The Enzyme Database

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EC 1.1.1.41     
Accepted name: isocitrate dehydrogenase (NAD+)
Reaction: isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH
For diagram of the citric-acid cycle, click here
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
Other name(s): isocitric dehydrogenase; β-ketoglutaric-isocitric carboxylase; isocitric acid dehydrogenase; NAD dependent isocitrate dehydrogenase; NAD isocitrate dehydrogenase; NAD-linked isocitrate dehydrogenase; NAD-specific isocitrate dehydrogenase; NAD isocitric dehydrogenase; isocitrate dehydrogenase (NAD); IDH (ambiguous); nicotinamide adenine dinucleotide isocitrate dehydrogenase
Systematic name: isocitrate:NAD+ oxidoreductase (decarboxylating)
Comments: Requires Mn2+ or Mg2+ for activity. Unlike EC 1.1.1.42, isocitrate dehydrogenase (NADP+), oxalosuccinate cannot be used as a substrate. In eukaryotes, isocitrate dehydrogenase exists in two forms: an NAD+-linked enzyme found only in mitochondria and displaying allosteric properties, and a non-allosteric, NADP+-linked enzyme that is found in both mitochondria and cytoplasm [7]. The enzyme from some species can also use NADP+ but much more slowly [9].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9001-58-5
References:
1.  Hathaway, J.A. and Atkinson, D.E. The effect of adenylic acid on yeast nicotinamide adenine dinucleotide isocitrate dehydrogenase, a possible metabolic control mechanism. J. Biol. Chem. 238 (1963) 2875–2881. [PMID: 14063317]
2.  Kornberg, A. and Pricer, W.E. Di- and triphosphopyridine nucleotide isocitric dehydrogenase in yeast. J. Biol. Chem. 189 (1951) 123–136. [PMID: 14832224]
3.  Plaut, G.W.E. Isocitrate dehydrogenases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 105–126.
4.  Plaut, G.W.E. and Sung, S.-C. Diphosphopyridine nucleotide isocitric dehydrogenase from animal tissues. J. Biol. Chem. 207 (1954) 305–314. [PMID: 13152105]
5.  Ramakrishnan, C.V. and Martin, S.M. Isocitric dehydrogenase in Aspergillus niger. Arch. Biochem. Biophys. 55 (1955) 403–407.
6.  Vickery, H.B. A suggested new nomenclature for the isomers of isocitric acid. J. Biol. Chem. 237 (1962) 1739–1741. [PMID: 13925783]
7.  Camacho, M.L., Brown, R.A., Bonete, M.J., Danson, M.J. and Hough, D.W. Isocitrate dehydrogenases from Haloferax volcanii and Sulfolobus solfataricus: enzyme purification, characterisation and N-terminal sequence. FEMS Microbiol. Lett. 134 (1995) 85–90. [DOI] [PMID: 8593959]
8.  Kim, Y.O., Koh, H.J., Kim, S.H., Jo, S.H., Huh, J.W., Jeong, K.S., Lee, I.J., Song, B.J. and Huh, T.L. Identification and functional characterization of a novel, tissue-specific NAD+-dependent isocitrate dehydrogenase β subunit isoform. J. Biol. Chem. 274 (1999) 36866–36875. [DOI] [PMID: 10601238]
9.  Inoue, H., Tamura, T., Ehara, N., Nishito, A., Nakayama, Y., Maekawa, M., Imada, K., Tanaka, H. and Inagaki, K. Biochemical and molecular characterization of the NAD+-dependent isocitrate dehydrogenase from the chemolithotroph Acidithiobacillus thiooxidans. FEMS Microbiol. Lett. 214 (2002) 127–132. [DOI] [PMID: 12204383]
[EC 1.1.1.41 created 1961, modified 2005]
 
 
EC 1.1.1.42     
Accepted name: isocitrate dehydrogenase (NADP+)
Reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+ (overall reaction)
(1a) isocitrate + NADP+ = oxalosuccinate + NADPH + H+
(1b) oxalosuccinate = 2-oxoglutarate + CO2
For diagram of the citric-acid cycle, click here
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
oxalosuccinate = 1-oxopropane-1,2,3-tricarboxylate
Other name(s): oxalosuccinate decarboxylase; oxalsuccinic decarboxylase; isocitrate (NADP) dehydrogenase; isocitrate (nicotinamide adenine dinucleotide phosphate) dehydrogenase; NADP-specific isocitrate dehydrogenase; NADP-linked isocitrate dehydrogenase; NADP-dependent isocitrate dehydrogenase; NADP isocitric dehydrogenase; isocitrate dehydrogenase (NADP-dependent); NADP-dependent isocitric dehydrogenase; triphosphopyridine nucleotide-linked isocitrate dehydrogenase-oxalosuccinate carboxylase; NADP+-linked isocitrate dehydrogenase; IDH (ambiguous); dual-cofactor-specific isocitrate dehydrogenase; NADP+-ICDH; NADP+-IDH; IDP; IDP1; IDP2; IDP3
Systematic name: isocitrate:NADP+ oxidoreductase (decarboxylating)
Comments: Requires Mn2+ or Mg2+ for activity. Unlike EC 1.1.1.41, isocitrate dehydrogenase (NAD+), oxalosuccinate can be used as a substrate. In eukaryotes, isocitrate dehydrogenase exists in two forms: an NAD+-linked enzyme found only in mitochondria and displaying allosteric properties, and a non-allosteric, NADP+-linked enzyme that is found in both mitochondria and cytoplasm [6]. The enzyme from some species can also use NAD+ but much more slowly [6,7].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9028-48-2
References:
1.  Agosin, M.U. and Weinbach, E.C. Partial purification and characterization of the isocitric dehydrogenase from Trypanosoma cruzi. Biochim. Biophys. Acta 21 (1956) 117–126. [DOI] [PMID: 13363868]
2.  Moyle, J. and Dixon, M. Purification of the isocitrate enzyme (triphosphopyridine nucleotide-linked isocitrate dehydrogenase-oxalosuccinate carboxylase). Biochem. J. 63 (1956) 548–552. [PMID: 13355848]
3.  Plaut, G.W.E. Isocitrate dehydrogenases. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 7, Academic Press, New York, 1963, pp. 105–126.
4.  Siebert, G., Dubuc, J., Warner, R.C. and Plaut, G.W.E. The preparation of isocitrate dehydrogenase from mammalian heart. J. Biol. Chem. 226 (1957) 965–975. [PMID: 13438885]
5.  Vickery, H.B. A suggested new nomenclature for the isomers of isocitric acid. J. Biol. Chem. 237 (1962) 1739–1741. [PMID: 13925783]
6.  Camacho, M.L., Brown, R.A., Bonete, M.J., Danson, M.J. and Hough, D.W. Isocitrate dehydrogenases from Haloferax volcanii and Sulfolobus solfataricus: enzyme purification, characterisation and N-terminal sequence. FEMS Microbiol. Lett. 134 (1995) 85–90. [DOI] [PMID: 8593959]
7.  Steen, I.H., Lien, T. and Birkeland, N.-K. Biochemical and phylogenetic characterization of isocitrate dehydrogenase from a hyperthermophilic archaeon, Archaeoglobus fulgidus. Arch. Microbiol. 168 (1997) 412–420. [PMID: 9325430]
8.  Koh, H.J., Lee, S.M., Son, B.G., Lee, S.H., Ryoo, Z.Y., Chang, K.T., Park, J.W., Park, D.C., Song, B.J., Veech, R.L., Song, H. and Huh, T.L. Cytosolic NADP+-dependent isocitrate dehydrogenase plays a key role in lipid metabolism. J. Biol. Chem. 279 (2004) 39968–39974. [DOI] [PMID: 15254034]
9.  Ceccarelli, C., Grodsky, N.B., Ariyaratne, N., Colman, R.F. and Bahnson, B.J. Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate. Insights into the enzyme mechanism. J. Biol. Chem. 277 (2002) 43454–43462. [DOI] [PMID: 12207025]
[EC 1.1.1.42 created 1961, modified 2005]
 
 
EC 1.1.1.87     
Accepted name: homoisocitrate dehydrogenase
Reaction: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
For diagram of l-lysine synthesis, click here
Glossary: homoisocitrate = (-)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): 2-hydroxy-3-carboxyadipate dehydrogenase; 3-carboxy-2-hydroxyadipate dehydrogenase; homoisocitric dehydrogenase; (-)-1-hydroxy-1,2,4-butanetricarboxylate:NAD+ oxidoreductase (decarboxylating); 3-carboxy-2-hydroxyadipate:NAD+ oxidoreductase (decarboxylating); HICDH
Systematic name: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate:NAD+ oxidoreductase (decarboxylating)
Comments: Forms part of the lysine biosynthesis pathway in fungi [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9067-90-7
References:
1.  Strassman, M. and Ceci, L.N. Enzymatic formation of α-ketoadipic acid from homoisocitric acid. J. Biol. Chem. 240 (1965) 4357–4361. [PMID: 4284830]
2.  Rowley, B. and Tucci, A.F. Homoisocitric dehydrogenase from yeast. Arch. Biochem. Biophys. 141 (1970) 499–510. [DOI] [PMID: 4395693]
3.  Zabriskie, T.M. and Jackson, M.D. Lysine biosynthesis and metabolism in fungi. Nat. Prod. Rep. 17 (2000) 85–97. [PMID: 10714900]
[EC 1.1.1.87 created 1972 (EC 1.1.1.155 created 1976, incorporated 2004)]
 
 
EC 1.1.1.155      
Deleted entry: homoisocitrate dehydrogenase. The enzyme is identical to EC 1.1.1.87, homoisocitrate dehydrogenase
[EC 1.1.1.155 created 1976, deleted 2004]
 
 
EC 1.1.1.286     
Accepted name: isocitrate—homoisocitrate dehydrogenase
Reaction: (1) isocitrate + NAD+ = 2-oxoglutarate + CO2 + NADH
(2) (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate + NAD+ = 2-oxoadipate + CO2 + NADH + H+
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
homoisocitrate = (-)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): homoisocitrate—isocitrate dehydrogenase; PH1722
Systematic name: isocitrate(homoisocitrate):NAD+ oxidoreductase (decarboxylating)
Comments: Requires Mn2+ and K+ or NH4+ for activity. Unlike EC 1.1.1.41, isocitrate dehydrogenase (NAD+) and EC 1.1.1.87, homoisocitrate dehydrogenase, this enzyme, from Pyrococcus horikoshii, can use both isocitrate and homoisocitrate as substrates. The enzyme may play a role in both the lysine and glutamate biosynthesis pathways.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Miyazaki, K. Bifunctional isocitrate-homoisocitrate dehydrogenase: a missing link in the evolution of β-decarboxylating dehydrogenase. Biochem. Biophys. Res. Commun. 331 (2005) 341–346. [DOI] [PMID: 15845397]
[EC 1.1.1.286 created 2005]
 
 
EC 1.16.1.9     
Accepted name: ferric-chelate reductase (NADPH)
Reaction: 2 Fe(II)-siderophore + NADP+ + H+ = 2 Fe(III)-siderophore + NADPH
Other name(s): ferric chelate reductase (ambiguous); iron chelate reductase (ambiguous); NADPH:Fe3+-EDTA reductase; NADPH-dependent ferric reductase; yqjH (gene name); Fe(II):NADP+ oxidoreductase
Systematic name: Fe(II)-siderophore:NADP+ oxidoreductase
Comments: Contains FAD. The enzyme, which is widespread among bacteria, catalyses the reduction of ferric iron bound to a variety of iron chelators (siderophores), including ferric triscatecholates and ferric dicitrate, resulting in the release of ferrous iron. The enzyme from the bacterium Escherichia coli has the highest efficiency with the hydrolysed ferric enterobactin complex ferric N-(2,3-dihydroxybenzoyl)-L-serine [3]. cf. EC 1.16.1.7, ferric-chelate reductase (NADH) and EC 1.16.1.10, ferric-chelate reductase [NAD(P)H].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 120720-17-4
References:
1.  Bamford, V.A., Armour, M., Mitchell, S.A., Cartron, M., Andrews, S.C. and Watson, K.A. Preliminary X-ray diffraction analysis of YqjH from Escherichia coli: a putative cytoplasmic ferri-siderophore reductase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 792–796. [DOI] [PMID: 18765906]
2.  Wang, S., Wu, Y. and Outten, F.W. Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli. J. Bacteriol. 193 (2011) 563–574. [DOI] [PMID: 21097627]
3.  Miethke, M., Hou, J. and Marahiel, M.A. The siderophore-interacting protein YqjH acts as a ferric reductase in different iron assimilation pathways of Escherichia coli. Biochemistry 50 (2011) 10951–10964. [DOI] [PMID: 22098718]
[EC 1.16.1.9 created 1992 as EC 1.6.99.13, transferred 2002 to EC 1.16.1.7, transferred 2011 to EC 1.16.1.9, modified 2012, modified 2014]
 
 
EC 1.16.99.1     
Accepted name: [Co(II) methylated amine-specific corrinoid protein] reductase
Reaction: (1) ATP + a [Co(II) methylamine-specific corrinoid protein] + reduced acceptor + H2O = ADP + phosphate + a [Co(I) methylamine-specific corrinoid protein] + acceptor
(2) ATP + a [Co(II) dimethylamine-specific corrinoid protein] + reduced acceptor + H2O = ADP + phosphate + a [Co(I) dimethylamine-specific corrinoid protein] + acceptor
(3) ATP + a [Co(II) trimethylamine-specific corrinoid protein] + reduced acceptor + H2O = ADP + phosphate + a [Co(I) trimethylamine-specific corrinoid protein] + acceptor
Glossary: ramA (gene name)
Systematic name: acceptor:[cobalt(II) methylated amines-specific corrinoid protein] oxidoreductase (ATP-hydrolysing)
Comments: Methyltrophic corrinoid proteins must have the cobalt atom in the active cobalt(I) state to become methylated. Because the cobalt(I)/cobalt(II) transformation has a very low redox potential the corrinoid cofactor is subject to adventitious oxidation to the cobalt(II) state, which renders the proteins inactive. This enzyme, characterized from the methanogenic archaeon Methanosarcina barkeri, reduces cobalt(II) back to cobalt(I), restoring activity. The enzyme acts on the corrinoid proteins involved in methanogenesis from methylamine, dimethylamine, and trimethylamine, namely MtmC, MtbC, and MttC, respectively. While in vitro the enzyme can use Ti(III)-citrate as the electron donor, the in vivo donor is not known. The enzyme from Methanosarcina barkeri contains a C-terminal [4Fe-4S] ferredoxin-like domain.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ferguson, T., Soares, J.A., Lienard, T., Gottschalk, G. and Krzycki, J.A. RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea. J. Biol. Chem. 284 (2009) 2285–2295. [DOI] [PMID: 19043046]
2.  Durichen, H., Diekert, G. and Studenik, S. Redox potential changes during ATP-dependent corrinoid reduction determined by redox titrations with europium(II)-DTPA. Protein Sci. 28 (2019) 1902–1908. [DOI] [PMID: 31359509]
[EC 1.16.99.1 created 2021]
 
 
EC 2.1.1.144     
Accepted name: trans-aconitate 2-methyltransferase
Reaction: S-adenosyl-L-methionine + trans-aconitate = S-adenosyl-L-homocysteine + (E)-3-(methoxycarbonyl)pent-2-enedioate
For diagram of reaction, click here
Glossary: trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
Systematic name: S-adenosyl-L-methionine:(E)-prop-1-ene-1,2,3-tricarboxylate 2′-O-methyltransferase
Comments: Also catalyses the formation of the methyl monoester of cis-aconitate, isocitrate and citrate, but more slowly. While the enzyme from Escherichia coli forms (E)-3-(methoxycarbonyl)-pent-2-enedioate as the product, that from Saccharomyces cerevisiae forms (E)-2-(methoxycarbonylmethyl)butenedioate and is therefore classified as a separate enzyme (cf. EC 2.1.1.145, trans-aconitate 3-methyltransferase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 235107-12-7
References:
1.  Cai, H. and Clarke, S. A novel methyltransferase catalyzes the esterification of trans-aconitate in Escherichia coli. J. Biol. Chem. 274 (1999) 13470–13479. [DOI] [PMID: 10224113]
2.  Cai, H., Strouse, J., Dumlao, D., Jung, M.E. and Clarke, S. Distinct reactions catalyzed by bacterial and yeast trans-aconitate methyltransferase. Biochemistry 40 (2001) 2210–2219. [DOI] [PMID: 11329290]
3.  Cai, H., Dumlao, D., Katz, J.E. and Clarke, S. Identification of the gene and characterization of the activity of the trans-aconitate methyltransferase from Saccharomyces cerevisiae. Biochemistry 40 (2001) 13699–13709. [DOI] [PMID: 11695919]
[EC 2.1.1.144 created 2002]
 
 
EC 2.1.1.145     
Accepted name: trans-aconitate 3-methyltransferase
Reaction: S-adenosyl-L-methionine + trans-aconitate = S-adenosyl-L-homocysteine + (E)-2-(methoxycarbonylmethyl)butenedioate
For diagram of reaction, click here
Glossary: trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
Systematic name: S-adenosyl-L-methionine:(E)-prop-1-ene-1,2,3-tricarboxylate 3′-O-methyltransferase
Comments: Also catalyses the formation of the methyl monoester of cis-aconitate, isocitrate and citrate, but more slowly. While the enzyme from Saccharomyces cerevisiae forms (E)-2-(methoxycarbonylmethyl)butenedioate as the product, that from Escherichia coli forms (E)-3-(methoxycarbonyl)-pent-2-enedioate and is therefore classified as a separate enzyme (cf. EC 2.1.1.144, trans-aconitate 2-methyltransferase)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 235107-12-7
References:
1.  Cai, H. and Clarke, S. A novel methyltransferase catalyzes the esterification of trans-aconitate in Escherichia coli. J. Biol. Chem. 274 (1999) 13470–13479. [DOI] [PMID: 10224113]
2.  Cai, H., Strouse, J., Dumlao, D., Jung, M.E. and Clarke, S. Distinct reactions catalyzed by bacterial and yeast trans-aconitate methyltransferase. Biochemistry 40 (2001) 2210–2219. [DOI] [PMID: 11329290]
[EC 2.1.1.145 created 2002]
 
 
EC 2.3.1.49     
Accepted name: deacetyl-[citrate-(pro-3S)-lyase] S-acetyltransferase
Reaction: S-acetylphosphopantetheine + holo-[citrate (pro-3S)-lyase] = phosphopantetheine + acetyl-[citrate (pro-3S)-lyase]
Other name(s): S-acetyl phosphopantetheine:deacetyl citrate lyase S-acetyltransferase; deacetyl-[citrate-(pro-3S)-lyase] acetyltransferase; S-acetylphosphopantetheine:deacetyl-[citrate-oxaloacetate-lyase((pro-3S)-CH2COO-→acetate)] S-acetyltransferase
Systematic name: S-acetylphosphopantetheine:holo-[citrate (pro-3S)-lyase] S-acetyltransferase
Comments: Both this enzyme and EC 6.2.1.22, [citrate (pro-3S)-lyase] ligase, acetylate and activate EC 4.1.3.6, citrate (pro-3S)-lyase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 42616-18-2
References:
1.  Singh, M., Böttger, B., Brooks, G.C. and Srere, P.A. S-Acetyl phosphopantetheine: deacetyl citrate lyase S-acetyl transferase from Klebsiella aerogenes. Biochem. Biophys. Res. Commun. 53 (1973) 1–9. [DOI] [PMID: 4741546]
[EC 2.3.1.49 created 1976]
 
 
EC 2.3.1.126     
Accepted name: isocitrate O-dihydroxycinnamoyltransferase
Reaction: caffeoyl-CoA + isocitrate = CoA + 2-O-caffeoylisocitrate
Glossary: 2-O-caffeoylisocitrate = (1R,2S)-1-{[3-(E)-(3,4-dihydroxyphenyl)acryloyl]oxy}propane-1,2,3-tricarboxylate = (3S,4R)-3-carboxy-2,3-dideoxy-4-O-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]pentarate
isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate = threo-Ds-isocitrate
Systematic name: caffeoyl-CoA:isocitrate 2-O-(3,4-dihydroxycinnamoyl)transferase
Comments: Feruloyl-CoA and 4-coumaroyl-CoA can also act as donors.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 112352-88-2
References:
1.  Strack, D., Leicht, P., Bokern, M., Wray, V. and Grotjahn, L. Hydroxycinnamic acid-esters of isocitric acid - accumulation and enzymatic-synthesis in Amaranthus cruentus. Phytochemistry 26 (1987) 2919–2922.
[EC 2.3.1.126 created 1990]
 
 
EC 2.3.3.1     
Accepted name: citrate (Si)-synthase
Reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA
For diagram of the citric acid cycle, click here and for diagram of the glyoxylate cycle, click here
Other name(s): (R)-citric synthase; citrate oxaloacetate-lyase [(pro-3S)-CH2COO-→acetyl-CoA]
Systematic name: acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-S)-carboxymethyl-forming]
Comments: The stereospecificity of this enzyme is opposite to that of EC 2.3.3.3, citrate (Re)-synthase, which is found in some anaerobes. Citrate synthase for which the stereospecificity with respect to C-2 of oxaloacetate has not been established are included in EC 2.3.3.16, citrate synthase (unknown stereospecificity).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-96-7
References:
1.  Lenz, H., Buckel, W., Wunderwald, P., Biedermann, G., Buschmeier, V., Eggerer, H., Cornforth, J.W., Redmond, J.W. and Mallaby, R. Stereochemistry of si-citrate synthase and ATP-citrate-lyase reactions. Eur. J. Biochem. 24 (1971) 207–215. [DOI] [PMID: 5157292]
2.  Karpusas, M., Branchaud, B. and Remington, S.J. Proposed mechanism for the condensation reaction of citrate synthase: 1.9-Å structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A. Biochemistry 29 (1990) 2213–2219. [PMID: 2337600]
3.  van Rooyen, J.P., Mienie, L.J., Erasmus, E., De Wet, W.J., Ketting, D., Duran, M. and Wadman, S.K. Identification of the stereoisomeric configurations of methylcitric acid produced by si-citrate synthase and methylcitrate synthase using capillary gas chromatography-mass spectrometry. J. Inherit. Metab. Dis. 17 (1994) 738–747. [PMID: 7707698]
[EC 2.3.3.1 created 1961 as EC 4.1.3.7, transferred 2002 to EC 2.3.3.1, modified 2014]
 
 
EC 2.3.3.2     
Accepted name: decylcitrate synthase
Reaction: lauroyl-CoA + H2O + oxaloacetate = (2S,3S)-2-hydroxytridecane-1,2,3-tricarboxylate + CoA
For diagram of reaction, click here
Other name(s): 2-decylcitrate synthase; (2S,3S)-2-hydroxytridecane-1,2,3-tricarboxylate oxaloacetate-lyase (CoA-acylating)
Systematic name: dodecanoyl-CoA:oxaloacetate C-dodecanoyltransferase (thioester-hydrolysing, 1-carboxyundecyl-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9068-72-8
References:
1.  Maahlén, A. and Gatenbeck, S. A metabolic variation in Penicillium spiculisporum Lehman. II. Purification and some properties of the enzyme synthesizing (-)-decylcitric acid. Acta Chem. Scand. 22 (1968) 2617–2623. [PMID: 5719165]
2.  Maahlén, A. Properties of 2-decylcitrate synthase from Penicillium spiculisporum Lehman. Eur. J. Biochem. 22 (1971) 104–114. [DOI] [PMID: 5099208]
[EC 2.3.3.2 created 1972 as EC 4.1.3.23, transferred 2002 to EC 2.3.3.2]
 
 
EC 2.3.3.3     
Accepted name: citrate (Re)-synthase
Reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA
For diagram of the reactions of the citrate synthases, click here
Other name(s): (R)-citrate synthase; Re-citrate-synthase; citrate oxaloacetate-lyase [(pro-3R)-CH2COO-→acetyl-CoA]
Systematic name: acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-R)-carboxymethyl-forming]
Comments: This enzyme is inactivated by oxygen and is found in some anaerobes. Its stereospecificity is opposite to that of EC 2.3.3.1, citrate (Si)-synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9077-70-7
References:
1.  Dittbrenner, S., Chowdhury, A.A. and Gottschalk, G. The stereospecificity of the (R)-citrates synthase in the presence of p-chloromercuribenzoate. Biochem. Biophys. Res. Commun. 36 (1969) 802–808. [DOI] [PMID: 5808294]
2.  Gottschalk, G. Partial purification and some properties of the (R)-citrate synthase from Clostridium acidi-urici. Eur. J. Biochem. 7 (1969) 301–306. [DOI] [PMID: 4974734]
3.  Gottschalk, G. and Barker, H.A. Synthesis of glutamate and citrate by Clostridium kluyveri. A new type of citrate synthase. Biochemistry 5 (1966) 1125–1133. [PMID: 5958189]
[EC 2.3.3.3 created 1972 as EC 4.1.3.28, transferred 2002 to EC 2.3.3.3]
 
 
EC 2.3.3.4     
Accepted name: decylhomocitrate synthase
Reaction: dodecanoyl-CoA + H2O + 2-oxoglutarate = (3S,4S)-3-hydroxytetradecane-1,3,4-tricarboxylate + CoA
For diagram of reaction, click here
Other name(s): 2-decylhomocitrate synthase; 3-hydroxytetradecane-1,3,4-tricarboxylate 2-oxoglutarate-lyase (CoA-acylating)
Systematic name: dodecanoyl-CoA:2-oxoglutarate C-dodecanoyltransferase (thioester-hydrolysing, 1-carboxyundecyl-forming)
Comments: Decanoyl-CoA can act instead of dodecanoyl-CoA, but 2-oxoglutarate cannot be replaced by oxaloacetate or pyruvate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 51845-40-0
References:
1.  Maahlén, A. Purification and some properties of 2-decylhomocitrate synthase from Penicillium spiculisporum. Eur. J. Biochem. 38 (1973) 32–39. [DOI] [PMID: 4774124]
2.  Brandäge, S., Dahlman, O., Lindqvist, B., Maahlén, A. and Mörch, L. Absolute configuration and enantiospecific synthesis of spiculisporic acid. Acta Chem. Scand. 38B (1984) 837–844.
[EC 2.3.3.4 created 1976 as EC 4.1.3.29, transferred 2002 to EC 2.3.3.4]
 
 
EC 2.3.3.5     
Accepted name: 2-methylcitrate synthase
Reaction: propanoyl-CoA + H2O + oxaloacetate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate + CoA
For diagram of reaction, click here
Glossary: 2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
Other name(s): 2-methylcitrate oxaloacetate-lyase; MCS; methylcitrate synthase; methylcitrate synthetase
Systematic name: propanoyl-CoA:oxaloacetate C-propanoyltransferase (thioester-hydrolysing, 1-carboxyethyl-forming)
Comments: The enzyme acts on acetyl-CoA, propanoyl-CoA, butanoyl-CoA and pentanoyl-CoA. The relative rate of condensation of acetyl-CoA and oxaloacetate is 140% of that of propanoyl-CoA and oxaloacetate, but the enzyme is distinct from EC 2.3.3.1, citrate (Si)-synthase. Oxaloacetate cannot be replaced by glyoxylate, pyruvate or 2-oxoglutarate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 57827-78-8
References:
1.  Uchiyama, H. and Tabuchi, T. Properties of methylcitrate synthase from Candida lipolytica. Agric. Biol. Chem. 40 (1976) 1411–1418.
2.  Textor, S., Wendisch, V.F., De Graaf, A.A., Muller, U., Linder, M.I., Linder, D. and Buckel, W. Propionate oxidation in Escherichia coli: evidence for operation of a methylcitrate cycle in bacteria. Arch. Microbiol. 168 (1997) 428–436. [PMID: 9325432]
3.  Horswill, A.R. and Escalante-Semerena, J.C. Salmonella typhimurium LT2 catabolizes propionate via the 2-methylcitric acid cycle. J. Bacteriol. 181 (1999) 5615–5623. [PMID: 10482501]
4.  Brock, M., Maerker, C., Schütz, A., Völker, U. and Buckel, W. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. Eur. J. Biochem. 269 (2002) 6184–6194. [DOI] [PMID: 12473114]
5.  Domin, N., Wilson, D. and Brock, M. Methylcitrate cycle activation during adaptation of Fusarium solani and Fusarium verticillioides to propionyl-CoA-generating carbon sources. Microbiology 155 (2009) 3903–3912. [DOI] [PMID: 19661181]
[EC 2.3.3.5 created 1978 as EC 4.1.3.31, transferred 2002 to EC 2.3.3.5, modified 2015]
 
 
EC 2.3.3.8     
Accepted name: ATP citrate synthase
Reaction: ADP + phosphate + acetyl-CoA + oxaloacetate = ATP + citrate + CoA
Other name(s): ATP-citric lyase; ATP:citrate oxaloacetate-lyase [(pro-S)-CH2COO-→acetyl-CoA] (ATP-dephosphorylating); acetyl-CoA:oxaloacetate acetyltransferase (isomerizing; ADP-phosphorylating); adenosine triphosphate citrate lyase; citrate cleavage enzyme; citrate-ATP lyase; citric cleavage enzyme; ATP citrate (pro-S)-lyase
Systematic name: acetyl-CoA:oxaloacetate C-acetyltransferase [(pro-S)-carboxymethyl-forming, ADP-phosphorylating]
Comments: The enzyme can be dissociated into components, two of which are identical with EC 4.1.3.34 (citryl-CoA lyase) and EC 6.2.1.18 (citrate—CoA ligase).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9027-95-6
References:
1.  Lill, U., Schreil, A. and Eggerer, H. Isolation of enzymically active fragments formed by limited proteolysis of ATP citrate lyase. Eur. J. Biochem. 125 (1982) 645–650. [DOI] [PMID: 6749502]
2.  Srere, P.A. and Lipmann, F. An enzymatic reaction between citrate, adenosine triphosphate and coenzyme A. J. Am. Chem. Soc. 75 (1953) 4874.
[EC 2.3.3.8 created 1965 as EC 4.1.3.8, modified 1986, transferred 2002 to EC 2.3.3.8]
 
 
EC 2.3.3.14     
Accepted name: homocitrate synthase
Reaction: acetyl-CoA + H2O + 2-oxoglutarate = (2R)-2-hydroxybutane-1,2,4-tricarboxylate + CoA
For diagram of L-Lysine synthesis, click here
Glossary: (R)-homocitrate = (2R)-2-hydroxybutane-1,2,4-tricarboxylate
Other name(s): 2-hydroxybutane-1,2,4-tricarboxylate 2-oxoglutarate-lyase (CoA-acetylating); acetyl-coenzyme A:2-ketoglutarate C-acetyl transferase; homocitrate synthetase; HCS
Systematic name: acetyl-CoA:2-oxoglutarate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming)
Comments: Belongs in the α-aminoadipate pathway of lysine synthesis, along with EC 4.2.1.36, homoaconitate hydratase. The enzyme also acts with oxaloacetate as substrate, but more slowly [2,3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9075-60-9
References:
1.  Strassman, M. and Ceci, L.N. Enzymatic formation of homocitric acid, an intermediate in lysine biosynthesis. Biochem. Biophys. Res. Commun. 14 (1964) 262–267. [DOI] [PMID: 5836514]
2.  Wulandari, A.P., Miyazaki, J., Kobashi, N., Nishiyama, M., Hoshino, T. and Yamane, H. Characterization of bacterial homocitrate synthase involved in lysine biosynthesis. FEBS Lett. 522 (2002) 35–40. [DOI] [PMID: 12095615]
3.  Andi, B., West, A.H. and Cook, P.F. Kinetic mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae. Biochemistry 43 (2004) 11790–11795. [DOI] [PMID: 15362863]
[EC 2.3.3.14 created 1972 as EC 4.1.3.21, transferred 2002 to EC 2.3.3.14]
 
 
EC 2.3.3.16     
Accepted name: citrate synthase (unknown stereospecificity)
Reaction: acetyl-CoA + H2O + oxaloacetate = citrate + CoA
Other name(s): citrate condensing enzyme; CoA-acetylating citrate oxaloacetate-lyase; citrate synthetase; citric synthase; citric-condensing enzyme; citrogenase; condensing enzyme (ambiguous); oxaloacetate transacetase; oxalacetic transacetase
Systematic name: acetyl-CoA:oxaloacetate C-acetyltransferase (thioester-hydrolysing)
Comments: This entry has been included to accommodate those citrate synthases for which the stereospecificity with respect to C-2 of oxaloacetate has not been established [cf. EC 2.3.3.1, citrate (Si)-synthase and EC 2.3.3.3, citrate (Re)-synthase].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lohlein-Werhahn, G., Goepfert, P. and Eggerer, H. Purification and properties of an archaebacterial enzyme: citrate synthase from Sulfolobus solfataricus. Biol. Chem. Hoppe Seyler 369 (1988) 109–113. [PMID: 3130075]
2.  Sievers, M., Stockli, M. and Teuber, M. Purification and properties of citrate synthase from Acetobacter europaeus. FEMS Microbiol. Lett. 146 (1997) 53–58. [DOI] [PMID: 8997706]
3.  Belova, L.L., Sokolov, A.P., Morgunov, I.G. and Trotsenko YuA. Purification and characterization of citrate synthase from Methylobacterium extorquens—a methylotrophic producer of polyhydroxybutyrate. Biochemistry (Mosc.) 62 (1997) 71–76. [PMID: 9113733]
4.  Lee, S., Park, C. and Yim, J. Characterization of citrate synthase purified from Drosophila melanogaster. Mol. Cells 7 (1997) 599–604. [PMID: 9387145]
5.  Maurus, R., Nguyen, N.T., Stokell, D.J., Ayed, A., Hultin, P.G., Duckworth, H.W. and Brayer, G.D. Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases. Biochemistry 42 (2003) 5555–5565. [DOI] [PMID: 12741811]
[EC 2.3.3.16 created 2014]
 
 
EC 2.3.3.18     
Accepted name: 2-phosphinomethylmalate synthase
Reaction: acetyl-CoA + H2O + 3-(hydroxyphosphinoyl)pyruvate = phosphinomethylmalate + CoA
Other name(s): pmmS (gene name)
Systematic name: acetyl-CoA:phosphinopyruvate C-acetyltransferase (thioester-hydrolysing, phosphinomethylmalate-forming)
Comments: The enzyme, characterized from the bacterium Streptomyces hygroscopicus, participates in the pathway for bialaphos biosynthesis. It requires a divalent metal ion and can also act on oxaloacetate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Shimotohno, K.W., Seto, H., Otake, N., Imai, S. and Murakami, T. Studies on the biosynthesis of bialaphos (SF-1293). 8. Purification and characterization of 2-phosphinomethylmalic acid synthase from Streptomyces hygroscopicus SF-1293. J. Antibiot. (Tokyo) 41 (1988) 1057–1065. [PMID: 3170341]
2.  Shimotohno, K.W., Imai, S., Murakami, T. and Seto, H. Purification and characterization of citrate synthase from Streptomyces hygroscopicus SF-1293 and comparison of its properties with those of 2-phosphinomethylmalic acid synthase. Agric. Biol. Chem. 54 (1990) 463–470. [PMID: 1368511]
[EC 2.3.3.18 created 2017]
 
 
EC 2.3.3.19     
Accepted name: 2-phosphonomethylmalate synthase
Reaction: acetyl-CoA + H2O + 3-phosphonopyruvate = (R)-2-(phosphonomethyl)malate + CoA
Other name(s): 2-phosphinomethylmalic acid synthase; PMM synthase
Systematic name: acetyl-CoA:3-phosphonopyruvate C-acetyltransferase
Comments: The enzyme, isolated from several Streptomyces species, participate in the biosynthesis of certain phosphonate antibiotics. The enzyme is analogous to EC 2.3.3.1 (Si)-citrate synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Shimotohno, K., Seto, H., Otake, N., Imai, S. and Satoh, A. Studies on the biosynthesis of bialaphos (SE-1293). 7. The absolute configuration of 2-phosphinomethylmalic acid, a biosynthetic intermediate of bialaphos. J. Antibiot. (Tokyo) 39 (1986) 1356–1359. [PMID: 3781934]
2.  Shimotohno, K.W., Seto, H., Otake, N., Imai, S. and Murakami, T. Studies on the biosynthesis of bialaphos (SF-1293). 8. Purification and characterization of 2-phosphinomethylmalic acid synthase from Streptomyces hygroscopicus SF-1293. J. Antibiot. (Tokyo) 41 (1988) 1057–1065. [PMID: 3170341]
3.  Eliot, A.C., Griffin, B.M., Thomas, P.M., Johannes, T.W., Kelleher, N.L., Zhao, H. and Metcalf, W.W. Cloning, expression, and biochemical characterization of Streptomyces rubellomurinus genes required for biosynthesis of antimalarial compound FR900098. Chem. Biol. 15 (2008) 765–770. [DOI] [PMID: 18721747]
[EC 2.3.3.19 created 2017]
 
 
EC 2.4.2.52     
Accepted name: triphosphoribosyl-dephospho-CoA synthase
Reaction: ATP + 3′-dephospho-CoA = 2′-(5-triphospho-α-D-ribosyl)-3′-dephospho-CoA + adenine
For diagram of holo-citrate-lyase biosynthesis, click here
Other name(s): 2′-(5′′-triphosphoribosyl)-3-dephospho-CoA synthase; ATP:dephospho-CoA 5-triphosphoribosyl transferase; CitG; ATP:dephospho-CoA 5′-triphosphoribosyl transferase; MdcB; ATP:3-dephospho-CoA 5′′-triphosphoribosyltransferase; MadG
Systematic name: ATP:3′-dephospho-CoA 5-triphospho-α-D-ribosyltransferase
Comments: ATP cannot be replaced by GTP, CTP, UTP, ADP or AMP. The reaction involves the formation of a new α (1′′→2′) glycosidic bond between the two ribosyl moieties, with concomitant displacement of the adenine moiety of ATP [1,4]. The 2′-(5-triphosphoribosyl)-3′-dephospho-CoA produced can be transferred by EC 2.7.7.61, citrate lyase holo-[acyl-carrier protein] synthase, to the apo-acyl-carrier protein subunit (γ-subunit) of EC 4.1.3.6, citrate (pro-3S) lyase, thus converting it from an apo-enzyme into a holo-enzyme [1,3]. Alternatively, it can be transferred to the apo-ACP subunit of malonate decarboxylase by the action of EC 2.7.7.66, malonate decarboxylase holo-[acyl-carrier protein] synthase [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 313345-38-9
References:
1.  Schneider, K., Dimroth, P. and Bott, M. Biosynthesis of the prosthetic group of citrate lyase. Biochemistry 39 (2000) 9438–9450. [DOI] [PMID: 10924139]
2.  Schneider, K., Dimroth, P. and Bott, M. Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group. FEBS Lett. 483 (2000) 165–168. [DOI] [PMID: 11042274]
3.  Schneider, K., Kästner, C.N., Meyer, M., Wessel, M., Dimroth, P. and Bott, M. Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group. J. Bacteriol. 184 (2002) 2439–2446. [DOI] [PMID: 11948157]
4.  Hoenke, S., Wild, M.R. and Dimroth, P. Biosynthesis of triphosphoribosyl-dephospho-coenzyme A, the precursor of the prosthetic group of malonate decarboxylase. Biochemistry 39 (2000) 13223–13232. [DOI] [PMID: 11052675]
[EC 2.4.2.52 created 2002 as EC 2.7.8.25, modified 2008, transferred 2013 to EC 2.4.2.52]
 
 
EC 2.7.1.37      
Transferred entry: protein kinase. Now divided into EC 2.7.11.1 (non-specific serine/threonine protein kinase), EC 2.7.11.8 (Fas-activated serine/threonine kinase), EC 2.7.11.9 (Goodpasture-antigen-binding protein kinase), EC 2.7.11.10 (IκB kinase), EC 2.7.11.11 (cAMP-dependent protein kinase), EC 2.7.11.12 (cGMP-dependent protein kinase), EC 2.7.11.13 (protein kinase C), EC 2.7.11.21 (polo kinase), EC 2.7.11.22 (cyclin-dependent kinase), EC 2.7.11.24 (mitogen-activated protein kinase), EC 2.7.11.25 (mitogen-activated protein kinase kinase kinase), EC 2.7.11.30 (receptor protein serine/threonine kinase) and EC 2.7.12.1 (dual-specificity kinase)
[EC 2.7.1.37 created 1961 (EC 2.7.1.70 incorporated 2004), deleted 2005]
 
 
EC 2.7.1.116      
Transferred entry: [isocitrate dehydrogenase (NADP+)] kinase. Now EC 2.7.11.5, [isocitrate dehydrogenase (NADP+)] kinase
[EC 2.7.1.116 created 1986, deleted 2005]
 
 
EC 2.7.1.128      
Transferred entry: [acetyl-CoA carboxylase] kinase. Now EC 2.7.11.27, [acetyl-CoA carboxylase] kinase
[EC 2.7.1.128 created 1990 (EC 2.7.1.111 created 1984, incorporated 1992), deleted 2005]
 
 
EC 2.7.7.61     
Accepted name: citrate lyase holo-[acyl-carrier protein] synthase
Reaction: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA + apo-[citrate (pro-3S)-lyase] = diphosphate + holo-[citrate (pro-3S)-lyase]
For diagram of reaction, click here
Other name(s): 2′-(5′′-phosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase; CitX; holo-ACP synthase (ambiguous); 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase adenylyltransferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase adenylyltransferase; holo-citrate lyase synthase (incorrect); 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Systematic name: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-[citrate (pro-3S)-lyase] 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Comments: The γ-subunit of EC 4.1.3.6, citrate (pro-3S) lyase, serves as an acyl-carrier protein (ACP) and contains the prosthetic group 2′-(5-triphosphoribosyl)-3′-dephospho-CoA [1,3]. Synthesis and attachment of the prosthetic group requires the concerted action of this enzyme and EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase [1]. In the enzyme from Escherichia coli, the prosthetic group is attached to serine-14 of the ACP via a phosphodiester bond.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 312492-44-7
References:
1.  Schneider, K., Dimroth, P. and Bott, M. Biosynthesis of the prosthetic group of citrate lyase. Biochemistry 39 (2000) 9438–9450. [DOI] [PMID: 10924139]
2.  Schneider, K., Dimroth, P. and Bott, M. Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group. FEBS Lett. 483 (2000) 165–168. [DOI] [PMID: 11042274]
3.  Schneider, K., Kästner, C.N., Meyer, M., Wessel, M., Dimroth, P. and Bott, M. Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group. J. Bacteriol. 184 (2002) 2439–2446. [DOI] [PMID: 11948157]
[EC 2.7.7.61 created 2002, modified 2008]
 
 
EC 2.7.7.66     
Accepted name: malonate decarboxylase holo-[acyl-carrier protein] synthase
Reaction: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA + malonate decarboxylase apo-[acyl-carrier protein] = malonate decarboxylase holo-[acyl-carrier protein] + diphosphate
For diagram of reaction, click here
Other name(s): holo ACP synthase (ambiguous); 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo ACP 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA transferase; MdcG; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-malonate-decarboxylase adenylyltransferase; holo-malonate-decarboxylase synthase (incorrect)
Systematic name: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-malonate-decarboxylase 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Comments: The δ subunit of malonate decarboxylase serves as an an acyl-carrier protein (ACP) and contains the prosthetic group 2-(5-triphosphoribosyl)-3-dephospho-CoA. Two reactions are involved in the production of the holo-ACP form of this enzyme. The first reaction is catalysed by EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase. The resulting prosthetic group is then attached to the ACP subunit via a phosphodiester linkage to a serine residue, thus forming the holo form of the enzyme, in a manner analogous to that of EC 2.7.7.61, citrate lyase holo-[acyl-carrier protein] synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hoenke, S., Wild, M.R. and Dimroth, P. Biosynthesis of triphosphoribosyl-dephospho-coenzyme A, the precursor of the prosthetic group of malonate decarboxylase. Biochemistry 39 (2000) 13223–13232. [DOI] [PMID: 11052675]
2.  Hoenke, S., Schmid, M. and Dimroth, P. Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases. Biochemistry 39 (2000) 13233–13240. [DOI] [PMID: 11052676]
[EC 2.7.7.66 created 2008]
 
 
EC 2.7.8.25      
Transferred entry: triphosphoribosyl-dephospho-CoA synthase. Now EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase
[EC 2.7.8.25 created 2002, modified 2008, deleted 2013]
 
 
EC 2.7.11.5     
Accepted name: [isocitrate dehydrogenase (NADP+)] kinase
Reaction: ATP + [isocitrate dehydrogenase (NADP+)] = ADP + [isocitrate dehydrogenase (NADP+)] phosphate
Other name(s): [isocitrate dehydrogenase (NADP)] kinase; ICDH kinase/phosphatase; IDH kinase; IDH kinase/phosphatase; IDH-K/P; IDHK/P; isocitrate dehydrogenase kinase (phosphorylating); isocitrate dehydrogenase kinase/phosphatase; STK3
Systematic name: ATP:[isocitrate dehydrogenase (NADP+)] phosphotransferase
Comments: The enzyme has no activating compound but is specific for its substrate. Phosphorylates and inactivates EC 1.1.1.42, isocitrate dehydrogenase (NADP+).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 83682-93-3
References:
1.  Wang, J.Y.J. and Koshland, D.E., Jr. The reversible phosphorylation of isocitrate dehydrogenase of Salmonella typhimurium. Arch. Biochem. Biophys. 218 (1982) 59–67. [DOI] [PMID: 6756316]
2.  Miller, S.P., Karschnia, E.J., Ikeda, T.P. and LaPorte, D.C. Isocitrate dehydrogenase kinase/phosphatase. Kinetic characteristics of the wild-type and two mutant proteins. J. Biol. Chem. 271 (1996) 19124–19128. [DOI] [PMID: 8702587]
3.  Singh, S.K., Matsuno, K., LaPorte, D.C. and Banaszak, L.J. Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 Å. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase. J. Biol. Chem. 276 (2001) 26154–26163. [DOI] [PMID: 11290745]
4.  Oudot, C., Cortay, J.C., Blanchet, C., Laporte, D.C., Di Pietro, A., Cozzone, A.J. and Jault, J.M. The "catalytic" triad of isocitrate dehydrogenase kinase/phosphatase from E. coli and its relationship with that found in eukaryotic protein kinases. Biochemistry 40 (2001) 3047–3055. [DOI] [PMID: 11258918]
[EC 2.7.11.5 created 1986 as EC 2.7.1.116, transferred 2005 to EC 2.7.11.5]
 
 
EC 2.7.11.27     
Accepted name: [acetyl-CoA carboxylase] kinase
Reaction: ATP + [acetyl-CoA carboxylase] = ADP + [acetyl-CoA carboxylase] phosphate
Other name(s): acetyl coenzyme A carboxylase kinase (phosphorylating); acetyl-CoA carboxylase bound kinase; acetyl-CoA carboxylase kinase; acetyl-CoA carboxylase kinase (cAMP-independent); acetyl-CoA carboxylase kinase 2; acetyl-CoA carboxylase kinase-2; acetyl-CoA carboxylase kinase-3 (AMP-activated); acetyl-coenzyme A carboxylase kinase; ACK2; ACK3; AMPK; I-peptide kinase; STK5
Systematic name: ATP:[acetyl-CoA carboxylase] phosphotransferase
Comments: Phosphorylates and inactivates EC 6.4.1.2, acetyl-CoA carboxylase, which can be dephosphorylated and reactivated by EC 3.1.3.17, [phosphorylase] phosphatase. The enzyme is more active towards the dimeric form of acetyl-CoA carboxylase than the polymeric form [5]. Phosphorylates serine residues.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 77000-06-7
References:
1.  Jamil, H. and Madsen, N.B. Phosphorylation state of acetyl-coenzyme A carboxylase. I. Linear inverse relationship to activity ratios at different citrate concentrations. J. Biol. Chem. 262 (1987) 630–637. [PMID: 2879833]
2.  Lent, B. and Kim, K.H. Purification and properties of a kinase which phosphorylates and inactivates acetyl-CoA carboxylase. J. Biol. Chem. 257 (1982) 1897–1901. [PMID: 6120170]
3.  Munday, M.R. and Hardie, D.G. Isolation of three cyclic-AMP-independent acetyl-CoA carboxylase kinases from lactating rat mammary gland and characterization of their effects on enzyme activity. Eur. J. Biochem. 141 (1984) 617–627. [DOI] [PMID: 6146523]
4.  Mohamed, A.H., Huang, W.Y., Huang, W., Venkatachalam, K.V. and Wakil, S.J. Isolation and characterization of a novel acetyl-CoA carboxylase kinase from rat liver. J. Biol. Chem. 269 (1994) 6859–6865. [PMID: 7907095]
5.  Heesom, K.J., Moule, S.K. and Denton, R.M. Purification and characterisation of an insulin-stimulated protein-serine kinase which phosphorylates acetyl-CoA carboxylase. FEBS Lett. 422 (1998) 43–46. [DOI] [PMID: 9475166]
[EC 2.7.11.27 created 1990 as EC 2.7.1.128 (EC 2.7.1.111 created 1984, incorporated 1992), transferred 2005 to EC 2.7.11.27]
 
 
EC 2.8.3.10     
Accepted name: citrate CoA-transferase
Reaction: acetyl-CoA + citrate = acetate + (3S)-citryl-CoA
Systematic name: acetyl-CoA:citrate CoA-transferase
Comments: The enzyme is a component of EC 4.1.3.6 [citrate (pro-3S)-lyase]. Also catalyses the transfer of thioacyl carrier protein from its acetyl thioester to citrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 65187-14-6
References:
1.  Dimroth, P., Loyal, R. and Eggerer, H. Characterization of the isolated transferase subunit of citrate lyase as a CoA-transferase. Evidence against a covalent enzyme-substrate intermediate. Eur. J. Biochem. 80 (1977) 479–488. [DOI] [PMID: 336371]
[EC 2.8.3.10 created 1984]
 
 
EC 2.8.3.11     
Accepted name: citramalate CoA-transferase
Reaction: acetyl-CoA + citramalate = acetate + (3S)-citramalyl-CoA
Systematic name: acetyl-CoA:citramalate CoA-transferase
Comments: The enzyme is a component of EC 4.1.3.22 citramalate lyase. Also catalyses the transfer of thioacyl carrier protein from its acetyl thioester to citramalate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9033-60-7
References:
1.  Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469–477. [DOI] [PMID: 923590]
[EC 2.8.3.11 created 1984]
 
 
EC 3.1.2.16     
Accepted name: citrate-lyase deacetylase
Reaction: acetyl-[citrate (pro-3S)-lyase] + H2O = holo-[citrate (pro-3S)-lyase] + acetate
Other name(s): [citrate-(pro-3S)-lyase] thiolesterase; acetyl-S-(acyl-carrier protein) enzyme thioester hydrolase; citrate lyase deacetylase; [citrate-(pro-3S)-lyase](acetyl-form) hydrolase
Systematic name: acetyl-[citrate-(pro-3S)-lyase] hydrolase
Comments: In the proteobacterium Rubrivivax gelatinosus, this enzyme modulates the activity of EC 4.1.3.6, citrate (pro-3S)-lyase, by converting it from its active acetyl form into its inactive thiol form by removal of its acetyl groups [2]. The activity of citrate-lyase deacetylase is itself inhibited by L-glutamate [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 58319-93-0
References:
1.  Giffhorn, F. and Gottschalk, G. Inactivation of citrate lyase from Rhodopseudomonas gelatinosa by a specific deacetylase and inhibition of this inactivation by L-(+)-glutamate. J. Bacteriol. 124 (1975) 1052–1061. [PMID: 356]
2.  Giffhorn, F., Rode, H., Kuhn, A. and Gottschalk, G. Citrate lyase deacetylase of Rhodopseudomonas gelatinosa. Isolation of the enzyme and studies on the inhibition by L-glutamate. Eur. J. Biochem. 111 (1980) 461–471. [DOI] [PMID: 7460909]
[EC 3.1.2.16 created 1989]
 
 
EC 3.1.2.29     
Accepted name: fluoroacetyl-CoA thioesterase
Reaction: fluoroacetyl-CoA + H2O = fluoroacetate + CoA
Systematic name: fluoroacetyl-CoA hydrolase
Comments: Fluoroacetate is extremely toxic. It reacts with CoA to form fluoroacetyl-CoA, which substitutes for acetyl CoA and reacts with EC 2.3.3.1 (citrate synthase) to produce fluorocitrate, a metabolite of which binds very tightly to EC 4.2.1.3 (aconitase) and halts the TCA cycle. This enzyme hydrolyses fluoroacetyl-CoA before it can react with citrate synthase, and thus confers fluoroacetate resistance on the organisms that produce it. It has been described in the poisonous plant Dichapetalum cymosum and the bacterium Streptomyces cattleya, both of which are fluoroacetate producers.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Meyer, J.J.M., Grobbelaar, N., Vleggaar, R. and Louw, A.I. Fluoroacetyl-coenzyme-A hydrolase-like activity in Dichapetalum cymosum. J. Plant Physiol. 139 (1992) 369–372.
2.  Huang, F., Haydock, S.F., Spiteller, D., Mironenko, T., Li, T.L., O'Hagan, D., Leadlay, P.F. and Spencer, J.B. The gene cluster for fluorometabolite biosynthesis in Streptomyces cattleya: a thioesterase confers resistance to fluoroacetyl-coenzyme A. Chem. Biol. 13 (2006) 475–484. [DOI] [PMID: 16720268]
3.  Dias, M.V., Huang, F., Chirgadze, D.Y., Tosin, M., Spiteller, D., Dry, E.F., Leadlay, P.F., Spencer, J.B. and Blundell, T.L. Structural basis for the activity and substrate specificity of fluoroacetyl-CoA thioesterase FlK. J. Biol. Chem. 285 (2010) 22495–22504. [DOI] [PMID: 20430898]
[EC 3.1.2.29 created 2011]
 
 
EC 3.4.13.20     
Accepted name: β-Ala-His dipeptidase
Reaction: Preferential hydrolysis of the β-Ala┼His dipeptide (carnosine), and also anserine, Xaa┼His dipeptides and other dipeptides including homocarnosine
Other name(s): serum carnosinase
Comments: Present in the serum of humans and higher primates, but not in the serum of other mammals. Activated by Cd2+ and citrate. Belongs in peptidase family M20.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 525589-43-9
References:
1.  Lenney, J.F., George, R.P., Weiss, A.M., Kucera, C.M., Chan, P.W.H. and Rinzler, G.S. Human serum carnosinase: characterization, distinction from cellular carnosinase, and activation by cadmium. Clin. Chim. Acta 123 (1982) 221–231. [DOI] [PMID: 7116644]
2.  Jackson, M.C., Kucera, C.M. and Lenney, J.F. Purification and properties of human serum carnosinase. Clin. Chim. Acta 196 (1991) 193–206. [DOI] [PMID: 1903095]
[EC 3.4.13.20 created 1992]
 
 
EC 3.6.3.34      
Transferred entry: iron-chelate-transporting ATPase; now recognized to be at least 3 separate enzymes EC 7.2.2.16, iron(III) hydroxamate ABC transporter, EC 7.2.2.17, ferric enterobactin ABC transporter, and EC 7.2.2.18, ferric citrate ABC transporter
[EC 3.6.3.34 created 2000, deleted 2018]
 
 
EC 3.11.1.3     
Accepted name: phosphonopyruvate hydrolase
Reaction: 3-phosphonopyruvate + H2O = pyruvate + phosphate
For diagram of phosphonate metabolism, click here
Other name(s): PPH
Comments: Highly specific for phosphonopyruvate as substrate [2]. The reaction is not inhibited by phosphate but is inhibited by the phosphonates phosphonoformic acid, hydroxymethylphosphonic acid and 3-phosphonopropanoic acid [2]. The enzyme is activated by the divalent cations Co2+, Mg2+ and Mn2+. This enzyme is a member of the phosphoenolpyruvate mutase/isocitrate lyase superfamily [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ternan, N.G., Hamilton, J.T. and Quinn, J.P. Initial in vitro characterisation of phosphonopyruvate hydrolase, a novel phosphate starvation-independent, carbon-phosphorus bond cleavage enzyme in Burkholderia cepacia Pal6. Arch. Microbiol. 173 (2000) 35–41. [PMID: 10648102]
2.  Kulakova, A.N., Wisdom, G.B., Kulakov, L.A. and Quinn, J.P. The purification and characterization of phosphonopyruvate hydrolase, a novel carbon-phosphorus bond cleavage enzyme from Variovorax sp. Pal2. J. Biol. Chem. 278 (2003) 23426–23431. [DOI] [PMID: 12697754]
3.  Chen, C.C., Han, Y., Niu, W., Kulakova, A.N., Howard, A., Quinn, J.P., Dunaway-Mariano, D. and Herzberg, O. Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily. Biochemistry 45 (2006) 11491–11504. [DOI] [PMID: 16981709]
[EC 3.11.1.3 created 2007]
 
 
EC 4.1.1.112     
Accepted name: oxaloacetate decarboxylase
Reaction: oxaloacetate = pyruvate + CO2
Other name(s): oxaloacetate β-decarboxylase; oxalacetic acid decarboxylase; oxalate β-decarboxylase; oxaloacetate carboxy-lyase
Systematic name: oxaloacetate carboxy-lyase (pyruvate-forming)
Comments: Requires a divalent metal cation. The enzymes from the fish Gadus morhua (Atlantic cod) and the bacterium Micrococcus luteus prefer Mn2+, while those from the bacteria Pseudomonas putida and Pseudomonas aeruginosa prefer Mg2+. Unlike EC 7.2.4.2 [oxaloacetate decarboxylase (Na+ extruding)], there is no evidence of the enzyme’s involvement in Na+ transport.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-98-0
References:
1.  Schmitt, A., Bottke, I. and Siebert, G. Eigenschaften einer Oxaloacetat-Decarboxylase aus Dorschmuskulatur. Hoppe-Seyler's Z. Physiol. Chem. 347 (1966) 18–34. [PMID: 5972993]
2.  Herbert, D. Oxalacetic carboxylase of Micrococcus lysodeikticus. Methods Enzymol. 1 (1955) 753–757.
3.  Horton, A.A. and Kornberg, H.L. Oxaloacetate 4-carboxy-lyase from Pseudomonas ovalis chester. Biochim. Biophys. Acta 89 (1964) 381–383. [PMID: 14205502]
4.  Sender, P.D., Martin, M.G., Peiru, S. and Magni, C. Characterization of an oxaloacetate decarboxylase that belongs to the malic enzyme family. FEBS Lett. 570 (2004) 217–222. [PMID: 15251467]
5.  Narayanan, B.C., Niu, W., Han, Y., Zou, J., Mariano, P.S., Dunaway-Mariano, D. and Herzberg, O. Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily. Biochemistry 47 (2008) 167–182. [PMID: 18081320]
[EC 4.1.1.112 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, part transferred 2018 to EC 4.1.1.112]
 
 
EC 4.1.3.1     
Accepted name: isocitrate lyase
Reaction: isocitrate = succinate + glyoxylate
For diagram of the glyoxylate cycle, click here
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
Other name(s): isocitrase; isocitritase; isocitratase; threo-Ds-isocitrate glyoxylate-lyase; isocitrate glyoxylate-lyase
Systematic name: isocitrate glyoxylate-lyase (succinate-forming)
Comments: The isomer of isocitrate involved is (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate [3].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9045-78-7
References:
1.  McFadden, B.A. and Howes, W.V. Crystallisation and some properties of isocitrate lyase from Pseudomonas indigofera. J. Biol. Chem. 238 (1963) 1737–1742.
2.  Shiio, I., Shiio, T. and McFadden, B.A. Isocitrate lyase from Pseudomonas indigofera. I. Preparation, amino acid composition and molecular weight. Biochim. Biophys. Acta 96 (1965) 114–122. [DOI] [PMID: 14285253]
3.  Vickery, H.B. A suggested new nomenclature for the isomers of isocitric acid. J. Biol. Chem. 237 (1962) 1739–1741. [PMID: 13925783]
[EC 4.1.3.1 created 1961]
 
 
EC 4.1.3.6     
Accepted name: citrate (pro-3S)-lyase
Reaction: citrate = acetate + oxaloacetate
Other name(s): citrase; citratase; citritase; citridesmolase; citrate aldolase; citric aldolase; citrate lyase; citrate oxaloacetate-lyase; citrate oxaloacetate-lyase [(pro-3S)-CH2COO-→acetate]
Systematic name: citrate oxaloacetate-lyase (forming acetate from the pro-S carboxymethyl group of citrate)
Comments: The enzyme can be dissociated into components, two of which are identical with EC 2.8.3.10 (citrate CoA-transferase) and EC 4.1.3.34 (citryl-CoA lyase). EC 3.1.2.16, citrate lyase deacetylase, deacetylates and inactivates the enzyme.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9012-83-3
References:
1.  Dagley, S. and Dawes, E.A. Citridesmolase: its properties and mode of action. Biochim. Biophys. Acta 17 (1955) 177–184. [DOI] [PMID: 13239657]
2.  Dimroth, P., Loyal, R. and Eggerer, H. Characterization of the isolated transferase subunit of citrate lyase as a CoA-transferase. Evidence against a covalent enzyme-substrate intermediate. Eur. J. Biochem. 80 (1977) 479–488. [DOI] [PMID: 336371]
[EC 4.1.3.6 created 1961]
 
 
EC 4.1.3.7      
Transferred entry: citrate (Si)-synthase. Now EC 2.3.3.1, citrate (Si)-synthase
[EC 4.1.3.7 created 1961, deleted 2002]
 
 
EC 4.1.3.8      
Transferred entry: ATP citrate (pro-S)-lyase. Now EC 2.3.3.8, ATP citrate synthase
[EC 4.1.3.8 created 1965, modified 1986, deleted 2002]
 
 
EC 4.1.3.21      
Transferred entry: homocitrate synthase. Now EC 2.3.3.14, homocitrate synthase
[EC 4.1.3.21 created 1972, deleted 2002]
 
 
EC 4.1.3.22     
Accepted name: citramalate lyase
Reaction: (2S)-2-hydroxy-2-methylbutanedioate = acetate + pyruvate
For diagram of reaction, click here
Glossary: (+)-citramalate = (2S)-2-hydroxy-2-methylbutanedioate
Other name(s): citramalate pyruvate-lyase; citramalate synthase; citramalic-condensing enzyme; citramalate synthetase; citramalic synthase; (S)-citramalate lyase; (+)-citramalate pyruvate-lyase; citramalate pyruvate lyase; (3S)-citramalate pyruvate-lyase; (2S)-2-hydroxy-2-methylbutanedioate pyruvate-lyase
Systematic name: (2S)-2-hydroxy-2-methylbutanedioate pyruvate-lyase (acetate-forming)
Comments: The enzyme can be dissociated into components, two of which are identical with EC 2.8.3.11 (citramalate CoA-transferase) and EC 4.1.3.25 (citramalyl-CoA lyase).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9027-93-4
References:
1.  Barker, H.A. Citramalate lyase of Clostridium tetanomorphum. Arch. Mikrobiol. 59 (1967) 4–12. [PMID: 4301387]
2.  Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469–477. [DOI] [PMID: 923590]
[EC 4.1.3.22 created 1972]
 
 
EC 4.1.3.23      
Transferred entry: decylcitrate synthase. Now EC 2.3.3.2, decylcitrate synthase
[EC 4.1.3.23 created 1972, deleted 2002]
 
 
EC 4.1.3.24     
Accepted name: malyl-CoA lyase
Reaction: (1) (S)-malyl-CoA = acetyl-CoA + glyoxylate
(2) (2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate
For diagram of the 3-hydroxypropanoate cycle, click here
Glossary: (S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
(2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): malyl-coenzyme A lyase; (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase; mclA (gene name); mcl1 (gene name); (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase (acetyl-CoA-forming); L-malyl-CoA lyase
Systematic name: (S)-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)
Comments: The enzymes from Rhodobacter species catalyse a step in the ethylmalonyl-CoA pathway for acetate assimilation [3,5]. The enzyme from halophilic bacteria participate in the methylaspartate cycle and catalyse the reaction in the direction of malyl-CoA formation [6]. The enzyme from the bacterium Chloroflexus aurantiacus, which participates in the 3-hydroxypropanoate cycle for carbon assimilation, also has the activity of EC 4.1.3.25, (3S)-citramalyl-CoA lyase [2,4].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 37290-67-8
References:
1.  Tuboi, S. and Kikuchi, G. Enzymic cleavage of malyl-Coenzyme A into acetyl-Coenzyme A and glyoxylic acid. Biochim. Biophys. Acta 96 (1965) 148–153. [DOI] [PMID: 14285256]
2.  Herter, S., Busch, A. and Fuchs, G. L-Malyl-coenzyme A lyase/β-methylmalyl-coenzyme A lyase from Chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic CO2 fixation. J. Bacteriol. 184 (2002) 5999–6006. [DOI] [PMID: 12374834]
3.  Meister, M., Saum, S., Alber, B.E. and Fuchs, G. L-Malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. J. Bacteriol. 187 (2005) 1415–1425. [DOI] [PMID: 15687206]
4.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [DOI] [PMID: 17259315]
5.  Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249–1258. [DOI] [PMID: 20047909]
6.  Borjian, F., Han, J., Hou, J., Xiang, H., Zarzycki, J. and Berg, I.A. Malate Synthase and β-Methylmalyl Coenzyme A Lyase Reactions in the Methylaspartate Cycle in Haloarcula hispanica. J. Bacteriol. 199 (2017) . [DOI] [PMID: 27920298]
[EC 4.1.3.24 created 1972, modified 2014]
 
 
EC 4.1.3.25     
Accepted name: (S)-citramalyl-CoA lyase
Reaction: (3S)-citramalyl-CoA = acetyl-CoA + pyruvate
For diagram of the 3-hydroxypropanoate cycle, click here
Other name(s): citramalyl coenzyme A lyase (ambiguous); (+)-CMA-CoA lyase; (3S)-citramalyl-CoA pyruvate-lyase; Mcl (ambiguous); citramalyl-CoA lyase (ambiguous)
Systematic name: (3S)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)
Comments: Requires Mg2+ ions for activity [3]. The enzyme from the bacterium Clostridium tetanomorphum is a component of EC 4.1.3.22, citramalate lyase [2]. It also acts on (3S)-citramalyl thioacyl-carrier protein [2]. The enzyme from the bacterium Chloroflexus aurantiacus also has the activity of EC 4.1.3.24, malyl-CoA lyase [3]. It has no activity with (3R)-citramalyl-CoA (cf. EC 4.1.3.46, (R)-citramalyl-CoA lyase) [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37290-68-9
References:
1.  Cooper, R.A. and Kornberg, H.L. The utilization of itaconate by Pseudomonas sp. Biochem. J. 91 (1964) 82–91. [PMID: 4284209]
2.  Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469–477. [DOI] [PMID: 923590]
3.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [DOI] [PMID: 17259315]
[EC 4.1.3.25 created 1972, modified 2014]
 
 
EC 4.1.3.28      
Transferred entry: citrate (Re)-synthase. Now EC 2.3.3.3, citrate (Re)-synthase
[EC 4.1.3.28 created 1972, deleted 2002]
 
 
EC 4.1.3.29      
Transferred entry: decylhomocitrate synthase. Now EC 2.3.3.4, decylhomocitrate synthase
[EC 4.1.3.29 created 1976, deleted 2002]
 
 
EC 4.1.3.30     
Accepted name: methylisocitrate lyase
Reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = succinate + pyruvate
Glossary: (2S,3R)-2-methylisocitrate = (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = threo-Ds-2-methylisocitrate
Other name(s): 2-methylisocitrate lyase; MICL; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase
Systematic name: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming)
Comments: The enzyme acts on threo-Ds-2-methylisocitrate, but not on threo-Ds-isocitrate, threo-DL-isocitrate or erythro-Ls-isocitrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 57827-77-7
References:
1.  Tabuchi, T. and Satoh, T. Distinction between isocitrate lyase and methylisocitrate lyase in Candida lipolytica. Agric. Biol. Chem. 40 (1976) 1863–1869.
2.  Tabuchi, T. and Satoh, T. Purification and properties of methylisocitrate lyase, a key enzyme in propionate metabolism, from Candida lipolytica. Agric. Biol. Chem. 41 (1977) 169–174.
[EC 4.1.3.30 created 1978]
 
 


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