The Enzyme Database

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

Proposed Changes to the Enzyme List

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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

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


Contents

EC 1.1.1.293 deleted
*EC 1.1.3.17 choline oxidase
*EC 1.3.1.53 (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate dehydrogenase
EC 1.3.1.61 deleted
EC 2.1.1.161 dimethylglycine N-methyltransferase
EC 2.1.1.162 glycine/sarcosine/dimethylglycine N-methyltransferase
EC 2.3.1.182 (R)-citramalate synthase
EC 2.3.1.183 phosphinothricin acetyltransferase
EC 2.3.1.184 acyl-homoserine-lactone synthase
*EC 2.4.2.29 tRNA-guanosine34 transglycosylase
EC 2.6.1.85 aminodeoxychorismate synthase
*EC 2.7.1.26 riboflavin kinase
*EC 2.7.7.2 FAD synthetase
EC 3.1.1.81 quorum-quenching N-acyl-homoserine lactonase
EC 3.2.1.164 galactan endo-1,6-β-galactosidase
EC 3.4.15.6 cyanophycinase
*EC 3.4.21.94 proprotein convertase 2
EC 3.4.22.67 zingipain
EC 3.5.1.97 acyl-homoserine-lactone acylase
EC 4.1.99.12 3,4-dihydroxy-2-butanone-4-phosphate synthase
EC 4.2.1.113 o-succinylbenzoate synthase
EC 4.2.2.22 pectate trisaccharide-lyase
EC 5.1.1.18 serine racemase
EC 6.1.1.26 pyrrolysine—tRNAPyl ligase
EC 6.3.2.29 cyanophycin synthase (L-aspartate-adding)
EC 6.3.2.30 cyanophycin synthase (L-arginine-adding)
EC 6.3.5.8 transferred


EC 1.1.1.293
Deleted entry: tropinone reductase I. This enzyme was already in the Enzyme List as EC 1.1.1.206, tropine dehydrogenase so EC 1.1.1.293 has been withdrawn at the public-review stage
[EC 1.1.1.293 created 2007, withdrawn while undergoing public review]
 
 
*EC 1.1.3.17
Accepted name: choline oxidase
Reaction: choline + 2 O2 + H2O = betaine + 2 H2O2 (overall reaction)
(1a) choline + O2 = betaine aldehyde + H2O2
(1b) betaine aldehyde + O2 + H2O = betaine + H2O2
Glossary: choline = (2-hydroxyethyl)trimethylammonium
betaine aldehyde = N,N,N-trimethyl-2-oxoethylammonium
betaine = glycine betaine = N,N,N-trimethylglycine = N,N,N-trimethylammonioacetate
Systematic name: choline:oxygen 1-oxidoreductase
Comments: A flavoprotein (FAD). In many bacteria, plants and animals, the osmoprotectant betaine is synthesized using different enzymes to catalyse the conversion of (1) choline into betaine aldehyde and (2) betaine aldehyde into betaine. In plants, the first reaction is catalysed by EC 1.14.15.7, choline monooxygenase, whereas in animals and many bacteria, it is catalysed by either membrane-bound choline dehydrogenase (EC 1.1.99.1) or soluble choline oxidase (EC 1.1.3.17) [6]. The enzyme involved in the second step, EC 1.2.1.8, betaine-aldehyde dehydrogenase, appears to be the same in those plants, animals and bacteria that use two separate enzymes.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9028-67-5
References:
1.  Ikuta, S., Imamura, S., Misaki, H. and Horiuti, Y. Purification and characterization of choline oxidase from Arthrobacter globiformis. J. Biochem. (Tokyo) 82 (1977) 1741–1749. [PMID: 599154]
2.  Rozwadowski, K.L., Khachatourians, G.G. and Selvaraj, G. Choline oxidase, a catabolic enzyme in Arthrobacter pascens, facilitates adaptation to osmotic stress in Escherichia coli. J. Bacteriol. 173 (1991) 472–478. [PMID: 1987142]
3.  Rand, T., Halkier, T. and Hansen, O.C. Structural characterization and mapping of the covalently linked FAD cofactor in choline oxidase from Arthrobacter globiformis. Biochemistry 42 (2003) 7188–7194. [PMID: 12795615]
4.  Gadda, G., Powell, N.L. and Menon, P. The trimethylammonium headgroup of choline is a major determinant for substrate binding and specificity in choline oxidase. Arch. Biochem. Biophys. 430 (2004) 264–273. [PMID: 15369826]
5.  Fan, F. and Gadda, G. On the catalytic mechanism of choline oxidase. J. Am. Chem. Soc. 127 (2005) 2067–2074. [PMID: 15713082]
6.  Waditee, R., Tanaka, Y., Aoki, K., Hibino, T., Jikuya, H., Takano, J., Takabe, T. and Takabe, T. Isolation and functional characterization of N-methyltransferases that catalyze betaine synthesis from glycine in a halotolerant photosynthetic organism Aphanothece halophytica. J. Biol. Chem. 278 (2003) 4932–4942. [PMID: 12466265]
7.  Fan, F., Ghanem, M. and Gadda, G. Cloning, sequence analysis, and purification of choline oxidase from Arthrobacter globiformis: a bacterial enzyme involved in osmotic stress tolerance. Arch. Biochem. Biophys. 421 (2004) 149–158. [PMID: 14678796]
8.  Gadda, G. Kinetic mechanism of choline oxidase from Arthrobacter globiformis. Biochim. Biophys. Acta 1646 (2003) 112–118. [PMID: 12637017]
[EC 1.1.3.17 created 1978, modified 2005, modified 2007]
 
 
*EC 1.3.1.53
Accepted name: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate dehydrogenase
Reaction: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate + NAD+ = 3,4-dihydroxybenzoate + CO2 + NADH
Glossary: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate = cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,4-dicarboxylate
Other name(s): (1R,2S)-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase; terephthalate 1,2-cis-dihydrodiol dehydrogenase; cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,4-dicarboxylate:NAD+ oxidoreductase (decarboxylating)
Systematic name: (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate:NAD+ oxidoreductase
Comments: Requires FeII. Involved in the terephthalate degradation pathway in bacteria [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, UM-BBD, CAS registry number: 162032-77-1
References:
1.  Saller, E., Laue, H.R., Schläfli Oppenberg, H.R. and Cook, A.M. Purification and some properties of (1R,2S)-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase from Comamonas testosteroni T-2. FEMS Microbiol. Lett. 130 (1996) 97–102.
2.  Wang, Y.Z., Zhou, Y. and Zylstra, G.J. Molecular analysis of isophthalate and terephthalate degradation by Comamonas testosteroni YZW-D. Environ. Health Perspect. 103, Suppl. 5 (1995) 9–12. [PMID: 8565920]
[EC 1.3.1.53 created 1999 (EC 1.3.1.61 created 2000, incorporated 2007)]
 
 
EC 1.3.1.61
Deleted entry: terephthalate 1,2-cis-dihydrodiol dehydrogenase. Enzyme is identical to EC 1.3.1.53, (3S,4R)-3,4-dihydroxycyclohexa-1,5-diene-1,4-dicarboxylate dehydrogenase
[EC 1.3.1.61 created 2000, deleted 2007]
 
 
EC 2.1.1.161
Accepted name: dimethylglycine N-methyltransferase
Reaction: S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine
Glossary: betaine = glycine betaine = N,N,N-trimethylglycine = N,N,N-trimethylammonioacetate
Other name(s): BsmB; DMT
Systematic name: S-adenosyl-L-methionine:N,N-dimethylglycine N-methyltransferase (betaine-forming)
Comments: This enzyme, from the marine cyanobacterium Synechococcus sp. WH8102, differs from EC 2.1.1.157, sarcosine/dimethylglycine N-methyltransferase in that it cannot use sarcosine as an alternative substrate [1]. Betaine is a ’compatible solute’ that enables cyanobacteria to cope with osmotic stress by maintaining a positive cellular turgor.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lu, W.D., Chi, Z.M. and Su, C.D. Identification of glycine betaine as compatible solute in Synechococcus sp. WH8102 and characterization of its N-methyltransferase genes involved in betaine synthesis. Arch. Microbiol. 186 (2006) 495–506. [PMID: 17019606]
[EC 2.1.1.161 created 2007]
 
 
EC 2.1.1.162
Accepted name: glycine/sarcosine/dimethylglycine N-methyltransferase
Reaction: 3 S-adenosyl-L-methionine + glycine = 3 S-adenosyl-L-homocysteine + betaine (overall reaction)
(1a) S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
(1b) S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine
(1c) S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine
Glossary: sarcosine = N-methylglycine
betaine = glycine betaine = N,N,N-trimethylglycine = N,N,N-trimethylammonioacetate
Other name(s): GSDMT; glycine sarcosine dimethylglycine N-methyltransferase
Systematic name: S-adenosyl-L-methionine:glycine(or sarcosine or N,N-dimethylglycine) N-methyltransferase [sarcosine(or N,N-dimethylglycine or betaine)-forming]
Comments: Unlike EC 2.1.1.156 (glycine/sarcosine N-methyltransferase), EC 2.1.1.157 (sarcosine/dimethylglycine N-methyltransferase) and EC 2.1.1.161 (dimethylglycine N-methyltransferase), this enzyme, from the halophilic methanoarchaeon Methanohalophilus portucalensis, can methylate glycine and all of its intermediates to form the compatible solute betaine [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lai, M.C., Wang, C.C., Chuang, M.J., Wu, Y.C. and Lee, Y.C. Effects of substrate and potassium on the betaine-synthesizing enzyme glycine sarcosine dimethylglycine N-methyltransferase from a halophilic methanoarchaeon Methanohalophilus portucalensis. Res. Microbiol. 157 (2006) 948–955. [PMID: 17098399]
[EC 2.1.1.162 created 2007]
 
 
EC 2.3.1.182
Accepted name: (R)-citramalate synthase
Reaction: acetyl-CoA + pyruvate + H2O = CoA + (2R)-2-hydroxy-2-methylbutanedioate
Glossary: (-)-citramalate = (2R)-2-methylmalate = (2R)-2-hydroxy-2-methylbutanedioate
α-ketoisovalerate = 3-methyl-2-oxobutanoate
α-ketobutyrate = 2-oxobutanoate
α-ketoisocaproate = 4-methyl-2-oxopentanoate
α-ketopimelate = 2-oxohexanoate
α-ketoglutarate = 2-oxoglutarate
Other name(s): CimA
Comments: One of the enzymes involved in a novel pyruvate pathway for isoleucine biosynthesis that is found in some, mainly archaeal, bacteria [1,2]. The enzyme can be inhibited by isoleucine, the end-product of the pathway, but not by leucine [2]. The enzyme is highly specific for pyruvate as substrate, as the 2-oxo acids 3-methyl-2-oxobutanoate, 2-oxobutanoate, 4-methyl-2-oxopentanoate, 2-oxohexanoate and 2-oxoglutarate cannot act as substrate [1,2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Howell, D.M., Xu, H. and White, R.H. (R)-Citramalate synthase in methanogenic archaea. J. Bacteriol. 181 (1999) 331–333. [PMID: 9864346]
2.  Xu, H., Zhang, Y., Guo, X., Ren, S., Staempfli, A.A., Chiao, J., Jiang, W. and Zhao, G. Isoleucine biosynthesis in Leptospira interrogans serotype 1ai strain 56601 proceeds via a threonine-independent pathway. J. Bacteriol. 186 (2004) 5400–5409. [PMID: 15292141]
[EC 2.3.1.182 created 2007]
 
 
EC 2.3.1.183
Accepted name: phosphinothricin acetyltransferase
Reaction: acetyl-CoA + phosphinothricin = CoA + N-acetylphosphinothricin
Glossary: phosphinothricin = glufosinate = 2-amino-4-[hydroxy(methyl)phosphoryl]butanoate
Other name(s): PAT; PPT acetyltransferase; Pt-N-acetyltransferase; ac-Pt
Systematic name: acetyl-CoA:phosphinothricin N-acetyltransferase
Comments: The substrate phosphinothricin is used as a nonselective herbicide and is a potent inhibitor of EC 6.3.1.2, glutamate—ammonia ligase, a key enzyme of nitrogen metabolism in plants [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Botterman, J., Gosselé, V., Thoen, C. and Lauwereys, M. Characterization of phosphinothricin acetyltransferase and C-terminal enzymatically active fusion proteins. Gene 102 (1991) 33–37. [PMID: 1864506]
2.  Dröge-Laser, W., Siemeling, U., Pühler, A. and Broer, I. The metabolites of the herbicide L-phosphinothricin (glufosinate) (identification, stability, and mobility in transgenic, herbicide-resistant, and untransformed plants). Plant Physiol. 105 (1994) 159–166. [PMID: 12232195]
[EC 2.3.1.183 created 2007]
 
 
EC 2.3.1.184
Accepted name: acyl-homoserine-lactone synthase
Reaction: an acyl-[acyl-carrier protein] + S-adenosyl-L-methionine = an [acyl-carrier protein] + S-methyl-5′-thioadenosine + an N-acyl-L-homoserine lactone
For diagram of reaction, click here
Other name(s): acyl-homoserine lactone synthase; acyl homoserine lactone synthase; acyl-homoserinelactone synthase; acylhomoserine lactone synthase; AHL synthase; AHS; AHSL synthase; AhyI; AinS; AinS protein; autoinducer synthase; autoinducer synthesis protein rhlI; EsaI; ExpISCC1; ExpISCC3065; LasI; LasR; LuxI; LuxI protein; LuxM; N-acyl homoserine lactone synthase; RhlI; YspI ; acyl-[acyl carrier protein]:S-adenosyl-L-methionine acyltranserase (lactone-forming, methylthioadenosine-releasing)
Systematic name: acyl-[acyl-carrier protein]:S-adenosyl-L-methionine acyltranserase (lactone-forming, methylthioadenosine-releasing)
Comments: Acyl-homoserine lactones (AHLs) are produced by a number of bacterial species and are used by them to regulate the expression of virulence genes in a process known as quorum-sensing. Each bacterial cell has a basal level of AHL and, once the population density reaches a critical level, it triggers AHL-signalling which, in turn, initiates the expression of particular virulence genes [5]. N-(3-Oxohexanoyl)-[acyl-carrier protein] and hexanoyl-[acyl-carrier protein] are the best substrates [1]. The fatty-acyl substrate is derived from fatty-acid biosynthesis through acyl-[acyl-carrier protein] rather than from fatty-acid degradation through acyl-CoA [1]. S-Adenosyl-L-methionine cannot be replaced by methionine, S-adenosylhomocysteine, homoserine or homoserine lactone [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 176023-66-8
References:
1.  Schaefer, A.L., Val, D.L., Hanzelka, B.L., Cronan, J.E., Jr. and Greenberg, E.P. Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein. Proc. Natl. Acad. Sci. USA 93 (1996) 9505–9509. [PMID: 8790360]
2.  Watson, W.T., Murphy, F.V., 4th, Gould, T.A., Jambeck, P., Val, D.L., Cronan, J.E., Jr., Beck von Bodman, S. and Churchill, M.E. Crystallization and rhenium MAD phasing of the acyl-homoserinelactone synthase EsaI. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 1945–1949. [PMID: 11717525]
3.  Chakrabarti, S. and Sowdhamini, R. Functional sites and evolutionary connections of acylhomoserine lactone synthases. Protein Eng. 16 (2003) 271–278. [PMID: 12736370]
4.  Hanzelka, B.L., Parsek, M.R., Val, D.L., Dunlap, P.V., Cronan, J.E., Jr. and Greenberg, E.P. Acylhomoserine lactone synthase activity of the Vibrio fischeri AinS protein. J. Bacteriol. 181 (1999) 5766–5770. [PMID: 10482519]
5.  Parsek, M.R., Val, D.L., Hanzelka, B.L., Cronan, J.E., Jr. and Greenberg, E.P. Acyl homoserine-lactone quorum-sensing signal generation. Proc. Natl. Acad. Sci. USA 96 (1999) 4360–4365. [PMID: 10200267]
6.  Ulrich, R.L. Quorum quenching: enzymatic disruption of N-acylhomoserine lactone-mediated bacterial communication in Burkholderia thailandensis. Appl. Environ. Microbiol. 70 (2004) 6173–6180. [PMID: 15466564]
7.  Gould, T.A., Schweizer, H.P. and Churchill, M.E. Structure of the Pseudomonas aeruginosa acyl-homoserinelactone synthase LasI. Mol. Microbiol. 53 (2004) 1135–1146. [PMID: 15306017]
8.  Raychaudhuri, A., Jerga, A. and Tipton, P.A. Chemical mechanism and substrate specificity of RhlI, an acylhomoserine lactone synthase from Pseudomonas aeruginosa. Biochemistry 44 (2005) 2974–2981. [PMID: 15723540]
9.  Gould, T.A., Herman, J., Krank, J., Murphy, R.C. and Churchill, M.E. Specificity of acyl-homoserine lactone synthases examined by mass spectrometry. J. Bacteriol. 188 (2006) 773–783. [PMID: 16385066]
[EC 2.3.1.184 created 2007]
 
 
*EC 2.4.2.29
Accepted name: tRNA-guanosine34 transglycosylase
Reaction: (1) guanine34 in tRNA + queuine = queuine34 in tRNA + guanine
(2) guanine34 in tRNA + 7-aminomethyl-7-carbaguanine = 7-aminomethyl-7-carbaguanine34 in tRNA + guanine
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
queuine = base Q = 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-1,7-dihydropyrrolo[3,2-e]pyrimidin-4-one
Other name(s): guanine insertion enzyme (ambiguous); tRNA transglycosylase (ambiguous); Q-insertase (ambiguous); queuine34 transfer ribonucleate ribosyltransferase; transfer ribonucleate glycosyltransferase (ambiguous); tRNA guanine34 transglycosidase; queuine tRNA-ribosyltransferase (ambiguous); TGT; [tRNA]-guanine34:queuine tRNA-D-ribosyltransferase; transfer ribonucleic acid guanine34 transglycosylase
Systematic name: tRNA-guanosine34:queuine tRNA-D-ribosyltransferase
Comments: Certain prokaryotic and eukaryotic tRNAs contain the modified base queuine at position 34. In eukaryotes queuine is salvaged from food and incorporated into tRNA directly via a base-exchange reaction, replacing guanine. In eubacteria, which produce queuine de novo, the enzyme catalyses the exchange of guanine with the queuine precursor preQ1, which is ultimately modified to queuosine [4,5]. The eubacterial enzyme can also use an earlier intermediate, preQ0, to replace guanine in unmodified tRNATyr and tRNAAsn [2]. This enzyme acts after EC 1.7.1.13, preQ1 synthase, in the queuine-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 72162-89-1
References:
1.  Howes, N.K. and Farkas, W.R. Studies with a homogeneous enzyme from rabbit erythrocytes catalyzing the insertion of guanine into tRNA. J. Biol. Chem. 253 (1978) 9082–9087. [PMID: 721832]
2.  Okada, N., Noguchi, S., Kasai, H., Shindo-Okada, N., Ohgi, T., Goto, T. and Nishimura, S. Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. J. Biol. Chem. 254 (1979) 3067–3073. [PMID: 372186]
3.  Shindo-Okada, N., Okada, N., Ohgi, T., Goto, T. and Nishimura, S. Transfer ribonucleic acid guanine transglycosylase isolated from rat liver. Biochemistry 19 (1980) 395–400. [PMID: 6986171]
4.  Todorov, K.A. and Garcia, G.A. Role of aspartate 143 in Escherichia coli tRNA-guanine transglycosylase: alteration of heterocyclic substrate specificity. Biochemistry 45 (2006) 617–625. [PMID: 16401090]
5.  Boland, C., Hayes, P., Santa-Maria, I., Nishimura, S. and Kelly, V.P. Queuosine formation in eukaryotic tRNA occurs via a mitochondria-localized heteromeric transglycosylase. J. Biol. Chem. 284 (2009) 18218–18227. [PMID: 19414587]
[EC 2.4.2.29 created 1984, modified 2007, modified 2012]
 
 
EC 2.6.1.85
Accepted name: aminodeoxychorismate synthase
Reaction: chorismate + L-glutamine = 4-amino-4-deoxychorismate + L-glutamate
For diagram of the late stages of folate biosynthesis, click here
Other name(s): ADC synthase; 4-amino-4-deoxychorismate synthase; PabB; chorismate:L-glutamine amido-ligase (incorrect)
Systematic name: chorismate:L-glutamine aminotransferase
Comments: The enzyme is composed of two parts, PabA and PabB. In the absence of PabA and glutamine, PabB converts ammonia and chorismate into 4-amino-4-deoxychorismate (in the presence of Mg2+). PabA converts glutamine into glutamate only in the presence of stoichiometric amounts of PabB. This enzyme is coupled with EC 4.1.3.38, aminodeoxychorismate lyase, to form 4-aminobenzoate.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Ye, Q.Z., Liu, J. and Walsh, C.T. p-Aminobenzoate synthesis in Escherichia coli: purification and characterization of PabB as aminodeoxychorismate synthase and enzyme X as aminodeoxychorismate lyase. Proc. Natl. Acad. Sci. USA 87 (1990) 9391–9395. [PMID: 2251281]
2.  Viswanathan, V.K., Green, J.M. and Nichols, B.P. Kinetic characterization of 4-amino 4-deoxychorismate synthase from Escherichia coli. J. Bacteriol. 177 (1995) 5918–5923. [PMID: 7592344]
[EC 2.6.1.85 created 2003 as EC 6.3.5.8, transferred 2007 to EC 2.6.1.85]
 
 
*EC 2.7.1.26
Accepted name: riboflavin kinase
Reaction: ATP + riboflavin = ADP + FMN
For diagram of FAD biosynthesis, click here
Other name(s): flavokinase; FK; RFK
Systematic name: ATP:riboflavin 5′-phosphotransferase
Comments: The cofactors FMN and FAD participate in numerous processes in all organisms, including mitochondrial electron transport, photosynthesis, fatty-acid oxidation, and metabolism of vitamin B6, vitamin B12 and folates [5]. While monofunctional riboflavin kinase is found in eukaryotes, some bacteria have a bifunctional enzyme that exhibits both this activity and that of EC 2.7.7.2, FMN adenylyltransferase [5]. A divalent metal cation is required for activity (with different species preferring Mg2+, Mn2+ or Zn2+). In Bacillus subtilis, ATP can be replaced by other phosphate donors but with decreasing enzyme activity in the order ATP > dATP > CTP > UTP [6].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 9032-82-0
References:
1.  Chassy, B.M., Arsenis, C. and McCormick, D.B. The effect of the length of the side chain of flavins on reactivity with flavokinase. J. Biol. Chem. 240 (1965) 1338–1340. [PMID: 14284745]
2.  Giri, K.V., Krishnaswamy, P.R. and Rao, N.A. Studies on plant flavokinase. Biochem. J. 70 (1958) 66–71. [PMID: 13584303]
3.  Kearney, E.B. The interaction of yeast flavokinase with riboflavin analogues. J. Biol. Chem. 194 (1952) 747–754. [PMID: 14927668]
4.  McCormick, D.B. and Butler, R.C. Substrate specificity of liver flavokinase. Biochim. Biophys. Acta 65 (1962) 326–332.
5.  Sandoval, F.J. and Roje, S. An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Biol. Chem. 280 (2005) 38337–38345. [PMID: 16183635]
6.  Solovieva, I.M., Tarasov, K.V. and Perumov, D.A. Main physicochemical features of monofunctional flavokinase from Bacillus subtilis. Biochemistry (Mosc) 68 (2003) 177–181. [PMID: 12693963]
7.  Solovieva, I.M., Kreneva, R.A., Leak, D.J. and Perumov, D.A. The ribR gene encodes a monofunctional riboflavin kinase which is involved in regulation of the Bacillus subtilis riboflavin operon. Microbiology 145 (1999) 67–73. [PMID: 10206712]
[EC 2.7.1.26 created 1961, modified 2007]
 
 
*EC 2.7.7.2
Accepted name: FAD synthetase
Reaction: ATP + FMN = diphosphate + FAD
For diagram of FAD biosynthesis, click here
Other name(s): FAD pyrophosphorylase; riboflavin mononucleotide adenylyltransferase; adenosine triphosphate-riboflavin mononucleotide transadenylase; adenosine triphosphate-riboflavine mononucleotide transadenylase; riboflavin adenine dinucleotide pyrophosphorylase; riboflavine adenine dinucleotide adenylyltransferase; flavin adenine dinucleotide synthetase; FADS; FMN adenylyltransferase
Systematic name: ATP:FMN adenylyltransferase
Comments: Requires Mg2+ and is highly specific for ATP as phosphate donor [5]. The cofactors FMN and FAD participate in numerous processes in all organisms, including mitochondrial electron transport, photosynthesis, fatty-acid oxidation, and metabolism of vitamin B6, vitamin B12 and folates [3]. While monofunctional FAD synthetase is found in eukaryotes and in some prokaryotes, most prokaryotes have a bifunctional enzyme that exhibits both this activity and that of EC 2.7.1.26, riboflavin kinase [3,5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 9026-37-3
References:
1.  Giri, K.V., Rao, N.A., Cama, H.R. and Kumar, S.A. Studies on flavinadenine dinucleotide-synthesizing enzyme in plants. Biochem. J. 75 (1960) 381–386. [PMID: 13828163]
2.  Schrecker, A.W. and Kornberg, A. Reversible enzymatic synthesis of flavin-adenine dinucleotide. J. Biol. Chem. 182 (1950) 795–803.
3.  Sandoval, F.J. and Roje, S. An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Biol. Chem. 280 (2005) 38337–38345. [PMID: 16183635]
4.  Oka, M. and McCormick, D.B. Complete purification and general characterization of FAD synthetase from rat liver. J. Biol. Chem. 262 (1987) 7418–7422. [PMID: 3034893]
5.  Brizio, C., Galluccio, M., Wait, R., Torchetti, E.M., Bafunno, V., Accardi, R., Gianazza, E., Indiveri, C. and Barile, M. Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase. Biochem. Biophys. Res. Commun. 344 (2006) 1008–1016. [PMID: 16643857]
[EC 2.7.7.2 created 1961, modified 2007]
 
 
EC 3.1.1.81
Accepted name: quorum-quenching N-acyl-homoserine lactonase
Reaction: an N-acyl-L-homoserine lactone + H2O = an N-acyl-L-homoserine
Other name(s): acyl homoserine degrading enzyme; acyl-homoserine lactone acylase; AHL lactonase; AHL-degrading enzyme; AHL-inactivating enzyme; AHLase; AhlD; AhlK; AiiA; AiiA lactonase; AiiA-like protein; AiiB; AiiC; AttM; delactonase; lactonase-like enzyme; N-acyl homoserine lactonase; N-acyl homoserine lactone hydrolase; N-acyl-homoserine lactone lactonase; N-acyl-L-homoserine lactone hydrolase; quorum-quenching lactonase; quorum-quenching N-acyl homoserine lactone hydrolase
Systematic name: N-acyl-L-homoserine-lactone lactonohydrolase
Comments: Acyl-homoserine lactones (AHLs) are produced by a number of bacterial species and are used by them to regulate the expression of virulence genes in a process known as quorum-sensing. Each bacterial cell has a basal level of AHL and, once the population density reaches a critical level, it triggers AHL-signalling which, in turn, initiates the expression of particular virulence genes [5]. Plants or animals capable of degrading AHLs would have a therapeutic advantage in avoiding bacterial infection as they could prevent AHL-signalling and the expression of virulence genes in quorum-sensing bacteria [5]. N-(3-Oxohexanoyl)-L-homoserine lactone, N-(3-oxododecanoyl)-L-homoserine lactone, N-butanoyl-L-homoserine lactone and N-(3-oxooctanoyl)-L-homoserine lactone can act as substrates [5].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 389867-43-0
References:
1.  Thomas, P.W., Stone, E.M., Costello, A.L., Tierney, D.L. and Fast, W. The quorum-quenching lactonase from Bacillus thuringiensis is a metalloprotein. Biochemistry 44 (2005) 7559–7569. [PMID: 15895999]
2.  Dong, Y.H., Gusti, A.R., Zhang, Q., Xu, J.L. and Zhang, L.H. Identification of quorum-quenching N-acyl homoserine lactonases from Bacillus species. Appl. Environ. Microbiol. 68 (2002) 1754–1759. [PMID: 11916693]
3.  Wang, L.H., Weng, L.X., Dong, Y.H. and Zhang, L.H. Specificity and enzyme kinetics of the quorum-quenching N-acyl homoserine lactone lactonase (AHL-lactonase). J. Biol. Chem. 279 (2004) 13645–13651. [PMID: 14734559]
4.  Dong, Y.H., Xu, J.L., Li, X.Z. and Zhang, L.H. AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. Proc. Natl. Acad. Sci. USA 97 (2000) 3526–3531. [PMID: 10716724]
5.  Dong, Y.H., Wang, L.H., Xu, J.L., Zhang, H.B., Zhang, X.F. and Zhang, L.H. Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature 411 (2001) 813–817. [PMID: 11459062]
6.  Lee, S.J., Park, S.Y., Lee, J.J., Yum, D.Y., Koo, B.T. and Lee, J.K. Genes encoding the N-acyl homoserine lactone-degrading enzyme are widespread in many subspecies of Bacillus thuringiensis. Appl. Environ. Microbiol. 68 (2002) 3919–3924. [PMID: 12147491]
7.  Park, S.Y., Lee, S.J., Oh, T.K., Oh, J.W., Koo, B.T., Yum, D.Y. and Lee, J.K. AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria. Microbiology 149 (2003) 1541–1550. [PMID: 12777494]
8.  Ulrich, R.L. Quorum quenching: enzymatic disruption of N-acylhomoserine lactone-mediated bacterial communication in Burkholderia thailandensis. Appl. Environ. Microbiol. 70 (2004) 6173–6180. [PMID: 15466564]
9.  Kim, M.H., Choi, W.C., Kang, H.O., Lee, J.S., Kang, B.S., Kim, K.J., Derewenda, Z.S., Oh, T.K., Lee, C.H. and Lee, J.K. The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase. Proc. Natl. Acad. Sci. USA 102 (2005) 17606–17611. [PMID: 16314577]
10.  Liu, D., Lepore, B.W., Petsko, G.A., Thomas, P.W., Stone, E.M., Fast, W. and Ringe, D. Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis. Proc. Natl. Acad. Sci. USA 102 (2005) 11882–11887. [PMID: 16087890]
11.  Yang, F., Wang, L.H., Wang, J., Dong, Y.H., Hu, J.Y. and Zhang, L.H. Quorum quenching enzyme activity is widely conserved in the sera of mammalian species. FEBS Lett. 579 (2005) 3713–3717. [PMID: 15963993]
[EC 3.1.1.81 created 2007]
 
 
EC 3.2.1.164
Accepted name: galactan endo-1,6-β-galactosidase
Reaction: Endohydrolysis of (1→6)-β-D-galactosidic linkages in arabinogalactan proteins and (1→3):(1→6)-β-galactans to yield galactose and (1→6)-β-galactobiose as the final products
Other name(s): endo-1,6-β-galactanase
Systematic name: endo-β-(1→6)-galactanase
Comments: The enzyme specifically hydrolyses 1,6-β-D-galactooligosaccharides with a degree of polymerization (DP) higher than 3, and their acidic derivatives with 4-O-methylglucosyluronate or glucosyluronate groups at the non-reducing terminals [2]. 1,3-β-D- and 1,4-β-D-galactosyl residues cannot act as substrates. The enzyme can also hydrolyse α-L-arabinofuranosidase-treated arabinogalactan protein (AGP) extracted from radish roots [2,3]. AGPs are thought to be involved in many physiological events, such as cell division, cell expansion and cell death [3].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Brillouet, J.-M., Williams, P. and Moutounet, M. Purification and some properties of a novel endo-β-(1→6)-D-galactanase from Aspergillus niger. Agric. Biol. Chem. 55 (1991) 1565–1571.
2.  Okemoto, K., Uekita, T., Tsumuraya, Y., Hashimoto, Y. and Kasama, T. Purification and characterization of an endo-β-(1→6)-galactanase from Trichoderma viride. Carbohydr. Res. 338 (2003) 219–230. [PMID: 12543554]
3.  Kotake, T., Kaneko, S., Kubomoto, A., Haque, M.A., Kobayashi, H. and Tsumuraya, Y. Molecular cloning and expression in Escherichia coli of a Trichoderma viride endo-β-(1→6)-galactanase gene. Biochem. J. 377 (2004) 749–755. [PMID: 14565843]
[EC 3.2.1.164 created 2007]
 
 
EC 3.4.15.6
Accepted name: cyanophycinase
Reaction: [L-Asp(4-L-Arg)]n + H2O = [L-Asp(4-L-Arg)]n-1 + L-Asp(4-L-Arg)
For diagram of cyanophycin biosynthesis, click here
Glossary: cyanophycin = [L-Asp(4-L-Arg)]n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]n = poly{N4-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}
Other name(s): cyanophycin degrading enzyme; β-Asp-Arg hydrolysing enzyme; CGPase; CphB; CphE; cyanophycin granule polypeptidase; extracellular CGPase
Comments: The enzyme is highly specific for the branched polypeptide cyanophycin and does not hydrolyse poly-L-aspartate or poly-L-arginine [3]. A serine-type exopeptidase that belongs in peptidase family S51.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, MEROPS, CAS registry number: 131554-16-0
References:
1.  Obst, M., Krug, A., Luftmann, H. and Steinbüchel, A. Degradation of cyanophycin by Sedimentibacter hongkongensis strain KI and Citrobacter amalonaticus strain G isolated from an anaerobic bacterial consortium. Appl. Environ. Microbiol. 71 (2005) 3642–3652. [PMID: 16000772]
2.  Obst, M., Oppermann-Sanio, F.B., Luftmann, H. and Steinbüchel, A. Isolation of cyanophycin-degrading bacteria, cloning and characterization of an extracellular cyanophycinase gene (cphE) from Pseudomonas anguilliseptica strain BI. The cphE gene from P. anguilliseptica BI encodes a cyanophycin-hydrolyzing enzyme. J. Biol. Chem. 277 (2002) 25096–25105. [PMID: 11986309]
3.  Richter, R., Hejazi, M., Kraft, R., Ziegler, K. and Lockau, W. Cyanophycinase, a peptidase degrading the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartic acid (cyanophycin): molecular cloning of the gene of Synechocystis sp. PCC 6803, expression in Escherichia coli, and biochemical characterization of the purified enzyme. Eur. J. Biochem. 263 (1999) 163–169. [PMID: 10429200]
[EC 3.4.15.6 created 2007]
 
 
*EC 3.4.21.94
Accepted name: proprotein convertase 2
Reaction: Release of protein hormones and neuropeptides from their precursors, generally by hydrolysis of -Lys-Arg┼ bonds
Other name(s): neuroendocrine convertase 2; PC2
Comments: A Ca2+-dependent enzyme, maximally active at about pH 5.5. Specificity is broader than that of prohormone convertase 1. Substrates include pro-opiomelanocortin, proenkephalin, prodynorphin, proglucagon, proinsulin and proluteinizing-hormone-releasing-hormone. Does not hydrolyse prorenin or prosomatostatin, however. Unusually, processing of prodynorphin occurs at a bond in which P2 is Thr. Present in the regulated secretory pathway of neuroendocrine cells, commonly acting co-operatively with prohormone convertase 1. In peptidase family S8 (subtilisin family)
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, MEROPS, CAS registry number: 388092-42-0
References:
1.  Seidah, N.G., Gaspar, L., Mion, P., Marcinkiewicz, M., Mbikay, M. and Chrétien, M. cDNA sequence of two distinct pituitary proteins homologous to Kex2 and furin gene products: tissue-specific mRNAs encoding candidates for pro-hormone processing proteinases. DNA Cell Biol. 9 (1990) 415–424. [PMID: 2169760]
2.  Smeekens, S.P. and Steiner, D.F. Identification of a human insulinoma cDNA encoding a novel mammalian protein structurally related to the yeast dibasic processing protease Kex2. J. Biol. Chem. 265 (1990) 2997–3000. [PMID: 2154467]
3.  Rouillé, Y., Westermark, G., Martin, S.K. and Steiner, D.F. Proglucagon is processed to glucagon by prohormone convertase PC2 in alphaTC1-6 cells. Proc. Natl. Acad. Sci. USA 91 (1994) 3242–3246. [PMID: 8159732]
4.  Seidah, N.G. and Chrétien, M. Pro-protein convertases of the subtilisin/kexin family. Methods Enzymol. 244 (1994) 175–188. [PMID: 7845206]
[EC 3.4.21.94 created 1996]
 
 
EC 3.4.22.67
Accepted name: zingipain
Reaction: Preferential cleavage of peptides with a proline residue at the P2 position
Other name(s): ginger protease; GP-I; GP-II; ginger protease II (Zingiber officinale); zingibain
Comments: This enzyme is found in ginger (Zingiber officinale) rhizome and is a member of the papain family. GP-II contains two glycosylation sites. The enzyme is inhibited by some divalent metal ions, such as Hg2+, Cu2+, Cd2+ and Zn2+ [2]. Belongs in peptidase family C1.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Choi, K.H. and Laursen, R.A. Amino-acid sequence and glycan structures of cysteine proteases with proline specificity from ginger rhizome Zingiber officinale. Eur. J. Biochem. 267 (2000) 1516–1526. [PMID: 10691991]
2.  Ohtsuki, K., Taguchi, K., Sato, K. and Kawabata, M. Purification of ginger proteases by DEAE-Sepharose and isoelectric focusing. Biochim. Biophys. Acta 1243 (1995) 181–184. [PMID: 7873561]
3.  Choi, K.H., Laursen, R.A. and Allen, K.N. The 2.1 Å structure of a cysteine protease with proline specificity from ginger rhizome, Zingiber officinale. Biochemistry 38 (1999) 11624–11633. [PMID: 10512617]
[EC 3.4.22.67 created 2007]
 
 
EC 3.5.1.97
Accepted name: acyl-homoserine-lactone acylase
Reaction: an N-acyl-L-homoserine lactone + H2O = L-homoserine lactone + a carboxylate
Other name(s): acyl-homoserine lactone acylase; AHL-acylase; AiiD; N-acyl-homoserine lactone acylase; PA2385 protein; quorum-quenching AHL acylase; quorum-quenching enzyme; QuiP
Systematic name: N-acyl-L-homoserine-lactone amidohydrolase
Comments: Acyl-homoserine lactones (AHLs) are produced by a number of bacterial species and are used by them to regulate the expression of virulence genes in a process known as quorum-sensing. Each bacterial cell has a basal level of AHL and, once the population density reaches a critical level, it triggers AHL-signalling which, in turn, initiates the expression of particular virulence genes. Plants or animals capable of degrading AHLs would have a therapeutic advantage in avoiding bacterial infection as they could prevent AHL-signalling and the expression of virulence genes in quorum-sensing bacteria. This quorum-quenching enzyme removes the fatty-acid side chain from the homoserine lactone ring of AHL-dependent quorum-sensing signal molecules. It has broad specificity for AHLs with side changes ranging in length from 11 to 14 carbons. Substituents at the 3′-position, as found in N-(3-oxododecanoyl)-L-homoserine lactone, do not affect this activity.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Lin, Y.H., Xu, J.L., Hu, J., Wang, L.H., Ong, S.L., Leadbetter, J.R. and Zhang, L.H. Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes. Mol. Microbiol. 47 (2003) 849–860. [PMID: 12535081]
2.  Sio, C.F., Otten, L.G., Cool, R.H., Diggle, S.P., Braun, P.G., Bos, R., Daykin, M., Cámara, M., Williams, P. and Quax, W.J. Quorum quenching by an N-acyl-homoserine lactone acylase from Pseudomonas aeruginosa PAO1. Infect. Immun. 74 (2006) 1673–1682. [PMID: 16495538]
[EC 3.5.1.97 created 2007]
 
 
EC 4.1.99.12
Accepted name: 3,4-dihydroxy-2-butanone-4-phosphate synthase
Reaction: D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
For diagram of riboflavin biosynthesis (late stages), click here
Other name(s): DHBP synthase; L-3,4-dihydroxybutan-2-one-4-phosphate synthase
Systematic name: D-ribulose 5-phosphate formate-lyase (L-3,4-dihydroxybutan-2-one 4-phosphate-forming)
Comments: Requires a divalent cation, preferably Mg2+, for activity [1]. The reaction involves an intramolecular skeletal rearrangement, with the bonds in D-ribulose 5-phosphate that connect C-3 and C-5 to C-4 being broken, C-4 being removed as formate and reconnection of C-3 and C-5 [1]. The phosphorylated four-carbon product (L-3,4-dihydroxybutan-2-one 4-phosphate) is an intermediate in the biosynthesis of riboflavin [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Volk, R. and Bacher, A. Studies on the 4-carbon precursor in the biosynthesis of riboflavin. Purification and properties of L-3,4-dihydroxy-2-butanone-4-phosphate synthase. J. Biol. Chem. 265 (1990) 19479–19485. [PMID: 2246238]
2.  Liao, D.I., Calabrese, J.C., Wawrzak, Z., Viitanen, P.V. and Jordan, D.B. Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis. Structure 9 (2001) 11–18. [PMID: 11342130]
3.  Kelly, M.J., Ball, L.J., Krieger, C., Yu, Y., Fischer, M., Schiffmann, S., Schmieder, P., Kühne, R., Bermel, W., Bacher, A., Richter, G. and Oschkinat, H. The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site. Proc. Natl. Acad. Sci. USA 98 (2001) 13025–13030. [PMID: 11687623]
4.  Liao, D.I., Zheng, Y.J., Viitanen, P.V. and Jordan, D.B. Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase. Biochemistry 41 (2002) 1795–1806. [PMID: 11827524]
5.  Fischer, M., Römisch, W., Schiffmann, S., Kelly, M., Oschkinat, H., Steinbacher, S., Huber, R., Eisenreich, W., Richter, G. and Bacher, A. Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii. J. Biol. Chem. 277 (2002) 41410–41416. [PMID: 12200440]
6.  Steinbacher, S., Schiffmann, S., Richter, G., Huber, R., Bacher, A. and Fischer, M. Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism. J. Biol. Chem. 278 (2003) 42256–42265. [PMID: 12904291]
7.  Steinbacher, S., Schiffmann, S., Bacher, A. and Fischer, M. Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1338–1340. [PMID: 15213409]
8.  Echt, S., Bauer, S., Steinbacher, S., Huber, R., Bacher, A. and Fischer, M. Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans. J. Mol. Biol. 341 (2004) 1085–1096. [PMID: 15328619]
[EC 4.1.99.12 created 2007]
 
 
EC 4.2.1.113
Accepted name: o-succinylbenzoate synthase
Reaction: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O
For diagram of vitamin K biosynthesis, click here
Glossary: 2-succinylbenzoate = o-succinylbenzoate = 4-(2-carboxyphenyl)-4-oxobutanoate
Other name(s): o-succinylbenzoic acid synthase; OSB synthase; OSBS; 2-succinylbenzoate synthase; MenC
Systematic name: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydro-lyase (2-succinylbenzoate-forming)
Comments: Belongs to the enolase superfamily and requires divalent cations, preferably Mg2+ or Mn2+, for activity. Forms part of the vitamin-K-biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB, CAS registry number: 97089-83-3
References:
1.  Sharma, V., Meganathan, R. and Hudspeth, M.E. Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli. J. Bacteriol. 175 (1993) 4917–4921. [PMID: 8335646]
2.  Klenchin, V.A., Taylor Ringia, E.A., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli. Biochemistry 42 (2003) 14427–14433. [PMID: 14661953]
3.  Palmer, D.R., Garrett, J.B., Sharma, V., Meganathan, R., Babbitt, P.C. and Gerlt, J.A. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry 38 (1999) 4252–4258. [PMID: 10194342]
4.  Thompson, T.B., Garrett, J.B., Taylor, E.A., Meganathan, R., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate. Biochemistry 39 (2000) 10662–10676. [PMID: 10978150]
5.  Taylor Ringia, E.A., Garrett, J.B., Thoden, J.B., Holden, H.M., Rayment, I. and Gerlt, J.A. Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry 43 (2004) 224–229. [PMID: 14705949]
[EC 4.2.1.113 created 2007]
 
 
EC 4.2.2.22
Accepted name: pectate trisaccharide-lyase
Reaction: eliminative cleavage of unsaturated trigalacturonate as the major product from the reducing end of polygalacturonic acid/pectate
Other name(s): exopectate-lyase; pectate lyase A; PelA
Systematic name: (1→4)-α-D-galacturonan reducing-end-trisaccharide-lyase
Comments: Differs in specificity from EC 4.2.2.9, pectate disaccharide-lyase, as the predominant action is removal of a trisaccharide rather than a disaccharide from the reducing end. Disaccharides and tetrasaccharides may also be removed [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG
References:
1.  Kluskens, L.D., van Alebeek, G.J., Voragen, A.G., de Vos, W.M. and van der Oost, J. Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima. Biochem. J. 370 (2003) 651–659. [PMID: 12443532]
2.  Tamaru, Y. and Doi, R.H. Pectate lyase A, an enzymatic subunit of the Clostridium cellulovorans cellulosome. Proc. Natl. Acad. Sci. USA 98 (2001) 4125–4129. [PMID: 11259664]
3.  Berensmeier, S., Singh, S.A., Meens, J. and Buchholz, K. Cloning of the pelA gene from Bacillus licheniformis 14A and biochemical characterization of recombinant, thermostable, high-alkaline pectate lyase. Appl. Microbiol. Biotechnol. 64 (2004) 560–567. [PMID: 14673544]
[EC 4.2.2.22 created 2007]
 
 
EC 5.1.1.18
Accepted name: serine racemase
Reaction: L-serine = D-serine
Other name(s): SRR
Systematic name: serine racemase
Comments: A pyridoxal-phosphate protein that is highly selective for L-serine as substrate. D-Serine is found in type-II astrocytes in mammalian brain, where it appears to be an endogenous ligand of the glycine site of N-methyl-D-aspartate (NMDA) receptors [1,2]. The reaction can also occur in the reverse direction but does so more slowly at physiological serine concentrations [4].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 77114-08-0
References:
1.  Wolosker, H., Blackshaw, S. and Snyder, S.H. Serine racemase: a glial enzyme synthesizing D-serine to regulate glutamate-N-methyl-D-aspartate neurotransmission. Proc. Natl. Acad. Sci. USA 96 (1999) 13409–13414. [PMID: 10557334]
2.  Wolosker, H., Sheth, K.N., Takahashi, M., Mothet, J.P., Brady, R.O., Jr., Ferris, C.D. and Snyder, S.H. Purification of serine racemase: biosynthesis of the neuromodulator D-serine. Proc. Natl. Acad. Sci. USA 96 (1999) 721–725. [PMID: 9892700]
3.  De Miranda, J., Santoro, A., Engelender, S. and Wolosker, H. Human serine racemase: moleular cloning, genomic organization and functional analysis. Gene 256 (2000) 183–188. [PMID: 11054547]
4.  Foltyn, V.N., Bendikov, I., De Miranda, J., Panizzutti, R., Dumin, E., Shleper, M., Li, P., Toney, M.D., Kartvelishvily, E. and Wolosker, H. Serine racemase modulates intracellular D-serine levels through an α,β-elimination activity. J. Biol. Chem. 280 (2005) 1754–1763. [PMID: 15536068]
[EC 5.1.1.18 created 2007]
 
 
EC 6.1.1.26
Accepted name: pyrrolysine—tRNAPyl ligase
Reaction: ATP + L-pyrrolysine + tRNAPyl = AMP + diphosphate + L-pyrrolysyl-tRNAPyl
Glossary: pyrrolysine = N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine
Other name(s): PylS; pyrrolysyl-tRNA synthetase
Systematic name: L-pyrrolysine:tRNAPyl ligase (AMP-forming)
Comments: In organisms such as Methanosarcina barkeri that incorporate the modified amino acid pyrrolysine (Pyl) into certain methylamine methyltransferases, an unusual tRNAPyl, with a CUA anticodon, can be charged directly with pyrrolysine by this class II aminoacyl—tRNA ligase. The enzyme is specific for pyrrolysine as substrate as it cannot be replaced by lysine or any of the other natural amino acids [1].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, PDB
References:
1.  Blight, S.K., Larue, R.C., Mahapatra, A., Longstaff, D.G., Chang, E., Zhao, G., Kang, P.T., Green-Church, K.B., Chan, M.K. and Krzycki, J.A. Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431 (2004) 333–335. [PMID: 15329732]
2.  Polycarpo, C., Ambrogelly, A., Bérubé, A., Winbush, S.M., McCloskey, J.A., Crain, P.F., Wood, J.L. and Söll, D. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc. Natl. Acad. Sci. USA 101 (2004) 12450–12454. [PMID: 15314242]
3.  Schimmel, P. and Beebe, K. Molecular biology: genetic code seizes pyrrolysine. Nature 431 (2004) 257–258. [PMID: 15372017]
[EC 6.1.1.26 created 2007]
 
 
EC 6.3.2.29
Accepted name: cyanophycin synthase (L-aspartate-adding)
Reaction: ATP + [L-Asp(4-L-Arg)]n + L-Asp = ADP + phosphate + [L-Asp(4-L-Arg)]n-L-Asp
For diagram of cyanophycin biosynthesis, click here
Glossary: cyanophycin = [L-Asp(4-L-Arg)]n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]n = poly{N4-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}
Other name(s): CphA (ambiguous); CphA1 (ambiguous); CphA2 (ambiguous); cyanophycin synthetase (ambiguous); multi-L-arginyl-poly-L-aspartate synthase (ambiguous)
Systematic name: cyanophycin:L-aspartate ligase (ADP-forming)
Comments: Requires Mg2+ for activity. Both this enzyme and EC 6.3.2.30, cyanophycin synthase (L-arginine-adding), are required for the elongation of cyanophycin, which is a protein-like cell inclusion that is unique to cyanobacteria and acts as a temporary nitrogen store [2]. Both enzymes are found in the same protein but have different active sites [2,4]. Both L-Asp and L-Arg must be present before either enzyme will display significant activity [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 131554-17-1
References:
1.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308. Arch. Microbiol. 174 (2000) 297–306. [PMID: 11131019]
2.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Purification of Synechocystis sp. strain PCC6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. Appl. Environ. Microbiol. 67 (2001) 2176–2182. [PMID: 11319097]
3.  Allen, M.M., Hutchison, F. and Weathers, P.J. Cyanophycin granule polypeptide formation and degradation in the cyanobacterium Aphanocapsa 6308. J. Bacteriol. 141 (1980) 687–693. [PMID: 6767688]
4.  Berg, H., Ziegler, K., Piotukh, K., Baier, K., Lockau, W. and Volkmer-Engert, R. Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers. Eur. J. Biochem. 267 (2000) 5561–5570. [PMID: 10951215]
5.  Ziegler, K., Deutzmann, R. and Lockau, W. Cyanophycin synthetase-like enzymes of non-cyanobacterial eubacteria: characterization of the polymer produced by a recombinant synthetase of Desulfitobacterium hafniense. Z. Naturforsch. [C] 57 (2002) 522–529. [PMID: 12132696]
6.  Ziegler, K., Diener, A., Herpin, C., Richter, R., Deutzmann, R. and Lockau, W. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Eur. J. Biochem. 254 (1998) 154–159. [PMID: 9652408]
[EC 6.3.2.29 created 2007]
 
 
EC 6.3.2.30
Accepted name: cyanophycin synthase (L-arginine-adding)
Reaction: ATP + [L-Asp(4-L-Arg)]n-L-Asp + L-Arg = ADP + phosphate + [L-Asp(4-L-Arg)]n+1
For diagram of cyanophycin biosynthesis, click here
Glossary: cyanophycin = [L-Asp(4-L-Arg)]n = N-β-aspartylarginine = [L-4-(L-arginin-2-N-yl)aspartic acid]n = poly{N4-[(1S)-1-carboxy-4-guanidinobutyl]-L-asparagine}
Other name(s): CphA (ambiguous); CphA1 (ambiguous); CphA2 (ambiguous); cyanophycin synthetase (ambiguous); multi-L-arginyl-poly-L-aspartate synthase (ambiguous)
Systematic name: cyanophycin:L-arginine ligase (ADP-forming)
Comments: Requires Mg2+ for activity. Both this enzyme and EC 6.3.2.29, cyanophycin synthase (L-aspartate-adding), are required for the elongation of cyanophycin, which is a protein-like cell inclusion that is unique to cyanobacteria and acts as a temporary nitrogen store [2]. Both enzymes are found in the same protein but have different active sites [2,4]. Both L-Asp and L-Arg must be present before either enzyme will display significant activity [2]. Canavanine and lysine can be incoporated into the polymer instead of arginine [2].
Links to other databases: BRENDA, EXPASY, IUBMB, KEGG, CAS registry number: 131554-17-1
References:
1.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Molecular characterization of the cyanophycin synthetase from Synechocystis sp. strain PCC6308. Arch. Microbiol. 174 (2000) 297–306. [PMID: 11131019]
2.  Aboulmagd, E., Oppermann-Sanio, F.B. and Steinbüchel, A. Purification of Synechocystis sp. strain PCC6308 cyanophycin synthetase and its characterization with respect to substrate and primer specificity. Appl. Environ. Microbiol. 67 (2001) 2176–2182. [PMID: 11319097]
3.  Allen, M.M., Hutchison, F. and Weathers, P.J. Cyanophycin granule polypeptide formation and degradation in the cyanobacterium Aphanocapsa 6308. J. Bacteriol. 141 (1980) 687–693. [PMID: 6767688]
4.  Berg, H., Ziegler, K., Piotukh, K., Baier, K., Lockau, W. and Volkmer-Engert, R. Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers. Eur. J. Biochem. 267 (2000) 5561–5570. [PMID: 10951215]
5.  Ziegler, K., Deutzmann, R. and Lockau, W. Cyanophycin synthetase-like enzymes of non-cyanobacterial eubacteria: characterization of the polymer produced by a recombinant synthetase of Desulfitobacterium hafniense. Z. Naturforsch. [C] 57 (2002) 522–529. [PMID: 12132696]
6.  Ziegler, K., Diener, A., Herpin, C., Richter, R., Deutzmann, R. and Lockau, W. Molecular characterization of cyanophycin synthetase, the enzyme catalyzing the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin). Eur. J. Biochem. 254 (1998) 154–159. [PMID: 9652408]
[EC 6.3.2.30 created 2007]
 
 
EC 6.3.5.8
Transferred entry: aminodeoxychorismate synthase. Now EC 2.6.1.85, aminodeoxychorismate synthase. As ATP is not hydrolysed during the reaction, the classification of the enzyme as a ligase was incorrect
[EC 6.3.5.8 created 2003, deleted 2007]
 
 


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