The Enzyme Database

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EC 6.2.1.20     
Accepted name: long-chain-fatty-acid—[acyl-carrier-protein] ligase
Reaction: ATP + a long-chain fatty acid + an [acyl-carrier protein] = AMP + diphosphate + a long-chain acyl-[acyl-carrier protein]
Other name(s): acyl-[acyl-carrier-protein] synthetase (ambiguous); acyl-ACP synthetase (ambiguous); stearoyl-ACP synthetase; acyl-acyl carrier protein synthetase (ambiguous); long-chain-fatty-acid:[acyl-carrier-protein] ligase (AMP-forming)
Systematic name: long-chain-fatty-acid:[acyl-carrier protein] ligase (AMP-forming)
Comments: The enzyme ligates long chain fatty acids (with aliphatic chain of 13-22 carbons) to an acyl-carrier protein. Not identical with EC 6.2.1.3 long-chain-fatty-acid—CoA ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 77322-37-3
References:
1.  Ray, T.K. and Cronan, J.E., Jr. Activation of long chain fatty acids with acyl carrier protein: demonstration of a new enzyme, acyl-acyl carrier protein synthetase, in Escherichia coli. Proc. Natl. Acad. Sci. USA 73 (1976) 4374–4378. [DOI] [PMID: 794875]
2.  Kaczmarzyk, D. and Fulda, M. Fatty acid activation in cyanobacteria mediated by acyl-acyl carrier protein synthetase enables fatty acid recycling. Plant Physiol. 152 (2010) 1598–1610. [DOI] [PMID: 20061450]
[EC 6.2.1.20 created 1986]
 
 
EC 6.2.1.21      
Deleted entry:  phenylacetate—CoA ligase. Activity covered by EC 6.2.1.30, phenylacetate—CoA ligase
[EC 6.2.1.21 created 1986, deleted 2001]
 
 
EC 6.2.1.22     
Accepted name: [citrate (pro-3S)-lyase] ligase
Reaction: ATP + acetate + holo-[citrate (pro-3S)-lyase] = AMP + diphosphate + acetyl-[citrate (pro-3S)-lyase]
Glossary: citrate = 2-hydroxypropane-1,2,3-tricarboxylate
Other name(s): citrate lyase ligase; citrate lyase synthetase; acetate: SH-[acyl-carrier-protein] enzyme ligase (AMP); acetate:HS-citrate lyase ligase; acetate:citrate-(pro-3S)-lyase(thiol-form) ligase (AMP-forming); acetate:[citrate-(pro-3S)-lyase](thiol-form) ligase (AMP-forming)
Systematic name: acetate:holo-[citrate-(pro-3S)-lyase] ligase (AMP-forming)
Comments: Both this enzyme and EC 2.3.1.49,deacetyl-[citrate-(pro-3S)-lyase] S-acetyltransferase, acetylate and activate EC 4.1.3.6, citrate (pro-3S)-lyase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 52660-22-7
References:
1.  Antranikian, G. and Gottschalk, G. Copurification of citrate lyase and citrate lyase ligase from Rhodopseudomonas gelatinosa and subsequent separation of the two enzymes. Eur. J. Biochem. 126 (1982) 43–47. [DOI] [PMID: 7128585]
2.  Antranikian, G., Herzberg, C. and Gottschalk, G. Covalent modification of citrate lyase ligase from Clostridium sphenoides by phosphorylation/dephosphorylation. Eur. J. Biochem. 153 (1985) 413–420. [DOI] [PMID: 3935436]
3.  Quentmeier, A. and Antranikian, G. Characterization of citrate lyase from Clostridium sporosphaeroides. Arch. Microbiol. 141 (1985) 85–90. [PMID: 3994485]
4.  Schmellenkamp, H. and Eggerer, H. Mechanism of enzymic acetylation of des-acetyl citrate lyase. Proc. Natl. Acad. Sci. USA 71 (1974) 1987–1991. [DOI] [PMID: 4365579]
[EC 6.2.1.22 created 1989]
 
 
EC 6.2.1.23     
Accepted name: dicarboxylate—CoA ligase
Reaction: ATP + an α,ω-dicarboxylate + CoA = AMP + diphosphate + an ω-carboxyacyl-CoA
Other name(s): carboxylyl-CoA synthetase; dicarboxylyl-CoA synthetase
Systematic name: ω-dicarboxylate:CoA ligase (AMP-forming)
Comments: Acts on dicarboxylic acids of chain length C5 to C16; the best substrate is dodecanedioic acid.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 99332-77-1
References:
1.  Vamecq, J., de Hoffmann, E. and van Hoof, F. The microsomal dicarboxylyl-CoA synthetase. Biochem. J. 230 (1985) 683–693. [PMID: 4062873]
[EC 6.2.1.23 created 1989, modified 2011]
 
 
EC 6.2.1.24     
Accepted name: phytanate—CoA ligase
Reaction: ATP + phytanate + CoA = AMP + diphosphate + phytanoyl-CoA
Other name(s): phytanoyl-CoA ligase
Systematic name: phytanate:CoA ligase (AMP-forming)
Comments: Not identical with EC 6.2.1.20 long-chain-fatty-acid—[acyl-carrier-protein] ligase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 105238-50-4
References:
1.  Muralidharan, F.N. and Muralidharan, V.B. Phytanoyl-CoA ligase activity in rat liver. Biochem. Int. 13 (1986) 123–130. [PMID: 3753503]
[EC 6.2.1.24 created 1989]
 
 
EC 6.2.1.25     
Accepted name: benzoate—CoA ligase
Reaction: ATP + benzoate + CoA = AMP + diphosphate + benzoyl-CoA
For diagram of Benzoyl-CoA catabolism, click here
Other name(s): benzoate—coenzyme A ligase; benzoyl-coenzyme A synthetase; benzoyl CoA synthetase (AMP forming)
Systematic name: benzoate:CoA ligase (AMP-forming)
Comments: Also acts on 2-, 3- and 4-fluorobenzoate, but only very slowly on the corresponding chlorobenzoates.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 95329-17-2
References:
1.  Hutber, G.N. and Ribbons, D.W. Involvement of coenzyme-A esters in the metabolism of benzoate and cyclohexanecarboxylate by Rhodopseudomonas palustris. J. Gen. Microbiol. 129 (1983) 2413–2420.
2.  Schennen, U., Braun, K. and Knackmuss, H.-J. Anaerobic degradation of 2-fluorobenzoate by benzoate-degrading, denitrifying bacteria. J. Bacteriol. 161 (1985) 321–325. [PMID: 2857161]
[EC 6.2.1.25 created 1989]
 
 
EC 6.2.1.26     
Accepted name: o-succinylbenzoate—CoA ligase
Reaction: ATP + 2-succinylbenzoate + CoA = AMP + diphosphate + 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA
For diagram of vitamin K biosynthesis, click here
Glossary: 2-succinylbenzoate = o-succinylbenzoate = 4-(2-carboxyphenyl)-4-oxobutanoate
Other name(s): o-succinylbenzoyl-coenzyme A synthetase; o-succinylbenzoate:CoA ligase (AMP-forming)
Systematic name: 2-succinylbenzoate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72506-70-8
References:
1.  Heide, L., Arendt, S. and Leistner, E. Enzymatic-synthesis, characterization, and metabolism of the coenzyme-A ester of o-succinylbenzoic acid, an intermediate in menaquinone (vitamin K2) biosynthesis. J. Biol. Chem. 257 (1982) 7396–7400. [PMID: 7045104]
2.  Kolkmann, R. and Leistner, E. 4-(2′-Carboxyphenyl)-4-oxobutyryl coenzyme A ester, an intermediate in vitamin K2 (menaquinone) biosynthesis. Z. Naturforsch. C: Sci. 42 (1987) 1207–1214. [PMID: 2966501]
3.  Meganathan, R. and Bentley, R. Menaquinone (vitamin K2) biosynthesis: conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid by Mycobacterium phlei enzymes. J. Bacteriol. 140 (1979) 92–98. [PMID: 500558]
[EC 6.2.1.26 created 1992]
 
 
EC 6.2.1.27     
Accepted name: 4-hydroxybenzoate—CoA ligase
Reaction: ATP + 4-hydroxybenzoate + CoA = AMP + diphosphate + 4-hydroxybenzoyl-CoA
Other name(s): 4-hydroxybenzoate-CoA synthetase; 4-hydroxybenzoate—coenzyme A ligase (AMP-forming); 4-hydroxybenzoyl coenzyme A synthetase; 4-hydroxybenzoyl-CoA ligase
Systematic name: 4-hydroxybenzoate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 119699-80-8
References:
1.  Merkel, S.M., Eberhard, A.E., Gibson, J. and Harwood, C.S. Involvement of coenzyme A thioesters in anaerobic metabolism of 4-hydroxybenzoate by Rhodopseudomonas palustris. J. Bacteriol. 171 (1989) 1–7. [DOI] [PMID: 2914844]
[EC 6.2.1.27 created 1992]
 
 
EC 6.2.1.28     
Accepted name: 3α,7α-dihydroxy-5β-cholestanate—CoA ligase
Reaction: ATP + (25R)-3α,7α-dihydroxy-5β-cholestan-26-oate + CoA = AMP + diphosphate + (25R)-3α,7α-dihydroxy-5β-cholestanoyl-CoA
For diagram of cholic-acid biosynthesis (sidechain), click here
Other name(s): 3α,7α-dihydroxy-5β-cholestanoyl coenzyme A synthetase; DHCA-CoA ligase; 3α,7α-dihydroxy-5β-cholestanate:CoA ligase (AMP-forming)
Systematic name: (25R)-3α,7α-dihydroxy-5β-cholestan-26-oate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 118732-03-9
References:
1.  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]
[EC 6.2.1.28 created 1992]
 
 
EC 6.2.1.29      
Deleted entry:  3α,7α,12α-trihydroxy-5β-cholestanate—CoA ligase. The enzyme is identical to EC 6.2.1.7, cholate—CoA ligase
[EC 6.2.1.29 created 1992, deleted 2005]
 
 
EC 6.2.1.30     
Accepted name: phenylacetate—CoA ligase
Reaction: ATP + phenylacetate + CoA = AMP + diphosphate + phenylacetyl-CoA
For diagram of aerobic phenylacetate catabolism, click here
Other name(s): phenacyl coenzyme A synthetase; phenylacetyl-CoA ligase; PA-CoA ligase; phenylacetyl-CoA ligase (AMP-forming)
Systematic name: phenylacetate:CoA ligase (AMP-forming)
Comments: Also acts, more slowly, on acetate, propanoate and butanoate, but not on hydroxy derivatives of phenylacetate and related compounds.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 57219-71-3
References:
1.  Martinez-Blanco, H., Reglero, A., Rodriguez-Asparicio, L.B. and Luengo, J.M. Purification and biochemical characterization of phenylacetyl-CoA ligase from Pseudomonas putida. A specific enzyme for the catabolism of phenylacetic acid. J. Biol. Chem. 265 (1990) 7084–7090. [PMID: 2324116]
[EC 6.2.1.30 created 1992 (EC 6.2.1.21 created 1986, incorporated 2001)]
 
 
EC 6.2.1.31     
Accepted name: 2-furoate—CoA ligase
Reaction: ATP + 2-furoate + CoA = AMP + diphosphate + 2-furoyl-CoA
For diagram of reaction, click here
Other name(s): 2-furoyl coenzyme A synthetase
Systematic name: 2-furoate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number: 122320-08-5
References:
1.  Koenig, K. and Andreesen, J.R. Molybdenum involvement in aerobic degradation of 2-furoic acid by Pseudomonas putida FU1. Appl. Environ. Microbiol. 55 (1989) 1829–1834. [PMID: 16347977]
[EC 6.2.1.31 created 1992]
 
 
EC 6.2.1.32     
Accepted name: anthranilate—CoA ligase
Reaction: ATP + anthranilate + CoA = AMP + diphosphate + anthraniloyl-CoA
For diagram of acridone alkaloid biosynthesis, click here
Glossary: anthraniloyl-CoA = 2-aminobenzoyl-CoA
Other name(s): anthraniloyl coenzyme A synthetase; 2-aminobenzoate—CoA ligase; 2-aminobenzoate—coenzyme A ligase; 2-aminobenzoate coenzyme A ligase
Systematic name: anthranilate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 112692-58-7
References:
1.  Altenschmidt, U., Eckerskorn, C. and Fuchs, G. Evidence that enzymes of a novel aerobic 2-amino-benzoate metabolism in denitrifying Pseudomonas are coded on a small plasmid. Eur. J. Biochem. 194 (1990) 647–653. [DOI] [PMID: 2176602]
[EC 6.2.1.32 created 1992]
 
 
EC 6.2.1.33     
Accepted name: 4-chlorobenzoate—CoA ligase
Reaction: 4-chlorobenzoate + CoA + ATP = 4-chlorobenzoyl-CoA + AMP + diphosphate
Systematic name: 4-chlorobenzoate:CoA ligase
Comments: Requires Mg2+. This enzyme is part of the bacterial 2,4-dichlorobenzoate degradation pathway.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 141583-20-2
References:
1.  Dunaway-Mariano, D., Babbitt, P.C. On the origins and functions of the enzymes of the 4-chlorobenzoate to 4-hydroxybenzoate converting pathway. Biodegradation 5 (1994) 259–276. [PMID: 7765837]
2.  Loffler, F., Muller, R., Lingens, F. Purification and properties of 4-halobenzoate-coenzyme A ligase from Pseudomonas sp. CBS3. Biol. Chem. Hoppe-Seyler 373 (1992) 1001–1007. [PMID: 1418673]
3.  Chang, K.H., Liang, P.H., Beck, W., Scholten, J.D., Dunaway-Mariano, D. Isolation and characterization of the three polypeptide components of 4-chlorobenzoate dehalogenase from Pseudomonas sp. strain CBS-3. Biochemistry 31 (1992) 5605–5610. [PMID: 1610806]
[EC 6.2.1.33 created 1999]
 
 
EC 6.2.1.34     
Accepted name: trans-feruloyl-CoA synthase
Reaction: ferulic acid + CoA + ATP = feruloyl-CoA + products of ATP breakdown
For diagram of reaction, click here
Other name(s): trans-feruloyl-CoA synthetase; trans-ferulate:CoASH ligase (ATP-hydrolysing); ferulate:CoASH ligase (ATP-hydrolysing)
Systematic name: ferulate:CoA ligase (ATP-hydrolysing)
Comments: Requires Mg2+. It has not yet been established whether AMP + diphosphate or ADP + phosphate are formed in this reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397–1405. [DOI] [PMID: 9611814]
2.  Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582–1585. [PMID: 6870241]
[EC 6.2.1.34 created 2000]
 
 
EC 6.2.1.35     
Accepted name: acetate—[acyl-carrier protein] ligase
Reaction: ATP + acetate + an [acyl-carrier protein] = AMP + diphosphate + an acetyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): HS-acyl-carrier protein:acetate ligase; [acyl-carrier protein]:acetate ligase; MadH; ACP-SH:acetate ligase
Systematic name: acetate:[acyl-carrier-protein] ligase (AMP-forming)
Comments: This enzyme, from the anaerobic bacterium Malonomonas rubra, is a component of the multienzyme complex EC 7.2.4.4, biotin-dependent malonate decarboxylase. The enzyme uses the energy from hydrolysis of ATP to convert the thiol group of the acyl-carrier-protein-bound 2′-(5-phosphoribosyl)-3′-dephospho-CoA cofactor into its acetyl thioester [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hilbi, H., Dehning, I., Schink, B. and Dimroth, P. Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme. Eur. J. Biochem. 207 (1992) 117–123. [DOI] [PMID: 1628643]
2.  Berg, M., Hilbi, H. and Dimroth, P. The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2′-(5"-phosphoribosyl)-3′-dephosphocoenzyme A as a prosthetic group. Biochemistry 35 (1996) 4689–4696. [DOI] [PMID: 8664258]
3.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [DOI] [PMID: 9128730]
4.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 6.2.1.35 created 2008, modified 2018]
 
 
EC 6.2.1.36     
Accepted name: 3-hydroxypropionyl-CoA synthase
Reaction: 3-hydroxypropanoate + ATP + CoA = 3-hydroxypropanoyl-CoA + AMP + diphosphate
For diagram of the 3-hydroxypropanoate cycle, click here and for diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Glossary: 3-hydroxypropionyl-CoA = 3-hydroxypropanoyl-CoA
Other name(s): 3-hydroxypropionyl-CoA synthetase (AMP-forming); 3-hydroxypropionate—CoA ligase
Systematic name: hydroxypropanoate:CoA ligase (AMP-forming)
Comments: Catalyses a step in the 3-hydroxypropanoate/4-hydroxybutanoate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [1,2].The enzymes from Metallosphaera sedula and Sulfolobus tokodaii can also use propionate, acrylate, acetate, and butanoate as substrates [2], and are thus different from EC 6.2.1.17 (propionate—CoA ligase), which does not accept acetate or butanoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782–1786. [DOI] [PMID: 18079405]
2.  Alber, B.E., Kung, J.W. and Fuchs, G. 3-Hydroxypropionyl-coenzyme A synthetase from Metallosphaera sedula, an enzyme involved in autotrophic CO2 fixation. J. Bacteriol. 190 (2008) 1383–1389. [DOI] [PMID: 18165310]
[EC 6.2.1.36 created 2009]
 
 
EC 6.2.1.37     
Accepted name: 3-hydroxybenzoate—CoA ligase
Reaction: ATP + 3-hydroxybenzoate + CoA = AMP + diphosphate + 3-hydroxybenzoyl-CoA
Other name(s): 3-hydroxybenzoyl-CoA synthetase; 3-hydroxybenzoate—coenzyme A ligase (AMP-forming); 3-hydroxybenzoyl coenzyme A synthetase; 3-hydroxybenzoyl-CoA ligase
Systematic name: 3-hydroxybenzoate:CoA ligase (AMP-forming)
Comments: The enzyme works equally well with 4-hydroxybenzoate but shows low activity towards benzoate, 4-aminobenzoate, 3-aminobenzoate, 3-fluorobenzoate, 4-fluorobenzoate, 3-chlorobenzoate, and 4-chlorobenzoate. There is no activity with 3,4-dihydroxybenzoate, 2,3-dihydroxybenzoate, and 2-hydroxybenzoate as substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Laempe, D., Jahn, M., Breese, K., Schägger, H. and Fuchs, G. Anaerobic metabolism of 3-hydroxybenzoate by the denitrifying bacterium Thauera aromatica. J. Bacteriol. 183 (2001) 968–979. [DOI] [PMID: 11208796]
[EC 6.2.1.37 created 2011]
 
 
EC 6.2.1.38     
Accepted name: (2,2,3-trimethyl-5-oxocyclopent-3-enyl)acetyl-CoA synthase
Reaction: [(1R)-2,2,3-trimethyl-5-oxocyclopent-3-enyl]acetate + ATP + CoA = AMP + diphosphate + [(1R)-2,2,3-trimethyl-5-oxocyclopent-3-enyl]acetyl-CoA
For diagram of camphor catabolism, click here
Other name(s): 2-oxo-Δ3-4,5,5-trimethylcyclopentenylacetyl-CoA synthetase
Systematic name: [(1R)-2,2,3-trimethyl-5-oxocyclopent-3-enyl]acetate:CoA ligase (AMP-forming)
Comments: Isolated from Pseudomonas putida. Forms part of the pathway of camphor catabolism.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc
References:
1.  Ougham, H.J., Taylor, D.G. and Trudgill, P.W. Camphor revisited: involvement of a unique monooxygenase in metabolism of 2-oxo-Δ3-4,5,5-trimethylcyclopentenylacetic acid by Pseudomonas putida. J. Bacteriol. 153 (1983) 140–152. [PMID: 6848481]
[EC 6.2.1.38 created 2012]
 
 
EC 6.2.1.39     
Accepted name: [butirosin acyl-carrier protein]—L-glutamate ligase
Reaction: (1) ATP + L-glutamate + BtrI acyl-carrier protein = ADP + phosphate + L-glutamyl-[BtrI acyl-carrier protein]
(2) ATP + L-glutamate + 4-amino butanoyl-[BtrI acyl-carrier protein] = ADP + phosphate + 4-(γ-L-glutamylamino)butanoyl-[BtrI acyl-carrier protein]
Other name(s): [BtrI acyl-carrier protein]—L-glutamate ligase; BtrJ
Systematic name: [BtrI acyl-carrier protein]:L-glutamate ligase (ADP-forming)
Comments: Catalyses two steps in the biosynthesis of the side chain of the aminoglycoside antibiotics of the butirosin family. The enzyme adds one molecule of L-glutamate to a dedicated acyl-carrier protein, and following decarboxylation of the product by EC 4.1.1.95, L-glutamyl-[BtrI acyl-carrier protein] decarboxylase, adds a second L-glutamate molecule. Requires Mg2+ or Mn2+, and activity is enhanced in the presence of Mn2+.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Li, Y., Llewellyn, N.M., Giri, R., Huang, F. and Spencer, J.B. Biosynthesis of the unique amino acid side chain of butirosin: possible protective-group chemistry in an acyl carrier protein-mediated pathway. Chem. Biol. 12 (2005) 665–675. [DOI] [PMID: 15975512]
[EC 6.2.1.39 created 2012]
 
 
EC 6.2.1.40     
Accepted name: 4-hydroxybutyrate—CoA ligase (AMP-forming)
Reaction: ATP + 4-hydroxybutanoate + CoA = AMP + diphosphate + 4-hydroxybutanoyl-CoA
For diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Other name(s): 4-hydroxybutyrate-CoA synthetase (ambiguous); 4-hydroxybutyrate:CoA ligase (ambiguous); hbs (gene name); 4-hydroxybutyrate—CoA ligase
Systematic name: 4-hydroxybutanoate:CoA ligase (AMP-forming)
Comments: Isolated from the archaeon Metallosphaera sedula. Involved in the 3-hydroxypropanoate/4-hydroxybutanoate cycle. cf. EC 6.2.1.56, 4-hydroxybutyrate—CoA ligase (ADP-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ramos-Vera, W.H., Weiss, M., Strittmatter, E., Kockelkorn, D. and Fuchs, G. Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota. J. Bacteriol. 193 (2011) 1201–1211. [DOI] [PMID: 21169482]
2.  Hawkins, A.S., Han, Y., Bennett, R.K., Adams, M.W. and Kelly, R.M. Role of 4-hydroxybutyrate-CoA synthetase in the CO2 fixation cycle in thermoacidophilic archaea. J. Biol. Chem. 288 (2013) 4012–4022. [DOI] [PMID: 23258541]
[EC 6.2.1.40 created 2014, modified 2019]
 
 
EC 6.2.1.41     
Accepted name: 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate—CoA ligase
Reaction: ATP + 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + CoA = AMP + diphosphate + 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoyl-CoA
For diagram of cholesterol catabolism, click here
Glossary: 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate = HIP
Other name(s): fadD3 (gene name); HIP—CoA ligase
Systematic name: 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from actinobacterium Mycobacterium tuberculosis, catalyses a step in the degradation of cholesterol and cholate. The enzyme is very specific for its substrate, and requires that the side chain at C17 is completely removed.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc
References:
1.  Horinouchi, M., Hayashi, T., Koshino, H. and Kudo, T. ORF18-disrupted mutant of Comamonas testosteroni TA441 accumulates significant amounts of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid and its derivatives after incubation with steroids. J. Steroid Biochem. Mol. Biol. 101 (2006) 78–84. [DOI] [PMID: 16891113]
2.  Casabon, I., Crowe, A.M., Liu, J. and Eltis, L.D. FadD3 is an acyl-CoA synthetase that initiates catabolism of cholesterol rings C and D in actinobacteria. Mol. Microbiol. 87 (2013) 269–283. [DOI] [PMID: 23146019]
[EC 6.2.1.41 created 2014]
 
 
EC 6.2.1.42     
Accepted name: 3-oxocholest-4-en-26-oate—CoA ligase
Reaction: ATP + (25S)-3-oxocholest-4-en-26-oate + CoA = AMP + diphosphate + (25S)-3-oxocholest-4-en-26-oyl-CoA
For diagram of cholic acid biosynthesis (sidechain), click here
Other name(s): fadD19 (gene name)
Systematic name: (25S)-3-oxocholest-4-en-26-oate:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from actinobacterium Mycobacterium tuberculosis, catalyses a step in the degradation of cholesterol. It is responsible for the activation of the C8 side chain. 3β-hydroxycholest-5-en-26-oate can also be used as substrate.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc
References:
1.  Wilbrink, M.H., Petrusma, M., Dijkhuizen, L. and van der Geize, R. FadD19 of Rhodococcus rhodochrous DSM43269, a steroid-coenzyme A ligase essential for degradation of C-24 branched sterol side chains. Appl. Environ. Microbiol. 77 (2011) 4455–4464. [DOI] [PMID: 21602385]
2.  Casabon, I., Swain, K., Crowe, A.M., Eltis, L.D. and Mohn, W.W. Actinobacterial acyl coenzyme a synthetases involved in steroid side-chain catabolism. J. Bacteriol. 196 (2014) 579–587. [DOI] [PMID: 24244004]
[EC 6.2.1.42 created 2014]
 
 
EC 6.2.1.43     
Accepted name: 2-hydroxy-7-methoxy-5-methyl-1-naphthoate—CoA ligase
Reaction: ATP + 2-hydroxy-7-methoxy-5-methyl-1-naphthoate + CoA = AMP + diphosphate + 2-hydroxy-7-methoxy-5-methyl-1-naphthoyl-CoA
For diagram of neocarzinostatin biosynthesis, click here
Other name(s): NcsB2
Systematic name: 2-hydroxy-7-methoxy-5-methyl-1-naphthoate:CoA ligase
Comments: The enzyme from the bacterium Streptomyces carzinostaticus is involved in the attachment of the 2-hydroxy-7-methoxy-5-methyl-1-naphthoate moiety of the antibiotic neocarzinostatin. In vitro the enzyme also catalyses the activation of other 1-naphthoic acid analogues, e.g. 2-hydroxy-5-methyl-1-naphthoate or 2,7-dihydroxy-5-methyl-1-naphthoate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cooke, H.A., Zhang, J., Griffin, M.A., Nonaka, K., Van Lanen, S.G., Shen, B. and Bruner, S.D. Characterization of NcsB2 as a promiscuous naphthoic acid/coenzyme A ligase integral to the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin. J. Am. Chem. Soc. 129 (2007) 7728–7729. [DOI] [PMID: 17539640]
[EC 6.2.1.43 created 2014]
 
 
EC 6.2.1.44     
Accepted name: 3-(methylthio)propionyl—CoA ligase
Reaction: ATP + 3-(methylsulfanyl)propanoate + CoA = AMP + diphosphate + 3-(methylsulfanyl)propanoyl-CoA
For diagram of 3-(dimethylsulfonio)propanoate metabolism, click here
Other name(s): DmdB; MMPA-CoA ligase; methylmercaptopropionate-coenzyme A ligase; 3-methylmercaptopropionyl-CoA ligase; 3-(methylthio)propanoate:CoA ligase (AMP-forming)
Systematic name: 3-(methylsulfanyl)propanoate:CoA ligase (AMP-forming)
Comments: The enzyme is part of a dimethylsulfoniopropanoate demethylation pathway in the marine bacteria Ruegeria pomeroyi and Pelagibacter ubique. It also occurs in some nonmarine bacteria capable of metabolizing dimethylsulfoniopropionate (e.g. Burkholderia thailandensis, Pseudomonas aeruginosa, and Silicibacter lacuscaerulensis). It requires Mg2+ [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Reisch, C.R., Stoudemayer, M.J., Varaljay, V.A., Amster, I.J., Moran, M.A. and Whitman, W.B. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473 (2011) 208–211. [DOI] [PMID: 21562561]
2.  Bullock, H.A., Reisch, C.R., Burns, A.S., Moran, M.A. and Whitman, W.B. Regulatory and functional diversity of methylmercaptopropionate coenzyme A ligases from the dimethylsulfoniopropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria. J. Bacteriol. 196 (2014) 1275–1285. [DOI] [PMID: 24443527]
[EC 6.2.1.44 created 2014]
 
 
EC 6.2.1.45     
Accepted name: E1 ubiquitin-activating enzyme
Reaction: ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
Other name(s): ubiquitin activating enzyme; E1; ubiquitin-activating enzyme E1
Systematic name: ubiquitin:[E1 ubiquitin-activating enzyme] ligase (AMP-forming)
Comments: Catalyses the ATP-dependent activation of ubiquitin through the formation of a thioester bond between the C-terminal glycine of ubiquitin and the sulfhydryl side group of a cysteine residue in the E1 protein. The two-step reaction consists of the ATP-dependent formation of an E1-ubiquitin adenylate intermediate in which the C-terminal glycine of ubiquitin is bound to AMP via an acyl-phosphate linkage, then followed by the conversion to an E1-ubiquitin thioester bond via the cysteine residue on E1 in the second step.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Haas, A.L., Warms, J.V., Hershko, A. and Rose, I.A. Ubiquitin-activating enzyme. Mechanism and role in protein-ubiquitin conjugation. J. Biol. Chem. 257 (1982) 2543–2548. [PMID: 6277905]
2.  Huzil, J.T., Pannu, R., Ptak, C., Garen, G. and Ellison, M.J. Direct catalysis of lysine 48-linked polyubiquitin chains by the ubiquitin-activating enzyme. J. Biol. Chem. 282 (2007) 37454–37460. [DOI] [PMID: 17951259]
3.  Zheng, M., Liu, J., Yang, Z., Gu, X., Li, F., Lou, T., Ji, C. and Mao, Y. Expression, purification and characterization of human ubiquitin-activating enzyme, UBE1. Mol. Biol. Rep. 37 (2010) 1413–1419. [DOI] [PMID: 19343538]
4.  Carvalho, A.F., Pinto, M.P., Grou, C.P., Vitorino, R., Domingues, P., Yamao, F., Sa-Miranda, C. and Azevedo, J.E. High-yield expression in Escherichia coli and purification of mouse ubiquitin-activating enzyme E1. Mol Biotechnol 51 (2012) 254–261. [DOI] [PMID: 22012022]
[EC 6.2.1.45 created 2015]
 
 
EC 6.2.1.46     
Accepted name: L-allo-isoleucine—holo-[CmaA peptidyl-carrier protein] ligase
Reaction: ATP + L-allo-isoleucine + holo-[CmaA peptidyl-carrier protein] = AMP + diphosphate + L-allo-isoleucyl-[CmaA peptidyl-carrier protein]
Other name(s): CmaA
Systematic name: L-allo-isoleucine:holo-[CmaA peptidyl-carrier protein] ligase (AMP-forming)
Comments: This two-domain protein from the bacterium Pseudomonas syringae contains an adenylation domain (A domain) and a thiolation domain (T domain). It catalyses the adenylation of L-allo-isoleucine and its attachment to the T domain. The enzyme is involved in the biosynthesis of the toxin coronatine, which mimics the plant hormone jasmonic acid isoleucine. Coronatine promotes opening of the plant stomata allowing bacterial invasion, which is followed by bacterial growth in the apoplast, systemic susceptibility, and disease.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Couch, R., O'Connor, S.E., Seidle, H., Walsh, C.T. and Parry, R. Characterization of CmaA, an adenylation-thiolation didomain enzyme involved in the biosynthesis of coronatine. J. Bacteriol. 186 (2004) 35–42. [DOI] [PMID: 14679222]
[EC 6.2.1.46 created 2015]
 
 
EC 6.2.1.47     
Accepted name: medium-chain-fatty-acid—[acyl-carrier-protein] ligase
Reaction: ATP + a medium-chain fatty acid + a holo-[acyl-carrier protein] = AMP + diphosphate + a medium-chain acyl-[acyl-carrier protein]
Other name(s): jamA (gene name)
Systematic name: medium-chain-fatty-acid:[acyl-carrier protein] ligase (AMP-forming)
Comments: The enzyme ligates medium chain fatty acids (with aliphatic chain of 6-12 carbons) to an acyl-carrier protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 77322-37-3
References:
1.  Edwards, D.J., Marquez, B.L., Nogle, L.M., McPhail, K., Goeger, D.E., Roberts, M.A. and Gerwick, W.H. Structure and biosynthesis of the jamaicamides, new mixed polyketide-peptide neurotoxins from the marine cyanobacterium Lyngbya majuscula. Chem. Biol. 11 (2004) 817–833. [DOI] [PMID: 15217615]
2.  Zhu, X., Liu, J. and Zhang, W. De novo biosynthesis of terminal alkyne-labeled natural products. Nat. Chem. Biol. 11 (2015) 115–120. [DOI] [PMID: 25531891]
[EC 6.2.1.47 created 2016]
 
 
EC 6.2.1.48     
Accepted name: carnitine—CoA ligase
Reaction: ATP + L-carnitine + CoA = AMP + diphosphate + L-carnitinyl-CoA
Glossary: carnitine = 3-hydroxy-4-(trimethylammonio)butanoate
crotonobetaine = (E)-4-(trimethylammonio)but-2-enoate
γ-butyrobetaine = 4-(trimethylammonio)butanoate
Other name(s): caiC (gene name)
Systematic name: L-carnitine:CoA ligase (AMP-forming)
Comments: The enzyme, originally characterized from the bacterium Escherichia coli, can catalyse the transfer of CoA to L-carnitine, crotonobetaine and γ-butyrobetaine. In vitro the enzyme also exhibits the activity of EC 2.8.3.21, L-carnitine CoA-transferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Eichler, K., Bourgis, F., Buchet, A., Kleber, H.P. and Mandrand-Berthelot, M.A. Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coli. Mol. Microbiol. 13 (1994) 775–786. [DOI] [PMID: 7815937]
2.  Bernal, V., Arense, P., Blatz, V., Mandrand-Berthelot, M.A., Canovas, M. and Iborra, J.L. Role of betaine:CoA ligase (CaiC) in the activation of betaines and the transfer of coenzyme A in Escherichia coli. J. Appl. Microbiol. 105 (2008) 42–50. [DOI] [PMID: 18266698]
[EC 6.2.1.48 created 2017]
 
 
EC 6.2.1.49     
Accepted name: long-chain fatty acid adenylyltransferase FadD28
Reaction: ATP + a long-chain fatty acid + holo-[mycocerosate synthase] = AMP + diphosphate + a long-chain acyl-[mycocerosate synthase] (overall reaction)
(1a) ATP + a long-chain fatty acid = diphosphate + a long-chain acyl-adenylate ester
(1b) a long-chain acyl-adenylate ester + holo-[mycocerosate synthase] = AMP + a long-chain acyl-[mycocerosate synthase]
Other name(s): fadD28 (gene name)
Systematic name: long-chain fatty acid:holo-[mycocerosate synthase] ligase (AMP-forming)
Comments: The enzyme, found in certain mycobacteria, activates long-chain fatty acids by adenylation and transfers them to EC 2.3.1.111, mycocerosate synthase. The enzyme participates in the biosynthesis of the virulent lipids dimycocerosates (DIM) and dimycocerosyl triglycosyl phenolphthiocerol (PGL).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Fitzmaurice, A.M. and Kolattukudy, P.E. Open reading frame 3, which is adjacent to the mycocerosic acid synthase gene, is expressed as an acyl coenzyme A synthase in Mycobacterium bovis BCG. J. Bacteriol. 179 (1997) 2608–2615. [DOI] [PMID: 9098059]
2.  Goyal, A., Yousuf, M., Rajakumara, E., Arora, P., Gokhale, R.S. and Sankaranarayanan, R. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of FadD28, a fatty-acyl AMP ligase from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (2006) 350–352. [DOI] [PMID: 16582482]
3.  Arora, P., Goyal, A., Natarajan, V.T., Rajakumara, E., Verma, P., Gupta, R., Yousuf, M., Trivedi, O.A., Mohanty, D., Tyagi, A., Sankaranarayanan, R. and Gokhale, R.S. Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat. Chem. Biol. 5 (2009) 166–173. [DOI] [PMID: 19182784]
4.  Menendez-Bravo, S., Comba, S., Sabatini, M., Arabolaza, A. and Gramajo, H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab. Eng. 24 (2014) 97–106. [DOI] [PMID: 24831705]
5.  Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040–1050. [DOI] [PMID: 25561717]
[EC 6.2.1.49 created 2016 as EC 2.7.7.95, transferred 2017 to EC 6.2.1.49]
 
 
EC 6.2.1.50     
Accepted name: 4-hydroxybenzoate adenylyltransferase FadD22
Reaction: ATP + 4-hydroxybenzoate + holo-[4-hydroxyphenylalkanoate synthase] = AMP + diphosphate + 4-hydroxybenzoyl-[4-hydroxyphenylalkanoate synthase] (overall reaction)
(1a) ATP + 4-hydroxybenzoate = 4-hydroxybenzoyl-adenylate + diphosphate
(1b) 4-hydroxybenzoyl-adenylate + holo-[4-hydroxyphenylalkanoate synthase] = AMP + 4-hydroxybenzoyl-[4-hydroxyphenylalkanoate synthase]
Other name(s): fadD22 (gene name); 4-hydroxybenzoate adenylase
Systematic name: 4-hydroxybenzoate:holo-[4-hydroxyphenylalkanoate synthase] ligase (AMP-forming)
Comments: This mycobacterial enzyme participates in the biosynthesis of phenolphthiocerols. Following the substrate’s activation by adenylation, it is transferred to an acyl-carrier protein domain within the enzyme, from which it is transferred to EC 2.3.1.261, 4-hydroxyphenylalkanoate synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715–2725. [DOI] [PMID: 20553505]
2.  Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040–1050. [DOI] [PMID: 25561717]
[EC 6.2.1.50 created 2017 as EC 2.7.7.98, transferred 2017 to EC 6.2.1.50]
 
 
EC 6.2.1.51     
Accepted name: 4-hydroxyphenylalkanoate adenylyltransferase FadD29
Reaction: (1) ATP + 17-(4-hydroxyphenyl)heptadecanoate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + diphosphate + 17-(4-hydroxyphenyl)heptadecanoyl-[(phenol)carboxyphthiodiolenone synthase]
(1a) ATP + 17-(4-hydroxyphenyl)heptadecanoate = diphosphate + 17-(4-hydroxyphenyl)heptadecanoyl-adenylate
(1b) 17-(4-hydroxyphenyl)heptadecanoyl-adenylate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + 17-(4-hydroxyphenyl)heptadecanoyl-[(phenol)carboxyphthiodiolenone synthase]
(2) ATP + 19-(4-hydroxyphenyl)nonadecanoate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + diphosphate + 19-(4-hydroxyphenyl)nonadecanoyl-[(phenol)carboxyphthiodiolenone synthase]
(2a) ATP + 19-(4-hydroxyphenyl)nonadecanoate = diphosphate + 19-(4-hydroxyphenyl)nonadecanoyl-adenylate
(2b) 19-(4-hydroxyphenyl)nonadecanoyl-adenylate + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + 19-(4-hydroxyphenyl)nonadecanoyl-[(phenol)carboxyphthiodiolenone synthase]
Other name(s): fadD29 (gene name); 4-hydroxyphenylalkanoate adenylase
Systematic name: 4-hydroxyphenylalkanoate:holo-[(phenol)carboxyphthiodiolenone synthase] ligase
Comments: The mycobacterial enzyme participates in the biosynthesis of phenolphthiocerols. Following the substrate’s activation by adenylation, it is transferred to an acyl-carrier protein domain within the enzyme, from which it is transferred to the phenolphthiocerol/phthiocerol polyketide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715–2725. [DOI] [PMID: 20553505]
2.  Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040–1050. [DOI] [PMID: 25561717]
[EC 6.2.1.51 created 2016 as EC 2.7.7.94, transferred 2017 to EC 6.2.1.51]
 
 
EC 6.2.1.52     
Accepted name: L-firefly luciferin—CoA ligase
Reaction: ATP + L-firefly luciferin + CoA = AMP + diphosphate + L-firefly luciferyl-CoA
Glossary: L-firefly luciferin = (R)-4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazole-4-carboxylate
Other name(s): LUC
Systematic name: (R)-4,5-dihydro-2-(6-hydroxy-1,3-benzothiazol-2-yl)thiazole-4-carboxylate:CoA ligase (AMP-forming)
Comments: This is an alternative activity of the firefly luciferase (EC 1.13.12.7), which the enzyme exhibits under normal conditions only when acting on the L-enantiomer of its substrate. The D-isomer can act as a substrate for the CoA—ligase activity in vitro only under low oxygen conditions that are not found in vivo. The activation of L-firefly luciferin to a CoA ester is a step in a recycling pathway that results in its epimerization to the D enantiomer, which is the only substrate whose oxygenation results in light emission.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fraga, H., Esteves da Silva, J.C. and Fontes, R. Identification of luciferyl adenylate and luciferyl coenzyme a synthesized by firefly luciferase. ChemBioChem 5 (2004) 110–115. [DOI] [PMID: 14695520]
2.  Nakamura, M., Maki, S., Amano, Y., Ohkita, Y., Niwa, K., Hirano, T., Ohmiya, Y. and Niwa, H. Firefly luciferase exhibits bimodal action depending on the luciferin chirality. Biochem. Biophys. Res. Commun. 331 (2005) 471–475. [DOI] [PMID: 15850783]
3.  Viviani, V.R., Scorsato, V., Prado, R.A., Pereira, J.G., Niwa, K., Ohmiya, Y. and Barbosa, J.A. The origin of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase): luciferin stereoselectivity as a switch for the oxygenase activity. Photochem Photobiol Sci 9 (2010) 1111–1119. [DOI] [PMID: 20526507]
4.  Maeda, J., Kato, D.I., Okuda, M., Takeo, M., Negoro, S., Arima, K., Ito, Y. and Niwa, K. Biosynthesis-inspired deracemizative production of D-luciferin by combining luciferase and thioesterase. Biochim. Biophys. Acta 1861 (2017) 2112–2118. [DOI] [PMID: 28454735]
[EC 6.2.1.52 created 2017]
 
 
EC 6.2.1.53     
Accepted name: L-proline—[L-prolyl-carrier protein] ligase
Reaction: ATP + L-proline + holo-[L-prolyl-carrier protein] = AMP + diphosphate + L-prolyl-[L-prolyl-carrier protein] (overall reaction)
(1a) ATP + L-proline = diphosphate + (L-prolyl)adenylate
(1b) (L-prolyl)adenylate + holo-[L-prolyl-carrier protein] = AMP + L-prolyl-[L-prolyl-carrier protein]
Other name(s): pltF (gene name); bmp4 (gene name); pigI (gene name)
Systematic name: L-proline:[L-prolyl-carrier protein] ligase (AMP-forming)
Comments: The enzyme participates in the biosynthesis of several pyrrole-containing compounds, such as undecylprodigiosin, prodigiosin, pyoluteorin, and coumermycin A1. It catalyses the activation of L-proline to an adenylate form, followed by its transfer to the 4′-phosphopantheine moiety of an L-prolyl-carrier protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Thomas, M.G., Burkart, M.D. and Walsh, C.T. Conversion of L-proline to pyrrolyl-2-carboxyl-S-PCP during undecylprodigiosin and pyoluteorin biosynthesis. Chem. Biol. 9 (2002) 171–184. [DOI] [PMID: 11880032]
2.  Harris, A.K., Williamson, N.R., Slater, H., Cox, A., Abbasi, S., Foulds, I., Simonsen, H.T., Leeper, F.J. and Salmond, G.P. The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation. Microbiology 150 (2004) 3547–3560. [DOI] [PMID: 15528645]
3.  Williamson, N.R., Simonsen, H.T., Ahmed, R.A., Goldet, G., Slater, H., Woodley, L., Leeper, F.J. and Salmond, G.P. Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Mol. Microbiol. 56 (2005) 971–989. [DOI] [PMID: 15853884]
[EC 6.2.1.53 created 2018]
 
 
EC 6.2.1.54     
Accepted name: D-alanine—[D-alanyl-carrier protein] ligase
Reaction: ATP + D-alanine + holo-[D-alanyl-carrier protein] = AMP + diphosphate + D-alanyl-[D-alanyl-carrier protein] (overall reaction)
(1a) ATP + D-alanine = (D-alanyl)adenylate + diphosphate
(1b) (D-alanyl)adenylate + holo-[D-alanyl-carrier protein] = AMP + D-alanyl-[D-alanyl-carrier protein]
Other name(s): dltA (gene name); Dcl
Systematic name: D-alanine:[D-alanyl-carrier protein] ligase
Comments: The enzyme is involved in the modification of wall teichoic acids, as well as type I and IV lipoteichoic acids, with D-alanine residues. It activates D-alanine using ATP to form a high-energy (D-alanyl)adenylate intermediate and subsequently transfers the alanyl moiety to the covalently-bound phosphopantheinyl cofactor of a D-alanyl-carrier protein (DltC).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Perego, M., Glaser, P., Minutello, A., Strauch, M.A., Leopold, K. and Fischer, W. Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. Identification of genes and regulation. J. Biol. Chem. 270 (1995) 15598–15606. [DOI] [PMID: 7797557]
2.  Yonus, H., Neumann, P., Zimmermann, S., May, J.J., Marahiel, M.A. and Stubbs, M.T. Crystal structure of DltA. Implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains. J. Biol. Chem. 283 (2008) 32484–32491. [DOI] [PMID: 18784082]
3.  Du, L., He, Y. and Luo, Y. Crystal structure and enantiomer selection by D-alanyl carrier protein ligase DltA from Bacillus cereus. Biochemistry 47 (2008) 11473–11480. [DOI] [PMID: 18847223]
4.  Osman, K.T., Du, L., He, Y. and Luo, Y. Crystal structure of Bacillus cereus D-alanyl carrier protein ligase (DltA) in complex with ATP. J. Mol. Biol. 388 (2009) 345–355. [DOI] [PMID: 19324056]
[EC 6.2.1.54 created 2018]
 
 
EC 6.2.1.55     
Accepted name: E1 SAMP-activating enzyme
Reaction: ATP + [SAMP]-Gly-Gly + [E1 SAMP-activating enzyme]-L-cysteine = S-[[SAMP]-Gly-Gly]-[[E1 SAMP-activating enzyme]-L-cysteine] + AMP + diphosphate (overall reaction)
(1a) ATP + [SAMP]-Gly-Gly = diphosphate + [SAMP]-Gly-Gly-AMP
(1b) [SAMP]-Gly-Gly-AMP + [E1 SAMP-activating enzyme]-L-cysteine = S-[[SAMP]-Gly-Gly]-[[E1 SAMP-activating enzyme]-L-cysteine] + AMP
Glossary: SAMP = small archaeal modifier protein = ubiquitin-like small archaeal modifier protein
Other name(s): UbaA; SAMP-activating enzyme E1
Systematic name: [SAMP]:[E1 SAMP-activating enzyme] ligase (AMP-forming)
Comments: Contains Zn2+. The enzyme catalyses the activation of SAMPs (Small Archaeal Modifier Proteins), which are ubiquitin-like proteins found only in the Archaea. SAMPs are involved in protein degradation, and also act as sulfur carriers involved in thiolation of tRNA and other metabolites such as molybdopterin. The enzyme catalyses the ATP-dependent formation of a SAMP adenylate intermediate in which the C-terminal glycine of SAMP is bound to AMP via an acyl-phosphate linkage (reaction 1). This intermediate can accept a sulfur atom to form a thiocarboxylate moiety in a mechanism that is not yet understood. Alternatively, the E1 enzyme can transfer SAMP from its activated form to an internal cysteine residue, releasing AMP (reaction 2). In this case SAMP is subsequently transferred to a lysine residue in a target protein in a process termed SAMPylation. Auto-SAMPylation (attachment of SAMP to lysine residues within the E1 enzyme) has been observed. cf. EC 2.7.7.100, SAMP-activating enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miranda, H.V., Nembhard, N., Su, D., Hepowit, N., Krause, D.J., Pritz, J.R., Phillips, C., Soll, D. and Maupin-Furlow, J.A. E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc. Natl. Acad. Sci. USA 108 (2011) 4417–4422. [DOI] [PMID: 21368171]
2.  Maupin-Furlow, J.A. Ubiquitin-like proteins and their roles in archaea. Trends Microbiol. 21 (2013) 31–38. [DOI] [PMID: 23140889]
3.  Miranda, H.V., Antelmann, H., Hepowit, N., Chavarria, N.E., Krause, D.J., Pritz, J.R., Basell, K., Becher, D., Humbard, M.A., Brocchieri, L. and Maupin-Furlow, J.A. Archaeal ubiquitin-like SAMP3 is isopeptide-linked to proteins via a UbaA-dependent mechanism. Mol. Cell. Proteomics 13 (2014) 220–239. [DOI] [PMID: 24097257]
4.  Hepowit, N.L., de Vera, I.M., Cao, S., Fu, X., Wu, Y., Uthandi, S., Chavarria, N.E., Englert, M., Su, D., Söll, D., Kojetin, D.J. and Maupin-Furlow, J.A. Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea. FEBS J. 283 (2016) 3567–3586. [DOI] [PMID: 27459543]
[EC 6.2.1.55 created 2018]
 
 
EC 6.2.1.56     
Accepted name: 4-hydroxybutyrate—CoA ligase (ADP-forming)
Reaction: ATP + 4-hydroxybutanoate + CoA = ADP + phosphate + 4-hydroxybutanoyl-CoA
For diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Other name(s): Nmar_0206 (locus name)
Systematic name: 4-hydroxybutanoate:CoA ligase (ADP-forming)
Comments: The enzyme, characterized from the marine ammonia-oxidizing archaeon Nitrosopumilus maritimus, participates in a variant of the 3-hydroxypropanoate/4-hydroxybutanate CO2 fixation cycle. cf. EC 6.2.1.40, 4-hydroxybutyrate—CoA ligase (AMP-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Konneke, M., Schubert, D.M., Brown, P.C., Hugler, M., Standfest, S., Schwander, T., Schada von Borzyskowski, L., Erb, T.J., Stahl, D.A. and Berg, I.A. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc. Natl. Acad. Sci. USA 111 (2014) 8239–8244. [PMID: 24843170]
[EC 6.2.1.56 created 2019]
 
 
EC 6.2.1.57     
Accepted name: long-chain fatty acid adenylase/transferase FadD23
Reaction: (1) ATP + stearate + a holo-[(hydroxy)phthioceranic acid synthase] = AMP + diphosphate + a stearoyl-[(hydroxy)phthioceranic acid synthase] (overall reaction)
(1a) ATP + stearate = diphosphate + (stearoyl)adenylate
(1b) (stearoyl)adenylate + a holo-[(hydroxy)phthioceranic acid synthase] = AMP + a stearoyl-[(hydroxy)phthioceranic acid synthase]
(2) ATP + palmitate + a holo-[(hydroxy)phthioceranic acid synthase] = AMP + diphosphate + a palmitoyl-[(hydroxy)phthioceranic acid synthase] (overall reaction)
(2a) ATP + palmitate = diphosphate + (palmitoyl)adenylate
(2b) (palmitoyl)adenylate + a holo-[(hydroxy)phthioceranic acid synthase] = AMP + a palmitoyl-[(hydroxy)phthioceranic acid synthase]
Other name(s): fadD23 (gene name); long-chain fatty acid adenylyltransferase FadD23
Systematic name: palmitate:holo-[(hydroxy)phthioceranic acid synthase] ligase
Comments: This mycobacterial enzyme activates palmitate and stearate by adenylation, followed by their loading onto the polyketide synthase EC 2.3.1.287, phthioceranic/hydroxyphthioceranic acid synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gokhale, R.S., Saxena, P., Chopra, T. and Mohanty, D. Versatile polyketide enzymatic machinery for the biosynthesis of complex mycobacterial lipids. Nat. Prod. Rep. 24 (2007) 267–277. [PMID: 17389997]
2.  Lynett, J. and Stokes, R.W. Selection of transposon mutants of Mycobacterium tuberculosis with increased macrophage infectivity identifies fadD23 to be involved in sulfolipid production and association with macrophages. Microbiology 153 (2007) 3133–3140. [PMID: 17768256]
[EC 6.2.1.57 created 2019]
 
 
EC 6.2.1.58     
Accepted name: isophthalate—CoA ligase
Reaction: ATP + isophthalate + CoA = AMP + diphosphate + isophthalyl-CoA
Other name(s): IPCL
Systematic name: isophthalate:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from the bacterium Syntrophorhabdus aromaticivorans, catalyses the first step in an anaerobic isophthalate degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Junghare, M., Spiteller, D. and Schink, B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME J. 13 (2019) 1252–1268. [PMID: 30647456]
[EC 6.2.1.58 created 2019]
 
 
EC 6.2.1.59     
Accepted name: long-chain fatty acid adenylase/transferase FadD26
Reaction: ATP + a long-chain fatty acid + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + diphosphate + a long-chain acyl-[(phenol)carboxyphthiodiolenone synthase] (overall reaction)
(1a) ATP + a long-chain fatty acid = diphosphate + a long-chain fatty-acyl adenylate ester
(1b) a long-chain fatty-acyl adenylate ester + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + a long-chain acyl-[(phenol)carboxyphthiodiolenone synthase]
Glossary: phthiocerols = linear carbohydrates containing one methoxyl group, one methyl group, and two secondary hydroxyl groups that serve as a backbone for certain lipids and glycolipids found in many species of Mycobacteriaceae
arachidate = icosanoate
behenate = docosanoate
lignocerate= tetracosanoate
Other name(s): FadD26
Systematic name: long-chain fatty acid:holo-[(phenol)carboxyphthiodiolenone synthase] ligase (AMP-forming)
Comments: The enzyme, present in pathogenic species of mycobacteria, participates in the pathway for biosynthesis of phthiocerols. It catalyses the adenylation of the long-chain fatty acids arachidate (C20) or behenate (C22) [1] and potentially the very-long-chain fatty acid lignocerate (C24) [2]. The activated fatty acids are then loaded to EC 2.3.1.292, (phenol)carboxyphthiodiolenone synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Azad, A.K., Sirakova, T.D., Fernandes, N.D. and Kolattukudy, P.E. Gene knockout reveals a novel gene cluster for the synthesis of a class of cell wall lipids unique to pathogenic mycobacteria. J. Biol. Chem. 272 (1997) 16741–16745. [PMID: 9201977]
2.  Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715–2725. [DOI] [PMID: 20553505]
3.  Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040–1050. [DOI] [PMID: 25561717]
[EC 6.2.1.59 created 2019]
 
 
EC 6.2.1.60     
Accepted name: marinolic acid—CoA ligase
Reaction: (1) ATP + a marinolic acid + CoA = AMP + diphosphate + a marinoloyl-CoA
(2) ATP + a pseudomonic acid + CoA = AMP + diphosphate + a pseudomonoyl-CoA
Glossary: thiomarinols = natural products that combine monic acid and the compact holothin core of the dithiolopyrrolones.
Other name(s): tmlU (gene name)
Systematic name: marinolic acid:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from the bacterium Pseudoalteromonas sp. SANK 73390, catalyses the CoA acylation of pseudomonic and marinolic acids, as part of the biosynthesis of thiomarinols and related compounds.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dunn, Z.D., Wever, W.J., Economou, N.J., Bowers, A.A. and Li, B. Enzymatic basis of "hybridity" in thiomarinol biosynthesis. Angew. Chem. Int. Ed. Engl. 54 (2015) 5137–5141. [PMID: 25726835]
[EC 6.2.1.60 created 2019]
 
 
EC 6.2.1.61     
Accepted name: salicylate—[aryl-carrier protein] ligase
Reaction: ATP + salicylate + holo-[non-ribosomal peptide synthase] = AMP + diphosphate + salicyl-[non-ribosomal peptide synthase] (overall reaction)
(1a) ATP + salicylate = diphosphate + (salicyl)adenylate
(1b) (salicyl)adenylate + holo-[non-ribosomal peptide synthase] = AMP + salicyl-[non-ribosomal peptide synthase]
Other name(s): pmsE (gene name); pchD (gene name)
Systematic name: salicylate:holo-[non-ribosomal peptide synthase] ligase
Comments: The enzyme catalyses the activation of salicylate to (salicyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of an aryl-carrier protein, which is often a domain of a larger non-ribosimal peptide synthase. The PmsE enzyme is involved in pseudomonine biosynthesis and transfers the activated salicylate first to itself, and then to a PmsG protein. The PchD enzyme is involved in pyochelin biosynthesis and transfers the activated salicylate directly to the PchE protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Quadri, L.E., Keating, T.A., Patel, H.M. and Walsh, C.T. Assembly of the Pseudomonas aeruginosa nonribosomal peptide siderophore pyochelin: In vitro reconstitution of aryl-4, 2-bisthiazoline synthetase activity from PchD, PchE, and PchF. Biochemistry 38 (1999) 14941–14954. [PMID: 10555976]
2.  Sattely, E.S. and Walsh, C.T. A latent oxazoline electrophile for N-O-C bond formation in pseudomonine biosynthesis. J. Am. Chem. Soc. 130 (2008) 12282–12284. [DOI] [PMID: 18710233]
[EC 6.2.1.61 created 2019]
 
 
EC 6.2.1.62     
Accepted name: 3,4-dihydroxybenzoate—[aryl-carrier protein] ligase
Reaction: ATP + 3,4-dihydroxybenzoate + holo-[aryl-carrier protein] = AMP + diphosphate + 3,4-dihydroxybenzoyl-[aryl-carrier protein] (overall reaction)
(1a) ATP + 3,4-dihydroxybenzoate = diphosphate + (3,4-dihydroxybenzoyl)adenylate
(1b) (3,4-dihydroxybenzoyl)adenylate + holo-[aryl-carrier protein] = AMP + 3,4-dihydroxybenzoyl-[aryl-carrier protein]
Other name(s): asbC (gene name)
Systematic name: 3,4-dihydroxybenzoate:[aryl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of 3,4-dihydroxybenzoate to (3,4-dihydroxybenzoyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of an aryl-carrier protein domain. The aryl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pfleger, B.F., Lee, J.Y., Somu, R.V., Aldrich, C.C., Hanna, P.C. and Sherman, D.H. Characterization and analysis of early enzymes for petrobactin biosynthesis in Bacillus anthracis. Biochemistry 46 (2007) 4147–4157. [PMID: 17346033]
[EC 6.2.1.62 created 2020]
 
 
EC 6.2.1.63     
Accepted name: L-arginine—[L-arginyl-carrier protein] ligase
Reaction: ATP + L-arginine + holo-[L-arginyl-carrier protein] = AMP + diphosphate + L-arginyl-[L-arginyl-carrier protein] (overall reaction)
(1a) ATP + L-arginine = diphosphate + (L-arginyl)adenylate
(1b) (L-arginyl)adenylate + holo-[L-arginyl-carrier protein] = AMP + L-arginyl-[L-arginyl-carrier protein]
Other name(s): vabF (gene name)
Systematic name: L-arginine:[L-arginyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-arginine to (L-arginyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Balado, M., Osorio, C.R. and Lemos, M.L. A gene cluster involved in the biosynthesis of vanchrobactin, a chromosome-encoded siderophore produced by Vibrio anguillarum. Microbiology 152 (2006) 3517–3528. [PMID: 17159203]
[EC 6.2.1.63 created 2020]
 
 
EC 6.2.1.64     
Accepted name: E1 NEDD8-activating enzyme
Reaction: ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Glossary: NEDD = Neural-precursor-cell Expressed Developmentally Down-regulated protein
Other name(s): NEDD-activating enzyme E1; NAE1 (gene name); UBA3 (gene name)
Systematic name: [NEDD8 protein]:[E1 NEDD8-activating enzyme] ligase (AMP-forming)
Comments: Some RING-type E3 ubiquitin transferase (EC 2.3.2.27) are not able to bind a substrate protein directly. Instead, they form complexes with a cullin scaffold protein and a substrate recognition module, which are known as CRL (Cullin-RING-Ligase) complexes. The cullin protein needs to be activated by the ubiquitin-like protein NEDD8 in a process known as neddylation. Like ubiquitin, the NEDD8 protein ends with two glycine residues. The E1 NEDD8-activating enzyme activates NEDD8 in an ATP-dependent reaction by forming a high-energy thioester intermediate between NEDD8 and one of its cysteine residues. The activated NEDD8 is subsequently transferred to a cysteine residue of EC 2.3.2.34, E2 NEDD8-conjugating enzyme, and is eventually conjugated to a lysine residue of specific substrates in the presence of the appropriate E3 transferase (EC 2.3.2.32, cullin-RING-type E3 NEDD8 transferase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Osaka, F., Kawasaki, H., Aida, N., Saeki, M., Chiba, T., Kawashima, S., Tanaka, K. and Kato, S. A new NEDD8-ligating system for cullin-4A. Genes Dev. 12 (1998) 2263–2268. [PMID: 9694792]
2.  Gong, L. and Yeh, E.T. Identification of the activating and conjugating enzymes of the NEDD8 conjugation pathway. J. Biol. Chem. 274 (1999) 12036–12042. [PMID: 10207026]
[EC 6.2.1.64 created 2020]
 
 
EC 6.2.1.65     
Accepted name: salicylate—CoA ligase
Reaction: ATP + salicylate + CoA = AMP + diphosphate + 2-hydroxybenzoyl-CoA (overall reaction)
(1a) ATP + salicylate = diphosphate + (2-hydroxybenzoyl)adenylate
(1b) (2-hydroxybenzoyl)adenylate + CoA = AMP + 2-hydroxybenzoyl-CoA
Glossary: 2-hydroxybenzoyl-CoA = salicyloyl-CoA
Other name(s): sdgA (gene name)
Systematic name: salicylate:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from the bacteria Thauera aromatica and Streptomyces sp. WA46, participates in a salicylate degradation pathway. It activates salicylate by its adenylation to (2-hydroxybenzoyl)adenylate, followed by the transfer of the activated compound to coenzyme A.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bonting, C.F. and Fuchs, G. Anaerobic metabolism of 2-hydroxybenzoic acid (salicylic acid) by a denitrifying bacterium. Arch. Microbiol. 165 (1996) 402–408. [PMID: 8661934]
2.  Ishiyama, D., Vujaklija, D. and Davies, J. Novel pathway of salicylate degradation by Streptomyces sp. strain WA46. Appl. Environ. Microbiol. 70 (2004) 1297–1306. [DOI] [PMID: 15006746]
[EC 6.2.1.65 created 2020]
 
 
EC 6.2.1.66     
Accepted name: glyine—[glycyl-carrier protein] ligase
Reaction: ATP + glycine + holo-[glycyl-carrier protein] = AMP + diphosphate + glycyl-[glycyl-carrier protein] (overall reaction)
(1a) ATP + glycine = diphosphate + (glycyl)adenylate
(1b) (glycyl)adenylate + holo-[glycyl-carrier protein] = AMP + glycyl-[glycyl-carrier protein]
Other name(s): dhbF (gene name); sfmB (gene name)
Systematic name: glycine:[glycyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of glycine to (glycyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein (as in the case of DhbF in bacillibactin biosynthesis), or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  May, J.J., Wendrich, T.M. and Marahiel, M.A. The dhb operon of Bacillus subtilis encodes the biosynthetic template for the catecholic siderophore 2,3-dihydroxybenzoate-glycine-threonine trimeric ester bacillibactin. J. Biol. Chem. 276 (2001) 7209–7217. [DOI] [PMID: 11112781]
2.  Li, L., Deng, W., Song, J., Ding, W., Zhao, Q.F., Peng, C., Song, W.W., Tang, G.L. and Liu, W. Characterization of the saframycin A gene cluster from Streptomyces lavendulae NRRL 11002 revealing a nonribosomal peptide synthetase system for assembling the unusual tetrapeptidyl skeleton in an iterative manner. J. Bacteriol. 190 (2008) 251–263. [DOI] [PMID: 17981978]
[EC 6.2.1.66 created 2021]
 
 
EC 6.2.1.67     
Accepted name: L-alanine—[L-alanyl-carrier protein] ligase
Reaction: ATP + L-alanine + holo-[L-alanyl-carrier protein] = AMP + diphosphate + L-alanyl-[L-alanyl-carrier protein] (overall reaction)
(1a) ATP + L-alanine = diphosphate + (L-alanyl)adenylate
(1b) (L-alanyl)adenylate + holo-[L-alanyl-carrier protein] = AMP + L-alanyl-[L-alanyl-carrier protein]
Other name(s): ambB (gene name); phsB (gene name)
Systematic name: L-alanine:[L-alanyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-alanine to (L-alanyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Schwartz, D., Grammel, N., Heinzelmann, E., Keller, U. and Wohlleben, W. Phosphinothricin tripeptide synthetases in Streptomyces viridochromogenes Tu494. Antimicrob. Agents Chemother. 49 (2005) 4598–4607. [DOI] [PMID: 16251301]
2.  Rojas Murcia, N., Lee, X., Waridel, P., Maspoli, A., Imker, H.J., Chai, T., Walsh, C.T. and Reimmann, C. The Pseudomonas aeruginosa antimetabolite L -2-amino-4-methoxy-trans-3-butenoic acid (AMB) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor. Front. Microbiol. 6:170 (2015). [DOI] [PMID: 25814981]
[EC 6.2.1.67 created 2021]
 
 
EC 6.2.1.68     
Accepted name: L-glutamate—[L-glutamyl-carrier protein] ligase
Reaction: ATP + L-glutamate + holo-[L-glutamyl-carrier protein] = AMP + diphosphate + L-glutamyl-[L-glutamyl-carrier protein] (overall reaction)
(1a) ATP + L-glutamate = diphosphate + (L-glutamyl)adenylate
(1b) (L-glutamyl)adenylate + holo-[L-glutamyl-carrier protein] = AMP + L-glutamyl-[L-glutamyl-carrier protein]
Other name(s): ambE (gene name)
Systematic name: L-glutamate:[L-glutamyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-glutamate to (L-glutamyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Rojas Murcia, N., Lee, X., Waridel, P., Maspoli, A., Imker, H.J., Chai, T., Walsh, C.T. and Reimmann, C. The Pseudomonas aeruginosa antimetabolite L -2-amino-4-methoxy-trans-3-butenoic acid (AMB) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor. Front. Microbiol. 6:170 (2015). [DOI] [PMID: 25814981]
[EC 6.2.1.68 created 2021]
 
 
EC 6.2.1.69     
Accepted name: L-cysteine—[L-cysteinyl-carrier protein] ligase
Reaction: ATP + L-cysteine + holo-[L-cysteinyl-carrier protein] = AMP + diphosphate + L-cysteinyl-[L-cysteinyl-carrier protein] (overall reaction)
(1a) ATP + L-cysteine = diphosphate + (L-cysteinyl)adenylate
(1b) (L-cysteinyl)adenylate + holo-[L-cysteinyl-carrier protein] = AMP + L-cysteinyl-[L-cysteinyl-carrier protein]
Other name(s): pchE (gene name); pchF (gene name); angR (gene name)
Systematic name: L-cysteine:[L-cysteinyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-cysteine to (L-cysteinyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Quadri, L.E., Keating, T.A., Patel, H.M. and Walsh, C.T. Assembly of the Pseudomonas aeruginosa nonribosomal peptide siderophore pyochelin: In vitro reconstitution of aryl-4, 2-bisthiazoline synthetase activity from PchD, PchE, and PchF. Biochemistry 38 (1999) 14941–14954. [PMID: 10555976]
[EC 6.2.1.69 created 2021]
 
 


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