The Enzyme Database

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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 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, 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 4.2.1.3     
Accepted name: aconitate hydratase
Reaction: citrate = isocitrate (overall reaction)
(1a) citrate = cis-aconitate + H2O
(1b) cis-aconitate + H2O = isocitrate
For diagram of the citric acid cycle, click here and for diagram of the glyoxylate cycle, click here
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
cis-aconitate = (Z)-prop-1-ene-1,2,3-tricarboxylate
Other name(s): cis-aconitase; aconitase; AcnB; 2-methylaconitate hydratase; citrate(isocitrate) hydro-lyase
Systematic name: citrate(isocitrate) hydro-lyase (cis-aconitate-forming)
Comments: Besides interconverting citrate and cis-aconitate, it also interconverts cis-aconitate with isocitrate and, hence, interconverts citrate and isocitrate. The equilibrium mixture is 91% citrate, 6% isocitrate and 3% aconitate. cis-Aconitate is used to designate the isomer (Z)-prop-1-ene-1,2,3-tricarboxylate. An iron-sulfur protein, containing a [4Fe-4S] cluster to which the substrate binds.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-25-3
References:
1.  Dickman, S.R. Aconitase. In: Boyer, P.D., Lardy, H. and Myrbäck, K (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 495–510.
2.  Morrison, J.F. The purification of aconitase. Biochem. J. 56 (1954) 99–105. [PMID: 13126098]
3.  Lauble, H., Kennedy, M.C., Beinert, H. and Stout, C.D. Crystal structures of aconitase with trans-aconitate and nitrocitrate bound. J. Mol. Biol. 237 (1994) 437–451. [DOI] [PMID: 8151704]
[EC 4.2.1.3 created 1961, modified 2003]
 
 
EC 4.2.1.4      
Deleted entry: citrate dehydratase. Now known to be a partial reaction catalysed by EC 4.2.1.3, aconitate hydratase.
[EC 4.2.1.4 created 1961, deleted 2013]
 
 
EC 4.2.1.79     
Accepted name: 2-methylcitrate dehydratase
Reaction: (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
Glossary: (2S,3S)-2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
cis-2-methylaconitate = (Z)-but-2-ene-1,2,3-tricarboxylate
Other name(s): 2-methylcitrate hydro-lyase; PrpD; 2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase
Systematic name: (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase [(Z)-but-2-ene-1,2,3-tricarboxylate-forming]
Comments: The enzyme is specific for (2S,3S)-methylcitrate, showing no activity with (2R,3S)-methylcitrate [2]. The enzyme can also use cis-aconitate as a substrate but more slowly [2]. Both this enzyme and EC 4.2.1.3, aconitate hydratase, are required to complete the isomerization of (2S,3S)-methylcitrate to (2R,3S)-2-methylisocitrate [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 80891-26-5
References:
1.  Aoki, H. and Tabuchi, T. Purification and properties of 2-methylcitrate dehydratase from Yarrowia lipolytica. Agric. Biol. Chem. 45 (1981) 2831–2837.
2.  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]
[EC 4.2.1.79 created 1984]
 
 
EC 4.2.1.114     
Accepted name: methanogen homoaconitase
Reaction: (R)-2-hydroxybutane-1,2,4-tricarboxylate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate (overall reaction)
(1a) (R)-2-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H2O
(1b) (Z)-but-1-ene-1,2,4-tricarboxylate + H2O = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
For diagram of the 2-aminoadipate pathway of L-lysine synthesis, click here
Glossary: cis-homoaconitate = (Z)-but-1-ene-1,2,4-tricarboxylate
(R)-homocitrate = (R)-2-hydroxybutane-1,2,4-tricarboxylate
homoisocitrate = (–)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): methanogen HACN
Systematic name: (R)-2-hydroxybutane-1,2,4-tricarboxylate hydro-lyase [(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate-forming]
Comments: This enzyme catalyses several reactions in the pathway of coenzyme-B biosynthesis in methanogenic archaea. Requires a [4Fe-4S] cluster for activity. In contrast to EC 4.2.1.36, homoaconitate hydratase, this enzyme can catalyse both the dehydration of (R)-homocitrate to form cis-homoaconitate and the subsequent hydration reaction that forms homoisocitrate. In addition to cis-homoaconitate, the enzyme can also catalyse the hydration of the physiological substrates dihomoaconitate and trihomoaconitate as well as the non-physiological substrate tetrahomoaconitate. cis-Aconitate and threo-DL-isocitrate cannot act as substrates, and (S)-homocitrate and trans-homoaconitate act as inhibitors of the enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Drevland, R.M., Jia, Y., Palmer, D.R. and Graham, D.E. Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis. J. Biol. Chem. 283 (2008) 28888–28896. [DOI] [PMID: 18765671]
[EC 4.2.1.114 created 2009]
 
 
EC 4.2.1.117     
Accepted name: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Reaction: (2S,3S)-2-methylcitrate = 2-methyl-trans-aconitate + H2O
Glossary: (2S,3S)-2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
2-methyl-trans-aconitate = (2E)-but-2-ene-1,2,3-tricarboxylate
Systematic name: (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase (2-methyl-trans-aconitate-forming)
Comments: Catalyses the dehydration of (2S,3S)-2-methylcitrate, forming the trans isomer of 2-methyl-aconitate (unlike EC 4.2.1.79, which forms only the cis isomer). Part of a propionate degradation pathway. The enzyme from Shewanella oneidensis can also accept citrate and cis-aconitate, but activity with (2S,3S)-2-methylcitrate was approximately 2.5-fold higher. 2-methylisocitrate and isocitrate were not substrates [1]. An iron-sulfur protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Grimek, T.L. and Escalante-Semerena, J.C. The acnD genes of Shewenella oneidensis and Vibrio cholerae encode a new Fe/S-dependent 2-methylcitrate dehydratase enzyme that requires prpF function in vivo. J. Bacteriol. 186 (2004) 454–462. [DOI] [PMID: 14702315]
[EC 4.2.1.117 created 2009]
 
 
EC 5.3.3.7     
Accepted name: aconitate Δ-isomerase
Reaction: trans-aconitate = cis-aconitate
Glossary: cis-aconitate = (Z)-prop-1-ene-1,2,3-tricarboxylate
trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
Other name(s): aconitate isomerase
Systematic name: aconitate Δ23-isomerase
Comments: cis-Aconitate is used to designate the isomer (Z)-prop-1-ene-1,2,3-tricarboxylate. This isomerization could take place either in a direct cis-trans interconversion or by an allylic rearrangement; the enzyme has been shown to catalyse the latter change.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37318-48-2
References:
1.  Klinman, J.P. and Rose, I.A. Purification and kinetic properties of aconitate isomerase from Pseudomonas putida. Biochemistry 10 (1971) 2253–2259. [PMID: 5114987]
2.  Klinman, J.P. and Rose, I.A. Mechanism of the aconitate isomerase reaction. Biochemistry 10 (1971) 2259–2266. [PMID: 5114988]
[EC 5.3.3.7 created 1972]
 
 


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