The Enzyme Database

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EC 1.1.1.291     
Accepted name: 2-hydroxymethylglutarate dehydrogenase
Reaction: (S)-2-hydroxymethylglutarate + NAD+ = 2-formylglutarate + NADH + H+
For diagram of nicotinate catabolism, click here
Other name(s): HgD
Systematic name: (S)-2-hydroxymethylglutarate:NAD+ oxidoreductase
Comments: NADP+ cannot replace NAD+. Forms part of the nicotinate-fermentation catabolism pathway in Eubacterium barkeri. Other enzymes involved in this pathway are EC 1.17.1.5 (nicotinate dehydrogenase), EC 1.3.7.1 (6-hydroxynicotinate reductase), EC 3.5.2.18 (enamidase), EC 5.4.99.4 (2-methyleneglutarate mutase), EC 5.3.3.6 (methylitaconate Δ-isomerase), EC 4.2.1.85 (dimethylmaleate hydratase) and EC 4.1.3.32 (2,3-dimethylmalate lyase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1073478-76-8
References:
1.  Alhapel, A., Darley, D.J., Wagener, N., Eckel, E., Elsner, N. and Pierik, A.J. Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri. Proc. Natl. Acad. Sci. USA 103 (2006) 12341–12346. [DOI] [PMID: 16894175]
[EC 1.1.1.291 created 2006]
 
 
EC 2.8.3.7      
Deleted entry: succinate—citramalate CoA-transferase. The activity has now been shown to be due to two separate enzymes described by EC 2.8.3.22, succinyl-CoA—L-malate CoA-transferase, and EC 2.8.3.20, succinyl-CoA—D-citramalate CoA-transferase
[EC 2.8.3.7 created 1972, deleted 2014]
 
 
EC 2.8.3.20     
Accepted name: succinyl-CoA—D-citramalate CoA-transferase
Reaction: (1) succinyl-CoA + (R)-citramalate = succinate + (R)-citramalyl-CoA
(2) succinyl-CoA + (R)-malate = succinate + (R)-malyl-CoA
Glossary: (R)-citramalate = (2R)-2-hydroxy-2-methylbutanedioate
(R)-malate = (2R)-2-hydroxybutanedioate
(R)-malyl-CoA = (3R)-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): Sct
Systematic name: succinyl-CoA:(R)-citramalate CoA-transferase
Comments: The enzyme, purified from the bacterium Clostridium tetanomorphum, can also accept itaconate as acceptor, with lower efficiency.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Friedmann, S., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:D-citramalate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 6460–6468. [DOI] [PMID: 16952935]
[EC 2.8.3.20 created 2014]
 
 
EC 2.8.3.22     
Accepted name: succinyl-CoA—L-malate CoA-transferase
Reaction: (1) succinyl-CoA + (S)-malate = succinate + (S)-malyl-CoA
(2) succinyl-CoA + (S)-citramalate = succinate + (S)-citramalyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Glossary: (S)-citramalate = (2S)-2-hydroxy-2-methylbutanedioate
(S)-malate = (2S)-2-hydroxybutanedioate
(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
Other name(s): SmtAB
Systematic name: succinyl-CoA:(S)-malate CoA-transferase
Comments: The enzyme, purified from the bacterium Chloroflexus aurantiacus, can also accept itaconate as acceptor, with lower efficiency. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Friedmann, S., Steindorf, A., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 2646–2655. [DOI] [PMID: 16547052]
[EC 2.8.3.22 created 2014]
 
 
EC 3.5.2.18     
Accepted name: enamidase
Reaction: 6-oxo-1,4,5,6-tetrahydronicotinate + 2 H2O = 2-formylglutarate + NH3
For diagram of nicotinate catabolism, click here
Systematic name: 6-oxo-1,4,5,6-tetrahydronicotinate amidohydrolase
Comments: Contains iron and Zn2+. Forms part of the nicotinate-fermentation catabolism pathway in Eubacterium barkeri. Other enzymes involved in this pathway are EC 1.17.1.5 (nicotinate dehydrogenase), EC 1.3.7.1 (6-hydroxynicotinate reductase), EC 1.1.1.291 (2-hydroxymethylglutarate dehydrogenase), EC 5.4.99.4 (2-methyleneglutarate mutase), EC 5.3.3.6 (methylitaconate Δ-isomerase), EC 4.2.1.85 (dimethylmaleate hydratase) and EC 4.1.3.32 (2,3-dimethylmalate lyase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Alhapel, A., Darley, D.J., Wagener, N., Eckel, E., Elsner, N. and Pierik, A.J. Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri. Proc. Natl. Acad. Sci. USA 103 (2006) 12341–12346. [DOI] [PMID: 16894175]
[EC 3.5.2.18 created 2006]
 
 
EC 4.1.1.6     
Accepted name: cis-aconitate decarboxylase
Reaction: cis-aconitate = itaconate + CO2
Glossary: itaconate = 2-methylenesuccinate
cis-aconitate = (Z)-prop-1-ene-1,2,3-tricarboxylate
Other name(s): cis-aconitic decarboxylase; cis-aconitate carboxy-lyase; CAD1 (gene name); IRG1 (gene name)
Systematic name: cis-aconitate carboxy-lyase (itaconate-forming)
Comments: The enzyme has been characterized from the fungus Aspergillus terreus and from human macrophages. cf. EC 4.1.1.113, trans-aconitate decarboxylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9025-01-8
References:
1.  Bentley, R. and Thiessen, C.P. Biosynthesis of itaconic acid in Aspergillus terreus. III. The properties and reaction mechanism of cis-aconitic acid decarboxylase. J. Biol. Chem. 226 (1957) 703–720. [PMID: 13438855]
2.  Dwiarti, L., Yamane, K., Yamatani, H., Kahar, P. and Okabe, M. Purification and characterization of cis-aconitic acid decarboxylase from Aspergillus terreus TN484-M1. J. Biosci. Bioeng. 94 (2002) 29–33. [PMID: 16233265]
3.  Kanamasa, S., Dwiarti, L., Okabe, M. and Park, E.Y. Cloning and functional characterization of the cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus. Appl. Microbiol. Biotechnol. 80 (2008) 223–229. [PMID: 18584171]
4.  Michelucci, A., Cordes, T., Ghelfi, J., Pailot, A., Reiling, N., Goldmann, O., Binz, T., Wegner, A., Tallam, A., Rausell, A., Buttini, M., Linster, C.L., Medina, E., Balling, R. and Hiller, K. Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production. Proc. Natl. Acad. Sci. USA 110 (2013) 7820–7825. [DOI] [PMID: 23610393]
[EC 4.1.1.6 created 1961, modified 2018]
 
 
EC 4.1.1.113     
Accepted name: trans-aconitate decarboxylase
Reaction: trans-aconitate = itaconate + CO2
Glossary: trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
itaconate = 2-methylenesuccinate
Other name(s): TAD1 (gene name)
Systematic name: trans-aconitate carboxy-lyase (itaconate-forming)
Comments: The enzyme, characterized from the smut fungus Ustilago maydis, is involved in an alternative pathway for the biosynthesis of itaconate. cf. EC 4.1.1.6, cis-aconitate decarboxylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Geiser, E., Przybilla, S.K., Friedrich, A., Buckel, W., Wierckx, N., Blank, L.M. and Bolker, M. Ustilago maydis produces itaconic acid via the unusual intermediate trans-aconitate. Microb. Biotechnol. 9 (2016) 116–126. [PMID: 26639528]
[EC 4.1.1.113 created 2018]
 
 
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, PDB, 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 4.2.1.56     
Accepted name: itaconyl-CoA hydratase
Reaction: citramalyl-CoA = itaconyl-CoA + H2O
Other name(s): itaconyl coenzyme A hydratase; citramalyl-CoA hydro-lyase
Systematic name: citramalyl-CoA hydro-lyase (itaconyl-CoA-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37290-83-8
References:
1.  Cooper, R.A. and Kornberg, H.L. The utilization of itaconate by Pseudomonas sp. Biochem. J. 91 (1964) 82–91. [PMID: 4284209]
[EC 4.2.1.56 created 1972]
 
 
EC 5.3.3.6     
Accepted name: methylitaconate Δ-isomerase
Reaction: methylitaconate = 2,3-dimethylmaleate
For diagram of nicotinate catabolism, click here
Glossary: methylitaconate = 2-methylene-3-methylsuccinate
Other name(s): methylitaconate isomerase
Systematic name: methylitaconate Δ2-Δ3-isomerase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9059-08-9
References:
1.  Kung, H.-F. and Stadtman, T.C. Nicotinic acid metabolism. VI. Purification and properties of α-methyleneglutarate mutase (B12-dependent) and methylitaconate isomerase. J. Biol. Chem. 246 (1971) 3378–3388. [PMID: 5574401]
[EC 5.3.3.6 created 1972]
 
 
EC 5.4.99.4     
Accepted name: 2-methyleneglutarate mutase
Reaction: 2-methyleneglutarate = 2-methylene-3-methylsuccinate
For diagram of nicotinate catabolism, click here
Other name(s): α-methyleneglutarate mutase
Systematic name: 2-methyleneglutarate carboxy-methylenemethylmutase
Comments: Requires a cobamide cofactor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9059-10-3
References:
1.  Kung, H.-F., Cederbaum, S., Tsai, L. and Stadtman, T.C. Nicotinic acid metabolism. V. A cobamide coenzyme-dependent conversion of α-methyleneglutaric acid to dimethylmaleic acid. Proc. Natl. Acad. Sci. USA 65 (1970) 978–984. [DOI] [PMID: 5266166]
2.  Kung, H.-F. and Stadtman, T.C. Nicotinic acid metabolism. VI. Purification and properties of α-methyleneglutarate mutase (B12-dependent) and methylitaconate isomerase. J. Biol. Chem. 246 (1971) 3378–3388. [PMID: 5574401]
[EC 5.4.99.4 created 1972]
 
 
EC 6.2.1.4     
Accepted name: succinate—CoA ligase (GDP-forming)
Reaction: GTP + succinate + CoA = GDP + phosphate + succinyl-CoA
For diagram of the citric-acid cycle, click here
Other name(s): succinyl-CoA synthetase (GDP-forming); succinyl coenzyme A synthetase (guanosine diphosphate-forming); succinate thiokinase (ambiguous); succinic thiokinase (ambiguous); succinyl coenzyme A synthetase (ambiguous); succinate-phosphorylating enzyme (ambiguous); P-enzyme; SCS (ambiguous); G-STK; succinyl coenzyme A synthetase (GDP-forming); succinyl CoA synthetase (ambiguous)
Systematic name: succinate:CoA ligase (GDP-forming)
Comments: Itaconate can act instead of succinate, and ITP instead of GTP.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-36-2
References:
1.  Hager, L.P. Succinyl CoA synthetase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 6, Academic Press, New York, 1962, pp. 387–399.
2.  Kaufman, S., Gilvarg, C., Cori, O. and Ochoa, S. Enzymatic oxidation of α-ketoglutarate and coupled phosphorylation. J. Biol. Chem. 203 (1953) 869–888. [PMID: 13084656]
3.  Mazumder, R., Sanadi, D.R. and Rodwell, W.V. Purification and properties of hog kidney succinic thiokinase. J. Biol. Chem. 235 (1960) 2546–2550. [PMID: 13768680]
4.  Sanadi, D.R., Gibson, D.M. and Ayengar, P. Guanosine triphosphate, the primary product of phosphorylation coupled to the breakdown of succinyl coenzyme A. Biochim. Biophys. Acta 14 (1954) 434–436. [DOI] [PMID: 13181903]
[EC 6.2.1.4 created 1961]
 
 


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