The Enzyme Database

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EC 6.2.1.7     
Accepted name: cholate—CoA ligase
Reaction: (1) ATP + cholate + CoA = AMP + diphosphate + choloyl-CoA
(2) ATP + (25R)-3α,7α,12α-trihydroxy-5β-cholestan-26-oate + CoA = AMP + diphosphate + (25R)-3α,7α,12α-trihydroxy-5β-cholestanoyl-CoA
For diagram of cholic acid conjugates biosynthesis, click here and for diagram of cholic acid biosynthesis (sidechain), click here
Glossary: cholate = 3α,7α,12α-trihydroxy-5β-cholan-24-oate
trihydroxycoprostanoate = 3α,7α,12α-trihydroxy-5β-cholestan-26-oate
Other name(s): BAL; bile acid CoA ligase; bile acid coenzyme A ligase; choloyl-CoA synthetase; choloyl coenzyme A synthetase; cholic thiokinase; cholate thiokinase; cholic acid:CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanoyl coenzyme A synthetase; 3α,7α,12α-trihydroxy-5β-cholestanoate-CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanoate-CoA synthetase; THCA-CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanate—CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanate:CoA ligase (AMP-forming); cholyl-CoA synthetase; trihydroxycoprostanoyl-CoA synthetase
Systematic name: cholate:CoA ligase (AMP-forming)
Comments: Requires Mg2+ for activity. The mammalian enzyme is membrane-bound and catalyses the first step in the conjugation of bile acids with amino acids, converting bile acids into their acyl-CoA thioesters. Chenodeoxycholate, deoxycholate, lithocholate and trihydroxycoprostanoate can also act as substrates [7]. The bacterial enzyme is soluble and participates in an anaerobic bile acid 7 α-dehydroxylation pathway [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-90-1
References:
1.  Elliott, W.H. The enzymic activation of cholic acid by guinea-pig-liver microsomes. Biochem. J. 62 (1956) 427–433. [PMID: 13303991]
2.  Elliott, W.H. The breakdown of adenosine triphosphate accompanying cholic acid activation by guinea-pig liver microsomes. Biochem. J. 65 (1957) 315–321. [PMID: 13403911]
3.  Prydz, K., Kase, B.F., Björkhem, I. and Pedersen, J.I. Subcellular localization of 3α,7α-dihydroxy- and 3α,7α,12α-trihydroxy-5β-cholestanoyl-coenzyme A ligase(s) in rat liver. J. Lipid Res. 29 (1988) 997–1004. [PMID: 3183523]
4.  Schepers, L., Casteels, M., Verheyden, K., Parmentier, G., Asselberghs, S., Eyssen, H.J. and Mannaerts, G.P. Subcellular distribution and characteristics of trihydroxycoprostanoyl-CoA synthetase in rat liver. Biochem. J. 257 (1989) 221–229. [PMID: 2521999]
5.  Mallonee, D.H., Adams, J.L. and Hylemon, P.B. The bile acid-inducible baiB gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme A ligase. J. Bacteriol. 174 (1992) 2065–2071. [DOI] [PMID: 1551828]
6.  Wheeler, J.B., Shaw, D.R. and Barnes, S. Purification and characterization of a rat liver bile acid coenzyme A ligase from rat liver microsomes. Arch. Biochem. Biophys. 348 (1997) 15–24. [DOI] [PMID: 9390170]
7.  Falany, C.N., Xie, X., Wheeler, J.B., Wang, J., Smith, M., He, D. and Barnes, S. Molecular cloning and expression of rat liver bile acid CoA ligase. J. Lipid Res. 43 (2002) 2062–2071. [PMID: 12454267]
[EC 6.2.1.7 created 1961 (EC 6.2.1.29 created 1992, incorporated 2005), modified 2005]
 
 
EC 6.2.1.70     
Accepted name: L-threonine—[L-threonyl-carrier protein] ligase
Reaction: ATP + L-threonine + holo-[L-threonyl-carrier protein] = AMP + diphosphate + L-threonyl-[L-threonyl-carrier protein] (overall reaction)
(1a) ATP + L-threonine = diphosphate + (L-threonyl)adenylate
(1b) (L-threonyl)adenylate + holo-[L-threonyl-carrier protein] = AMP + L-threonyl-[L-threonyl-carrier protein]
Other name(s): dhbF (gene name); pmsD (gene name); syrB1 (gene name)
Systematic name: L-threonine:[L-threonyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-threonine to (L-threonyl)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 (as in the case of PmsD in pseudomonine biosynthesis). This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Vaillancourt, F.H., Yin, J. and Walsh, C.T. SyrB2 in syringomycin E biosynthesis is a nonheme FeII α-ketoglutarate- and O2-dependent halogenase. Proc. Natl. Acad. Sci. USA 102 (2005) 10111–10116. [DOI] [PMID: 16002467]
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 6.2.1.70 created 2021]
 
 
EC 6.2.1.71     
Accepted name: 2,3-dihydroxybenzoate—[aryl-carrier protein] ligase
Reaction: ATP + 2,3-dihydroxybenzoate + holo-[aryl-carrier protein] = AMP + diphosphate + 2,3-dihydroxybenzoyl-[aryl-carrier protein] (overall reaction)
(1a) ATP + 2,3-dihydroxybenzoate = diphosphate + (2,3-dihydroxybenzoyl)adenylate
(1b) (2,3-dihydroxybenzoyl)adenylate + holo-[aryl-carrier protein] = AMP + 2,3-dihydroxybenzoyl-[aryl-carrier protein]
Other name(s): entE (gene name); vibE (gene name); dhbE (gene name); angE (gene name)
Systematic name: 2,3-dihydroxybenzoate:[aryl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of 2,3-dihydroxybenzoate to (2,3-dihydroxybenzoyl)adenylate, followed by the transfer the activated compound to the free thiol of a phosphopantetheine arm of an aryl-carrier protein domain of a specific non-ribosomal peptide synthase. For example, the EntE enzyme of Escherichia coli is part of the enterobactin synthase complex, the VibE enzyme of Vibrio cholerae is part of the vibriobactin synthase complex, and the DhbE enzyme of Bacillus subtilis is part of the bacillibactin synthase complex.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Gehring, A.M., Bradley, K.A. and Walsh, C.T. Enterobactin biosynthesis in Escherichia coli: isochorismate lyase (EntB) is a bifunctional enzyme that is phosphopantetheinylated by EntD and then acylated by EntE using ATP and 2,3-dihydroxybenzoate. Biochemistry 36 (1997) 8495–8503. [DOI] [PMID: 9214294]
2.  Wyckoff, E.E., Stoebner, J.A., Reed, K.E. and Payne, S.M. Cloning of a Vibrio cholerae vibriobactin gene cluster: identification of genes required for early steps in siderophore biosynthesis. J. Bacteriol. 179 (1997) 7055–7062. [PMID: 9371453]
3.  Ehmann, D.E., Shaw-Reid, C.A., Losey, H.C. and Walsh, C.T. The EntF and EntE adenylation domains of Escherichia coli enterobactin synthetase: sequestration and selectivity in acyl-AMP transfers to thiolation domain cosubstrates. Proc. Natl. Acad. Sci. USA 97 (2000) 2509–2514. [DOI] [PMID: 10688898]
4.  Keating, T.A., Marshall, C.G. and Walsh, C.T. Vibriobactin biosynthesis in Vibrio cholerae: VibH is an amide synthase homologous to nonribosomal peptide synthetase condensation domains. Biochemistry 39 (2000) 15513–15521. [PMID: 11112537]
5.  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]
6.  Sikora, A.L., Wilson, D.J., Aldrich, C.C. and Blanchard, J.S. Kinetic and inhibition studies of dihydroxybenzoate-AMP ligase from Escherichia coli. Biochemistry 49 (2010) 3648–3657. [DOI] [PMID: 20359185]
7.  Khalil, S. and Pawelek, P.D. Enzymatic adenylation of 2,3-dihydroxybenzoate is enhanced by a protein-protein interaction between Escherichia coli 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EntA) and 2,3-dihydroxybenzoate-AMP ligase (EntE). Biochemistry 50 (2011) 533–545. [DOI] [PMID: 21166461]
[EC 6.2.1.71 created 2021 (EC 2.7.7.58 created 1992, incorporated 2021)]
 
 
EC 6.2.1.72     
Accepted name: L-serine—[L-seryl-carrier protein] ligase
Reaction: ATP + L-serine + holo-[L-seryl-carrier protein] = AMP + diphosphate + L-seryl-[L-seryl-carrier protein] (overall reaction)
(1a) ATP + L-serine = diphosphate + (L-seryl)adenylate
(1b) (L-seryl)adenylate + holo-[L-seryl-carrier protein] = AMP + L-seryl-[L-seryl-carrier protein]
Other name(s): entF (gene name); zmaJ (gene name); gdnB (gene name); serine-activating enzyme
Systematic name: L-serine:[L-seryl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-serine to (L-seryl)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.  Pettis, G.S. and McIntosh, M.A. Molecular characterization of the Escherichia coli enterobactin cistron entF and coupled expression of entF and the fes gene. J. Bacteriol. 169 (1987) 4154–4162. [PMID: 3040679]
2.  Rusnak, F., Sakaitani, M., Drueckhammer, D., Reichert, J. and Walsh, C.T. Biosynthesis of the Escherichia coli siderophore enterobactin: sequence of the entF gene, expression and purification of EntF, and analysis of covalent phosphopantetheine. Biochemistry 30 (1991) 2916–2927. [PMID: 1826089]
3.  Reichert, J., Sakaitani, M. and Walsh, C.T. Characterization of EntF as a serine-activating enzyme. Protein Sci. 1 (1992) 549–556. [DOI] [PMID: 1338974]
4.  Ehmann, D.E., Shaw-Reid, C.A., Losey, H.C. and Walsh, C.T. The EntF and EntE adenylation domains of Escherichia coli enterobactin synthetase: sequestration and selectivity in acyl-AMP transfers to thiolation domain cosubstrates. Proc. Natl. Acad. Sci. USA 97 (2000) 2509–2514. [DOI] [PMID: 10688898]
5.  Chan, Y.A., Boyne, M.T., 2nd, Podevels, A.M., Klimowicz, A.K., Handelsman, J., Kelleher, N.L. and Thomas, M.G. Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. Proc. Natl. Acad. Sci. USA 103 (2006) 14349–14354. [DOI] [PMID: 16983083]
6.  Frueh, D.P., Arthanari, H., Koglin, A., Vosburg, D.A., Bennett, A.E., Walsh, C.T. and Wagner, G. Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase. Nature 454 (2008) 903–906. [DOI] [PMID: 18704088]
[EC 6.2.1.72 created 2021]
 
 
EC 6.2.1.73     
Accepted name: L-tryptophan—[L-tryptophyl-carrier protein] ligase
Reaction: ATP + L-tryptophan + holo-[L-tryptophyl-carrier protein] = AMP + diphosphate + -L-tryptophyl-[L-tryptophyl-carrier protein] (overall reaction)
(1a) ATP + tryptophan = diphosphate + (L-tryptophyl)adenylate
(1b) (L-tryptophyl)adenylate + holo-[L-tryptophyl-carrier protein] = AMP + L-tryptophyl-[L-tryptophyl-carrier protein]
Other name(s): ecm13 (gene name); swb11 (gene name)
Systematic name: L-tryptophan:[L-tryptophyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-tryptophan to (L-tryptophyl)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.  Zhang, C., Kong, L., Liu, Q., Lei, X., Zhu, T., Yin, J., Lin, B., Deng, Z. and You, D. In vitro characterization of echinomycin biosynthesis: formation and hydroxylation of L-tryptophanyl-S-enzyme and oxidation of (2S,3S) β-hydroxytryptophan. PLoS One 8:e56772 (2013). [DOI] [PMID: 23437232]
[EC 6.2.1.73 created 2021]
 
 
EC 6.2.1.74     
Accepted name: 3-amino-5-hydroxybenzoate—[acyl-carrier protein] ligase
Reaction: ATP + 3-amino-5-hydroxybenzoate + a holo-[acyl-carrier protein] = 3-amino-5-hydroxybenzoyl-[acyl-carrier protein] + AMP + diphosphate
Other name(s): rifA (gene name); mitE (gene name)
Systematic name: 3-amino-5-hydroxybenzoate:[acyl carrier protein] ligase (AMP-forming)
Comments: During the biosynthesis of most ansamycin antibiotics such as rifamycins, streptovaricins, naphthomycins, and chaxamycins, the activity is catalysed by the loading domain of the respective polyketide synthase (PKS), which transfers the substrate to the acyl-carrier protein domain of the first extension module of the PKS. During the biosynthesis of the mitomycins the reaction is catalysed by the MitE protein, which transfers the substrate to a dedicated acyl-carrier protein (MmcB).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Admiraal, S.J., Walsh, C.T. and Khosla, C. The loading module of rifamycin synthetase is an adenylation-thiolation didomain with substrate tolerance for substituted benzoates. Biochemistry 40 (2001) 6116–6123. [PMID: 11352749]
2.  Admiraal, S.J., Khosla, C. and Walsh, C.T. The loading and initial elongation modules of rifamycin synthetase collaborate to produce mixed aryl ketide products. Biochemistry 41 (2002) 5313–5324. [PMID: 11955082]
3.  Admiraal, S.J., Khosla, C. and Walsh, C.T. A Switch for the transfer of substrate between nonribosomal peptide and polyketide modules of the rifamycin synthetase assembly line. J. Am. Chem. Soc. 125 (2003) 13664–13665. [DOI] [PMID: 14599196]
4.  Chamberland, S., Gruschow, S., Sherman, D.H. and Williams, R.M. Synthesis of potential early-stage intermediates in the biosynthesis of FR900482 and mitomycin C. Org. Lett. 11 (2009) 791–794. [DOI] [PMID: 19161340]
[EC 6.2.1.74 created 2021]
 
 
EC 6.2.1.75     
Accepted name: indoleacetate—CoA ligase
Reaction: ATP + (indol-3-yl)acetate + CoA = AMP + diphosphate + (indol-3-yl)acetyl-CoA
Other name(s): iaaB (gene name)
Systematic name: (indol-3-yl)acetate:CoA ligase (AMP-forming)
Comments: The enzyme, characterized from the bacterium Aromatoleum aromaticum, is involved in degradation of (indol-3-yl)acetate. It is also active with phenylacetate and the non-physiological compound (2-naphthyl)acetate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schuhle, K., Nies, J. and Heider, J. An indoleacetate-CoA ligase and a phenylsuccinyl-CoA transferase involved in anaerobic metabolism of auxin. Environ. Microbiol. 18 (2016) 3120–3132. [DOI] [PMID: 27102732]
[EC 6.2.1.75 created 2022]
 
 
EC 6.2.1.76     
Accepted name: malonate—CoA ligase
Reaction: ATP + malonate + CoA = AMP + diphosphate + malonyl-CoA
Other name(s): ACSF3 (gene name); AAE13 (gene name); malonyl-CoA synthetase
Systematic name: malonate:CoA ligase (AMP-forming)
Comments: The enzyme, found in mitochondria, detoxifies malonate, which is a potent inhibitor of mitochondrial respiration, and provides malonyl-CoA to the mitochondrial fatty acid biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Gueguen, V., Macherel, D., Jaquinod, M., Douce, R. and Bourguignon, J. Fatty acid and lipoic acid biosynthesis in higher plant mitochondria. J. Biol. Chem. 275 (2000) 5016–5025. [DOI] [PMID: 10671542]
2.  Witkowski, A., Thweatt, J. and Smith, S. Mammalian ACSF3 protein is a malonyl-CoA synthetase that supplies the chain extender units for mitochondrial fatty acid synthesis. J. Biol. Chem. 286 (2011) 33729–33736. [DOI] [PMID: 21846720]
3.  Chen, H., Kim, H.U., Weng, H. and Browse, J. Malonyl-CoA synthetase, encoded by Acyl Activating Enzyme13, is essential for growth and development of Arabidopsis. Plant Cell 23 (2011) 2247–2262. [DOI] [PMID: 21642549]
4.  Guan, X. and Nikolau, B.J. AAE13 encodes a dual-localized malonyl-CoA synthetase that is crucial for mitochondrial fatty acid biosynthesis. Plant J. 85 (2016) 581–593. [DOI] [PMID: 26836315]
5.  Bowman, C.E., Rodriguez, S., Selen Alpergin, E.S., Acoba, M.G., Zhao, L., Hartung, T., Claypool, S.M., Watkins, P.A. and Wolfgang, M.J. The mammalian malonyl-CoA synthetase ACSF3 is required for mitochondrial protein malonylation and metabolic efficiency. Cell Chem. Biol. 24 (2017) 673–684.e4. [DOI] [PMID: 28479296]
6.  Bowman, C.E. and Wolfgang, M.J. Role of the malonyl-CoA synthetase ACSF3 in mitochondrial metabolism. Adv Biol Regul 71 (2019) 34–40. [DOI] [PMID: 30201289]
[EC 6.2.1.76 created 2022]
 
 


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