarkar, S., Martínez, M.J. and Martínez, A.T. The cloning of a new peroxidase found in lignocellulose cultures of Pleurotus eryngii and sequence comparison with other fungal peroxidases. FEMS Microbiol. Lett. 191 (2000) 37–43. [DOI] [PMID: 11004397]
7.  Ruiz-Dueñas, F.J., Camarero, S., Pérez-Boada, M., Martínez, M.J. and Martínez, A.T. A new versatile peroxidase from Pleurotus. Biochem. Soc. Trans. 29 (2001) 116–122. [PMID: 11356138]
8.  Banci, L., Camarero, S., Martínez, A.T., Martínez, M.J., Pérez-Boada, M., Pierattelli, R. and Ruiz-Dueñas, F.J. NMR study of manganese(II) binding by a new versatile peroxidase from the white-rot fungus Pleurotus eryngii. J. Biol. Inorg. Chem. 8 (2003) 751–760. [DOI] [PMID: 12884090]
9.  Pérez-Boada, M., Ruiz-Dueñas, F.J., Pogni, R., Basosi, R., Choinowski, T., Martínez, M.J., Piontek, K. and Martínez, A.T. Versatile peroxidase oxidation of high redox potential aromatic compounds: site-directed mutagenesis, spectroscopic and crystallographic investigation of three long-range electron transfer pathways. J. Mol. Biol. 354 (2005) 385–402. [DOI] [PMID: 16246366]
10.  Caramelo, L., Martínez, M.J. and Martínez, A.T. A search for ligninolytic peroxidases in the fungus Pleurotus eryngii involving α-keto-γ-thiomethylbutyric acid and lignin model dimer. Appl. Environ. Microbiol. 65 (1999) 916–922. [PMID: 10049842]
[EC 1.11.1.16 created 2006, modified 2016]
 
 
*EC 1.13.11.11
Accepted name: tryptophan 2,3-dioxygenase
Reaction: L-tryptophan + O2 = N-formyl-L-kynurenine
For diagram of tryptophan catabolism, click here
Other name(s): tryptophan pyrrolase (ambiguous); tryptophanase; tryptophan oxygenase; tryptamine 2,3-dioxygenase; tryptophan peroxidase; indoleamine 2,3-dioxygenase (ambiguous); indolamine 2,3-dioxygenase (ambiguous); L-tryptophan pyrrolase; TDO; L-tryptophan 2,3-dioxygenase; L-tryptophan:oxygen 2,3-oxidoreductase (decyclizing)
Systematic name: L-tryptophan:oxygen 2,3-oxidoreductase (ring-opening)
Comments: A protohemoprotein. In mammals, the enzyme appears to be located only in the liver. This enzyme, together with EC 1.13.11.52, indoleamine 2,3-dioxygenase, catalyses the first and rate-limiting step in the kynurenine pathway, the major pathway of tryptophan metabolism [5]. The enzyme is specific for tryptophan as substrate, but is far more active with L-tryptophan than with D-tryptophan [2].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9014-51-1
References:
1.  Uchida, K., Shimizu, T., Makino, R., Sakaguchi, K., Iizuka, T., Ishimura, Y., Nozawa, T. and Hatano, M. Magnetic and natural circular dichroism of L-tryptophan 2,3-dioxygenases and indoleamine 2,3-dioxygenase. I. Spectra of ferric and ferrous high spin forms. J. Biol. Chem. 258 (1983) 2519–2525. [PMID: 6600455]
2.  Ren, S., Liu, H., Licad, E. and Correia, M.A. Expression of rat liver tryptophan 2,3-dioxygenase in Escherichia coli: structural and functional characterization of the purified enzyme. Arch. Biochem. Biophys. 333 (1996) 96–102. [DOI] [PMID: 8806758]
3.  Leeds, J.M., Brown, P.J., McGeehan, G.M., Brown, F.K. and Wiseman, J.S. Isotope effects and alternative substrate reactivities for tryptophan 2,3-dioxygenase. J. Biol. Chem. 268 (1993) 17781–17786. [PMID: 8349662]
4.  Dang, Y., Dale, W.E. and Brown, O.R. Comparative effects of oxygen on indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase of the kynurenine pathway. Free Radic. Biol. Med. 28 (2000) 615–624. [DOI] [PMID: 10719243]
5.  Littlejohn, T.K., Takikawa, O., Truscott, R.J. and Walker, M.J. Asp274 and His346 are essential for heme binding and catalytic function of human indoleamine 2,3-dioxygenase. J. Biol. Chem. 278 (2003) 29525–29531. [DOI] [PMID: 12766158]
[EC 1.13.11.11 created 1961 as EC 1.11.1.4, deleted 1964, reinstated 1965 as EC 1.13.1.12, transferred 1972 to EC 1.13.11.11, modified 1989, modified 2006]
 
 
*EC 1.13.11.19
Accepted name: cysteamine dioxygenase
Reaction: cysteamine + O2 = hypotaurine
For diagram of taurine biosynthesis, click here
Glossary: cysteamine = 2-aminoethanethiol
Other name(s): ADO (gene name); persulfurase; cysteamine oxygenase; cysteamine:oxygen oxidoreductase
Systematic name: 2-aminoethanethiol:oxygen oxidoreductase
Comments: A non-heme iron protein that is involved in the biosynthesis of taurine. 3-Aminopropanethiol (homocysteamine) and 2-sulfanylethan-1-ol (2-mercaptoethanol) can also act as substrates, but glutathione, cysteine, and cysteine ethyl- and methyl esters are not good substrates [1,3].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9033-41-4
References:
1.  Cavallini, D., de Marco, C., Scandurra, R., Duprè, S. and Graziani, M.T. The enzymatic oxidation of cysteamine to hypotaurine. Purification and properties of the enzyme. J. Biol. Chem. 241 (1966) 3189–3196. [PMID: 5912113]
2.  Wood, J.L. and Cavallini, D. Enzymic oxidation of cysteamine to hypotaurine in the absence of a cofactor. Arch. Biochem. Biophys. 119 (1967) 368–372. [DOI] [PMID: 6052430]
3.  Cavallini, D., Federici, G., Ricci, G., Duprè, S. and Antonucci, A. The specificity of cysteamine oxygenase. FEBS Lett. 56 (1975) 348–351. [DOI] [PMID: 1157952]
4.  Richerson, R.B. and Ziegler, D.M. Cysteamine dioxygenase. Methods Enzymol. 143 (1987) 410–415. [DOI] [PMID: 3657558]
5.  Dominy, J.E., Jr., Simmons, C.R., Hirschberger, L.L., Hwang, J., Coloso, R.M. and Stipanuk, M.H. Discovery and characterization of a second mammalian thiol dioxygenase, cysteamine dioxygenase. J. Biol. Chem. 282 (2007) 25189–25198. [PMID: 17581819]
[EC 1.13.11.19 created 1972, modified 2006]
 
 
EC 1.13.11.42
Deleted entry:  indoleamine-pyrrole 2,3-dioxygenase. The enzyme was identical to EC 1.13.11.11, tryptophan 2,3-dioxygenase
[EC 1.13.11.42 created 1992, deleted 2006]
 
 
EC 1.13.11.52
Accepted name: indoleamine 2,3-dioxygenase
Reaction: (1) D-tryptophan + O2 = N-formyl-D-kynurenine
(2) L-tryptophan + O2 = N-formyl-L-kynurenine
For diagram of tryptophan catabolism, click here
Other name(s): IDO (ambiguous); tryptophan pyrrolase (ambiguous); D-tryptophan:oxygen 2,3-oxidoreductase (decyclizing)
Systematic name: D-tryptophan:oxygen 2,3-oxidoreductase (ring-opening)
Comments: A protohemoprotein. Requires ascorbic acid and methylene blue for activity. This enzyme has broader substrate specificity than EC 1.13.11.11, tryptophan 2,3-dioxygenase [1]. It is induced in response to pathological conditions and host-defense mechanisms and its distribution in mammals is not confined to the liver [2]. While the enzyme is more active with D-tryptophan than L-tryptophan, its only known function to date is in the metabolism of L-tryptophan [2,6]. Superoxide radicals can replace O2 as oxygen donor [4,7].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9014-51-1
References:
1.  Yamamoto, S. and Hayaishi, O. Tryptophan pyrrolase of rabbit intestine. D- and L-tryptophan-cleaving enzyme or enzymes. J. Biol. Chem. 242 (1967) 5260–5266. [PMID: 6065097]
2.  Yasui, H., Takai, K., Yoshida, R. and Hayaishi, O. Interferon enhances tryptophan metabolism by inducing pulmonary indoleamine 2,3-dioxygenase: its possible occurrence in cancer patients. Proc. Natl. Acad. Sci. USA 83 (1986) 6622–6626. [DOI] [PMID: 2428037]
3.  Takikawa, O., Yoshida, R., Kido, R. and Hayaishi, O. Tryptophan degradation in mice initiated by indoleamine 2,3-dioxygenase. J. Biol. Chem. 261 (1986) 3648–3653. [PMID: 2419335]
4.  Hirata, F., Ohnishi, T. and Hayaishi, O. Indoleamine 2,3-dioxygenase. Characterization and properties of enzyme. O2- complex. J. Biol. Chem. 252 (1977) 4637–4642. [PMID: 194886]
5.  Dang, Y., Dale, W.E. and Brown, O.R. Comparative effects of oxygen on indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase of the kynurenine pathway. Free Radic. Biol. Med. 28 (2000) 615–624. [DOI] [PMID: 10719243]
6.  Littlejohn, T.K., Takikawa, O., Truscott, R.J. and Walker, M.J. Asp274 and His346 are essential for heme binding and catalytic function of human indoleamine 2,3-dioxygenase. J. Biol. Chem. 278 (2003) 29525–29531. [DOI] [PMID: 12766158]
7.  Thomas, S.R. and Stocker, R. Redox reactions related to indoleamine 2,3-dioxygenase and tryptophan metabolism along the kynurenine pathway. Redox Rep. 4 (1999) 199–220. [DOI] [PMID: 10731095]
8.  Sono, M. Spectroscopic and equilibrium studies of ligand and organic substrate binding to indolamine 2,3-dioxygenase. Biochemistry 29 (1990) 1451–1460. [PMID: 2334706]
[EC 1.13.11.52 created 2006]
 
 
EC 1.13.11.53
Accepted name: acireductone dioxygenase (Ni2+-requiring)
Reaction: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 3-(methylsulfanyl)propanoate + formate + CO
For diagram of methionine salvage, click here and for diagram of reaction, click here
Glossary: acireductone = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
Other name(s): ARD; 2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase (ambiguous); acireductone dioxygenase (ambiguous); E-2; 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming)
Systematic name: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming)
Comments: Requires Ni2+. If iron(II) is bound instead of Ni2+, the reaction catalysed by EC 1.13.11.54, acireductone dioxygenase [iron(II)-requiring], occurs instead [1]. The enzyme from the bacterium Klebsiella oxytoca (formerly Klebsiella pneumoniae) ATCC strain 8724 is involved in the methionine salvage pathway.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Wray, J.W. and Abeles, R.H. A bacterial enzyme that catalyzes formation of carbon monoxide. J. Biol. Chem. 268 (1993) 21466–21469. [PMID: 8407993]
2.  Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147–3153. [DOI] [PMID: 7852397]
3.  Furfine, E.S. and Abeles, R.H. Intermediates in the conversion of 5′-S-methylthioadenosine to methionine in Klebsiella pneumoniae. J. Biol. Chem. 263 (1988) 9598–9606. [PMID: 2838472]
4.  Dai, Y., Wensink, P.C. and Abeles, R.H. One protein, two enzymes. J. Biol. Chem. 274 (1999) 1193–1195. [DOI] [PMID: 9880484]
5.  Mo, H., Dai, Y., Pochapsky, S.S. and Pochapsky, T.C. 1H, 13C and 15N NMR assignments for a carbon monoxide generating metalloenzyme from Klebsiella pneumoniae. J. Biomol. NMR 14 (1999) 287–288. [PMID: 10481280]
6.  Dai, Y., Pochapsky, T.C. and Abeles, R.H. Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae. Biochemistry 40 (2001) 6379–6387. [DOI] [PMID: 11371200]
7.  Al-Mjeni, F., Ju, T., Pochapsky, T.C. and Maroney, M.J. XAS investigation of the structure and function of Ni in acireductone dioxygenase. Biochemistry 41 (2002) 6761–6769. [DOI] [PMID: 12022880]
8.  Pochapsky, T.C., Pochapsky, S.S., Ju, T., Mo, H., Al-Mjeni, F. and Maroney, M.J. Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat. Struct. Biol. 9 (2002) 966–972. [DOI] [PMID: 12402029]
[EC 1.13.11.53 created 2006]
 
 
EC 1.13.11.54
Accepted name: acireductone dioxygenase [iron(II)-requiring]
Reaction: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 4-(methylsulfanyl)-2-oxobutanoate + formate
For diagram of methionine salvage, click here and for diagram of reaction, click here
Glossary: acireductone = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
Other name(s): ARD′; 2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase (ambiguous); acireductone dioxygenase (ambiguous); E-2′; E-3 dioxygenase; 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate-forming)
Systematic name: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one:oxygen oxidoreductase (formate-forming)
Comments: Requires iron(II). If Ni2+ is bound instead of iron(II), the reaction catalysed by EC 1.13.11.53, acireductone dioxygenase (Ni2+-requiring), occurs instead. The enzyme from the bacterium Klebsiella oxytoca (formerly Klebsiella pneumoniae) ATCC strain 8724 is involved in the methionine salvage pathway.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Wray, J.W. and Abeles, R.H. A bacterial enzyme that catalyzes formation of carbon monoxide. J. Biol. Chem. 268 (1993) 21466–21469. [PMID: 8407993]
2.  Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147–3153. [DOI] [PMID: 7852397]
3.  Furfine, E.S. and Abeles, R.H. Intermediates in the conversion of 5′-S-methylthioadenosine to methionine in Klebsiella pneumoniae. J. Biol. Chem. 263 (1988) 9598–9606. [PMID: 2838472]
4.  Dai, Y., Wensink, P.C. and Abeles, R.H. One protein, two enzymes. J. Biol. Chem. 274 (1999) 1193–1195. [DOI] [PMID: 9880484]
5.  Mo, H., Dai, Y., Pochapsky, S.S. and Pochapsky, T.C. 1H, 13C and 15N NMR assignments for a carbon monoxide generating metalloenzyme from Klebsiella pneumoniae. J. Biomol. NMR 14 (1999) 287–288. [PMID: 10481280]
6.  Dai, Y., Pochapsky, T.C. and Abeles, R.H. Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae. Biochemistry 40 (2001) 6379–6387. [DOI] [PMID: 11371200]
7.  Al-Mjeni, F., Ju, T., Pochapsky, T.C. and Maroney, M.J. XAS investigation of the structure and function of Ni in acireductone dioxygenase. Biochemistry 41 (2002) 6761–6769. [DOI] [PMID: 12022880]
8.  Pochapsky, T.C., Pochapsky, S.S., Ju, T., Mo, H., Al-Mjeni, F. and Maroney, M.J. Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat. Struct. Biol. 9 (2002) 966–972. [DOI] [PMID: 12402029]
[EC 1.13.11.54 created 2006]
 
 
EC 1.13.11.55
Accepted name: sulfur oxygenase/reductase
Reaction: 4 sulfur + 4 H2O + O2 = 2 hydrogen sulfide + 2 sulfite
Other name(s): SOR; sulfur oxygenase; sulfur oxygenase reductase
Systematic name: sulfur:oxygen oxidoreductase (hydrogen-sulfide- and sulfite-forming)
Comments: This enzyme, which is found in thermophilic microorganisms, contains one mononuclear none-heme iron centre per subunit. Elemental sulfur is both the electron donor and one of the two known acceptors, the other being oxygen. Thiosulfate is also observed as a product, but is likely formed non-enzymically by a reaction between sulfite and sulfur [1]. This enzyme differs from EC 1.13.11.18, persulfide dioxygenase and EC 1.12.98.4, sulfhydrogenase, in that both activities occur simultaneously.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 120598-92-7
References:
1.  Kletzin, A. Coupled enzymatic production of sulfite, thiosulfate, and hydrogen sulfide from sulfur: purification and properties of a sulfur oxygenase reductase from the facultatively anaerobic archaebacterium Desulfurolobus ambivalens. J. Bacteriol. 171 (1989) 1638–1643. [DOI] [PMID: 2493451]
2.  Kletzin, A. Molecular characterization of the sor gene, which encodes the sulfur oxygenase/reductase of the thermoacidophilic Archaeum Desulfurolobus ambivalens. J. Bacteriol. 174 (1992) 5854–5859. [DOI] [PMID: 1522063]
3.  Sun, C.W., Chen, Z.W., He, Z.G., Zhou, P.J. and Liu, S.J. Purification and properties of the sulfur oxygenase/reductase from the acidothermophilic archaeon, Acidianus strain S5. Extremophiles 7 (2003) 131–134. [DOI] [PMID: 12664265]
4.  Urich, T., Bandeiras, T.M., Leal, S.S., Rachel, R., Albrecht, T., Zimmermann, P., Scholz, C., Teixeira, M., Gomes, C.M. and Kletzin, A. The sulphur oxygenase reductase from Acidianus ambivalens is a multimeric protein containing a low-potential mononuclear non-haem iron centre. Biochem. J. 381 (2004) 137–146. [DOI] [PMID: 15030315]
[EC 1.13.11.55 created 2006]
 
 
EC 1.13.12.14
Transferred entry: chlorophyllide-a oxygenase. Now EC 1.14.13.122, chlorophyllide-a oxygenase
[EC 1.13.12.14 created 2006, deleted 2011]
 
 
EC 1.14.13.65
Deleted entry:  2-hydroxyquinoline 8-monooxygenase
[EC 1.14.13.65 created 1999, deleted 2006]
 
 
EC 1.14.13.101
Accepted name: senecionine N-oxygenase
Reaction: senecionine + NADPH + H+ + O2 = senecionine N-oxide + NADP+ + H2O
Other name(s): senecionine monooxygenase (N-oxide-forming); SNO
Systematic name: senecionine,NADPH:oxygen oxidoreductase (N-oxide-forming)
Comments: A flavoprotein. NADH cannot replace NADPH. While pyrrolizidine alkaloids of the senecionine and monocrotaline types are generally good substrates (e.g. senecionine, retrorsine and monocrotaline), the enzyme does not use ester alkaloids lacking an hydroxy group at C-7 (e.g. supinine and phalaenopsine), 1,2-dihydro-alkaloids (e.g. sarracine) or unesterified necine bases (e.g. senkirkine) as substrates [1]. Senecionine N-oxide is used by insects as a chemical defense: senecionine N-oxide is non-toxic, but it is bioactivated to a toxic form by the action of cytochrome P-450 oxidase when absorbed by insectivores.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 220581-68-0
References:
1.  Lindigkeit, R., Biller, A., Buch, M., Schiebel, H.M., Boppre, M. and Hartmann, T. The two facies of pyrrolizidine alkaloids: the role of the tertiary amine and its N-oxide in chemical defense of insects with acquired plant alkaloids. Eur. J. Biochem. 245 (1997) 626–636. [DOI] [PMID: 9182998]
2.  Naumann, C., Hartmann, T. and Ober, D. Evolutionary recruitment of a flavin-dependent monooxygenase for the detoxification of host plant-acquired pyrrolizidine alkaloids in the alkaloid-defended arctiid moth Tyria jacobaeae. Proc. Natl. Acad. Sci. USA 99 (2002) 6085–6090. [DOI] [PMID: 11972041]
[EC 1.14.13.101 created 2006]
 
 
*EC 1.14.99.3
Transferred entry: heme oxygenase (biliverdin-producing). Now EC 1.14.14.18, heme oxygenase (biliverdin-producing)
[EC 1.14.99.3 created 1972, modified 2006, deleted 2015]
 
 
EC 1.17.99.4
Accepted name: uracil/thymine dehydrogenase
Reaction: (1) uracil + H2O + acceptor = barbiturate + reduced acceptor
(2) thymine + H2O + acceptor = 5-methylbarbiturate + reduced acceptor
For diagram of pyrimidine catabolism, click here
Other name(s): uracil oxidase; uracil-thymine oxidase; uracil dehydrogenase
Systematic name: uracil:acceptor oxidoreductase
Comments: Forms part of the oxidative pyrimidine-degrading pathway in some microorganisms, along with EC 3.5.2.1 (barbiturase) and EC 3.5.1.95 (N-malonylurea hydrolase). Mammals, plants and other microorganisms utilize the reductive pathway, comprising EC 1.3.1.1 [dihydrouracil dehydrogenase (NAD+)] or EC 1.3.1.2 [dihydropyrimidine dehydrogenase (NADP+)], EC 3.5.2.2 (dihydropyrimidinase) and EC 3.5.1.6 (β-ureidopropionase), with the ultimate degradation products being an L-amino acid, NH3 and CO2 [5].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9029-00-9
References:
1.  Hayaishi, O. and Kornberg, A. Metabolism of cytosine, thymine, uracil, and barbituric acid by bacterial enzymes. J. Biol. Chem. 197 (1952) 717–723. [PMID: 12981104]
2.  Wang, T.P. and Lampen, J.O. Metabolism of pyrimidines by a soil bacterium. J. Biol. Chem. 194 (1952) 775–783. [PMID: 14927671]
3.  Wang, T.P. and Lampen, J.O. Uracil oxidase and the isolation of barbituric acid from uracil oxidation. J. Biol. Chem. 194 (1952) 785–791. [PMID: 14927672]
4.  Lara, F.J.S. On the decomposition of pyrimidines by bacteria. II. Studies with cell-free enzyme preparations. J. Bacteriol. 64 (1952) 279–285. [PMID: 14955523]
5.  Soong, C.L., Ogawa, J. and Shimizu, S. Novel amidohydrolytic reactions in oxidative pyrimidine metabolism: analysis of the barbiturase reaction and discovery of a novel enzyme, ureidomalonase. Biochem. Biophys. Res. Commun. 286 (2001) 222–226. [DOI] [PMID: 11485332]
[EC 1.17.99.4 created 1961 as EC 1.2.99.1, transferred 1984 to EC 1.1.99.19, transferred 2006 to EC 1.17.99.4]
 
 
*EC 2.1.2.10
Accepted name: aminomethyltransferase
Reaction: [protein]-S8-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3
For diagram of the glycine-cleavage system, click here
Glossary: dihydrolipoyl group
Other name(s): S-aminomethyldihydrolipoylprotein:(6S)-tetrahydrofolate aminomethyltransferase (ammonia-forming); T-protein; glycine synthase; tetrahydrofolate aminomethyltransferase; [protein]-8-S-aminomethyldihydrolipoyllysine:tetrahydrofolate aminomethyltransferase (ammonia-forming)
Systematic name: [protein]-S8-aminomethyldihydrolipoyllysine:tetrahydrofolate aminomethyltransferase (ammonia-forming)
Comments: A component, with EC 1.4.4.2 glycine dehydrogenase (decarboxylating) and EC 1.8.1.4, dihydrolipoyl dehydrogenanse, of the glycine cleavage system, formerly known as glycine synthase. The glycine cleavage system is composed of four components that only loosely associate: the P protein (EC 1.4.4.2), the T protein (EC 2.1.2.10), the L protein (EC 1.8.1.4) and the lipoyl-bearing H protein [3].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37257-08-2
References:
1.  Okamura-Ikeda, K., Fujiwara, K. and Motokawa, Y. Purification and characterization of chicken liver T-protein, a component of the glycine cleavage system. J. Biol. Chem. 257 (1982) 135–139. [PMID: 7053363]
2.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
3.  Nesbitt, N.M., Baleanu-Gogonea, C., Cicchillo, R.M., Goodson, K., Iwig, D.F., Broadwater, J.A., Haas, J.A., Fox, B.G. and Booker, S.J. Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase. Protein Expr. Purif. 39 (2005) 269–282. [DOI] [PMID: 15642479]
[EC 2.1.2.10 created 1972, modified 2003, modified 2006]
 
 
*EC 2.3.1.11
Accepted name: thioethanolamine S-acetyltransferase
Reaction: acetyl-CoA + 2-aminoethanethiol = CoA + S-(2-aminoethyl)thioacetate
Other name(s): thioltransacetylase B; thioethanolamine acetyltransferase; acetyl-CoA:thioethanolamine S-acetyltransferase
Systematic name: acetyl-CoA:2-aminoethanethiol S-acetyltransferase
Comments: 2-Sulfanylethan-1-ol (2-mercaptoethanol) can act as a substrate [1].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 9029-93-0
References:
1.  Brady, R.O. and Stadtman, E.R. Enzymatic thioltransacetylation. J. Biol. Chem. 211 (1954) 621–629. [PMID: 13221570]
2.  Gunsalus, I.C. Group transfer and acyl-generating functions of lipoic acid derivatives. In: McElroy, W.D. and Glass, B. (Ed.), A Symposium on the Mechanism of Enzyme Action, Johns Hopkins Press, Baltimore, 1954, pp. 545–580.
[EC 2.3.1.11 created 1961, modified 2006]
 
 
*EC 2.3.1.38
Accepted name: [acyl-carrier-protein] S-acetyltransferase
Reaction: acetyl-CoA + an [acyl-carrier protein] = CoA + an acetyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): acetyl coenzyme A-acyl-carrier-protein transacylase; [acyl-carrier-protein]-acetyltransferase; [ACP]-acetyltransferase; acetyl-CoA:[acyl-carrier-protein] S-acetyltransferase
Systematic name: acetyl-CoA:[acyl-carrier protein] S-acetyltransferase
Comments: This enzyme, along with EC 2.3.1.39, [acyl-carrier-protein] S-malonyltransferase, is essential for the initiation of fatty-acid biosynthesis in bacteria. The substrate acetyl-CoA protects the enzyme against inhibition by N-ethylmaleimide or iodoacetamide [4]. This is one of the activities associated with β-ketoacyl-[acyl-carrier-protein] synthase III (EC 2.3.1.180) [5].
Links to other databases: BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 37257-16-2
References:
1.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [PMID: 4561013]
2.  Vance, D.E., Mituhashi, O. and Bloch, K. Purification and properties of the fatty acid synthetase from Mycobacterium phlei. J. Biol. Chem. 248 (1973) 2303–2309. [PMID: 4698221]
3.  Williamson, I.P. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVII. Preparation and general properties of acetyl coenzyme A and malonyl coenzyme A-acyl carrier protein transacylases. J. Biol. Chem. 241 (1966) 2326–2332. [DOI] [PMID: 5330116]
4.  Lowe, P.N. and Rhodes, S. Purification and characterization of [acyl-carrier-protein] acetyltransferase from Escherichia coli. Biochem. J. 250 (1988) 789–796. [PMID: 3291856]
5.  Tsay, J.T., Oh, W., Larson, T.J., Jackowski, S. and Rock, C.O. Isolation and characterization of the β-ketoacyl-acyl carrier protein synthase III gene (fabH) from Escherichia coli K-12. J. Biol. Chem. 267 (1992) 6807–6814. [PMID: 1551888]
6.  Rangan, V.S. and Smith, S. Alteration of the substrate specificity of the malonyl-CoA/acetyl-CoA:acyl carrier protein S-acyltransferase domain of the multifunctional fatty acid synthase by mutation of a single arginine residue. J. Biol. Chem. 272 (1997) 11975–11978. [DOI] [PMID: 9115261]
[EC 2.3.1.38 created 1972, modified 2006]
 
 
*EC 2.3.1.39
Accepted name: [acyl-carrier-protein] S-malonyltransferase
Reaction: malonyl-CoA + an [acyl-carrier protein] = CoA + a malonyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): [acyl carrier protein]malonyltransferase; FabD; malonyl coenzyme A-acyl carrier protein transacylase; malonyl transacylase; malonyl transferase; malonyl-CoA-acyl carrier protein transacylase; malonyl-CoA:[acyl-carrier-protein] S-malonyltransferase; malonyl-CoA:ACP transacylase; malonyl-CoA:ACP-SH transacylase; malonyl-CoA:AcpM transacylase; malonyl-CoA:acyl carrier protein transacylase; malonyl-CoA:acyl-carrier-protein transacylase; malonyl-CoA/dephospho-CoA acyltransferase; MAT; MCAT; MdcH
Systematic name: malonyl-CoA:[acyl-carrier protein] S-malonyltransferase
Comments: This enzyme, along with EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, is essential for the initiation of fatty-acid biosynthesis in bacteria. This enzyme also provides the malonyl groups for polyketide biosynthesis [7]. The product of the reaction, malonyl-ACP, is an elongation substrate in fatty-acid biosynthesis. In Mycobacterium tuberculosis, holo-ACP (the product of EC 2.7.8.7, holo-[acyl-carrier-protein] synthase) is the preferred substrate [5]. This enzyme also forms part of the multienzyme complexes EC 4.1.1.88, biotin-independent malonate decarboxylase and EC 7.2.4.4, biotin-dependent malonate decarboxylase. Malonylation of ACP is immediately followed by decarboxylation within the malonate-decarboxylase complex to yield acetyl-ACP, the catalytically active species of the decarboxylase [12]. In the enzyme from Klebsiella pneumoniae, methylmalonyl-CoA can also act as a substrate but acetyl-CoA cannot [10] whereas the enzyme from Pseudomonas putida can use both as substrates [11]. The ACP subunit found in fatty-acid biosynthesis contains a pantetheine-4′-phosphate cofactor; that from malonate decarboxylase also contains pantetheine-4′-phosphate but in the form of a 2′-(5-triphosphoribosyl)-3′-dephospho-CoA cofactor.
Links to other databases: BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 37257-17-3
References:
1.  Alberts, A.W., Majerus, P.W. and Vagelos, P.R. Acetyl-CoA acyl carrier protein transacylase. Methods Enzymol. 14 (1969) 50–53. [DOI]
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [PMID: 4561013]
3.  Williamson, I.P. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVII. Preparation and general properties of acetyl coenzyme A and malonyl coenzyme A-acyl carrier protein transacylases. J. Biol. Chem. 241 (1966) 2326–2332. [DOI] [PMID: 5330116]
4.  Joshi, V.C. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XXVI. Purification and properties of malonyl-coenzyme A--acyl carrier protein transacylase of Escherichia coli. Arch. Biochem. Biophys. 143 (1971) 493–505. [DOI] [PMID: 4934182]
5.  Kremer, L., Nampoothiri, K.M., Lesjean, S., Dover, L.G., Graham, S., Betts, J., Brennan, P.J., Minnikin, D.E., Locht, C. and Besra, G.S. Biochemical characterization of acyl carrier protein (AcpM) and malonyl-CoA:AcpM transacylase (mtFabD), two major components of Mycobacterium tuberculosis fatty acid synthase II. J. Biol. Chem. 276 (2001) 27967–27974. [DOI] [PMID: 11373295]
6.  Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J., O'Connell, J.D., 3rd, Khosla, C. and Stroud, R.M. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 11 (2003) 147–154. [DOI] [PMID: 12575934]
7.  Szafranska, A.E., Hitchman, T.S., Cox, R.J., Crosby, J. and Simpson, T.J. Kinetic and mechanistic analysis of the malonyl CoA:ACP transacylase from Streptomyces coelicolor indicates a single catalytically competent serine nucleophile at the active site. Biochemistry 41 (2002) 1421–1427. [DOI] [PMID: 11814333]
8.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [DOI] [PMID: 9208947]
9.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [DOI] [PMID: 10561613]
10.  Hoenke, S. and Dimroth, P. Formation of catalytically active acetyl-S-malonate decarboxylase requires malonyl-coenzyme A:acyl carrier protein transacylase as auxiliary enzyme. Eur. J. Biochem. 259 (1999) 181–187. [DOI] [PMID: 9914491]
11.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [DOI] [PMID: 9851033]
12.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 2.3.1.39 created 1972, modified 2006, modified 2008]
 
 
*EC 2.3.1.41
Accepted name: β-ketoacyl-[acyl-carrier-protein] synthase I
Reaction: an acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a 3-oxoacyl-[acyl-carrier protein] + CO2 + an [acyl-carrier protein]
Glossary: acyl-[acyl-carrier protein] = R-CO-[acyl-carrier protein]
malonyl-[acyl-carrier protein] = HOOC-CH2-CO-[acyl-carrier protein]
3-oxoacyl-[acyl-carrier protein] = R-CO-CH2-CO-[acyl-carrier protein]
Other name(s): β-ketoacyl-ACP synthase I; β-ketoacyl synthetase; β-ketoacyl-ACP synthetase; β-ketoacyl-acyl carrier protein synthetase; β-ketoacyl-[acyl carrier protein] synthase; β-ketoacylsynthase; condensing enzyme (ambiguous); 3-ketoacyl-acyl carrier protein synthase; fatty acid condensing enzyme; acyl-malonyl(acyl-carrier-protein)-condensing enzyme; acyl-malonyl acyl carrier protein-condensing enzyme; β-ketoacyl acyl carrier protein synthase; 3-oxoacyl-[acyl-carrier-protein] synthase; 3-oxoacyl:ACP synthase I; KASI; KAS I; FabF1; FabB; acyl-[acyl-carrier-protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Systematic name: acyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)
Comments: This enzyme is responsible for the chain-elongation step of dissociated (type II) fatty-acid biosynthesis, i.e. the addition of two C atoms to the fatty-acid chain. Escherichia coli mutants that lack this enzyme are deficient in unsaturated fatty acids. The enzyme can use fatty acyl thioesters of ACP (C2 to C16) as substrates, as well as fatty acyl thioesters of Co-A (C4 to C16) [4]. The substrate specificity is very similar to that of EC 2.3.1.179, β-ketoacyl-ACP synthase II, with the exception that the latter enzyme is far more active with palmitoleoyl-ACP (C16Δ9) as substrate, allowing the organism to regulate its fatty-acid composition with changes in temperature [4,5].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9077-10-5
References:
1.  Alberts, A.W., Majerus, P.W. and Vagelos, P.R. Acetyl-CoA acyl carrier protein transacylase. Methods Enzymol. 14 (1969) 50–53. [DOI]
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [PMID: 4561013]
3.  Toomey, R.E. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVI. Preparation and general properties of acyl-malonyl acyl carrier protein-condensing enzyme from Escherichia coli. J. Biol. Chem. 241 (1966) 1159–1165. [PMID: 5327099]
4.  D'Agnolo, G., Rosenfeld, I.S. and Vagelos, P.R. Multiple forms of β-ketoacyl-acyl carrier protein synthetase in Escherichia coli. J. Biol. Chem. 250 (1975) 5289–5294. [PMID: 237914]
5.  Garwin, J.L., Klages, A.L. and Cronan, J.E., Jr.. Structural, enzymatic, and genetic studies of β-ketoacyl-acyl carrier protein synthases I and II of Escherichia coli. J. Biol. Chem. 255 (1980) 11949–11956. [PMID: 7002930]
6.  Wang, H. and Cronan, J.E. Functional replacement of the FabA and FabB proteins of Escherichia coli fatty acid synthesis by Enterococcus faecalis FabZ and FabF homologues. J. Biol. Chem. 279 (2004) 34489–34495. [DOI] [PMID: 15194690]
7.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
[EC 2.3.1.41 created 1972, modified 2006]
 
 
*EC 2.3.1.109
Accepted name: arginine N-succinyltransferase
Reaction: succinyl-CoA + L-arginine = CoA + N2-succinyl-L-arginine
For diagram of arginine catabolism, click here
Other name(s): arginine succinyltransferase; AstA; arginine and ornithine N2-succinyltransferase; AOST; AST (ambiguous); succinyl-CoA:L-arginine 2-N-succinyltransferase
Systematic name: succinyl-CoA:L-arginine N2-succinyltransferase
Comments: Also acts on L-ornithine. This is the first enzyme in the arginine succinyltransferase (AST) pathway for the catabolism of arginine [1]. This pathway converts the carbon skeleton of arginine into glutamate, with the concomitant production of ammonia and conversion of succinyl-CoA into succinate and CoA. The five enzymes involved in this pathway are EC 2.3.1.109 (arginine N-succinyltransferase), EC 3.5.3.23 (N-succinylarginine dihydrolase), EC 2.6.1.81 (succinylornithine transaminase), EC 1.2.1.71 (succinylglutamate-semialdehyde dehydrogenase) and EC 3.5.1.96 (succinylglutamate desuccinylase) [2,6].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 99676-48-9
References:
1.  Vander Wauven, C., Jann, A., Haas, D., Leisinger, T. and Stalon, V. N2-succinylornithine in ornithine catabolism of Pseudomonas aeruginosa. Arch. Microbiol. 150 (1988) 400–404. [PMID: 3144259]
2.  Vander Wauven, C. and Stalon, V. Occurrence of succinyl derivatives in the catabolism of arginine in Pseudomonas cepacia. J. Bacteriol. 164 (1985) 882–886. [PMID: 2865249]
3.  Tricot, C., Vander Wauven, C., Wattiez, R., Falmagne, P. and Stalon, V. Purification and properties of a succinyltransferase from Pseudomonas aeruginosa specific for both arginine and ornithine. Eur. J. Biochem. 224 (1994) 853–861. [DOI] [PMID: 7523119]
4.  Itoh, Y. Cloning and characterization of the aru genes encoding enzymes of the catabolic arginine succinyltransferase pathway in Pseudomonas aeruginosa. J. Bacteriol. 179 (1997) 7280–7290. [DOI] [PMID: 9393691]
5.  Schneider, B.L., Kiupakis, A.K. and Reitzer, L.J. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180 (1998) 4278–4286. [PMID: 9696779]
6.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 50 (1986) 314–352. [PMID: 3534538]
7.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Erratum report: Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 51 (1987) 178. [PMID: 16350242]
[EC 2.3.1.109 created 1989, modified 2006]
 
 
EC 2.3.1.177
Accepted name: 3,5-dihydroxybiphenyl synthase
Reaction: 3 malonyl-CoA + benzoyl-CoA = 4 CoA + 3,5-dihydroxybiphenyl + 4 CO2
For diagram of polyketides biosynthesis, click here
Other name(s): BIS1; biphenyl synthase (ambiguous)
Systematic name: malonyl-CoA:benzoyl-CoA malonyltransferase
Comments: A polyketide synthase that is involved in the production of the phytoalexin aucuparin. 2-Hydroxybenzoyl-CoA can also act as substrate but it leads to the derailment product 4-hydroxycoumarin (cf. EC 2.3.1.208, 4-hydroxycoumarin synthase) [2]. This enzyme uses the same starter substrate as EC 2.3.1.151, benzophenone synthase.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 1217551-24-0
References:
1.  Liu, B., Beuerle, T., Klundt, T. and Beerhues, L. Biphenyl synthase from yeast-extract-treated cell cultures of Sorbus aucuparia. Planta 218 (2004) 492–496. [DOI] [PMID: 14595561]
2.  Liu, B., Raeth, T., Beuerle, T. and Beerhues, L. Biphenyl synthase, a novel type III polyketide synthase. Planta 225 (2007) 1495–1503. [DOI] [PMID: 17109150]
[EC 2.3.1.177 created 2006, modified 2012]
 
 
EC 2.3.1.178
Accepted name: diaminobutyrate acetyltransferase
Reaction: acetyl-CoA + L-2,4-diaminobutanoate = CoA + (2S)-4-acetamido-2-aminobutanoate
For diagram of ectoine biosynthesis, click here
Other name(s): L-2,4-diaminobutyrate acetyltransferase; L-2,4-diaminobutanoate acetyltransferase; EctA; diaminobutyric acid acetyltransferase; DABA acetyltransferase; 2,4-diaminobutanoate acetyltransferase; DAB acetyltransferase; DABAcT; acetyl-CoA:L-2,4-diaminobutanoate 4-N-acetyltransferase
Systematic name: acetyl-CoA:L-2,4-diaminobutanoate N4-acetyltransferase
Comments: Requires Na+ or K+ for maximal activity [3]. Ornithine, lysine, aspartate, and α-, β- and γ-aminobutanoate cannot act as substrates [3]. However, acetyl-CoA can be replaced by propanoyl-CoA, although the reaction proceeds more slowly [3]. Forms part of the ectoine-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 130456-92-7
References:
1.  Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157–162.
2.  Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91–99. [PMID: 9864317]
3.  Reshetnikov, A.S., Mustakhimov, I.I., Khmelenina, V.N. and Trotsenko, Y.A. Cloning, purification, and characterization of diaminobutyrate acetyltransferase from the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z. Biochemistry (Mosc.) 70 (2005) 878–883. [PMID: 16212543]
4.  Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772–783. [DOI] [PMID: 11823218]
5.  Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141–1149. [DOI] [PMID: 9141677]
[EC 2.3.1.178 created 2006]
 
 
EC 2.3.1.179
Accepted name: β-ketoacyl-[acyl-carrier-protein] synthase II
Reaction: a (Z)-hexadec-9-enoyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a (Z)-3-oxooctadec-11-enoyl-[acyl-carrier protein] + CO2 + an [acyl-carrier protein]
Glossary: palmitoleoyl-[acyl-carrier protein] = (Z)-hexadec-9-enoyl-[acyl-carrier protein]
cis-vaccenoyl-[acyl-carrier protein] = (Z)-octadec-11-enoyl-[acyl-carrier protein]
Other name(s): KASII; KAS II; FabF; 3-oxoacyl-acyl carrier protein synthase II; β-ketoacyl-ACP synthase II
Systematic name: (Z)-hexadec-9-enoyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)
Comments: Involved in the dissociated (or type II) fatty acid biosynthesis system that occurs in plants and bacteria. While the substrate specificity of this enzyme is very similar to that of EC 2.3.1.41, β-ketoacyl-[acyl-carrier-protein] synthase I, it differs in that palmitoleoyl-[acyl-carrier protein] is not a good substrate of EC 2.3.1.41 but is an excellent substrate of this enzyme [1,2]. The fatty-acid composition of Escherichia coli changes as a function of growth temperature, with the proportion of unsaturated fatty acids increasing with lower growth temperature. This enzyme controls the temperature-dependent regulation of fatty-acid composition, with mutants lacking this acivity being deficient in the elongation of palmitoleate to cis-vaccenate at low temperatures [3,4].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 1048648-42-5
References:
1.  D'Agnolo, G., Rosenfeld, I.S. and Vagelos, P.R. Multiple forms of β-ketoacyl-acyl carrier protein synthetase in Escherichia coli. J. Biol. Chem. 250 (1975) 5289–5294. [PMID: 237914]
2.  Garwin, J.L., Klages, A.L. and Cronan, J.E., Jr.. Structural, enzymatic, and genetic studies of β-ketoacyl-acyl carrier protein synthases I and II of Escherichia coli. J. Biol. Chem. 255 (1980) 11949–11956. [PMID: 7002930]
3.  Price, A.C., Rock, C.O. and White, S.W. The 1.3-Angstrom-resolution crystal structure of β-ketoacyl-acyl carrier protein synthase II from Streptococcus pneumoniae. J. Bacteriol. 185 (2003) 4136–4143. [DOI] [PMID: 12837788]
4.  Garwin, J.L., Klages, A.L. and Cronan, J.E., Jr. β-Ketoacyl-acyl carrier protein synthase II of Escherichia coli. Evidence for function in the thermal regulation of fatty acid synthesis. J. Biol. Chem. 255 (1980) 3263–3265. [PMID: 6988423]
5.  Magnuson, K., Carey, M.R. and Cronan, J.E., Jr. The putative fabJ gene of Escherichia coli fatty acid synthesis is the fabF gene. J. Bacteriol. 177 (1995) 3593–3595. [DOI] [PMID: 7768872]
6.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
[EC 2.3.1.179 created 2006, modified 2020]
 
 
EC 2.3.1.180
Accepted name: β-ketoacyl-[acyl-carrier-protein] synthase III
Reaction: acetyl-CoA + a malonyl-[acyl-carrier protein] = an acetoacetyl-[acyl-carrier protein] + CoA + CO2
Other name(s): 3-oxoacyl:ACP synthase III; 3-ketoacyl-acyl carrier protein synthase III; KASIII; KAS III; FabH; β-ketoacyl-acyl carrier protein synthase III; β-ketoacyl-ACP synthase III; β-ketoacyl (acyl carrier protein) synthase III; acetyl-CoA:malonyl-[acyl-carrier-protein] C-acyltransferase
Systematic name: acetyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme is responsible for initiating straight-chain fatty acid biosynthesis by the dissociated (or type II) fatty-acid biosynthesis system that occurs in plants and bacteria. In contrast to EC 2.3.1.41, β-ketoacyl-[acyl-carrier-protein] synthase I, and EC 2.3.1.179, β-ketoacyl-[acyl-carrier-protein] synthase II, this enzyme specifically uses short-chain acyl-CoA thioesters (preferably acetyl-CoA) rather than acyl-[acp] as its substrate [1]. The enzyme can also catalyse the reaction of EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, but to a much lesser extent [1]. The enzymes from some organisms (e.g. the Gram-positive bacterium Streptococcus pneumoniae) can accept branched-chain acyl-CoAs in addition to acetyl-CoA [5] (cf. EC 2.3.1.300, branched-chain β-ketoacyl-[acyl-carrier-protein] synthase).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 1048646-78-1
References:
1.  Tsay, J.T., Oh, W., Larson, T.J., Jackowski, S. and Rock, C.O. Isolation and characterization of the β-ketoacyl-acyl carrier protein synthase III gene (fabH) from Escherichia coli K-12. J. Biol. Chem. 267 (1992) 6807–6814. [PMID: 1551888]
2.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
3.  Han, L., Lobo, S. and Reynolds, K.A. Characterization of β-ketoacyl-acyl carrier protein synthase III from Streptomyces glaucescens and its role in initiation of fatty acid biosynthesis. J. Bacteriol. 180 (1998) 4481–4486. [DOI] [PMID: 9721286]
4.  Choi, K.H., Kremer, L., Besra, G.S. and Rock, C.O. Identification and substrate specificity of β-ketoacyl (acyl carrier protein) synthase III (mtFabH) from Mycobacterium tuberculosis. J. Biol. Chem. 275 (2000) 28201–28207. [DOI] [PMID: 10840036]
5.  Khandekar, S.S., Gentry, D.R., Van Aller, G.S., Warren, P., Xiang, H., Silverman, C., Doyle, M.L., Chambers, P.A., Konstantinidis, A.K., Brandt, M., Daines, R.A. and Lonsdale, J.T. Identification, substrate specificity, and inhibition of the Streptococcus pneumoniae β-ketoacyl-acyl carrier protein synthase III (FabH). J. Biol. Chem. 276 (2001) 30024–30030. [DOI] [PMID: 11375394]
6.  Qiu, X., Choudhry, A.E., Janson, C.A., Grooms, M., Daines, R.A., Lonsdale, J.T. and Khandekar, S.S. Crystal structure and substrate specificity of the β-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus. Protein Sci. 14 (2005) 2087–2094. [DOI] [PMID: 15987898]
7.  Li, Y., Florova, G. and Reynolds, K.A. Alteration of the fatty acid profile of Streptomyces coelicolor by replacement of the initiation enzyme 3-ketoacyl acyl carrier protein synthase III (FabH). J. Bacteriol. 187 (2005) 3795–3799. [DOI] [PMID: 15901703]
[EC 2.3.1.180 created 2006, modified 2021]
 
 
EC 2.3.1.181
Accepted name: lipoyl(octanoyl) transferase
Reaction: an octanoyl-[acyl-carrier protein] + a protein = a protein N6-(octanoyl)lysine + an [acyl-carrier protein]
Glossary: lipoyl group
Other name(s): LipB; lipoyl (octanoyl)-[acyl-carrier-protein]-protein N-lipoyltransferase; lipoyl (octanoyl)-acyl carrier protein:protein transferase; lipoate/octanoate transferase; lipoyltransferase; octanoyl-[acyl carrier protein]-protein N-octanoyltransferase; lipoyl(octanoyl)transferase; octanoyl-[acyl-carrier-protein]:protein N-octanoyltransferase
Systematic name: octanoyl-[acyl-carrier protein]:protein N-octanoyltransferase
Comments: This is the first committed step in the biosynthesis of lipoyl cofactor. Lipoylation is essential for the function of several key enzymes involved in oxidative metabolism, as it converts apoprotein into the biologically active holoprotein. Examples of such lipoylated proteins include pyruvate dehydrogenase (E2 domain), 2-oxoglutarate dehydrogenase (E2 domain), the branched-chain 2-oxoacid dehydrogenases and the glycine cleavage system (H protein) [2,3]. Lipoyl-ACP can also act as a substrate [4] although octanoyl-ACP is likely to be the true substrate [6]. The other enzyme involved in the biosynthesis of lipoyl cofactor is EC 2.8.1.8, lipoyl synthase. An alternative lipoylation pathway involves EC 6.3.1.20, lipoate—protein ligase, which can lipoylate apoproteins using exogenous lipoic acid (or its analogues).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 392687-64-8
References:
1.  Nesbitt, N.M., Baleanu-Gogonea, C., Cicchillo, R.M., Goodson, K., Iwig, D.F., Broadwater, J.A., Haas, J.A., Fox, B.G. and Booker, S.J. Expression, purification, and physical characterization of Escherichia coli lipoyl(octanoyl)transferase. Protein Expr. Purif. 39 (2005) 269–282. [DOI] [PMID: 15642479]
2.  Vanden Boom, T.J., Reed, K.E. and Cronan, J.E., Jr. Lipoic acid metabolism in Escherichia coli: isolation of null mutants defective in lipoic acid biosynthesis, molecular cloning and characterization of the E. coli lip locus, and identification of the lipoylated protein of the glycine cleavage system. J. Bacteriol. 173 (1991) 6411–6420. [DOI] [PMID: 1655709]
3.  Jordan, S.W. and Cronan, J.E., Jr. A new metabolic link. The acyl carrier protein of lipid synthesis donates lipoic acid to the pyruvate dehydrogenase complex in Escherichia coli and mitochondria. J. Biol. Chem. 272 (1997) 17903–17906. [DOI] [PMID: 9218413]
4.  Zhao, X., Miller, J.R., Jiang, Y., Marletta, M.A. and Cronan, J.E. Assembly of the covalent linkage between lipoic acid and its cognate enzymes. Chem. Biol. 10 (2003) 1293–1302. [DOI] [PMID: 14700636]
5.  Wada, M., Yasuno, R., Jordan, S.W., Cronan, J.E., Jr. and Wada, H. Lipoic acid metabolism in Arabidopsis thaliana: cloning and characterization of a cDNA encoding lipoyltransferase. Plant Cell Physiol. 42 (2001) 650–656. [PMID: 11427685]
6.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
[EC 2.3.1.181 created 2006, modified 2016]
 
 
*EC 2.4.1.195
Accepted name: N-hydroxythioamide S-β-glucosyltransferase
Reaction: (1) UDP-α-D-glucose + (Z)-2-phenyl-1-thioacetohydroximate = UDP + desulfoglucotropeolin
(2) UDP-α-D-glucose + an (E)-ω-(methylsulfanyl)alkyl-thiohydroximate = UDP + an aliphatic desulfoglucosinolate
(3) UDP-α-D-glucose + (E)-2-(1H-indol-3-yl)-1-thioacetohydroximate = UDP + desulfoglucobrassicin
For diagram of glucotropeolin biosynthesis, click here
Glossary: an aliphatic desulfoglucosinolate = an ω-(methylsulfanyl)alkylhydroximate S-glucoside
Other name(s): UGT74B1 (gene name); desulfoglucosinolate-uridine diphosphate glucosyltransferase; uridine diphosphoglucose-thiohydroximate glucosyltransferase; thiohydroximate β-D-glucosyltransferase; UDPG:thiohydroximate glucosyltransferase; thiohydroximate S-glucosyltransferase; thiohydroximate glucosyltransferase; UDP-glucose:thiohydroximate S-β-D-glucosyltransferase; UDP-glucose:N-hydroxy-2-phenylethanethioamide S-β-D-glucosyltransferase
Systematic name: UDP-α-D-glucose:N-hydroxy-2-phenylethanethioamide S-β-D-glucosyltransferase
Comments: The enzyme specifically glucosylates the thiohydroximate functional group. It is involved in the biosynthesis of glucosinolates in cruciferous plants, and acts on aliphatic, aromatic, and indolic substrates.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 9068-14-8
References:
1.  Jain, J.C., Reed, D.W., Groot Wassink, J.W.D. and Underhill, E.W. A radioassay of enzymes catalyzing the glucosylation and sulfation steps of glucosinolate biosynthesis in Brassica species. Anal. Biochem. 178 (1989) 137–140. [DOI] [PMID: 2524977]
2.  Reed, D.W., Davin, L., Jain, J.C., Deluca, V., Nelson, L. and Underhill, E.W. Purification and properties of UDP-glucose:thiohydroximate glucosyltransferase from Brassica napus L. seedlings. Arch. Biochem. Biophys. 305 (1993) 526–532. [DOI] [PMID: 8373190]
3.  Marillia, E.F., MacPherson, J.M., Tsang, E.W., Van Audenhove, K., Keller, W.A. and GrootWassink, J.W. Molecular cloning of a Brassica napus thiohydroximate S-glucosyltransferase gene and its expression in Escherichia coli. Physiol. Plant. 113 (2001) 176–184. [PMID: 12060294]
4.  Fahey, J.W., Zalcmann, A.T. and Talalay, P. The chemical diversity and distribution of glucosinolates and isothiocyanates among plants. Phytochemistry 56 (2001) 5–51. [DOI] [PMID: 11198818]
5.  Grubb, C.D., Zipp, B.J., Ludwig-Muller, J., Masuno, M.N., Molinski, T.F. and Abel, S. Arabidopsis glucosyltransferase UGT74B1 functions in glucosinolate biosynthesis and auxin homeostasis. Plant J. 40 (2004) 893–908. [DOI] [PMID: 15584955]
[EC 2.4.1.195 created 1992, modified 2006, modified 2018]
 
 
EC 2.4.1.223
Accepted name: glucuronosyl-galactosyl-proteoglycan 4-α-N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-α-D-glucosamine + [protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine = UDP + [protein]-3-O-(α-D-GlcNAc-(1→4)-β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine
For diagram of heparan biosynthesis (later stages), click here
Glossary: [protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine = [protein]-3-O-(β-D-glucuronosyl-(1→3)-β-D-galactosyl-(1→3)-β-D-galactosyl-(1→4)-β-D-xylosyl)-L-serine
Other name(s): α-N-acetylglucosaminyltransferase I; α1,4-N-acetylglucosaminyltransferase; glucuronosylgalactosyl-proteoglycan 4-α-N-acetylglucosaminyltransferase; UDP-N-acetyl-D-glucosamine:β-D-glucuronosyl-(1→3)-β-D-galactosyl-(1→3)-β-D-galactosyl-(1→4)-β-D-xylosyl-proteoglycan 4IV-α-N-acetyl-D-glucosaminyltransferase; glucuronyl-galactosyl-proteoglycan 4-α-N-acetylglucosaminyltransferase
Systematic name: UDP-N-acetyl-α-D-glucosamine:[protein]-3-O-(β-D-GlcA-(1→3)-β-D-Gal-(1→3)-β-D-Gal-(1→4)-β-D-Xyl)-L-serine 4IV-α-N-acetyl-D-glucosaminyltransferase (configuration-retaining)
Comments: Enzyme involved in the initiation of heparin and heparan sulfate synthesis, transferring GlcNAc to the (GlcA-Gal-Gal-Xyl-)Ser core. Apparently products of both the human EXTL2 and EXTL3 genes can catalyse this reaction. In Caenorhabditis elegans, the product of the rib-2 gene displays this activity as well as that of EC 2.4.1.224, glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-α-N-acetylglucosaminyltransferase. For explanation of the use of a superscript in the systematic name, see 2-Carb-37.2.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 179241-74-8
References:
1.  Kitagawa, H., Shimakawa, H. and Sugahara, K. The tumor suppressor EXT-like gene EXTL2 encodes an α1,4-N-acetylhexosaminyltransferase that transfers N-acetylgalactosamine and N-acetylglucosamine to the common glycosaminoglycan-protein linkage region. The key enzyme for the chain initiation of heparan sulfate. J. Biol. Chem. 274 (1999) 13933–13937. [DOI] [PMID: 10318803]
2.  Kitagawa, H., Egusa, N., Tamura, J.I., Kusche-Gullberg, M., Lindahl, U. and Sugahara, K. rib-2, a Caenorhabditis elegans homolog of the human tumor suppressor EXT genes encodes a novel α1,4-N-acetylglucosaminyltransferase involved in the biosynthetic initiation and elongation of heparan sulfate. J. Biol. Chem. 276 (2001) 4834–4838. [DOI] [PMID: 11121397]
[EC 2.4.1.223 created 2002, modified 2016]
 
 
EC 2.4.1.243
Accepted name: 6G-fructosyltransferase
Reaction: [1-β-D-fructofuranosyl-(2→1)-]m+1-α-D-glucopyranoside + [1-β-D-fructofuranosyl-(2→1)-]n-α-D-glucopyranoside = [1-β-D-fructofuranosyl-(2→1)-]m-α-D-glucopyranoside + [1-β-D-fructofuranosyl-(2→1)-]n-β-D-fructofuranosyl-(2→6)-α-D-glucopyranoside (m > 0; n ≥ 0)
Glossary: [1-β-D-fructofuranosyl-(2→1)-]n-α-D-glucopyranoside = inulin
Other name(s): fructan:fructan 6G-fructosyltransferase; 1F(1-β-D-fructofuranosyl)m sucrose:1F(1-β-D-fructofuranosyl)nsucrose 6G-fructosyltransferase; 6G-FFT; 6G-FT; 6G-fructotransferase
Systematic name: 1F-oligo[β-D-fructofuranosyl-(2→1)-]sucrose 6G-β-D-fructotransferase
Comments: Inulins are polysaccharides consisting of linear or branched D-fructofuranosyl chains attached to the fructosyl residue of sucrose by a β(2→1) linkage. This enzyme catalyses the transfer of the terminal (2→1)-linked -D-fructosyl group of an inulin chain onto O-6 position of the glucose residue of another inulin molecule [1]. For example, if 1-kestose [1F-(β-D-fructofuranosyl)sucrose] is both the donor and recipient in the reaction shown above, i.e., if m = 1 and n = 1, then the products will be sucrose and 6G-di-β-D-fructofuranosylsucrose. In this notation, the superscripts F and G are used to specify whether the fructose or glucose residue of the sucrose carries the substituent. Alternatively, this may be indicated by the presence and/or absence of primes (see http://www.chem.qmul.ac.uk/iupac/2carb/36.html#362). Sucrose cannot be a donor substrate in the reaction (i.e. m cannot be zero) and inulin cannot act as an acceptor. Side reactions catalysed are transfer of a β-D-fructosyl group between compounds of the structure 1F-(1-β-D-fructofuranosyl)m-6G-(1-β-D-fructofuranosyl)n sucrose, where m ≥ 0 and n = 1 for the donor, and m ≥ 0 and n ≥ 0 for the acceptor.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 79633-28-6
References:
1.  Shiomi, N. Purification and characterisation of 6G-fructosyltransferase from the roots of asparagus (Asparagus officinalis L.). Carbohydr. Res. 96 (1981) 281–292.
2.  Shiomi, N. Reverse reaction of fructosyl transfer catalysed by asparagus 6G-fructosyltransferase. Carbohydr. Res. 106 (1982) 166–169.
3.  Shiomi, N. and Ueno, K. Cloning and expression of genes encoding fructosyltransferases from higher plants in food technology. J. Appl. Glycosci. 51 (2004) 177–183.
4.  Ueno, K., Onodera, S., Kawakami, A., Yoshida, M. and Shiomi, N. Molecular characterization and expression of a cDNA encoding fructan:fructan 6G-fructosyltransferase from asparagus (Asparagus officinalis). New Phytol. 165 (2005) 813–824. [DOI] [PMID: 15720693]
[EC 2.4.1.243 created 2006]
 
 
EC 2.4.1.244
Accepted name: N-acetyl-β-glucosaminyl-glycoprotein 4-β-N-acetylgalactosaminyltransferase
Reaction: UDP-N-acetyl-α-D-galactosamine + N-acetyl-β-D-glucosaminyl group = UDP + N-acetyl-β-D-galactosaminyl-(1→4)-N-acetyl-β-D-glucosaminyl group
Glossary: N-acetyl-β-D-galactosaminyl-(1→4)-N-acetyl-β-D-glucosamine = N,N′-diacetyllactosediamine
Other name(s): β1,4-N-acetylgalactosaminyltransferase III; β4GalNAc-T3; β1,4-N-acetylgalactosaminyltransferase IV; β4GalNAc-T4; UDP-N-acetyl-D-galactosamine:N-acetyl-D-glucosaminyl-group β-1,4-N-acetylgalactosaminyltransferase; UDP-N-acetyl-D-galactosamine:N-acetyl-β-D-glucosaminyl-group 4-β-N-acetylgalactosaminyltransferase
Systematic name: UDP-N-acetyl-α-D-galactosamine:N-acetyl-β-D-glucosaminyl-group 4-β-N-acetylgalactosaminyltransferase
Comments: The enzyme from human can transfer N-acetyl-D-galactosamine (GalNAc) to N-glycan and O-glycan substrates that have N-acetyl-D-glucosamine (GlcNAc) but not D-glucuronic acid (GlcUA) at their non-reducing end. The N-acetyl-β-D-glucosaminyl group is normally on a core oligosaccharide although benzyl glycosides have been used in enzyme-characterization experiments. Some glycohormones, e.g. lutropin and thyrotropin contain the N-glycan structure containing the N-acetyl-β-D-galactosaminyl-(1→4)-N-acetyl-β-D-glucosaminyl group.
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Sato, T., Gotoh, M., Kiyohara, K., Kameyama, A., Kubota, T., Kikuchi, N., Ishizuka, Y., Iwasaki, H., Togayachi, A., Kudo, T., Ohkura, T., Nakanishi, H. and Narimatsu, H. Molecular cloning and characterization of a novel human β1,4-N-acetylgalactosaminyltransferase, β4GalNAc-T3, responsible for the synthesis of N,N'-diacetyllactosediamine, GalNAc β1-4GlcNAc. J. Biol. Chem. 278 (2003) 47534–47544. [DOI] [PMID: 12966086]
2.  Gotoh, M., Sato, T., Kiyohara, K., Kameyama, A., Kikuchi, N., Kwon, Y.D., Ishizuka, Y., Iwai, T., Nakanishi, H. and Narimatsu, H. Molecular cloning and characterization of β1,4-N-acetylgalactosaminyltransferases IV synthesizing N,N'-diacetyllactosediamine. FEBS Lett. 562 (2004) 134–140. [DOI] [PMID: 15044014]
[EC 2.4.1.244 created 2006]
 
 
*EC 2.6.1.52
Accepted name: phosphoserine transaminase
Reaction: (1) O-phospho-L-serine + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate
(2) 4-phosphooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4-phosphooxybutanoate + L-glutamate
For diagram of EC 2.6.1, click here, for diagram of serine biosynthesis, click here and for diagram of pyridoxal biosynthesis, click here
Other name(s): PSAT; phosphoserine aminotransferase; 3-phosphoserine aminotransferase; hydroxypyruvic phosphate-glutamic transaminase; L-phosphoserine aminotransferase; phosphohydroxypyruvate transaminase; phosphohydroxypyruvic-glutamic transaminase; 3-O-phospho-L-serine:2-oxoglutarate aminotransferase; SerC; PdxC; 3PHP transaminase
Systematic name: O-phospho-L-serine:2-oxoglutarate aminotransferase
Comments: A pyridoxal 5′-phosphate protein. This enzyme catalyses the second step in the phosphorylated pathway of serine biosynthesis [1,3] and the third step in pyridoxal 5′-phosphate biosynthesis in the bacterium Escherichia coli [3]. Pyridoxal 5′-phosphate is the cofactor for both activities and therefore seems to be involved in its own biosynthesis [4]. Non-phosphorylated forms of serine and threonine are not substrates [4]. The archaeal enzyme has a relaxed specificity and can act on L-cysteate and L-alanine as alternative substrates to O-phospho-L-serine [7].
Links to other databases: BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9030-90-4
References:
1.  Pizer, L.I. The pathway and control of serine biosynthesis in Escherichia coli. J. Biol. Chem. 238 (1963) 3934–3944. [PMID: 14086727]
2.  Hirsch, H. and Greenberg, D.M. Studies on phosphoserine aminotransferase of sheep brain. J. Biol. Chem. 242 (1967) 2283–2287. [PMID: 6022873]
3.  Zhao, G. and Winkler, M.E. A novel α-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria. J. Bacteriol. 178 (1996) 232–239. [DOI] [PMID: 8550422]
4.  Drewke, C., Klein, M., Clade, D., Arenz, A., Müller, R. and Leistner, E. 4-O-phosphoryl-L-threonine, a substrate of the pdxC(serC) gene product involved in vitamin B6 biosynthesis. FEBS Lett. 390 (1996) 179–182. [DOI] [PMID: 8706854]
5.  Zhao, G. and Winkler, M.E. 4-Phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal 5′-phosphate coenzyme biosynthesis in Escherichia coli K-12. FEMS Microbiol. Lett. 135 (1996) 275–280. [PMID: 8595869]
6.  Baek, J.Y., Jun, D.Y., Taub, D. and Kim, Y.H. Characterization of human phosphoserine aminotransferase involved in the phosphorylated pathway of L-serine biosynthesis. Biochem. J. 373 (2003) 191–200. [PMID: 12633500]
7.  Helgadottir, S., Rosas-Sandoval, G., Soll, D. and Graham, D.E. Biosynthesis of phosphoserine in the Methanococcales. J. Bacteriol. 189 (2007) 575–582. [PMID: 17071763]
[EC 2.6.1.52 created 1972, modified 2006]
 
 
*EC 2.6.1.76
Accepted name: diaminobutyrate—2-oxoglutarate transaminase
Reaction: L-2,4-diaminobutanoate + 2-oxoglutarate = L-aspartate 4-semialdehyde + L-glutamate
For diagram of ectoine biosynthesis, click here
Other name(s): L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase; 2,4-diaminobutyrate 4-aminotransferase; diaminobutyrate aminotransferase; DABA aminotransferase; DAB aminotransferase; EctB; diaminibutyric acid aminotransferase; L-2,4-diaminobutyrate:2-oxoglutarate 4-aminotransferase
Systematic name: L-2,4-diaminobutanoate:2-oxoglutarate 4-aminotransferase
Comments: A pyridoxal-phosphate protein that requires potassium for activity [4]. In the proteobacterium Acinetobacter baumannii, this enzyme is cotranscribed with the neighbouring ddc gene that also encodes EC 4.1.1.86, diaminobutyrate decarboxylase. Differs from EC 2.6.1.46, diaminobutyrate—pyruvate transaminase, which has pyruvate as the amino-group acceptor. This is the first enzyme in the ectoine-biosynthesis pathway, the other enzymes involved being EC 2.3.1.178, diaminobutyrate acetyltransferase and EC 4.2.1.108, ectoine synthase [3,4].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 196622-96-5
References:
1.  Ikai, H. and Yamamoto, S. Identification and analysis of a gene encoding L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase involved in the 1,3-diaminopropane production pathway in Acinetobacter baumannii. J. Bacteriol. 179 (1997) 5118–5125. [DOI] [PMID: 9260954]
2.  Ikai, H. and Yamamoto, S. Two genes involved in the 1,3-diaminopropane production pathway in Haemophilus influenzae. Biol. Pharm. Bull. 21 (1998) 170–173. [PMID: 9514614]
3.  Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157–162.
4.  Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91–99. [PMID: 9864317]
5.  Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772–783. [DOI] [PMID: 11823218]
6.  Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141–1149. [DOI] [PMID: 9141677]
[EC 2.6.1.76 created 2000, modified 2006]
 
 
EC 2.6.1.81
Accepted name: succinylornithine transaminase
Reaction: N2-succinyl-L-ornithine + 2-oxoglutarate = N-succinyl-L-glutamate 5-semialdehyde + L-glutamate
For diagram of arginine catabolism, click here
Other name(s): succinylornithine aminotransferase; N2-succinylornithine 5-aminotransferase; AstC; SOAT; 2-N-succinyl-L-ornithine:2-oxoglutarate 5-aminotransferase
Systematic name: N2-succinyl-L-ornithine:2-oxoglutarate 5-aminotransferase
Comments: A pyridoxal-phosphate protein. Also acts on N2-acetyl-L-ornithine and L-ornithine, but more slowly [3]. In Pseudomonas aeruginosa, the arginine-inducible succinylornithine transaminase, acetylornithine transaminase (EC 2.6.1.11) and ornithine aminotransferase (EC 2.6.1.13) activities are catalysed by the same enzyme, but this is not the case in all species [5]. This is the third enzyme in the arginine succinyltransferase (AST) pathway for the catabolism of arginine [1]. This pathway converts the carbon skeleton of arginine into glutamate, with the concomitant production of ammonia and conversion of succinyl-CoA into succinate and CoA. The five enzymes involved in this pathway are EC 2.3.1.109 (arginine N-succinyltransferase), EC 3.5.3.23 (N-succinylarginine dihydrolase), EC 2.6.1.81 (succinylornithine transaminase), EC 1.2.1.71 (succinylglutamate-semialdehyde dehydrogenase) and EC 3.5.1.96 (succinylglutamate desuccinylase) [3,6].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Vander Wauven, C. and Stalon, V. Occurrence of succinyl derivatives in the catabolism of arginine in Pseudomonas cepacia. J. Bacteriol. 164 (1985) 882–886. [PMID: 2865249]
2.  Schneider, B.L., Kiupakis, A.K. and Reitzer, L.J. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180 (1998) 4278–4286. [PMID: 9696779]
3.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 50 (1986) 314–352. [PMID: 3534538]
4.  Itoh, Y. Cloning and characterization of the aru genes encoding enzymes of the catabolic arginine succinyltransferase pathway in Pseudomonas aeruginosa. J. Bacteriol. 179 (1997) 7280–7290. [DOI] [PMID: 9393691]
5.  Stalon, V., Vander Wauven, C., Momin, P. and Legrain, C. Catabolism of arginine, citrulline and ornithine by Pseudomonas and related bacteria. J. Gen. Microbiol. 133 (1987) 2487–2495. [DOI] [PMID: 3129535]
[EC 2.6.1.81 created 2006]
 
 
EC 2.6.99.2
Accepted name: pyridoxine 5′-phosphate synthase
Reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5′-phosphate + phosphate + 2 H2O
For diagram of pyridoxal biosynthesis, click here
Other name(s): pyridoxine 5-phosphate phospho lyase; PNP synthase; PdxJ
Systematic name: 1-deoxy-D-xylulose-5-phosphate:3-amino-2-oxopropyl phosphate 3-amino-2-oxopropyltransferase (phosphate-hydrolysing; cyclizing)
Comments: In Escherichia coli, the cofactor pyridoxal 5′-phosphate is synthesized de novo by a pathway that involves EC 1.2.1.72 (erythrose-4-phosphate dehydrogenase), EC 1.1.1.290 (4-phosphoerythronate dehydrogenase), EC 2.6.1.52 (phosphoserine transaminase), EC 1.1.1.262 (4-hydroxythreonine-4-phosphate dehydrogenase), EC 2.6.99.2 (pyridoxine 5′-phosphate synthase) and EC 1.4.3.5 (with pyridoxine 5′-phosphate as substrate). 1-Deoxy-D-xylulose cannot replace 1-deoxy-D-xylulose 5-phosphate as a substrate [3].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 230310-47-1
References:
1.  Garrido-Franco, M. Pyridoxine 5′-phosphate synthase: de novo synthesis of vitamin B6 and beyond. Biochim. Biophys. Acta 1647 (2003) 92–97. [DOI] [PMID: 12686115]
2.  Garrido-Franco, M., Laber, B., Huber, R. and Clausen, T. Enzyme-ligand complexes of pyridoxine 5′-phosphate synthase: implications for substrate binding and catalysis. J. Mol. Biol. 321 (2002) 601–612. [DOI] [PMID: 12206776]
3.  Laber, B., Maurer, W., Scharf, S., Stepusin, K. and Schmidt, F.S. Vitamin B6 biosynthesis: formation of pyridoxine 5′-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. FEBS Lett. 449 (1999) 45–48. [DOI] [PMID: 10225425]
4.  Franco, M.G., Laber, B., Huber, R. and Clausen, T. Structural basis for the function of pyridoxine 5′-phosphate synthase. Structure 9 (2001) 245–253. [DOI] [PMID: 11286891]
[EC 2.6.99.2 created 2006]
 
 
*EC 2.7.1.151
Accepted name: inositol-polyphosphate multikinase
Reaction: 2 ATP + 1D-myo-inositol 1,4,5-trisphosphate = 2 ADP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate (overall reaction)
(1a) ATP + 1D-myo-inositol 1,4,5-trisphosphate = ADP + 1D-myo-inositol 1,4,5,6-tetrakisphosphate
(1b) ATP + 1D-myo-inositol 1,4,5,6-tetrakisphosphate = ADP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate
For diagram of myo-inositol-phosphate metabolism, click here
Other name(s): IpK2; IP3/IP4 6-/3-kinase; IP3/IP4 dual-specificity 6-/3-kinase; IpmK; ArgRIII; AtIpk2α; AtIpk2β; inositol polyphosphate 6-/3-/5-kinase
Systematic name: ATP:1D-myo-inositol-1,4,5-trisphosphate 6-phosphotransferase
Comments: This enzyme also phosphorylates Ins(1,4,5)P3 to Ins(1,3,4,5)P4, Ins(1,3,4,5)P4 to Ins(1,3,4,5,6)P5, and Ins(1,3,4,5,6)P4 to Ins(PP)P4, isomer unknown. The enzyme from the plant Arabidopsis thaliana can also phosphorylate Ins(1,3,4,6)P4 and Ins(1,2,3,4,6)P5 at the D-5-position to produce 1,3,4,5,6-pentakisphosphate and inositol hexakisphosphate (InsP6), respectively [3]. Yeast produce InsP6 from Ins(1,4,5)P3 by the actions of this enzyme and EC 2.7.1.158, inositol-pentakisphosphate 2-kinase [4].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9077-69-4
References:
1.  Saiardi, A., Erdjument-Bromage, H., Snowman, A.M., Tempst, P. and Snyder, S.H. Synthesis of diphosphoinositol pentakisphosphate by a newly identified family of higher inositol polyphosphate kinases. Curr. Biol. 9 (1999) 1323–1326. [DOI] [PMID: 10574768]
2.  Odom, A.R., Stahlberg, A., Wente, S.R. and York, J.D. A role for nuclear inositol 1,4,5-trisphosphate kinase in transcriptional control. Science 287 (2000) 2026–2029. [DOI] [PMID: 10720331]
3.  Stevenson-Paulik, J., Odom, A.R. and York, J.D. Molecular and biochemical characterization of two plant inositol polyphosphate 6-/3-/5-kinases. J. Biol. Chem. 277 (2002) 42711–42718. [DOI] [PMID: 12226109]
4.  Verbsky, J.W., Chang, S.C., Wilson, M.P., Mochizuki, Y. and Majerus, P.W. The pathway for the production of inositol hexakisphosphate in human cells. J. Biol. Chem. 280 (2005) 1911–1920. [DOI] [PMID: 15531582]
[EC 2.7.1.151 created 2002, modified 2006]
 
 
EC 2.7.1.158
Accepted name: inositol-pentakisphosphate 2-kinase
Reaction: ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol hexakisphosphate
Other name(s): IP5 2-kinase; Gsl1p; Ipk1p; inositol polyphosphate kinase; inositol 1,3,4,5,6-pentakisphosphate 2-kinase; Ins(1,3,4,5,6)P5 2-kinase
Systematic name: ATP:1D-myo-inositol 1,3,4,5,6-pentakisphosphate 2-phosphotransferase
Comments: The enzyme can also use Ins(1,4,5,6)P4 [2] and Ins(1,4,5)P3 [3] as substrate. Inositol hexakisphosphate (phytate) accumulates in storage protein bodies during seed development and, when hydrolysed, releases stored nutrients to the developing seedling before the plant is capable of absorbing nutrients from its environment [5].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  York, J.D., Odom, A.R., Murphy, R., Ives, E.B. and Wente, S.R. A phospholipase C-dependent inositol polyphosphate kinase pathway required for efficient messenger RNA export. Science 285 (1999) 96–100. [DOI] [PMID: 10390371]
2.  Phillippy, B.Q., Ullah, A.H. and Ehrlich, K.C. Purification and some properties of inositol 1,3,4,5,6-Pentakisphosphate 2-kinase from immature soybean seeds. J. Biol. Chem. 269 (1994) 28393–28399. [PMID: 7961779]
3.  Phillippy, B.Q., Ullah, A.H. and Ehrlich, K.C. Additions and corrections to Purification and some properties of inositol 1,3,4,5,6-pentakisphosphate 2-kinase from immature soybean seeds. J. Biol. Chem. 270 (1997) 7782.
4.  Ongusaha, P.P., Hughes, P.J., Davey, J. and Michell, R.H. Inositol hexakisphosphate in Schizosaccharomyces pombe: synthesis from Ins(1,4,5)P3 and osmotic regulation. Biochem. J. 335 (1998) 671–679. [PMID: 9794810]
5.  Miller, A.L., Suntharalingam, M., Johnson, S.L., Audhya, A., Emr, S.D. and Wente, S.R. Cytoplasmic inositol hexakisphosphate production is sufficient for mediating the Gle1-mRNA export pathway. J. Biol. Chem. 279 (2004) 51022–51032. [DOI] [PMID: 15459192]
6.  Stevenson-Paulik, J., Odom, A.R. and York, J.D. Molecular and biochemical characterization of two plant inositol polyphosphate 6-/3-/5-kinases. J. Biol. Chem. 277 (2002) 42711–42718. [DOI] [PMID: 12226109]
[EC 2.7.1.158 created 2006]
 
 
EC 2.7.1.159
Accepted name: inositol-1,3,4-trisphosphate 5/6-kinase
Reaction: (1) ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,5-tetrakisphosphate
(2) ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,6-tetrakisphosphate
Other name(s): Ins(1,3,4)P3 5/6-kinase; inositol trisphosphate 5/6-kinase
Systematic name: ATP:1D-myo-inositol 1,3,4-trisphosphate 5-phosphotransferase
Comments: In humans, this enzyme, along with EC 2.7.1.127 (inositol-trisphosphate 3-kinase), EC 2.7.1.140 (inositol-tetrakisphosphate 5-kinase) and EC 2.7.1.158 (inositol pentakisphosphate 2-kinase) is involved in the production of inositol hexakisphosphate (InsP6). InsP6 is involved in many cellular processes, including mRNA export from the nucleus [2]. Yeasts do not have this enzyme, so produce InsP6 from Ins(1,4,5)P3 by the actions of EC 2.7.1.151 (inositol-polyphosphate multikinase) and EC 2.7.1.158 (inositol-pentakisphosphate 2-kinase) [2]. The enzymes from animals and plants also have the activity of EC 2.7.1.134, inositol-tetrakisphosphate 1-kinase.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 288307-53-9
References:
1.  Wilson, M.P. and Majerus, P.W. Isolation of inositol 1,3,4-trisphosphate 5/6-kinase, cDNA cloning and expression of the recombinant enzyme. J. Biol. Chem. 271 (1996) 11904–11910. [DOI] [PMID: 8662638]
2.  Verbsky, J.W., Chang, S.C., Wilson, M.P., Mochizuki, Y. and Majerus, P.W. The pathway for the production of inositol hexakisphosphate in human cells. J. Biol. Chem. 280 (2005) 1911–1920. [DOI] [PMID: 15531582]
3.  Miller, G.J., Wilson, M.P., Majerus, P.W. and Hurley, J.H. Specificity determinants in inositol polyphosphate synthesis: crystal structure of inositol 1,3,4-trisphosphate 5/6-kinase. Mol. Cell. 18 (2005) 201–212. [DOI] [PMID: 15837423]
[EC 2.7.1.159 created 2006]
 
 
EC 2.7.4.22
Accepted name: UMP kinase
Reaction: ATP + UMP = ADP + UDP
Other name(s): uridylate kinase; UMPK; uridine monophosphate kinase; PyrH; UMP-kinase; SmbA
Systematic name: ATP:UMP phosphotransferase
Comments: This enzyme is strictly specific for UMP as substrate and is used by prokaryotes in the de novo synthesis of pyrimidines, in contrast to eukaryotes, which use the dual-specificity enzyme UMP/CMP kinase (EC 2.7.4.14) for the same purpose [2]. This enzyme is the subject of feedback regulation, being inhibited by UTP and activated by GTP [1].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9036-23-1
References:
1.  Serina, L., Blondin, C., Krin, E., Sismeiro, O., Danchin, A., Sakamoto, H., Gilles, A.M. and Bârzu, O. Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP. Biochemistry 34 (1995) 5066–5074. [PMID: 7711027]
2.  Marco-Marín, C., Gil-Ortiz, F. and Rubio, V. The crystal structure of Pyrococcus furiosus UMP kinase provides insight into catalysis and regulation in microbial pyrimidine nucleotide biosynthesis. J. Mol. Biol. 352 (2005) 438–454. [DOI] [PMID: 16095620]
[EC 2.7.4.22 created 2006]
 
 
EC 2.7.7.63
Transferred entry: lipoate—protein ligase. Now EC 6.3.1.20, lipoate—protein ligase.
[EC 2.7.7.63 created 2006, deleted 2016]
 
 
*EC 2.8.1.6
Accepted name: biotin synthase
Reaction: dethiobiotin + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + 2 reduced [2Fe-2S] ferredoxin = biotin + (sulfur carrier) + 2 L-methionine + 2 5′-deoxyadenosine + 2 oxidized [2Fe-2S] ferredoxin
Glossary: biotin = 5[(3aS,4S,6aR)-2-oxohexahydro(4H-thieno[4,5-d]imidazol-4-yl)]pentanoate
4,5-secobiotin = 6-[(4R,5R)-2-oxo-5-(sulfanylmethyl)imidazolidin-4-yl]hexanoate = 9-mercaptodethiobiotin
Other name(s): dethiobiotin:sulfur sulfurtransferase
Systematic name: dethiobiotin:sulfur-(sulfur carrier) sulfurtransferase
Comments: The enzyme binds a [4Fe-4S] and a [2Fe-2S] cluster. In every reaction cycle, the enzyme consumes two molecules of AdoMet. The first reaction produces 5′-deoxyadenosine and 4,5-secobiotin. Reaction with another equivalent of AdoMet results in abstraction of the C-6 methylene pro-S hydrogen atom from 4,5-secobiotin, and the resulting carbon radical is quenched via formation of an intramolecular C-S bond, thus closing the biotin tetrahydrothiophene ring. The sulfur donor is believed to be the [2Fe-2S] cluster, which is sacrificed in the process, so that in vitro the reaction is a single turnover. In vivo, the [2Fe-2S] cluster can be reassembled by the Isc or Suf iron-sulfur cluster assembly systems, to allow further catalysis.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 80146-93-6
References:
1.  Trainor, D.A., Parry, R.J. and Gitterman, A. Biotin biosynthesis. 2. Stereochemistry of sulfur introduction at C-4 of dethiobiotin. J. Am. Chem. Soc. 102 (1980) 1467–1468.
2.  Shiuan, D. and Campbell, A. Transcriptional regulation and gene arrangement of Escherichia coli, Citrobacter freundii and Salmonella typhimurium biotin operons. Gene 67 (1988) 203–211. [DOI] [PMID: 2971595]
3.  Zhang, S., Sanyal, I., Bulboaca, G.H., Rich, A. and Flint, D.H. The gene for biotin synthase from Saccharomyces cerevisiae: cloning, sequencing, and complementation of Escherichia coli strains lacking biotin synthase. Arch. Biochem. Biophys. 309 (1994) 29–35. [DOI] [PMID: 8117110]
4.  Ugulava, N.B., Gibney, B.R. and Jarrett, J.T. Biotin synthase contains two distinct iron-sulfur cluster binding sites: chemical and spectroelectrochemical analysis of iron-sulfur cluster interconversions. Biochemistry 40 (2001) 8343–8351. [DOI] [PMID: 11444981]
5.  Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T. and Drennan, C.L. Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 303 (2004) 76–79. [DOI] [PMID: 14704425]
6.  Lotierzo, M., Tse Sum Bui, B., Florentin, D., Escalettes, F. and Marquet, A. Biotin synthase mechanism: an overview. Biochem. Soc. Trans. 33 (2005) 820–823. [DOI] [PMID: 16042606]
7.  Taylor, A.M., Farrar, C.E. and Jarrett, J.T. 9-Mercaptodethiobiotin is formed as a competent catalytic intermediate by Escherichia coli biotin synthase. Biochemistry 47 (2008) 9309–9317. [DOI] [PMID: 18690713]
8.  Reyda, M.R., Fugate, C.J. and Jarrett, J.T. A complex between biotin synthase and the iron-sulfur cluster assembly chaperone HscA that enhances in vivo cluster assembly. Biochemistry 48 (2009) 10782–10792. [DOI] [PMID: 19821612]
[EC 2.8.1.6 created 1999, modified 2006, modified 2011, modified 2014]
 
 
EC 2.8.1.8
Accepted name: lipoyl synthase
Reaction: [protein]-N6-(octanoyl)-L-lysine + an [Fe-S] cluster scaffold protein carrying a [4Fe-4S]2+ cluster + 2 S-adenosyl-L-methionine + 2 oxidized [2Fe-2S] ferredoxin + 6 H+ = [protein]-N6-[(R)-dihydrolipoyl]-L-lysine + an [Fe-S] cluster scaffold protein + 2 sulfide + 4 Fe3+ + 2 L-methionine + 2 5′-deoxyadenosine + 2 reduced [2Fe-2S] ferredoxin
Other name(s): lipA (gene name); LS; lipoate synthase; protein 6-N-(octanoyl)lysine:sulfur sulfurtransferase; protein N6-(octanoyl)lysine:sulfur sulfurtransferase; protein N6-(octanoyl)lysine:sulfur-(sulfur carrier) sulfurtransferase
Systematic name: [protein]-N6-(octanoyl)-L-lysine:an [Fe-S] cluster scaffold protein carrying a [4Fe-4S]2+ cluster sulfurtransferase
Comments: This enzyme catalyses the final step in the de-novo biosynthesis of the lipoyl cofactor, the attachment of two sulfhydryl groups to C6 and C8 of a pendant octanoyl chain. It is a member of the ‘AdoMet radical’ (radical SAM) family, all members of which produce the 5′-deoxyadenosin-5′-yl radical and methionine from AdoMet (S-adenosylmethionine) by the addition of an electron from an iron-sulfur centre. The enzyme contains two [4Fe-4S] clusters. The first cluster produces the radicals, which are converted into 5′-deoxyadenosine when they abstract hydrogen atoms from C6 and C8, respectively, leaving reactive radicals at these positions that interact with sulfur atoms within the second (auxiliary) cluster. Having donated two sulfur atoms, the auxiliary cluster is degraded during catalysis, but is regenerated immediately by the transfer of a new cluster from iron-sulfur cluster carrier proteins [8]. Lipoylation is essential for the function of several key enzymes involved in oxidative metabolism, as it converts apoprotein into the biologically active holoprotein. Examples of such lipoylated proteins include pyruvate dehydrogenase (E2 domain), 2-oxoglutarate dehydrogenase (E2 domain), the branched-chain 2-oxoacid dehydrogenases and the glycine cleavage system (H protein) [1,2]. An alternative lipoylation pathway involves EC 6.3.1.20, lipoate—protein ligase, which can lipoylate apoproteins using exogenous lipoic acid (or its analogues) [4].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 189398-80-9
References:
1.  Cicchillo, R.M. and Booker, S.J. Mechanistic investigations of lipoic acid biosynthesis in Escherichia coli: both sulfur atoms in lipoic acid are contributed by the same lipoyl synthase polypeptide. J. Am. Chem. Soc. 127 (2005) 2860–2861. [DOI] [PMID: 15740115]
2.  Vanden Boom, T.J., Reed, K.E. and Cronan, J.E., Jr. Lipoic acid metabolism in Escherichia coli: isolation of null mutants defective in lipoic acid biosynthesis, molecular cloning and characterization of the E. coli lip locus, and identification of the lipoylated protein of the glycine cleavage system. J. Bacteriol. 173 (1991) 6411–6420. [DOI] [PMID: 1655709]
3.  Zhao, X., Miller, J.R., Jiang, Y., Marletta, M.A. and Cronan, J.E. Assembly of the covalent linkage between lipoic acid and its cognate enzymes. Chem. Biol. 10 (2003) 1293–1302. [DOI] [PMID: 14700636]
4.  Cicchillo, R.M., Iwig, D.F., Jones, A.D., Nesbitt, N.M., Baleanu-Gogonea, C., Souder, M.G., Tu, L. and Booker, S.J. Lipoyl synthase requires two equivalents of S-adenosyl-L-methionine to synthesize one equivalent of lipoic acid. Biochemistry 43 (2004) 6378–6386. [DOI] [PMID: 15157071]
5.  Jordan, S.W. and Cronan, J.E., Jr. A new metabolic link. The acyl carrier protein of lipid synthesis donates lipoic acid to the pyruvate dehydrogenase complex in Escherichia coli and mitochondria. J. Biol. Chem. 272 (1997) 17903–17906. [DOI] [PMID: 9218413]
6.  Miller, J.R., Busby, R.W., Jordan, S.W., Cheek, J., Henshaw, T.F., Ashley, G.W., Broderick, J.B., Cronan, J.E., Jr. and Marletta, M.A. Escherichia coli LipA is a lipoyl synthase: in vitro biosynthesis of lipoylated pyruvate dehydrogenase complex from octanoyl-acyl carrier protein. Biochemistry 39 (2000) 15166–15178. [DOI] [PMID: 11106496]
7.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
8.  McCarthy, E.L. and Booker, S.J. Destruction and reformation of an iron-sulfur cluster during catalysis by lipoyl synthase. Science 358 (2017) 373–377. [DOI] [PMID: 29051382]
[EC 2.8.1.8 created 2006, modified 2014, modified 2018]
 
 
EC 3.1.3.76
Accepted name: lipid-phosphate phosphatase
Reaction: (9S,10S)-10-hydroxy-9-(phosphooxy)octadecanoate + H2O = (9S,10S)-9,10-dihydroxyoctadecanoate + phosphate
Other name(s): hydroxy fatty acid phosphatase; dihydroxy fatty acid phosphatase; hydroxy lipid phosphatase; sEH (ambiguous); soluble epoxide hydrolase (ambiguous); (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate phosphohydrolase
Systematic name: (9S,10S)-10-hydroxy-9-(phosphooxy)octadecanoate phosphohydrolase
Comments: Requires Mg2+ for maximal activity. The enzyme from mammals is a bifunctional enzyme: the N-terminal domain exhibits lipid-phosphate-phosphatase activity and the C-terminal domain has the activity of EC 3.3.2.10, soluble epoxide hydrolase (sEH) [1]. The best substrates for this enzyme are 10-hydroxy-9-(phosphooxy)octadecanoates, with the threo- form being a better substrate than the erythro- form [1]. The phosphatase activity is not found in plant sEH or in EC 3.3.2.9, microsomal epoxide hydrolase, from mammals [1].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Newman, J.W., Morisseau, C., Harris, T.R. and Hammock, B.D. The soluble epoxide hydrolase encoded by EPXH2 is a bifunctional enzyme with novel lipid phosphate phosphatase activity. Proc. Natl. Acad. Sci. USA 100 (2003) 1558–1563. [DOI] [PMID: 12574510]
2.  Cronin, A., Mowbray, S., Dürk, H., Homburg, S., Fleming, I., Fisslthaler, B., Oesch, F. and Arand, M. The N-terminal domain of mammalian soluble epoxide hydrolase is a phosphatase. Proc. Natl. Acad. Sci. USA 100 (2003) 1552–1557. [DOI] [PMID: 12574508]
3.  Morisseau, C. and Hammock, B.D. Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles. Annu. Rev. Pharmacol. Toxicol. 45 (2005) 311–333. [DOI] [PMID: 15822179]
4.  Tran, K.L., Aronov, P.A., Tanaka, H., Newman, J.W., Hammock, B.D. and Morisseau, C. Lipid sulfates and sulfonates are allosteric competitive inhibitors of the N-terminal phosphatase activity of the mammalian soluble epoxide hydrolase. Biochemistry 44 (2005) 12179–12187. [DOI] [PMID: 16142916]
5.  Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
6.  Srivastava, P.K., Sharma, V.K., Kalonia, D.S. and Grant, D.F. Polymorphisms in human soluble epoxide hydrolase: effects on enzyme activity, enzyme stability, and quaternary structure. Arch. Biochem. Biophys. 427 (2004) 164–169. [DOI] [PMID: 15196990]
7.  Gomez, G.A., Morisseau, C., Hammock, B.D. and Christianson, D.W. Structure of human epoxide hydrolase reveals mechanistic inferences on bifunctional catalysis in epoxide and phosphate ester hydrolysis. Biochemistry 43 (2004) 4716–4723. [DOI] [PMID: 15096040]
[EC 3.1.3.76 created 2006]
 
 
EC 3.1.13.5
Accepted name: ribonuclease D
Reaction: Exonucleolytic cleavage that removes extra residues from the 3′-terminus of tRNA to produce 5′-mononucleotides
Other name(s): RNase D
Comments: Requires divalent cations for activity (Mg2+, Mn2+ or Co2+). Alteration of the 3′-terminal base has no effect on the rate of hydrolysis whereas modification of the 3′-terminal sugar has a major effect. tRNA terminating with a 3′-phosphate is completely inactive [3]. This enzyme can convert a tRNA precursor into a mature tRNA [2].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Ghosh, R.K. and Deutscher, M.P. Identification of an Escherichia coli nuclease acting on structurally altered transfer RNA molecules. J. Biol. Chem. 253 (1978) 997–1000. [PMID: 342522]
2.  Cudny, H., Zaniewski, R. and Deutscher, M.P. Escherichia coli RNase D. Purification and structural characterization of a putative processing nuclease. J. Biol. Chem. 256 (1981) 5627–5632. [PMID: 6263885]
3.  Cudny, H., Zaniewski, R. and Deutscher, M.P. Escherichia coli RNase D. Catalytic properties and substrate specificity. J. Biol. Chem. 256 (1981) 5633–5637. [PMID: 6263886]
4.  Zhang, J.R. and Deutscher, M.P. Cloning, characterization, and effects of overexpression of the Escherichia coli rnd gene encoding RNase D. J. Bacteriol. 170 (1988) 522–527. [DOI] [PMID: 2828310]
[EC 3.1.13.5 created 2006]
 
 
*EC 3.1.26.3
Accepted name: ribonuclease III
Reaction: Endonucleolytic cleavage to a 5′-phosphomonoester
Other name(s): RNase III; ribonuclease 3
Comments: This is an endoribonuclease that cleaves double-stranded RNA molecules [4]. The cleavage can be either a single-stranded nick or double-stranded break in the RNA, depending in part upon the degree of base-pairing in the region of the cleavage site [5]. Specificity is conferred by negative determinants, i.e., the presence of certain Watson-Crick base-pairs at specific positions that strongly inhibit cleavage [6]. RNase III is involved in both rRNA processing and mRNA processing and decay.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9073-62-5
References:
1.  Crouch, R.J. Ribonuclease 3 does not degrade deoxyribonucleic acid-ribonucleic acid hybrids. J. Biol. Chem. 249 (1974) 1314–1316. [PMID: 4592261]
2.  Rech, J., Cathala, G. and Jeanteur, P. Isolation and characterization of a ribonuclease activity specific for double-stranded RNA (RNase D) from Krebs II ascites cells. J. Biol. Chem. 255 (1980) 6700–6706. [PMID: 6248530]
3.  Robertson, H.D., Webster, R.E. and Zinder, N.D. Purification and properties of ribonuclease III from Escherichia coli. J. Biol. Chem. 243 (1968) 82–91. [PMID: 4865702]
4.  Grunberg-Manago, M. Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu. Rev. Genet. 33 (1999) 193–227. [DOI] [PMID: 10690408]
5.  Court, D. RNA processing and degradation by RNase III in control of mRNA stability. In: Belasco, J.G. and Brawerman, G. (Ed.), Control of Messenger RNA Stability, Academic Press, New York, 1993, pp. 71–116.
6.  Zhang, K. and Nicholson, A.W. Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc. Natl. Acad. Sci. USA 94 (1997) 13437–13441. [DOI] [PMID: 9391043]
[EC 3.1.26.3 created 1978, modified 2006]
 
 
*EC 3.2.1.81
Accepted name: β-agarase
Reaction: Hydrolysis of (1→4)-β-D-galactosidic linkages in agarose, giving the tetramer as the predominant product
Glossary: agarose = a linear polysaccharide produced by some members of the Rhodophyta (red algae) made up from alternating D-galactose and 3,6-anhydro-α-L-galactopyranose residues joined by α-(1→3)- and β-(1→4)-linkages. In the field of oligosaccharides derived from agarose, carrageenans, etc., in which alternate residues are 3,6-anhydro sugars, the prefix ’neo’ designates an oligosaccharide whose non-reducing end is the anhydro sugar, and the absence of this prefix means that it is not.
For example:
neoagarobiose = 3,6-anhydro-α-L-galactopyranosyl-(1→3)-D-galactose
agarobiose = β-D-galactopyranosyl-(1→4)-3,6-anhydro-L-galactose
Other name(s): agarase (ambiguous); AgaA; AgaB; endo-β-agarase; agarose 3-glycanohydrolase (incorrect)
Systematic name: agarose 4-glycanohydrolase
Comments: Also acts on porphyran, but more slowly [1]. This enzyme cleaves the β-(1→4) linkages of agarose in a random manner with retention of the anomeric-bond configuration, producing β-anomers that give rise progressively to α-anomers when mutarotation takes place [6]. The end products of hydrolysis are neoagarotetraose and neoagarohexaose in the case of AgaA from the marine bacterium Zobellia galactanivorans, and neoagarotetraose and neoagarobiose in the case of AgaB [6].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37288-57-6
References:
1.  Duckworth, M. and Turvey, J.R. The action of a bacterial agarase on agarose, porphyran and alkali-treated porphyran. Biochem. J. 113 (1969) 687–692. [PMID: 5386190]
2.  Allouch, J., Jam, M., Helbert, W., Barbeyron, T., Kloareg, B., Henrissat, B. and Czjzek, M. The three-dimensional structures of two β-agarases. J. Biol. Chem. 278 (2003) 47171–47180. [DOI] [PMID: 12970344]
3.  Ohta, Y., Nogi, Y., Miyazaki, M., Li, Z., Hatada, Y., Ito, S. and Horikoshi, K. Enzymatic properties and nucleotide and amino acid sequences of a thermostable β-agarase from the novel marine isolate, JAMB-A94. Biosci. Biotechnol. Biochem. 68 (2004) 1073–1081. [DOI] [PMID: 15170112]
4.  Ohta, Y., Hatada, Y., Nogi, Y., Miyazaki, M., Li, Z., Akita, M., Hidaka, Y., Goda, S., Ito, S. and Horikoshi, K. Enzymatic properties and nucleotide and amino acid sequences of a thermostable β-agarase from a novel species of deep-sea Microbulbifer. Appl. Microbiol. Biotechnol. 64 (2004) 505–514. [DOI] [PMID: 15088129]
5.  Sugano, Y., Terada, I., Arita, M., Noma, M. and Matsumoto, T. Purification and characterization of a new agarase from a marine bacterium, Vibrio sp. strain JT0107. Appl. Environ. Microbiol. 59 (1993) 1549–1554. [PMID: 8517750]
6.  Jam, M., Flament, D., Allouch, J., Potin, P., Thion, L., Kloareg, B., Czjzek, M., Helbert, W., Michel, G. and Barbeyron, T. The endo-β-agarases AgaA and AgaB from the marine bacterium Zobellia galactanivorans: two paralogue enzymes with different molecular organizations and catalytic behaviours. Biochem. J. 385 (2005) 703–713. [DOI] [PMID: 15456406]
[EC 3.2.1.81 created 1972, modified 2006]
 
 
*EC 3.2.1.83
Accepted name: κ-carrageenase
Reaction: Endohydrolysis of (1→4)-β-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose in κ-carrageenans
For diagram of reaction, click here
Glossary: In the field of oligosaccharides derived from agarose, carrageenans, etc., in which alternate residues are 3,6-anhydro sugars, the prefix ’neo’ designates an oligosaccharide whose non-reducing end is the anhydro sugar, and the absence of this prefix means that it is not.
For example:
ι-neocarrabiose = 3,6-anhydro-2-O-sulfo-α-D-galactopyranosyl-(1→3)-4-O-sulfo-D-galactose
ι-carrabiose = 4-O-sulfo- β-D-galactopyranosyl-(1→4)-3,6-anhydro-2-O-sulfo-D-galactose
Other name(s): κ-carrageenan 4-β-D-glycanohydrolase
Systematic name: κ-carrageenan 4-β-D-glycanohydrolase (configuration-retaining)
Comments: The main products of hydrolysis are neocarrabiose-sulfate and neocarratetraose-sulfate [5]. Unlike EC 3.2.1.157 (ι-carrageenase), but similar to EC 3.2.1.81 (β-agarase), this enzyme proceeds with retention of the anomeric configuration.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37288-59-8
References:
1.  Weigl, J. and Yashe, W. The enzymic hydrolysis of carrageenan by Pseudomonas carrageenovora: purification of a κ-carrageenase. Can. J. Microbiol. 12 (1966) 939–947. [PMID: 5972647]
2.  Potin, P., Sanseau, A., Le Gall, Y., Rochas, C. and Kloareg, B. Purification and characterization of a new κ-carrageenase from a marine Cytophaga-like bacterium. Eur. J. Biochem. 201 (1991) 241–247. [DOI] [PMID: 1915370]
3.  Potin, P., Richard, C., Barbeyron, T., Henrissat, B., Gey, C., Petillot, Y., Forest, E., Dideberg, O., Rochas, C. and Kloareg, B. Processing and hydrolytic mechanism of the cgkA-encoded κ-carrageenase of Alteromonas carrageenovora. Eur. J. Biochem. 228 (1995) 971–975. [DOI] [PMID: 7737202]
4.  Michel, G., Barbeyron, T., Flament, D., Vernet, T., Kloareg, B. and Dideberg, O. Expression, purification, crystallization and preliminary x-ray analysis of the κ-carrageenase from Pseudoalteromonas carrageenovora. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 918–920. [PMID: 10089334]
5.  Michel, G., Chantalat, L., Duee, E., Barbeyron, T., Henrissat, B., Kloareg, B. and Dideberg, O. The κ-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases. Structure 9 (2001) 513–525. [DOI] [PMID: 11435116]
[EC 3.2.1.83 created 1972, modified 2006]
 
 
EC 3.2.1.155
Accepted name: xyloglucan-specific endo-processive β-1,4-glucanase
Reaction: Hydrolysis of (1→4)-D-glucosidic linkages in xyloglucans so as to successively remove oligosaccharides from the newly-formed chain end after endo-initiation on a polymer molecule
Other name(s): Cel74A; [(1→6)-α-D-xylo]-(1→4)-β-D-glucan exo-glucohydrolase (ambiguous); xyloglucan-specific exo-β-1,4-glucanase (ambiguous)
Systematic name: [(1→6)-α-D-xylo]-(1→4)-β-D-glucan endo-processive glucohydrolase
Comments: The enzyme removes branched oligosaccharides, containing preferentially four glucoside residues in the main chain, from xyloglucan molecules in a processive manner after the initial endo-type attack on a polysaccharide [1-5]. Hydrolysis occurs at either the unsubstituted D-glucopyranose residue in the main backbone and/or the D-glucopyranose residue bearing a xylosyl group [1-5]. The enzyme does not display activity, or shows very low activity, towards other β-D-glucans [1,2,4,5].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 1000598-79-7
References:
1.  Grishutin, S.G., Gusakov, A.V., Markov, A.V., Ustinov, B.B., Semenova, M.V. and Sinitsyn, A.P. Specific xyloglucanases as a new class of polysaccharide-degrading enzymes. Biochim. Biophys. Acta 1674 (2004) 268–281. [DOI] [PMID: 15541296]
2.  Ichinose, H., Araki, Y., Michikawa, M., Harazono, K., Yaoi, K., Karita, S. and Kaneko, S. Characterization of an endo-processive-type xyloglucanase having a β-1,4-glucan-binding module and an endo-type xyloglucanase from Streptomyces avermitilis. Appl. Environ. Microbiol. 78 (2012) 7939–7945. [PMID: 22941084]
3.  Matsuzawa, T., Saito, Y. and Yaoi, K. Key amino acid residues for the endo-processive activity of GH74 xyloglucanase. FEBS Lett. 588 (2014) 1731–1738. [PMID: 24657616]
4.  Arnal, G., Stogios, P.J., Asohan, J., Skarina, T., Savchenko, A. and Brumer, H. Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74 endo-xyloglucanase. Biochem. J. 475 (2018) 3963–3978. [PMID: 30463871]
5.  Arnal, G., Stogios, P.J., Asohan, J., Attia, M.A., Skarina, T., Viborg, A.H., Henrissat, B., Savchenko, A. and Brumer, H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J. Biol. Chem. 294 (2019) 13233–13247. [PMID: 31324716]
6.  Gusakov, A.V. Additional sequence and structural characterization of an endo-processive GH74 xyloglucanase from Myceliophthora thermophila and the revision of the EC 3.2.1.155 entry. Biochim. Biophys. Acta. 1864:129511 (2020). [PMID: 31911243]
[EC 3.2.1.155 created 2005, withdrawn at public-review stage, modified and reinstated 2006, modified 2020]
 
 
EC 3.2.1.157
Accepted name: ι-carrageenase
Reaction: Endohydrolysis of (1→4)-β-D-linkages between D-galactose 4-sulfate and 3,6-anhydro-D-galactose-2-sulfate in ι-carrageenans
For diagram of reaction, click here
Glossary: In the field of oligosaccharides derived from agarose, carrageenans, etc., in which alternate residues are 3,6-anhydro sugars, the prefix ’neo’ designates an oligosaccharide whose non-reducing end is the anhydro sugar, and the absence of this prefix means that it is not.
For example:
ι-neocarrabiose = 3,6-anhydro-2-O-sulfo-α-D-galactopyranosyl-(1→3)-4-O-sulfo-D-galactose
ι-carrabiose = 4-O-sulfo-β-D-galactopyranosyl-(1→4)-3,6-anhydro-2-O-sulfo-D-galactose
Systematic name: ι-carrageenan 4-β-D-glycanohydrolase (configuration-inverting)
Comments: The main products of hydrolysis are ι-neocarratetraose sulfate and ι-neocarrahexaose sulfate. ι-Neocarraoctaose is the shortest substrate oligomer that can be cleaved. Unlike EC 3.2.1.81, β-agarase and EC 3.2.1.83, κ-carrageenase, this enzyme proceeds with inversion of the anomeric configuration. ι-Carrageenan differs from κ-carrageenan by possessing a sulfo group on O-2 of the 3,6-anhydro-D-galactose residues, in addition to that present in the κ-compound on O-4 of the D-galactose residues.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 50936-37-3
References:
1.  Barbeyron, T., Michel, G., Potin, P., Henrissat, B. and Kloareg, B. ι-Carrageenases constitute a novel family of glycoside hydrolases, unrelated to that of κ-carrageenases. J. Biol. Chem. 275 (2000) 35499–35505. [DOI] [PMID: 10934194]
2.  Michel, G., Chantalat, L., Fanchon, E., Henrissat, B., Kloareg, B. and Dideberg, O. The ι-carrageenase of Alteromonas fortis. A β-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide. J. Biol. Chem. 276 (2001) 40202–40209. [DOI] [PMID: 11493601]
3.  Michel, G., Helbert, W., Kahn, R., Dideberg, O. and Kloareg, B. The structural bases of the processive degradation of ι-carrageenan, a main cell wall polysaccharide of red algae. J. Mol. Biol. 334 (2003) 421–433. [DOI] [PMID: 14623184]
[EC 3.2.1.157 created 2006]
 
 
EC 3.2.1.158
Accepted name: α-agarase
Reaction: Endohydrolysis of (1→3)-α-L-galactosidic linkages in agarose, yielding agarotetraose as the major product
Glossary: agarose = a linear polysaccharide produced by some members of the Rhodophyta (red algae) made up from alternating D-galactose and 3,6-anhydro-α-L-galactopyranose residues joined by α-(1→3)- and β-(1→4)-linkages. In the field of oligosaccharides derived from agarose, carrageenans, etc., in which alternate residues are 3,6-anhydro sugars, the prefix ’neo’ designates an oligosaccharide whose non-reducing end is the anhydro sugar, and the absence of this prefix means that it is not.
For example:
neoagarobiose = 3,6-anhydro-α-L-galactopyranosyl-(1→3)-D-galactose
agarobiose = β-D-galactopyranosyl-(1→4)-3,6-anhydro-L-galactose
Other name(s): agarase (ambiguous); agaraseA33
Systematic name: agarose 3-glycanohydrolase
Comments: Requires Ca2+. The enzyme from Thalassomonas sp. can use agarose, agarohexaose and neoagarohexaose as substrate. The products of agarohexaose hydrolysis are dimers and tetramers, with agarotetraose being the predominant product, whereas hydrolysis of neoagarohexaose gives rise to two types of trimer. While the enzyme can also hydrolyse the highly sulfated agarose porphyran very efficiently, it cannot hydrolyse the related compounds κ-carrageenan (see EC 3.2.1.83) and ι-carrageenan (see EC 3.2.1.157) [2]. See also EC 3.2.1.81, β-agarase.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 63952-00-1
References:
1.  Potin, P., Richard, C., Rochas, C. and Kloareg, B. Purification and characterization of the α-agarase from Alteromonas agarlyticus (Cataldi) comb. nov., strain GJ1B. Eur. J. Biochem. 214 (1993) 599–607. [DOI] [PMID: 8513809]
2.  Ohta, Y., Hatada, Y., Miyazaki, M., Nogi, Y., Ito, S. and Horikoshi, K. Purification and characterization of a novel α-agarase from a Thalassomonas sp. Curr. Microbiol. 50 (2005) 212–216. [DOI] [PMID: 15902469]
[EC 3.2.1.158 created 2006]
 
 
EC 3.2.1.159
Accepted name: α-neoagaro-oligosaccharide hydrolase
Reaction: Hydrolysis of the (1→3)-α-L-galactosidic linkages of neoagaro-oligosaccharides that are smaller than a hexamer, yielding 3,6-anhydro-L-galactose and D-galactose
Glossary: In the field of oligosaccharides derived from agarose, carrageenans, etc., in which alternate residues are 3,6-anhydro sugars, the prefix ’neo’ designates an oligosaccharide whose non-reducing end is the anhydro sugar, and the absence of this prefix means that it is not.
For example:
neoagarobiose = 3,6-anhydro-α-L-galactopyranosyl-(1→3)-D-galactose
agarobiose = β-D-galactopyranosyl-(1→4)-3,6-anhydro-L-galactose
Other name(s): α-neoagarooligosaccharide hydrolase; α-NAOS hydrolase
Systematic name: α-neoagaro-oligosaccharide 3-glycohydrolase
Comments: When neoagarohexaose is used as a substrate, the oligosaccharide is cleaved at the non-reducing end to produce 3,6-anhydro-L-galactose and agaropentaose, which is further hydrolysed to agarobiose and agarotriose. With neoagarotetraose as substrate, the products are predominantly agarotriose and 3,6-anhydro-L-galactose. In Vibrio sp. the actions of EC 3.2.1.81, β-agarase and EC 3.2.1.159 can be used to degrade agarose to 3,6-anhydro-L-galactose and D-galactose.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 60063-77-6
References:
1.  Sugano, Y., Kodama, H., Terada, I., Yamazaki, Y. and Noma, M. Purification and characterization of a novel enzyme, α-neoagarooligosaccharide hydrolase (α-NAOS hydrolase), from a marine bacterium, Vibrio sp. strain JT0107. J. Bacteriol. 176 (1994) 6812–6818. [DOI] [PMID: 7961439]
[EC 3.2.1.159 created 2006]
 
 
EC 3.2.1.161
Accepted name: β-apiosyl-β-glucosidase
Reaction: 7-[β-D-apiofuranosyl-(1→6)-β-D-glucopyranosyloxy]isoflavonoid + H2O = a 7-hydroxyisoflavonoid + β-D-apiofuranosyl-(1→6)-D-glucose
Other name(s): isoflavonoid-7-O-β[D-apiosyl-(1→6)-β-D-glucoside] disaccharidase; isoflavonoid 7-O-β-apiosyl-glucoside β-glucosidase; furcatin hydrolase
Systematic name: 7-[β-D-apiofuranosyl-(1→6)-β-D-glucopyranosyloxy]isoflavonoid β-D-apiofuranosyl-(1→6)-D-glucohydrolase
Comments: The enzyme from the tropical tree Dalbergia nigrescens Kurz belongs in glycosyl hydrolase family 1. The enzyme removes disaccharides from the natural substrates dalpatein 7-O-β-D-apiofuranosyl-(1→6)-β-D-glucopyranoside and 7-hydroxy-2′,4′,5′,6-tetramethoxy-7-O-β-D-apiofuranosyl-(1→6)-β-D-glucopyranoside (dalnigrein 7-O-β-D-apiofuranosyl-(1→6)-β-D-glucopyranoside) although it can also remove a single glucose residue from isoflavonoid 7-O-glucosides [2]. Daidzin and genistin are also substrates.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 1000598-83-3
References:
1.  Hosel, W. and Barz, W. β-Glucosidases from Cicer arietinum L. Purification and Properties of isoflavone-7-O-glucoside-specific β-glucosidases. Eur. J. Biochem. 57 (1975) 607–616. [DOI] [PMID: 240725]
2.  Chuankhayan, P., Hua, Y., Svasti, J., Sakdarat, S., Sullivan, P.A. and Ketudat Cairns, J.R. Purification of an isoflavonoid 7-O-β-apiosyl-glucoside β-glycosidase and its substrates from Dalbergia nigrescens Kurz. Phytochemistry 66 (2005) 1880–1889. [DOI] [PMID: 16098548]
3.  Ahn, Y.O., Mizutani, M., Saino, H. and Sakata, K. Furcatin hydrolase from Viburnum furcatum Blume is a novel disaccharide-specific acuminosidase in glycosyl hydrolase family 1. J. Biol. Chem. 279 (2004) 23405–23414. [DOI] [PMID: 14976214]
[EC 3.2.1.161 created 2006]
 
 
EC 3.3.2.3
Transferred entry: epoxide hydrolase. Now known to comprise two enzymes, microsomal epoxide hydrolase (EC 3.3.2.9) and soluble epoxide hydrolase (EC 3.3.2.10)
[EC 3.3.2.3 created 1978, modified 1999, deleted 2006]
 
 
*EC 3.3.2.6
Accepted name: leukotriene-A4 hydrolase
Reaction: leukotriene A4 + H2O = leukotriene B4
Glossary: leukotriene A4 = (7E,9E,11Z,14Z)-(5S,6S)-5,6-epoxyicosa-7,9,11,14-tetraenoate
leukotriene B4 = (6Z,8E,10E,14Z)-(5S,12R)-5,12-dihydroxyicosa-6,8,10,14-tetraenoate
Other name(s): LTA4 hydrolase; LTA4H; leukotriene A4 hydrolase
Systematic name: (7E,9E,11Z,14Z)-(5S,6S)-5,6-epoxyicosa-7,9,11,14-tetraenoate hydrolase
Comments: This is a bifunctional zinc metalloprotease that displays both epoxide hydrolase and aminopeptidase activities [4,6]. It preferentially cleaves tripeptides at an arginyl bond, with dipeptides and tetrapeptides being poorer substrates [6] (see EC 3.4.11.6, aminopeptidase B). It also converts leukotriene A4 into leukotriene B4, unlike EC 3.3.2.10, soluble epoxide hydrolase, which converts leukotriene A4 into 5,6-dihydroxy-7,9,11,14-icosatetraenoic acid [3,4]. In vertebrates, five epoxide-hydrolase enzymes have been identified to date: EC 3.3.2.6 (leukotriene A4 hydrolase), EC 3.3.2.7 (hepoxilin-epoxide hydrolase), EC 3.3.2.9 (microsomal epoxide hydrolase), EC 3.3.2.10 (soluble epoxide hydrolase) and EC 3.3.2.11 (cholesterol-5,6-oxide hydrolase) [5].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 90119-07-6
References:
1.  Evans, J.F., Dupuis, P. and Ford-Hutchinson, A.W. Purification and characterisation of leukotriene A4 hydrolase from rat neutrophils. Biochim. Biophys. Acta 840 (1985) 43–50. [DOI] [PMID: 3995081]
2.  Minami, M., Ohno, S., Kawasaki, H., Rådmark, O., Samuelsson, B., Jörnvall, H., Shimizu, T., Seyama, Y. and Suzuki, K. Molecular cloning of a cDNA coding for human leukotriene A4 hydrolase - complete primary structure of an enzyme involved in eicosanoid synthesis. J. Biol. Chem. 262 (1987) 13873–13876. [PMID: 3654641]
3.  Haeggström, J., Meijer, J. and Rådmark, O. Leukotriene A4. Enzymatic conversion into 5,6-dihydroxy-7,9,11,14-eicosatetraenoic acid by mouse liver cytosolic epoxide hydrolase. J. Biol. Chem. 261 (1986) 6332–6337. [PMID: 3009453]
4.  Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
5.  Fretland, A.J. and Omiecinski, C.J. Epoxide hydrolases: biochemistry and molecular biology. Chem. Biol. Interact. 129 (2000) 41–59. [DOI] [PMID: 11154734]
6.  Orning, L., Gierse, J.K. and Fitzpatrick, F.A. The bifunctional enzyme leukotriene-A4 hydrolase is an arginine aminopeptidase of high efficiency and specificity. J. Biol. Chem. 269 (1994) 11269. [PMID: 8157657]
7.  Ohishi, N., Izumi, T., Minami, M., Kitamura, S., Seyama, Y., Ohkawa, S., Terao, S., Yotsumoto, H., Takaku, F. and Shimizu, T. Leukotriene A4 hydrolase in the human lung. Inactivation of the enzyme with leukotriene A4 isomers. J. Biol. Chem. 262 (1987) 10200–10205. [PMID: 3038871]
[EC 3.3.2.6 created 1989, modified 2006]
 
 
*EC 3.3.2.7
Accepted name: hepoxilin-epoxide hydrolase
Reaction: hepoxilin A3 + H2O = trioxilin A3
Glossary: hepoxilin A3 = (5Z,9E,14Z)-(8ξ,11R,12S)-11,12-epoxy-8-hydroxyicosa-5,9,14-trienoate
trioxilin A3 = (5Z,9E,14Z)-(8ξ,11ξ,12S)-8,11,12-trihydroxyicosa-5,9,14-trienoate
Other name(s): hepoxilin epoxide hydrolase; hepoxylin hydrolase; hepoxilin A3 hydrolase
Systematic name: (5Z,9E,14Z)-(8ξ,11R,12S)-11,12-epoxy-8-hydroxyicosa-5,9,14-trienoate hydrolase
Comments: Converts hepoxilin A3 into trioxilin A3. Highly specific for the substrate, having only slight activity with other epoxides such as leukotriene A4 and styrene oxide [2]. Hepoxilin A3 is an hydroxy-epoxide derivative of arachidonic acid that is formed via the 12-lipoxygenase pathway [2]. It is probable that this enzyme plays a modulatory role in inflammation, vascular physiology, systemic glucose metabolism and neurological function [4]. In vertebrates, five epoxide-hydrolase enzymes have been identified to date: EC 3.3.2.6 (leukotriene-A4 hydrolase), EC 3.3.2.7 (hepoxilin-epoxide hydrolase), EC 3.3.2.9 (microsomal epoxide hydrolase), EC 3.3.2.10 (soluble epoxide hydrolase) and EC 3.3.2.11 (cholesterol 5,6-oxide hydrolase) [3].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 122096-98-4
References:
1.  Pace-Asciak, C.R. Formation and metabolism of hepoxilin A3 by the rat brain. Biochem. Biophys. Res. Commun. 151 (1988) 493–498. [DOI] [PMID: 3348791]
2.  Pace-Asciak, C.R. and Lee, W.-S. Purification of hepoxilin epoxide hydrolase from rat liver. J. Biol. Chem. 264 (1989) 9310–9313. [PMID: 2722835]
3.  Fretland, A.J. and Omiecinski, C.J. Epoxide hydrolases: biochemistry and molecular biology. Chem. Biol. Interact. 129 (2000) 41–59. [DOI] [PMID: 11154734]
4.  Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
[EC 3.3.2.7 created 1992, modified 2006]
 
 
EC 3.3.2.9
Accepted name: microsomal epoxide hydrolase
Reaction: (1) cis-stilbene oxide + H2O = (1R,2R)-1,2-diphenylethane-1,2-diol
(2) 1-(4-methoxyphenyl)-N-methyl-N-[(3-methyloxetan-3-yl)methyl]methanamine + H2O = 2-({[(4-methoxyphenyl)methyl](methyl)amino}methyl)-2-methylpropane-1,3-diol
Glossary: oxirane = ethylene oxide = a 3-membered oxygen-containing ring
oxetane = 1,3-propylene oxide = a 4-membered oxygen-containing ring
Other name(s): microsomal oxirane/oxetane hydrolase; epoxide hydratase (ambiguous); microsomal epoxide hydratase (ambiguous); epoxide hydrase; microsomal epoxide hydrase; arene-oxide hydratase (ambiguous); benzo[a]pyrene-4,5-oxide hydratase; benzo(a)pyrene-4,5-epoxide hydratase; aryl epoxide hydrase (ambiguous); cis-epoxide hydrolase; mEH; EPHX1 (gene name)
Systematic name: cis-stilbene-oxide hydrolase
Comments: This is a key hepatic enzyme that catalyses the hydrolytic ring opening of oxiranes (epoxides) and oxetanes to give the corresponding diols. The enzyme is involved in the metabolism of numerous substrates including the stereoselective hydrolytic ring opening of 7-oxabicyclo[4.1.0]hepta-2,4-dienes (arene oxides) to the corresponding trans-dihydrodiols. The reaction proceeds via a triad mechanism and involves the formation of an hydroxyalkyl-enzyme intermediate. Five epoxide-hydrolase enzymes have been identified in vertebrates to date: EC 3.3.2.6 (leukotriene-A4 hydrolase), EC 3.3.2.7 (hepoxilin-epoxide hydrolase), EC 3.3.2.9 (microsomal epoxide hydrolase), EC 3.3.2.10 (soluble epoxide hydrolase) and EC 3.3.2.11 (cholesterol-5,6-oxide hydrolase).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Oesch, F. and Daly, J. Solubilization, purification, and properties of a hepatic epoxide hydrase. Biochim. Biophys. Acta 227 (1971) 692–697. [DOI] [PMID: 4998715]
2.  Jakoby, W.B. and Fjellstedt, T.A. Epoxidases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 199–212.
3.  Oesch, F. Mammalian epoxide hydrases: inducible enzymes catalysing the inactivation of carcinogenic and cytotoxic metabolites derived from aromatic and olefinic compounds. Xenobiotica 3 (1973) 305–340. [DOI] [PMID: 4584115]
4.  Oesch, F. Purification and specificity of a human microsomal epoxide hydratase. Biochem. J. 139 (1974) 77–88. [PMID: 4463951]
5.  Lu, A.Y., Ryan, D., Jerina, D.M., Daly, J.W. and Levin, W. Liver microsomal expoxide hydrase. Solubilization, purification, and characterization. J. Biol. Chem. 250 (1975) 8283–8288. [PMID: 240858]
6.  Bellucci, G., Chiappe, C. and Ingrosso, G. Kinetics and stereochemistry of the microsomal epoxide hydrolase-catalyzed hydrolysis of cis-stilbene oxides. Chirality 6 (1994) 577–582. [DOI] [PMID: 7986671]
7.  Fretland, A.J. and Omiecinski, C.J. Epoxide hydrolases: biochemistry and molecular biology. Chem. Biol. Interact. 129 (2000) 41–59. [DOI] [PMID: 11154734]
8.  Morisseau, C. and Hammock, B.D. Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles. Annu. Rev. Pharmacol. Toxicol. 45 (2005) 311–333. [DOI] [PMID: 15822179]
9.  Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
10.  Toselli, F., Fredenwall, M., Svensson, P., Li, X.Q., Johansson, A., Weidolf, L. and Hayes, M.A. Oxetane substrates of human microsomal epoxide hydrolase. Drug Metab. Dispos. 45 (2017) 966–973. [DOI] [PMID: 28600384]
[EC 3.3.2.9 created 2006 (EC 3.3.2.3 created 1978, modified 1999, part incorporated 2006), modified 2017]
 
 
EC 3.3.2.10
Accepted name: soluble epoxide hydrolase
Reaction: an epoxide + H2O = a glycol
Other name(s): epoxide hydrase (ambiguous); epoxide hydratase (ambiguous); arene-oxide hydratase (ambiguous); aryl epoxide hydrase (ambiguous); trans-stilbene oxide hydrolase; sEH; cytosolic epoxide hydrolase
Systematic name: epoxide hydrolase
Comments: Catalyses the hydrolysis of trans-substituted epoxides, such as trans-stilbene oxide, as well as various aliphatic epoxides derived from fatty-acid metabolism [7]. It is involved in the metabolism of arachidonic epoxides (epoxyicosatrienoic acids; EETs) and linoleic acid epoxides. The EETs, which are endogenous chemical mediators, act at the vascular, renal and cardiac levels to regulate blood pressure [4,5]. The enzyme from mammals is a bifunctional enzyme: the C-terminal domain exhibits epoxide-hydrolase activity and the N-terminal domain has the activity of EC 3.1.3.76, lipid-phosphate phosphatase [1,2]. Like EC 3.3.2.9, microsomal epoxide hydrolase, it is probable that the reaction involves the formation of an hydroxyalkyl—enzyme intermediate [4,6]. The enzyme can also use leukotriene A4, the substrate of EC 3.3.2.6, leukotriene-A4 hydrolase, but it forms 5,6-dihydroxy-7,9,11,14-icosatetraenoic acid rather than leukotriene B4 as the product [9,10]. In vertebrates, five epoxide-hydrolase enzymes have been identified to date: EC 3.3.2.6 (leukotriene-A4 hydrolase), EC 3.3.2.7 (hepoxilin-epoxide hydrolase), EC 3.3.2.9 (microsomal epoxide hydrolase), EC 3.3.2.10 (soluble epoxide hydrolase) and EC 3.3.2.11 (cholesterol 5,6-oxide hydrolase) [7].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 9048-63-9
References:
1.  Newman, J.W., Morisseau, C., Harris, T.R. and Hammock, B.D. The soluble epoxide hydrolase encoded by EPXH2 is a bifunctional enzyme with novel lipid phosphate phosphatase activity. Proc. Natl. Acad. Sci. USA 100 (2003) 1558–1563. [DOI] [PMID: 12574510]
2.  Cronin, A., Mowbray, S., Dürk, H., Homburg, S., Fleming, I., Fisslthaler, B., Oesch, F. and Arand, M. The N-terminal domain of mammalian soluble epoxide hydrolase is a phosphatase. Proc. Natl. Acad. Sci. USA 100 (2003) 1552–1557. [DOI] [PMID: 12574508]
3.  Oesch, F. Mammalian epoxide hydrases: inducible enzymes catalysing the inactivation of carcinogenic and cytotoxic metabolites derived from aromatic and olefinic compounds. Xenobiotica 3 (1973) 305–340. [DOI] [PMID: 4584115]
4.  Morisseau, C. and Hammock, B.D. Epoxide hydrolases: mechanisms, inhibitor designs, and biological roles. Annu. Rev. Pharmacol. Toxicol. 45 (2005) 311–333. [DOI] [PMID: 15822179]
5.  Yu, Z., Xu, F., Huse, L.M., Morisseau, C., Draper, A.J., Newman, J.W., Parker, C., Graham, L., Engler, M.M., Hammock, B.D., Zeldin, D.C. and Kroetz, D.L. Soluble epoxide hydrolase regulates hydrolysis of vasoactive epoxyeicosatrienoic acids. Circ. Res. 87 (2000) 992–998. [PMID: 11090543]
6.  Lacourciere, G.M. and Armstrong, R.N. The catalytic mechanism of microsomal epoxide hydrolase involves an ester intermediate. J. Am. Chem. Soc. 115 (1993) 10466.
7.  Fretland, A.J. and Omiecinski, C.J. Epoxide hydrolases: biochemistry and molecular biology. Chem. Biol. Interact. 129 (2000) 41–59. [DOI] [PMID: 11154734]
8.  Zeldin, D.C., Wei, S., Falck, J.R., Hammock, B.D., Snapper, J.R. and Capdevila, J.H. Metabolism of epoxyeicosatrienoic acids by cytosolic epoxide hydrolase: substrate structural determinants of asymmetric catalysis. Arch. Biochem. Biophys. 316 (1995) 443–451. [DOI] [PMID: 7840649]
9.  Haeggström, J., Meijer, J. and Rådmark, O. Leukotriene A4. Enzymatic conversion into 5,6-dihydroxy-7,9,11,14-eicosatetraenoic acid by mouse liver cytosolic epoxide hydrolase. J. Biol. Chem. 261 (1986) 6332–6337. [PMID: 3009453]
10.  Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
[EC 3.3.2.10 created 2006 (EC 3.3.2.3 created 1978, part incorporated 2006)]
 
 
EC 3.3.2.11
Accepted name: cholesterol-5,6-oxide hydrolase
Reaction: (1) 5,6α-epoxy-5α-cholestan-3β-ol + H2O = 5α-cholestane-3β,5α,6β-triol
(2) 5,6β-epoxy-5β-cholestan-3β-ol + H2O = 5α-cholestane-3β,5α,6β-triol
For diagram of reactions, click here
Glossary: cholesterol = cholest-5-en-3β-ol
Other name(s): cholesterol-epoxide hydrolase; ChEH
Systematic name: 5,6α-epoxy-5α-cholestan-3β-ol hydrolase
Comments: The enzyme appears to work equally well with either epoxide as substrate [3]. The product is a competitive inhibitor of the reaction. In vertebrates, five epoxide-hydrolase enzymes have been identified to date: EC 3.3.2.6 (leukotriene-A4 hydrolase), EC 3.3.2.7 (hepoxilin-epoxide hydrolase), EC 3.3.2.9 (microsomal epoxide hydrolase), EC 3.3.2.10 (soluble epoxide hydrolase) and EC 3.3.2.11 (cholesterol 5,6-oxide hydrolase) [3].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Levin, W., Michaud, D.P., Thomas, P.E. and Jerina, D.M. Distinct rat hepatic microsomal epoxide hydrolases catalyze the hydration of cholesterol 5,6 α-oxide and certain xenobiotic alkene and arene oxides. Arch. Biochem. Biophys. 220 (1983) 485–494. [DOI] [PMID: 6401984]
2.  Oesch, F., Timms, C.W., Walker, C.H., Guenthner, T.M., Sparrow, A., Watabe, T. and Wolf, C.R. Existence of multiple forms of microsomal epoxide hydrolases with radically different substrate specificities. Carcinogenesis 5 (1984) 7–9. [DOI] [PMID: 6690087]
3.  Sevanian, A. and McLeod, L.L. Catalytic properties and inhibition of hepatic cholesterol-epoxide hydrolase. J. Biol. Chem. 261 (1986) 54–59. [PMID: 3941086]
4.  Fretland, A.J. and Omiecinski, C.J. Epoxide hydrolases: biochemistry and molecular biology. Chem. Biol. Interact. 129 (2000) 41–59. [DOI] [PMID: 11154734]
5.  Newman, J.W., Morisseau, C. and Hammock, B.D. Epoxide hydrolases: their roles and interactions with lipid metabolism. Prog. Lipid Res. 44 (2005) 1–51. [DOI] [PMID: 15748653]
[EC 3.3.2.11 created 2006]
 
 
EC 3.4.21.87
Transferred entry: omptin. Now EC 3.4.23.49, omptin. The enzyme is not a serine protease, as thought previously, but an aspartate protease
[EC 3.4.21.87 created 1993, deleted 2006]
 
 
EC 3.4.23.49
Accepted name: omptin
Reaction: Has a virtual requirement for Arg in the P1 position and a slightly less stringent preference for this residue in the P1′ position, which can also contain Lys, Gly or Val.
Other name(s): protease VII; protease A; gene ompT proteins; ompT protease; protein a; Pla; OmpT
Comments: A product of the ompT gene of Escherichia coli, and associated with the outer membrane. Omptin shows a preference for cleavage between consecutive basic amino acids, but is capable of cleavage when P1′ is a non-basic residue [5,7]. Belongs in peptidase family A26.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 150770-86-8
References:
1.  Grodberg, J., Lundrigan, M.D., Toledo, D.L., Mangel, W.F. and Dunn, J.J. Complete nucleotide sequence and deduced amino acid sequence of the ompT gene of Escherichia coli K-12. Nucleic Acids Res. 16 (1988) 1209. [DOI] [PMID: 3278297]
2.  Sugimura, K. and Nishihara, T. Purification, characterization, and primary structure of Escherichia coli protease VII with specificity for paired basic residues: identity of protease VII and ompT. J. Bacteriol. 170 (1988) 5625–5632. [DOI] [PMID: 3056908]
3.  Hanke, C., Hess, J., Schumacher, G. and Goebel, W. Processing by OmpT of fusion proteins carrying the HlyA transport signal during secretion by the Escherichia coli hemolysin transport system. Mol. Gen. Genet. 233 (1992) 42–48. [PMID: 1603076]
4.  Dekker, N. Omptin. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Ed.), Handbook of Proteolytic Enzymes, 2nd edn, Elsevier, London, 2004, pp. 212–216.
5.  Vandeputte-Rutten, L., Kramer, R.A., Kroon, J., Dekker, N., Egmond, M.R. and Gros, P. Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site. EMBO J. 20 (2001) 5033–5039. [DOI] [PMID: 11566868]
6.  Kramer, R.A., Vandeputte-Rutten, L., de Roon, G.J., Gros, P., Dekker, N. and Egmond, M.R. Identification of essential acidic residues of outer membrane protease OmpT supports a novel active site. FEBS Lett. 505 (2001) 426–430. [DOI] [PMID: 11576541]
7.  McCarter, J.D., Stephens, D., Shoemaker, K., Rosenberg, S., Kirsch, J.F. and Georgiou, G. Substrate specificity of the Escherichia coli outer membrane protease OmpT. J. Bacteriol. 186 (2004) 5919–5925. [DOI] [PMID: 15317797]
[EC 3.4.23.49 created 1993 as EC 3.4.21.87, transferred 2006 to EC 3.4.23.49]
 
 
EC 3.5.1.94
Accepted name: γ-glutamyl-γ-aminobutyrate hydrolase
Reaction: 4-(γ-L-glutamylamino)butanoate + H2O = 4-aminobutanoate + L-glutamate
Glossary: 4-aminobutanoate = γ-aminobutyrate = GABA
Other name(s): γ-glutamyl-GABA hydrolase; PuuD; YcjL; 4-(γ-glutamylamino)butanoate amidohydrolase; 4-(L-γ-glutamylamino)butanoate amidohydrolase
Systematic name: 4-(γ-L-glutamylamino)butanoate amidohydrolase
Comments: Forms part of a putrescine-utilizing pathway in Escherichia coli, in which it has been hypothesized that putrescine is first glutamylated to form γ-glutamylputrescine, which is oxidized to 4-(γ-glutamylamino)butanal and then to 4-(γ-glutamylamino)butanoate. The enzyme can also catalyse the reactions of EC 3.5.1.35 (D-glutaminase) and EC 3.5.1.65 (theanine hydrolase).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Kurihara, S., Oda, S., Kato, K., Kim, H.G., Koyanagi, T., Kumagai, H. and Suzuki, H. A novel putrescine utilization pathway involves γ-glutamylated intermediates of Escherichia coli K-12. J. Biol. Chem. 280 (2005) 4602–4608. [DOI] [PMID: 15590624]
[EC 3.5.1.94 created 2006, modified 2011]
 
 
EC 3.5.1.95
Accepted name: N-malonylurea hydrolase
Reaction: 3-oxo-3-ureidopropanoate + H2O = malonate + urea
For pyrimidine catabolism, click here
Other name(s): ureidomalonase
Systematic name: 3-oxo-3-ureidopropanoate amidohydrolase (urea- and malonate-forming)
Comments: Forms part of the oxidative pyrimidine-degrading pathway in some microorganisms, along with EC 1.17.99.4 (uracil/thymine dehydrogenase) and EC 3.5.2.1 (barbiturase).
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 368888-22-6
References:
1.  Soong, C.L., Ogawa, J. and Shimizu, S. Novel amidohydrolytic reactions in oxidative pyrimidine metabolism: analysis of the barbiturase reaction and discovery of a novel enzyme, ureidomalonase. Biochem. Biophys. Res. Commun. 286 (2001) 222–226. [DOI] [PMID: 11485332]
2.  Soong, C.L., Ogawa, J., Sakuradani, E. and Shimizu, S. Barbiturase, a novel zinc-containing amidohydrolase involved in oxidative pyrimidine metabolism. J. Biol. Chem. 277 (2002) 7051–7058. [DOI] [PMID: 11748240]
[EC 3.5.1.95 created 2006]
 
 
EC 3.5.1.96
Accepted name: succinylglutamate desuccinylase
Reaction: N-succinyl-L-glutamate + H2O = succinate + L-glutamate
For diagram of arginine catabolism, click here
Other name(s): N2-succinylglutamate desuccinylase; SGDS; AstE
Systematic name: N-succinyl-L-glutamate amidohydrolase
Comments: Requires Co2+ for maximal activity [1]. N2-Acetylglutamate is not a substrate. This is the final enzyme in the arginine succinyltransferase (AST) pathway for the catabolism of arginine [1]. This pathway converts the carbon skeleton of arginine into glutamate, with the concomitant production of ammonia and conversion of succinyl-CoA into succinate and CoA. The five enzymes involved in this pathway are EC 2.3.1.109 (arginine N-succinyltransferase), EC 3.5.3.23 (N-succinylarginine dihydrolase), EC 2.6.1.11 (acetylornithine transaminase), EC 1.2.1.71 (succinylglutamate-semialdehyde dehydrogenase) and EC 3.5.1.96 (succinylglutamate desuccinylase).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 99676-40-1
References:
1.  Vander Wauven, C. and Stalon, V. Occurrence of succinyl derivatives in the catabolism of arginine in Pseudomonas cepacia. J. Bacteriol. 164 (1985) 882–886. [PMID: 2865249]
2.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 50 (1986) 314–352. [PMID: 3534538]
3.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Erratum report: Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 51 (1987) 178. [PMID: 16350242]
4.  Itoh, Y. Cloning and characterization of the aru genes encoding enzymes of the catabolic arginine succinyltransferase pathway in Pseudomonas aeruginosa. J. Bacteriol. 179 (1997) 7280–7290. [DOI] [PMID: 9393691]
5.  Schneider, B.L., Kiupakis, A.K. and Reitzer, L.J. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180 (1998) 4278–4286. [PMID: 9696779]
[EC 3.5.1.96 created 2006]
 
 
*EC 3.5.2.1
Accepted name: barbiturase
Reaction: barbiturate + H2O = 3-oxo-3-ureidopropanoate
For diagram of pyrimidine catabolism, click here
Glossary: barbiturate = 6-hydroxyuracil
Systematic name: barbiturate amidohydrolase (3-oxo-3-ureidopropanoate-forming)
Comments: Contains zinc and is specific for barbiturate as substrate [3]. Forms part of the oxidative pyrimidine-degrading pathway in some microorganisms, along with EC 1.17.99.4 (uracil/thymine dehydrogenase) and EC 3.5.1.95 (N-malonylurea hydrolase). It was previously thought that the end-products of the reaction were malonate and urea but this has since been disproved [2]. May be involved in the regulation of pyrimidine metabolism, along with EC 2.4.2.9, uracil phosphoribosyltransferase.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9025-16-5
References:
1.  Hayaishi, O. and Kornberg, A. Metabolism of cytosine, thymine, uracil, and barbituric acid by bacterial enzymes. J. Biol. Chem. 197 (1952) 717–723. [PMID: 12981104]
2.  Soong, C.L., Ogawa, J. and Shimizu, S. Novel amidohydrolytic reactions in oxidative pyrimidine metabolism: analysis of the barbiturase reaction and discovery of a novel enzyme, ureidomalonase. Biochem. Biophys. Res. Commun. 286 (2001) 222–226. [DOI] [PMID: 11485332]
3.  Soong, C.L., Ogawa, J., Sakuradani, E. and Shimizu, S. Barbiturase, a novel zinc-containing amidohydrolase involved in oxidative pyrimidine metabolism. J. Biol. Chem. 277 (2002) 7051–7058. [DOI] [PMID: 11748240]
[EC 3.5.2.1 created 1961, modified 2006]
 
 
EC 3.5.3.23
Accepted name: N-succinylarginine dihydrolase
Reaction: N2-succinyl-L-arginine + 2 H2O = N2-succinyl-L-ornithine + 2 NH3 + CO2
For diagram of arginine catabolism, click here
Other name(s): N2-succinylarginine dihydrolase; arginine succinylhydrolase; SADH; AruB; AstB; 2-N-succinyl-L-arginine iminohydrolase (decarboxylating)
Systematic name: N2-succinyl-L-arginine iminohydrolase (decarboxylating)
Comments: Arginine, N2-acetylarginine and N2-glutamylarginine do not act as substrates [3]. This is the second enzyme in the arginine succinyltransferase (AST) pathway for the catabolism of arginine [1]. This pathway converts the carbon skeleton of arginine into glutamate, with the concomitant production of ammonia and conversion of succinyl-CoA into succinate and CoA. The five enzymes involved in this pathway are EC 2.3.1.109 (arginine N-succinyltransferase), EC 3.5.3.23 (N-succinylarginine dihydrolase), EC 2.6.1.81 (succinylornithine transaminase), EC 1.2.1.71 (succinylglutamate-semialdehyde dehydrogenase) and EC 3.5.1.96 (succinylglutamate desuccinylase).
Links to other databases: BRENDA, EXPASY, GENE, KEGG, PDB
References:
1.  Schneider, B.L., Kiupakis, A.K. and Reitzer, L.J. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180 (1998) 4278–4286. [PMID: 9696779]
2.  Tocilj, A., Schrag, J.D., Li, Y., Schneider, B.L., Reitzer, L., Matte, A. and Cygler, M. Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli. J. Biol. Chem. 280 (2005) 15800–15808. [DOI] [PMID: 15703173]
3.  Vander Wauven, C. and Stalon, V. Occurrence of succinyl derivatives in the catabolism of arginine in Pseudomonas cepacia. J. Bacteriol. 164 (1985) 882–886. [PMID: 2865249]
4.  Cunin, R., Glansdorff, N., Pierard, A. and Stalon, V. Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 50 (1986) 314–352. [PMID: 3534538]
5.  Itoh, Y. Cloning and characterization of the aru genes encoding enzymes of the catabolic arginine succinyltransferase pathway in Pseudomonas aeruginosa. J. Bacteriol. 179 (1997) 7280–7290. [DOI] [PMID: 9393691]
[EC 3.5.3.23 created 2006]
 
 
*EC 3.6.3.5
Transferred entry: Zn2+-exporting ATPase. Now EC 7.2.2.12, Zn2+-exporting ATPase
[EC 3.6.3.5 created 2000, modified 2001, modified 2006, deleted 2018]
 
 
*EC 3.6.3.44
Transferred entry: xenobiotic-transporting ATPase. Now EC 7.6.2.2, ABC-type xenobiotic transporter
[EC 3.6.3.44 created 2000 (EC 3.6.3.45 incorporated 2006), modified 2006, deleted 2018]
 
 
EC 3.6.3.45
Deleted entry: steroid-transporting ATPase. Now included with EC 3.6.3.44, xenobiotic-transporting ATPase
[EC 3.6.3.45 created 2000, deleted 2006]
 
 
*EC 4.1.1.21
Accepted name: phosphoribosylaminoimidazole carboxylase
Reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO2
For diagram of the late stages of purine biosynthesis, click here
Other name(s): 5-phosphoribosyl-5-aminoimidazole carboxylase; 5-amino-1-ribosylimidazole 5-phosphate carboxylase; AIR carboxylase; 1-(5-phosphoribosyl)-5-amino-4-imidazolecarboxylate carboxy-lyase; ADE2; class II PurE; 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate carboxy-lyase
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate carboxy-lyase [5-amino-1-(5-phospho-D-ribosyl)imidazole-forming]
Comments: While this is the reaction that occurs in vertebrates during purine biosynthesis, two enzymes are required to carry out the same reaction in Escherichia coli, namely EC 6.3.4.18, 5-(carboxyamino)imidazole ribonucleotide synthase and EC 5.4.99.18, 5-(carboxyamino)imidazole ribonucleotide mutase [3]. 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole is not a substrate.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9032-04-6
References:
1.  Lukens, L.N. and Buchanan, J.M. Biosynthesis of purines. XXIV. The enzymatic synthesis of 5-amino-1-ribosyl-4-imidazolecarboxylic acid 5′-phosphate from 5-amino-1-ribosylimidazole 5′-phosphate and carbon dioxide. J. Biol. Chem. 234 (1959) 1799–1805. [PMID: 13672967]
2.  Firestine, S.M., Poon, S.W., Mueller, E.J., Stubbe, J. and Davisson, V.J. Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms. Biochemistry 33 (1994) 11927–11934. [PMID: 7918411]
3.  Firestine, S.M., Misialek, S., Toffaletti, D.L., Klem, T.J., Perfect, J.R. and Davisson, V.J. Biochemical role of the Cryptococcus neoformans ADE2 protein in fungal de novo purine biosynthesis. Arch. Biochem. Biophys. 351 (1998) 123–134. [DOI] [PMID: 9500840]
[EC 4.1.1.21 created 1961, modified 2000, modified 2006]
 
 
EC 4.1.1.86
Accepted name: diaminobutyrate decarboxylase
Reaction: L-2,4-diaminobutanoate = propane-1,3-diamine + CO2
For diagram of ectoine biosynthesis, click here
Other name(s): DABA DC; L-2,4-diaminobutyrate decarboxylase; L-2,4-diaminobutanoate carboxy-lyase
Systematic name: L-2,4-diaminobutanoate carboxy-lyase (propane-1,3-diamine-forming)
Comments: A pyridoxal-phosphate protein that requires a divalent cation for activity [1]. N4-Acetyl-L-2,4-diaminobutanoate, 2,3-diaminopropanoate, ornithine and lysine are not substrates. Found in the proteobacteria Haemophilus influenzae and Acinetobacter baumannii. In the latter, this enzyme is cotranscribed with the dat gene that encodes EC 2.6.1.76, diaminobutyrate—2-oxoglutarate transaminase, which can supply the substrate for this enzyme.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Yamamoto, S., Tsuzaki, Y., Tougou, K. and Shinoda, S. Purification and characterization of L-2,4-diaminobutyrate decarboxylase from Acinetobacter calcoaceticus. J. Gen. Microbiol. 138 (1992) 1461–1465. [DOI] [PMID: 1512577]
2.  Ikai, H. and Yamamoto, S. Cloning and expression in Escherichia coli of the gene encoding a novel L-2,4-diaminobutyrate decarboxylase of Acinetobacter baumannii. FEMS Microbiol. Lett. 124 (1994) 225–228. [DOI] [PMID: 7813892]
3.  Ikai, H. and Yamamoto, S. Identification and analysis of a gene encoding L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase involved in the 1,3-diaminopropane production pathway in Acinetobacter baumannii. J. Bacteriol. 179 (1997) 5118–5125. [DOI] [PMID: 9260954]
[EC 4.1.1.86 created 2006]
 
 
*EC 4.1.2.8
Accepted name: indole-3-glycerol-phosphate lyase
Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
For diagram of reaction, click here
Other name(s): tryptophan synthase α; TSA; indoleglycerolphosphate aldolase; indole glycerol phosphate hydrolase; indole synthase; indole-3-glycerolphosphate D-glyceraldehyde-3-phosphate-lyase; indole-3-glycerol phosphate lyase; IGL; BX1; (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate D-glyceraldehyde-3-phosphate-lyase
Systematic name: (1S,2R)-1-C-(indol-3-yl)glycerol-3-phosphate D-glyceraldehyde-3-phosphate-lyase (indole-forming)
Comments: Forms part of the defence mechanism against insects and microbial pathogens in the grass family, Gramineae, where it catalyses the first committed step in the formation of the cyclic hydroxamic acids 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) [1]. This enzyme resembles the α-subunit of EC 4.2.1.20, tryptophan synthase [3], for which, (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate is also a substrate, but, unlike tryptophan synthase, its activity is independent of the β-subunit and free indole is released [2].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9014-52-2
References:
1.  Yanofsky, C. The enzymatic conversion of anthranilic acid to indole. J. Biol. Chem. 223 (1956) 171–184. [PMID: 13376586]
2.  Frey, M., Chomet, P., Glawischnig, E., Stettner, C., Grün, S., Winklmair, A., Eisenreich, W., Bacher, A., Meeley, R.B., Briggs, S.P., Simcox, K. and Gierl, A. Analysis of a chemical plant defense mechanism in grasses. Science 277 (1997) 696–699. [DOI] [PMID: 9235894]
3.  Frey, M., Stettner, C., Paré, P.W., Schmelz, E.A., Tumlinson, J.H. and Gierl, A. An herbivore elicitor activates the gene for indole emission in maize. Proc. Natl. Acad. Sci. USA 97 (2000) 14801–14806. [DOI] [PMID: 11106389]
4.  Melanson, D., Chilton, M.D., Masters-Moore, D. and Chilton, W.S. A deletion in an indole synthase gene is responsible for the DIMBOA-deficient phenotype of bxbx maize. Proc. Natl. Acad. Sci. USA 94 (1997) 13345–13350. [DOI] [PMID: 9371848]
[EC 4.1.2.8 created 1961, deleted 1972, reinstated 2006]
 
 
EC 4.1.3.39
Accepted name: 4-hydroxy-2-oxovalerate aldolase
Reaction: (S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
For diagram of 3-phenylpropanoate catabolism, click here, for diagram of catechol catabolism (meta ring cleavage), click here and for diagram of cinnamate catabolism, click here
Glossary: (S)-4-hydroxy-2-oxopentanoate = (S)-4-hydroxy-2-oxovalerate
Other name(s): 4-hydroxy-2-ketovalerate aldolase; HOA; DmpG; 4-hydroxy-2-oxovalerate pyruvate-lyase; 4-hydroxy-2-oxopentanoate pyruvate-lyase; BphI; 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Systematic name: (S)-4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Comments: Requires Mn2+ for maximal activity [1]. The enzyme from the bacterium Pseudomonas putida is also stimulated by NADH [1]. In some bacterial species the enzyme forms a bifunctional complex with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). The enzymes from the bacteria Burkholderia xenovorans and Thermus thermophilus also perform the reaction of EC 4.1.3.43, 4-hydroxy-2-oxohexanoate aldolase [4,5].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 37325-52-3
References:
1.  Manjasetty, B.A., Powlowski, J. and Vrielink, A. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 6992–6997. [DOI] [PMID: 12764229]
2.  Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377–385. [DOI] [PMID: 8419288]
3.  Manjasetty, B.A., Croteau, N., Powlowski, J. and Vrielink, A. Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase—aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 582–585. [PMID: 11264589]
4.  Baker, P., Carere, J. and Seah, S.Y.K. Probing the molecular basis of substrate specificity, stereospecificity, and catalysis in the class II pyruvate aldolase, BphI. Biochemistry 50 (2011) 3559–3569. [DOI] [PMID: 21425833]
5.  Baker, P., Hillis, C., Carere, J. and Seah, S.Y.K. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 51 (2012) 1942–1952. [DOI] [PMID: 22316175]
6.  Baker, P. and Seah, S.Y.K. Rational design of stereoselectivity in the class II pyruvate aldolase BphI. J. Am. Chem. Soc. 134 (2012) 507–513. [DOI] [PMID: 22081904]
[EC 4.1.3.39 created 2006, modified 2011]
 
 
*EC 4.2.1.60
Deleted entry: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase. The reaction described is covered by EC 4.2.1.59.
[EC 4.2.1.60 created 1972, modified 2006, deleted 2012]
 
 
EC 4.2.1.108
Accepted name: ectoine synthase
Reaction: (2S)-4-acetamido-2-aminobutanoate = L-ectoine + H2O
For diagram of ectoine biosynthesis, click here
Glossary: ectoine = (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate
Other name(s): ectC (gene name); N-acetyldiaminobutyrate dehydratase; N-acetyldiaminobutanoate dehydratase; L-ectoine synthase; 4-N-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming); N4-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming)
Systematic name: (2S)-4-acetamido-2-aminobutanoate (L-ectoine-forming)
Comments: Ectoine is an osmoprotectant that is found in halophilic eubacteria. This enzyme is part of the ectoine biosynthesis pathway and only acts in the direction of ectoine formation. cf. EC 3.5.4.44, ectoine hydrolase.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157–162.
2.  Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91–99. [PMID: 9864317]
3.  Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772–783. [DOI] [PMID: 11823218]
4.  Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141–1149. [DOI] [PMID: 9141677]
5.  Schwibbert, K., Marin-Sanguino, A., Bagyan, I., Heidrich, G., Lentzen, G., Seitz, H., Rampp, M., Schuster, S.C., Klenk, H.P., Pfeiffer, F., Oesterhelt, D. and Kunte, H.J. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ. Microbiol. 13 (2011) 1973–1994. [DOI] [PMID: 20849449]
[EC 4.2.1.108 created 2006, modified 2017]
 
 
*EC 4.2.3.9
Accepted name: aristolochene synthase
Reaction: (2E,6E)-farnesyl diphosphate = aristolochene + diphosphate
For diagram of eremophilane and spirovetivane sesquiterpenoid biosynthesis, click here
Other name(s): sesquiterpene cyclase; trans,trans-farnesyl diphosphate aristolochene-lyase; trans,trans-farnesyl-diphosphate diphosphate-lyase (cyclizing, aristolochene-forming)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, aristolochene-forming)
Comments: The initial internal cyclization produces the monocyclic intermediate germacrene A; further cyclization and methyl transfer converts the intermediate into aristolochene. While in some species germacrene A remains as an enzyme-bound intermediate, it has been shown to be a minor product of the reaction in Penicillium roqueforti [5] (see also EC 4.2.3.23, germacrene-A synthase). The enzyme from Penicillium roqueforti requires Mg2+. Mn2+ can partially substitute, at low concentrations. Aristolochene is the likely parent compound for a number of sesquiterpenes produced by filamentous fungi.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 94185-89-4
References:
1.  Cane, D.E., Prabhakaran, P.C., Oliver, J.S. and McIlwaine, D.B. Aristolochene biosynthesis. Stereochemistry of the deprotonation steps in the enzymatic cyclization of farnesyl pyrophosphate. J. Am. Chem. Soc. 112 (1990) 3209–3210.
2.  Cane, D.E., Prabhakaran, P.C., Salaski, E.J., Harrison, P.M.H., Noguchi, H. and Rawlings, B.J. Aristolochene biosynthesis and enzymatic cyclization of farnesyl pyrophosphate. J. Am. Chem. Soc. 111 (1989) 8914–8916.
3.  Hohn, T.M. and Plattner, R.D. Purification and characterization of the sesquiterpene cyclase aristolochene synthase from Penicillium roqueforti. Arch. Biochem. Biophys. 272 (1989) 137–143. [DOI] [PMID: 2544140]
4.  Proctor, R.H. and Hohn, T.M. Aristolochene synthase. Isolation, characterization, and bacterial expression of a sesquiterpenoid biosynthetic gene (Ari1) from Penicillium roqueforti. J. Biol. Chem. 268 (1993) 4543–4548. [PMID: 8440737]
5.  Calvert, M.J., Ashton, P.R. and Allemann, R.K. Germacrene A is a product of the aristolochene synthase-mediated conversion of farnesylpyrophosphate to aristolochene. J. Am. Chem. Soc. 124 (2002) 11636–11641. [DOI] [PMID: 12296728]
[EC 4.2.3.9 created 1992 as EC 2.5.1.40, transferred 1999 to EC 4.1.99.7, transferred 2000 to EC 4.2.3.9, modified 2006]
 
 
EC 4.2.3.22
Accepted name: germacradienol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate
For diagram of germacrene-derived sesquiterpenoid biosynthesis, click here
Other name(s): germacradienol/germacrene-D synthase; 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol-forming]
Comments: Requires Mg2+ for activity. H-1si of farnesyl diphosphate is lost in the formation of (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol. Formation of (-)-germacrene D involves a stereospecific 1,3-hydride shift of H-1si of farnesyl diphosphate. Both products are formed from a common intermediate [2]. Other enzymes produce germacrene D as the sole product using a different mechanism. The enzyme mediates a key step in the biosynthesis of geosmin (see EC 4.1.99.16 geosmin synthase), a widely occurring metabolite of many streptomycetes, bacteria and fungi [2]. Also catalyses the reaction of EC 4.2.3.75, (-)-germacrene D synthase.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 211049-88-6
References:
1.  Cane, D.E. and Watt, R.M. Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis. Proc. Natl. Acad. Sci. USA 100 (2003) 1547–1551. [DOI] [PMID: 12556563]
2.  He, X. and Cane, D.E. Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2). J. Am. Chem. Soc. 126 (2004) 2678–2679. [DOI] [PMID: 14995166]
3.  Gust, B., Challis, G.L., Fowler, K., Kieser, T. and Chater, K.F. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl. Acad. Sci. USA 100 (2003) 1541–1546. [DOI] [PMID: 12563033]
[EC 4.2.3.22 created 2006, modified 2011]
 
 
EC 4.2.3.23
Accepted name: germacrene-A synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-(R)-gemacrene A + diphosphate
For diagram of germacrene sesquiterpenoid biosynthesis, click here
Other name(s): germacrene A synthase; (+)-germacrene A synthase; (+)-(10R)-germacrene A synthase; GAS; 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-(R)-germacrene-A-forming]
Comments: Requires Mg2+ for activity. While germacrene A is an enzyme-bound intermediate in the biosynthesis of a number of phytoalexins, e.g. EC 4.2.3.9 (aristolochene synthase) from some species and EC 4.2.3.21 (vetispiradiene synthase), it is the sole sesquiterpenoid product formed in chicory [1].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 213763-55-4
References:
1.  Bouwmeester, H.J., Kodde, J., Verstappen, F.W., Altug, I.G., de Kraker, J.W. and Wallaart, T.E. Isolation and characterization of two germacrene A synthase cDNA clones from chicory. Plant Physiol. 129 (2002) 134–144. [DOI] [PMID: 12011345]
2.  Prosser, I., Phillips, A.L., Gittings, S., Lewis, M.J., Hooper, A.M., Pickett, J.A. and Beale, M.H. (+)-(10R)-Germacrene A synthase from goldenrod, Solidago canadensis; cDNA isolation, bacterial expression and functional analysis. Phytochemistry 60 (2002) 691–702. [DOI] [PMID: 12127586]
3.  de Kraker, J.W., Franssen, M.C., de Groot, A., König, W.A. and Bouwmeester, H.J. (+)-Germacrene A biosynthesis . The committed step in the biosynthesis of bitter sesquiterpene lactones in chicory. Plant Physiol. 117 (1998) 1381–1392. [PMID: 9701594]
4.  Calvert, M.J., Ashton, P.R. and Allemann, R.K. Germacrene A is a product of the aristolochene synthase-mediated conversion of farnesylpyrophosphate to aristolochene. J. Am. Chem. Soc. 124 (2002) 11636–11641. [DOI] [PMID: 12296728]
5.  Chang, Y.J., Jin, J., Nam, H.Y. and Kim, S.U. Point mutation of (+)-germacrene A synthase from Ixeris dentata. Biotechnol. Lett. 27 (2005) 285–288. [DOI] [PMID: 15834787]
[EC 4.2.3.23 created 2006]
 
 
EC 4.2.3.24
Accepted name: amorpha-4,11-diene synthase
Reaction: (2E,6E)-farnesyl diphosphate = amorpha-4,11-diene + diphosphate
Other name(s): amorphadiene synthase
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (amorpha-4,11-diene-forming)
Comments: Requires Mg2+ and Mn2+ for activity. This is a key enzyme in the biosynthesis of the antimalarial endoperoxide artemisinin [3]. Catalyses the formation of both olefinic [e.g. amorpha-4,11-diene, amorpha-4,7(11)-diene, γ-humulene and β-sesquiphellandrene] and oxygenated (e.g. amorpha-4-en-7-ol) sesquiterpenes, with amorpha-4,11-diene being the major product. When geranyl diphosphate is used as a substrate, no monoterpenes are produced [2].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 259213-60-0
References:
1.  Wallaart, T.E., Bouwmeester, H.J., Hille, J., Poppinga, L. and Maijers, N.C. Amorpha-4,11-diene synthase: cloning and functional expression of a key enzyme in the biosynthetic pathway of the novel antimalarial drug artemisinin. Planta 212 (2001) 460–465. [DOI] [PMID: 11289612]
2.  Mercke, P., Bengtsson, M., Bouwmeester, H.J., Posthumus, M.A. and Brodelius, P.E. Molecular cloning, expression, and characterization of amorpha-4,11-diene synthase, a key enzyme of artemisinin biosynthesis in Artemisia annua L. Arch. Biochem. Biophys. 381 (2000) 173–180. [DOI] [PMID: 11032404]
3.  Bouwmeester, H.J., Wallaart, T.E., Janssen, M.H., van Loo, B., Jansen, B.J., Posthumus, M.A., Schmidt, C.O., De Kraker, J.W., König, W.A. and Franssen, M.C. Amorpha-4,11-diene synthase catalyses the first probable step in artemisinin biosynthesis. Phytochemistry 52 (1999) 843–854. [DOI] [PMID: 10626375]
4.  Chang, Y.J., Song, S.H., Park, S.H. and Kim, S.U. Amorpha-4,11-diene synthase of Artemisia annua: cDNA isolation and bacterial expression of a terpene synthase involved in artemisinin biosynthesis. Arch. Biochem. Biophys. 383 (2000) 178–184. [DOI] [PMID: 11185551]
5.  Martin, V.J., Pitera, D.J., Withers, S.T., Newman, J.D. and Keasling, J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21 (2003) 796–802. [DOI] [PMID: 12778056]
6.  Picaud, S., Mercke, P., He, X., Sterner, O., Brodelius, M., Cane, D.E. and Brodelius, P.E. Amorpha-4,11-diene synthase: Mechanism and stereochemistry of the enzymatic cyclization of farnesyl diphosphate. Arch. Biochem. Biophys. 448 (2006) 150–155. [DOI] [PMID: 16143293]
[EC 4.2.3.24 created 2006]
 
 
EC 4.2.3.25
Accepted name: S-linalool synthase
Reaction: geranyl diphosphate + H2O = (3S)-linalool + diphosphate
For diagram of acyclic monoterpenoid biosynthesis, click here
Glossary: (3S)-linalool = (3S)-3,7-dimethylocta-1,6-dien-3-ol
Other name(s): LIS; Lis; 3S-linalool synthase
Systematic name: geranyl-diphosphate diphosphate-lyase [(3S)-linalool-forming]
Comments: Requires Mn2+ or Mg2+ for activity. Neither (S)- nor (R)-linalyl diphosphate can act as substrate for the enzyme from the flower Clarkia breweri [1]. Unlike many other monoterpene synthases, only a single product, (3S)-linalool, is formed.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 160477-81-6
References:
1.  Pichersky, E., Lewinsohn, E. and Croteau, R. Purification and characterization of S-linalool synthase, an enzyme involved in the production of floral scent in Clarkia breweri. Arch. Biochem. Biophys. 316 (1995) 803–807. [DOI] [PMID: 7864636]
2.  Lücker, J., Bouwmeester, H.J., Schwab, W., Blaas, J., van der Plas, L.H. and Verhoeven, H.A. Expression of Clarkia S-linalool synthase in transgenic petunia plants results in the accumulation of S-linalyl-β-D-glucopyranoside. Plant J. 27 (2001) 315–324. [DOI] [PMID: 11532177]
3.  Dudareva, N., Cseke, L., Blanc, V.M. and Pichersky, E. Evolution of floral scent in Clarkia: novel patterns of S-linalool synthase gene expression in the C. breweri flower. Plant Cell 8 (1996) 1137–1148. [DOI] [PMID: 8768373]
[EC 4.2.3.25 created 2006]
 
 
EC 4.2.3.26
Accepted name: R-linalool synthase
Reaction: geranyl diphosphate + H2O = (3R)-linalool + diphosphate
For diagram of acyclic monoterpenoid biosynthesis, click here
Glossary: (3R)-linalool = (3R)-3,7-dimethylocta-1,6-dien-3-ol
Other name(s): (3R)-linalool synthase; (–)-3R-linalool synthase
Systematic name: geranyl-diphosphate diphosphate-lyase [(3R)-linalool-forming]
Comments: Geranyl diphosphate cannot be replaced by isopentenyl diphosphate (3-methylbut-3-en-1-yl diphosphate), prenyl diphosphate, farnesyl diphosphate or geranylgeranyl diphosphate as substrate [1]. Requires Mg2+ or Mn2+ for activity. Unlike many other monoterpene synthases, only a single product, (3R)-linalool, is formed.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 254993-26-5
References:
1.  Jia, J.W., Crock, J., Lu, S., Croteau, R. and Chen, X.Y. (3R)-Linalool synthase from Artemisia annua L.: cDNA isolation, characterization, and wound induction. Arch. Biochem. Biophys. 372 (1999) 143–149. [DOI] [PMID: 10562427]
2.  Crowell, A.L., Williams, D.C., Davis, E.M., Wildung, M.R. and Croteau, R. Molecular cloning and characterization of a new linalool synthase. Arch. Biochem. Biophys. 405 (2002) 112–121. [DOI] [PMID: 12176064]
[EC 4.2.3.26 created 2006]
 
 
EC 4.4.1.24
Accepted name: (2R)-sulfolactate sulfo-lyase
Reaction: (2R)-3-sulfolactate = pyruvate + hydrogensulfite
Other name(s): Suy; SuyAB; 3-sulfolactate bisulfite-lyase; sulfolactate sulfo-lyase (ambigious); (2R)-3-sulfolactate bisulfite-lyase (pyruvate-forming)
Systematic name: (2R)-3-sulfolactate hydrogensulfite-lyase (pyruvate-forming)
Comments: Requires iron(II). This inducible enzyme participates in cysteate degradation by the bacterium Paracoccus pantotrophus NKNCYSA and in 3-sulfolactate degradation by the bacterium Chromohalobacter salexigens. The enzyme is specific for the (R) isomer of its substrate.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 1256650-35-7
References:
1.  Graham, D.E. and White, R.H. Elucidation of methanogenic coenzyme biosyntheses: from spectroscopy to genomics. Nat. Prod. Rep. 19 (2002) 133–147. [PMID: 12013276]
2.  Rein, U., Gueta, R., Denger, K., Ruff, J., Hollemeyer, K. and Cook, A.M. Dissimilation of cysteate via 3-sulfolactate sulfo-lyase and a sulfate exporter in Paracoccus pantotrophus NKNCYSA. Microbiology 151 (2005) 737–747. [DOI] [PMID: 15758220]
3.  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. [DOI] [PMID: 20007648]
[EC 4.4.1.24 created 2006, modified 2011]
 
 
EC 4.4.1.25
Accepted name: L-cysteate sulfo-lyase
Reaction: L-cysteate + H2O = hydrogensulfite + pyruvate + NH3 (overall reaction)
(1a) L-cysteate = hydrogensulfite + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Glossary: L-cysteate = (2S)-2-amino-3-sulfopropanoate
Other name(s): L-cysteate sulfo-lyase (deaminating); CuyA; L-cysteate bisulfite-lyase (deaminating; pyruvate-forming)
Systematic name: L-cysteate hydrogensulfite-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme cleaves a carbon-sulfur bond, releasing hydrogensulfite and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The latter reaction, which can occur spontaneously, can also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. D-Cysteine can also act as a substrate, but more slowly. It is converted into hydrogen sulfide, pyruvate, and ammonia. This inducible enzyme from the marine bacterium Silicibacter pomeroyi DSS-3 forms part of the cysteate-degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Denger, K., Smits, T.H.M. and Cook, A.M. L-Cysteate sulpho-lyase, a widespread pyridoxal 5′-phosphate-coupled desulphonative enzyme purified from Silicibacter pomeroyi DSS-3(T). Biochem. J. 394 (2006) 657–664. [DOI] [PMID: 16302849]
[EC 4.4.1.25 created 2006]
 
 
EC 5.3.3.14
Accepted name: trans-2-decenoyl-[acyl-carrier protein] isomerase
Reaction: a trans-dec-2-enoyl-[acyl-carrier protein] = a cis-dec-3-enoyl-[acyl-carrier protein]
Other name(s): β-hydroxydecanoyl thioester dehydrase; trans-2-cis-3-decenoyl-ACP isomerase; trans-2,cis-3-decenoyl-ACP isomerase; trans-2-decenoyl-ACP isomerase; FabM; decenoyl-[acyl-carrier-protein] Δ2-trans-Δ3-cis-isomerase
Systematic name: decenoyl-[acyl-carrier protein] Δ2-trans-Δ3-cis-isomerase
Comments: While the enzyme from Escherichia coli is highly specific for the 10-carbon enoyl-ACP, the enzyme from Streptococcus pneumoniae can also use the 12-carbon enoyl-ACP as substrate in vitro but not 14- or 16-carbon enoyl-ACPs [3]. ACP can be replaced by either CoA or N-acetylcysteamine thioesters. The cis-3-enoyl product is required to form unsaturated fatty acids, such as palmitoleic acid and cis-vaccenic acid, in dissociated (or type II) fatty-acid biosynthesis.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9030-80-2
References:
1.  Brock, D.J.H., Kass, L.R. and Bloch, K. β-Hydroxydecanoyl thioester dehydrase. II. Mode of action. J. Biol. Chem. 242 (1967) 4432–4440. [PMID: 4863740]
2.  Bloch, K. Enzymatic synthesis of monounsaturated fatty acids. Acc. Chem. Res. 2 (1969) 193–202.
3.  Marrakchi, H., Choi, K.H. and Rock, C.O. A new mechanism for anaerobic unsaturated fatty acid formation in Streptococcus pneumoniae. J. Biol. Chem. 277 (2002) 44809–44816. [DOI] [PMID: 12237320]
4.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
[EC 5.3.3.14 created 2006]
 
 
EC 5.4.99.18
Accepted name: 5-(carboxyamino)imidazole ribonucleotide mutase
Reaction: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
For diagram of the late stages of purine biosynthesis, click here
Other name(s): N5-CAIR mutase; PurE; N5-carboxyaminoimidazole ribonucleotide mutase; class I PurE
Systematic name: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole carboxymutase
Comments: In eubacteria, fungi and plants, this enzyme, along with EC 6.3.4.18, 5-(carboxyamino)imidazole ribonucleotide synthase, is required to carry out the single reaction catalysed by EC 4.1.1.21, phosphoribosylaminoimidazole carboxylase, in vertebrates [6]. In the absence of EC 6.3.2.6, phosphoribosylaminoimidazolesuccinocarboxamide synthase, the reaction is reversible [3]. The substrate is readily converted into 5-amino-1-(5-phospho-D-ribosyl)imidazole by non-enzymic decarboxylation [3].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 255379-40-9
References:
1.  Meyer, E., Leonard, N.J., Bhat, B., Stubbe, J. and Smith, J.M. Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31 (1992) 5022–5032. [PMID: 1534690]
2.  Mueller, E.J., Meyer, E., Rudolph, J., Davisson, V.J. and Stubbe, J. N5-Carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. Biochemistry 33 (1994) 2269–2278. [PMID: 8117684]
3.  Meyer, E., Kappock, T.J., Osuji, C. and Stubbe, J. Evidence for the direct transfer of the carboxylate of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to generate 4-carboxy-5-aminoimidazole ribonucleotide catalyzed by Escherichia coli PurE, an N5-CAIR mutase. Biochemistry 38 (1999) 3012–3018. [DOI] [PMID: 10074353]
4.  Mathews, I.I., Kappock, T.J., Stubbe, J. and Ealick, S.E. Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway. Structure 7 (1999) 1395–1406. [DOI] [PMID: 10574791]
5.  Firestine, S.M., Poon, S.W., Mueller, E.J., Stubbe, J. and Davisson, V.J. Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms. Biochemistry 33 (1994) 11927–11934. [PMID: 7918411]
6.  Firestine, S.M., Misialek, S., Toffaletti, D.L., Klem, T.J., Perfect, J.R. and Davisson, V.J. Biochemical role of the Cryptococcus neoformans ADE2 protein in fungal de novo purine biosynthesis. Arch. Biochem. Biophys. 351 (1998) 123–134. [DOI] [PMID: 9500840]
[EC 5.4.99.18 created 2006]
 
 
EC 6.2.1.7
Accepted name: cholate—CoA ligase
Reaction: (1) ATP + cholate + CoA = AMP + diphosphate + choloyl-CoA
(2) ATP + (25R)-3α,7α,12α-trihydroxy-5β-cholestan-26-oate + CoA = AMP + diphosphate + (25R)-3α,7α,12α-trihydroxy-5β-cholestanoyl-CoA
For diagram of cholic acid conjugates biosynthesis, click here and for diagram of cholic acid biosynthesis (sidechain), click here
Glossary: cholate = 3α,7α,12α-trihydroxy-5β-cholan-24-oate
trihydroxycoprostanoate = 3α,7α,12α-trihydroxy-5β-cholestan-26-oate
Other name(s): BAL; bile acid CoA ligase; bile acid coenzyme A ligase; choloyl-CoA synthetase; choloyl coenzyme A synthetase; cholic thiokinase; cholate thiokinase; cholic acid:CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanoyl coenzyme A synthetase; 3α,7α,12α-trihydroxy-5β-cholestanoate-CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanoate-CoA synthetase; THCA-CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanate—CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanate:CoA ligase (AMP-forming); cholyl-CoA synthetase; trihydroxycoprostanoyl-CoA synthetase
Systematic name: cholate:CoA ligase (AMP-forming)
Comments: Requires Mg2+ for activity. The mammalian enzyme is membrane-bound and catalyses the first step in the conjugation of bile acids with amino acids, converting bile acids into their acyl-CoA thioesters. Chenodeoxycholate, deoxycholate, lithocholate and trihydroxycoprostanoate can also act as substrates [7]. The bacterial enzyme is soluble and participates in an anaerobic bile acid 7 α-dehydroxylation pathway [5].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9027-90-1
References:
1.  Elliott, W.H. The enzymic activation of cholic acid by guinea-pig-liver microsomes. Biochem. J. 62 (1956) 427–433. [PMID: 13303991]
2.  Elliott, W.H. The breakdown of adenosine triphosphate accompanying cholic acid activation by guinea-pig liver microsomes. Biochem. J. 65 (1957) 315–321. [PMID: 13403911]
3.  Prydz, K., Kase, B.F., Björkhem, I. and Pedersen, J.I. Subcellular localization of 3α,7α-dihydroxy- and 3α,7α,12α-trihydroxy-5β-cholestanoyl-coenzyme A ligase(s) in rat liver. J. Lipid Res. 29 (1988) 997–1004. [PMID: 3183523]
4.  Schepers, L., Casteels, M., Verheyden, K., Parmentier, G., Asselberghs, S., Eyssen, H.J. and Mannaerts, G.P. Subcellular distribution and characteristics of trihydroxycoprostanoyl-CoA synthetase in rat liver. Biochem. J. 257 (1989) 221–229. [PMID: 2521999]
5.  Mallonee, D.H., Adams, J.L. and Hylemon, P.B. The bile acid-inducible baiB gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme A ligase. J. Bacteriol. 174 (1992) 2065–2071. [DOI] [PMID: 1551828]
6.  Wheeler, J.B., Shaw, D.R. and Barnes, S. Purification and characterization of a rat liver bile acid coenzyme A ligase from rat liver microsomes. Arch. Biochem. Biophys. 348 (1997) 15–24. [DOI] [PMID: 9390170]
7.  Falany, C.N., Xie, X., Wheeler, J.B., Wang, J., Smith, M., He, D. and Barnes, S. Molecular cloning and expression of rat liver bile acid CoA ligase. J. Lipid Res. 43 (2002) 2062–2071. [PMID: 12454267]
[EC 6.2.1.7 created 1961 (EC 6.2.1.29 created 1992, incorporated 2005), modified 2005]
 
 
*EC 6.3.2.6
Accepted name: phosphoribosylaminoimidazolesuccinocarboxamide synthase
Reaction: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate = ADP + phosphate + (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate
For diagram of the late stages of purine biosynthesis, click here
Other name(s): phosphoribosylaminoimidazole-succinocarboxamide synthetase; PurC; SAICAR synthetase; 4-(N-succinocarboxamide)-5-aminoimidazole synthetase; 4-[(N-succinylamino)carbonyl]-5-aminoimidazole ribonucleotide synthetase; SAICARs; phosphoribosylaminoimidazolesuccinocarboxamide synthetase; 5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate:L-aspartate ligase (ADP-forming)
Comments: Forms part of the purine biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9023-67-0
References:
1.  Lukens, L.N. and Buchanan, J.M. Biosynthesis of purines. XXIV. The enzymatic synthesis of 5-amino-1-ribosyl-4-imidazolecarboxylic acid 5′-phosphate from 5-amino-1-ribosylimidazole 5′-phosphate and carbon dioxide. J. Biol. Chem. 234 (1959) 1799–1805. [PMID: 13672967]
2.  Parker, J. Identification of the purC gene product of Escherichia coli. J. Bacteriol. 157 (1984) 712–717. [PMID: 6365889]
3.  Ebbole, D.J. and Zalkin, H. Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J. Biol. Chem. 262 (1987) 8274–8287. [PMID: 3036807]
4.  Chen, Z.D., Dixon, J.E. and Zalkin, H. Cloning of a chicken liver cDNA encoding 5-aminoimidazole ribonucleotide carboxylase and 5-aminoimidazole-4-N-succinocarboxamide ribonucleotide synthetase by functional complementation of Escherichia coli pur mutants. Proc. Natl. Acad. Sci. USA 87 (1990) 3097–3101. [DOI] [PMID: 1691501]
5.  O'Donnell, A.F., Tiong, S., Nash, D. and Clark, D.V. The Drosophila melanogaster ade5 gene encodes a bifunctional enzyme for two steps in the de novo purine synthesis pathway. Genetics 154 (2000) 1239–1253. [PMID: 10757766]
6.  Nelson, S.W., Binkowski, D.J., Honzatko, R.B. and Fromm, H.J. Mechanism of action of Escherichia coli phosphoribosylaminoimidazolesuccinocarboxamide synthetase. Biochemistry 44 (2005) 766–774. [DOI] [PMID: 15641804]
[EC 6.3.2.6 created 1961, modified 2000, modified 2006]
 
 
*EC 6.3.2.27
Deleted entry: The activity is covered by two independent enzymes, EC 6.3.2.38 N2-citryl-N6-acetyl-N6-hydroxylysine synthase, and EC 6.3.2.39, aerobactin synthase
[EC 6.3.2.27 created 2002, modified 2006, deleted 2012]
 
 
EC 6.3.4.18
Accepted name: 5-(carboxyamino)imidazole ribonucleotide synthase
Reaction: ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
For diagram of the late stages of purine biosynthesis, click here
Other name(s): N5-CAIR synthetase; N5-carboxyaminoimidazole ribonucleotide synthetase; PurK
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming)
Comments: In Escherichia coli, this enzyme, along with EC 5.4.99.18, 5-(carboxyamino)imidazole ribonucleotide mutase, is required to carry out the single reaction catalysed by EC 4.1.1.21, phosphoribosylaminoimidazole carboxylase, in vertebrates. Belongs to the ATP grasp protein superfamily [3]. Carboxyphosphate is the putative acyl phosphate intermediate. Involved in the late stages of purine biosynthesis.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 255379-40-9
References:
1.  Meyer, E., Leonard, N.J., Bhat, B., Stubbe, J. and Smith, J.M. Purification and characterization of the purE, purK, and purC gene products: identification of a previously unrecognized energy requirement in the purine biosynthetic pathway. Biochemistry 31 (1992) 5022–5032. [PMID: 1534690]
2.  Mueller, E.J., Meyer, E., Rudolph, J., Davisson, V.J. and Stubbe, J. N5-Carboxyaminoimidazole ribonucleotide: evidence for a new intermediate and two new enzymatic activities in the de novo purine biosynthetic pathway of Escherichia coli. Biochemistry 33 (1994) 2269–2278. [PMID: 8117684]
3.  Thoden, J.B., Kappock, T.J., Stubbe, J. and Holden, H.M. Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily. Biochemistry 38 (1999) 15480–15492. [DOI] [PMID: 10569930]
[EC 6.3.4.18 created 2006]
 
 


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