The Enzyme Database

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EC 1.2.1.58     
Accepted name: phenylglyoxylate dehydrogenase (acylating)
Reaction: phenylglyoxylate + NAD+ + CoA = benzoyl-S-CoA + CO2 + NADH
Systematic name: phenylglyoxylate:NAD+ oxidoreductase
Comments: Requires thiamine diphosphate as cofactor. The enzyme from the denitrifying bacterium Azoarcus evansii is specific for phenylglyoxylate. 2-Oxoisovalerate is oxidized at 15% of the rate for phenylglyoxylate. Also reduces viologen dyes. Contains iron-sulfur centres and FAD.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 205510-78-7
References:
1.  Hirsch, W., Schägger, H. and Fuchs, G. Phenylglyoxylate:NAD+ oxidoreductase (CoA benzoylating), a new enzyme of anaerobic phenylalanine metabolism in the denitrifying bacterium Axoarcus evansii. Eur. J. Biochem. 251 (1998) 907–915. [DOI] [PMID: 9490067]
[EC 1.2.1.58 created 1999]
 
 
EC 1.2.2.2      
Deleted entry: pyruvate dehydrogenase (cytochrome). Now covered by EC 1.2.5.1, pyruvate dehydrogenase (quinone)
[EC 1.2.2.2 created 1961, deleted 2010]
 
 
EC 1.2.3.3     
Accepted name: pyruvate oxidase
Reaction: pyruvate + phosphate + O2 = acetyl phosphate + CO2 + H2O2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): pyruvic oxidase; phosphate-dependent pyruvate oxidase
Systematic name: pyruvate:oxygen 2-oxidoreductase (phosphorylating)
Comments: A flavoprotein (FAD) requiring thiamine diphosphate. Two reducing equivalents are transferred from the resonant carbanion/enamine forms of 2-hydroxyethyl-thiamine-diphosphate to the adjacent flavin cofactor, yielding 2-acetyl-thiamine diphosphate (AcThDP) and reduced flavin. FADH2 is reoxidized by O2 to yield H2O2 and FAD and AcThDP is cleaved phosphorolytically to acetyl phosphate and thiamine diphosphate [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9001-96-1
References:
1.  Williams, F.R. and Hager, L.P. Crystalline flavin pyruvate oxidase from Escherichia coli. I. Isolation and properties of the flavoprotein. Arch. Biochem. Biophys. 116 (1966) 168–176. [PMID: 5336022]
2.  Tittmann, K., Wille, G., Golbik, R., Weidner, A., Ghisla, S. and Hübner, G. Radical phosphate transfer mechanism for the thiamin diphosphate- and FAD-dependent pyruvate oxidase from Lactobacillus plantarum. Kinetic coupling of intercofactor electron transfer with phosphate transfer to acetyl-thiamin diphosphate via a transient FAD semiquinone/hydroxyethyl-ThDP radical pair. Biochemistry 44 (2005) 13291–13303. [DOI] [PMID: 16201755]
[EC 1.2.3.3 created 1961]
 
 
EC 1.2.4.1     
Accepted name: pyruvate dehydrogenase (acetyl-transferring)
Reaction: pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO2
For diagram of oxo-acid dehydrogenase complexes, click here
Glossary: dihydrolipoyl group
thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): pyruvate decarboxylase (ambiguous); pyruvate dehydrogenase (ambiguous); pyruvate dehydrogenase (lipoamide); pyruvate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-acetylating); pyruvic acid dehydrogenase; pyruvic dehydrogenase (ambiguous)
Systematic name: pyruvate:[dihydrolipoyllysine-residue acetyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-acetylating)
Comments: Contains thiamine diphosphate. It is a component (in multiple copies) of the multienzyme pyruvate dehydrogenase complex, EC 1.2.1.104, in which it is bound to a core of molecules of EC 2.3.1.12, dihydrolipoyllysine-residue acetyltransferase, which also binds multiple copies of EC 1.8.1.4, dihydrolipoyl dehydrogenase. It does not act on free lipoamide or lipoyllysine, but only on the lipoyllysine residue in EC 2.3.1.12.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9014-20-4
References:
1.  Ochoa, S. Enzymic mechanisms in the citric acid cycle. Adv. Enzymol. Relat. Subj. Biochem. 15 (1954) 183–270. [PMID: 13158180]
2.  Scriba, P. and Holzer, H. Gewinnung von αHydroxyäthyl-2-thiaminpyrophosphat mit Pyruvatoxydase aus Schweineherzmuskel. Biochem. Z. 334 (1961) 473–486. [PMID: 13749426]
3.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
[EC 1.2.4.1 created 1961, modified 2003]
 
 
EC 1.2.4.2     
Accepted name: oxoglutarate dehydrogenase (succinyl-transferring)
Reaction: 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO2
For diagram of the citric acid cycle, click here and for diagram of oxo-acid dehydrogenase complexes, click here
Glossary: dihydrolipoyl group
thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): 2-ketoglutarate dehydrogenase; 2-oxoglutarate dehydrogenase; 2-oxoglutarate: lipoate oxidoreductase; 2-oxoglutarate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-succinylating); α-ketoglutarate dehydrogenase; alphaketoglutaric acid dehydrogenase; α-ketoglutaric dehydrogenase; α-oxoglutarate dehydrogenase; AKGDH; OGDC; ketoglutaric dehydrogenase; oxoglutarate decarboxylase (misleading); oxoglutarate dehydrogenase; oxoglutarate dehydrogenase (lipoamide)
Systematic name: 2-oxoglutarate:[dihydrolipoyllysine-residue succinyltransferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-succinylating)
Comments: Contains thiamine diphosphate. It is a component of the multienzyme 2-oxoglutarate dehydrogenase complex, EC 1.2.1.105, in which multiple copies of it are bound to a core of molecules of EC 2.3.1.61, dihydrolipoyllysine-residue succinyltransferase, which also binds multiple copies of EC 1.8.1.4, dihydrolipoyl dehydrogenase. It does not act on free lipoamide or lipoyllysine, but only on the lipoyllysine residue in EC 2.3.1.61.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9031-02-1
References:
1.  Massey, V. The composition of the ketoglutarate dehydrogenase complex. Biochim. Biophys. Acta 38 (1960) 447–460. [DOI] [PMID: 14422131]
2.  Ochoa, S. Enzymic mechanisms in the citric acid cycle. Adv. Enzymol. Relat. Subj. Biochem. 15 (1954) 183–270. [PMID: 13158180]
3.  Sanadi, D.R., Littlefield, J.W. and Bock, R.M. Studies on α-ketoglutaric oxidase. II. Purification and properties. J. Biol. Chem. 197 (1952) 851–862. [PMID: 12981117]
4.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
[EC 1.2.4.2 created 1961, modified 1980, modified 1986, modified 2003]
 
 
EC 1.2.4.4     
Accepted name: 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
Reaction: 3-methyl-2-oxobutanoate + [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] lipoyllysine = [dihydrolipoyllysine-residue (2-methylpropanoyl)transferase] S-(2-methylpropanoyl)dihydrolipoyllysine + CO2
For diagram of oxo-acid-dehydrogenase complexes, click here
Glossary: dihydrolipoyl group
thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): 2-oxoisocaproate dehydrogenase; 2-oxoisovalerate (lipoate) dehydrogenase; 3-methyl-2-oxobutanoate dehydrogenase (lipoamide); 3-methyl-2-oxobutanoate:lipoamide oxidoreductase (decarboxylating and acceptor-2-methylpropanoylating); α-keto-α-methylvalerate dehydrogenase; α-ketoisocaproate dehydrogenase; α-ketoisocaproic dehydrogenase; α-ketoisocaproic-α-keto-α-methylvaleric dehydrogenase; α-ketoisovalerate dehydrogenase; α-oxoisocaproate dehydrogenase; BCKDH (ambiguous); BCOAD; branched chain keto acid dehydrogenase; branched-chain (-2-oxoacid) dehydrogenase (BCD); branched-chain 2-keto acid dehydrogenase; branched-chain 2-oxo acid dehydrogenase; branched-chain α-keto acid dehydrogenase; branched-chain α-oxo acid dehydrogenase; branched-chain keto acid dehydrogenase; branched-chain ketoacid dehydrogenase; dehydrogenase, 2-oxoisovalerate (lipoate); dehydrogenase, branched chain α-keto acid
Systematic name: 3-methyl-2-oxobutanoate:[dihydrolipoyllysine-residue (2-methylpropanoyl)transferase]-lipoyllysine 2-oxidoreductase (decarboxylating, acceptor-2-methylpropanoylating)
Comments: Contains thiamine diphosphate. It acts not only on 3-methyl-2-oxobutanaoate, but also on 4-methyl-2-oxopentanoate and (S)-3-methyl-2-oxopentanoate, so that it acts on the 2-oxo acids that derive from the action of transaminases on valine, leucine and isoleucine. It is a component of the multienzyme 3-methyl-2-oxobutanoate dehydrogenase complex in which multiple copies of it are bound to a core of molecules of EC 2.3.1.168, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase, which also binds multiple copies of EC 1.8.1.4, dihydrolipoyl dehydrogenase. It does not act on free lipoamide or lipoyllysine, but only on the lipoyllysine residue in EC 2.3.1.168.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9082-72-8
References:
1.  Bowden, J.A. and Connelly, J.L. Branched chain α-keto acid metabolism. II. Evidence for the common identity of α-ketoisocaproic acid and α-keto-β-methyl-valeric acid dehydrogenases. J. Biol. Chem. 243 (1968) 3526–3531. [PMID: 5656388]
2.  Connelly, J.L., Danner, D.J. and Bowden, J.A. Branched chain α-keto acid metabolism. I. Isolation, purification, and partial characterization of bovine liver α-ketoisocaproic:α-keto-β-methylvaleric acid dehydrogenase. J. Biol. Chem. 243 (1968) 1198–1203. [PMID: 5689906]
3.  Danner, D.J., Lemmon, S.K., Beharse, J.C. and Elsas, L.J., II Purification and characterization of branched chain α-ketoacid dehydrogenase from bovine liver mitochondria. J. Biol. Chem. 254 (1979) 5522–5526. [PMID: 447664]
4.  Pettit, F.H., Yeaman, S.J. and Reed, L.J. Purification and characterization of branched chain α-keto acid dehydrogenase complex of bovine kidney. Proc. Natl. Acad. Sci. USA 75 (1978) 4881–4885. [DOI] [PMID: 283398]
5.  Perham, R.N. Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu. Rev. Biochem. 69 (2000) 961–1004. [DOI] [PMID: 10966480]
[EC 1.2.4.4 created 1972 (EC 1.2.4.3 created 1972, incorporated 1978), modified 2003]
 
 
EC 1.2.5.1     
Accepted name: pyruvate dehydrogenase (quinone)
Reaction: pyruvate + ubiquinone + H2O = acetate + CO2 + ubiquinol
Other name(s): pyruvate dehydrogenase (ambiguous); pyruvic dehydrogenase (ambiguous); pyruvic (cytochrome b1) dehydrogenase (incorrect); pyruvate:ubiquinone-8-oxidoreductase; pyruvate oxidase (ambiguous); pyruvate dehydrogenase (cytochrome) (incorrect)
Systematic name: pyruvate:ubiquinone oxidoreductase
Comments: Flavoprotein (FAD) [1]. This bacterial enzyme is located on the inner surface of the cytoplasmic membrane and coupled to the respiratory chain via ubiquinone [2,3]. Does not accept menaquinone. Activity is greatly enhanced by lipids [4,5,6]. Requires thiamine diphosphate [7]. The enzyme can also form acetoin [8].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Recny, M.A. and Hager, L.P. Reconstitution of native Escherichia coli pyruvate oxidase from apoenzyme monomers and FAD. J. Biol. Chem. 257 (1982) 12878–12886. [PMID: 6752142]
2.  Cunningham, C.C. and Hager, L.P. Reactivation of the lipid-depleted pyruvate oxidase system from Escherichia coli with cell envelope neutral lipids. J. Biol. Chem. 250 (1975) 7139–7146. [PMID: 1100621]
3.  Koland, J.G., Miller, M.J. and Gennis, R.B. Reconstitution of the membrane-bound, ubiquinone-dependent pyruvate oxidase respiratory chain of Escherichia coli with the cytochrome d terminal oxidase. Biochemistry 23 (1984) 445–453. [PMID: 6367818]
4.  Grabau, C. and Cronan, J.E., Jr. In vivo function of Escherichia coli pyruvate oxidase specifically requires a functional lipid binding site. Biochemistry 25 (1986) 3748–3751. [PMID: 3527254]
5.  Wang, A.Y., Chang, Y.Y. and Cronan, J.E., Jr. Role of the tetrameric structure of Escherichia coli pyruvate oxidase in enzyme activation and lipid binding. J. Biol. Chem. 266 (1991) 10959–10966. [PMID: 2040613]
6.  Chang, Y.Y. and Cronan, J.E., Jr. Sulfhydryl chemistry detects three conformations of the lipid binding region of Escherichia coli pyruvate oxidase. Biochemistry 36 (1997) 11564–11573. [DOI] [PMID: 9305946]
7.  O'Brien, T.A., Schrock, H.L., Russell, P., Blake, R., 2nd and Gennis, R.B. Preparation of Escherichia coli pyruvate oxidase utilizing a thiamine pyrophosphate affinity column. Biochim. Biophys. Acta 452 (1976) 13–29. [DOI] [PMID: 791368]
8.  Bertagnolli, B.L. and Hager, L.P. Role of flavin in acetoin production by two bacterial pyruvate oxidases. Arch. Biochem. Biophys. 300 (1993) 364–371. [DOI] [PMID: 8424670]
[EC 1.2.5.1 created 2010]
 
 
EC 1.2.7.1     
Accepted name: pyruvate synthase
Reaction: pyruvate + CoA + 2 oxidized ferredoxin = acetyl-CoA + CO2 + 2 reduced ferredoxin + 2 H+
For diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Other name(s): pyruvate oxidoreductase; pyruvate synthetase; pyruvate:ferredoxin oxidoreductase; pyruvic-ferredoxin oxidoreductase; 2-oxobutyrate synthase; α-ketobutyrate-ferredoxin oxidoreductase; 2-ketobutyrate synthase; α-ketobutyrate synthase; 2-oxobutyrate-ferredoxin oxidoreductase; 2-oxobutanoate:ferredoxin 2-oxidoreductase (CoA-propionylating); 2-oxobutanoate:ferredoxin 2-oxidoreductase (CoA-propanoylating)
Systematic name: pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
Comments: Contains thiamine diphosphate and [4Fe-4S] clusters. The enzyme also decarboxylates 2-oxobutyrate with lower efficiency, but shows no activity with 2-oxoglutarate. This enzyme is a member of the 2-oxoacid oxidoreductases, a family of enzymes that oxidatively decarboxylate different 2-oxoacids to form their CoA derivatives, and are differentiated based on their substrate specificity. For examples of other members of this family, see EC 1.2.7.3, 2-oxoglutarate synthase and EC 1.2.7.7, 3-methyl-2-oxobutanoate dehydrogenase (ferredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9082-51-3
References:
1.  Evans, M.C.W. and Buchanan, B.B. Photoreduction of ferredoxin and its use in carbon dioxide fixation by a subcellular system from a photosynthetic bacterium. Proc. Natl. Acad. Sci. USA 53 (1965) 1420–1425. [DOI] [PMID: 5217644]
2.  Gehring, U. and Arnon, D.I. Purification and properties of α-ketoglutarate synthase from a photosynthetic bacterium. J. Biol. Chem. 247 (1972) 6963–6969. [PMID: 4628267]
3.  Uyeda, K. and Rabinowitz, J.C. Pyruvate-ferredoxin oxidoreductase. 3. Purification and properties of the enzyme. J. Biol. Chem. 246 (1971) 3111–3119. [PMID: 5574389]
4.  Uyeda, K. and Rabinowitz, J.C. Pyruvate-ferredoxin oxidoreductase. IV. Studies on the reaction mechanism. J. Biol. Chem. 246 (1971) 3120–3125. [PMID: 4324891]
5.  Charon, M.-H., Volbeda, A., Chabriere, E., Pieulle, L. and Fontecilla-Camps, J.C. Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase. Curr. Opin. Struct. Biol. 9 (1999) 663–669. [DOI] [PMID: 10607667]
[EC 1.2.7.1 created 1972, modified 2003, modified 2013]
 
 
EC 1.2.7.3     
Accepted name: 2-oxoglutarate synthase
Reaction: 2-oxoglutarate + CoA + 2 oxidized ferredoxin = succinyl-CoA + CO2 + 2 reduced ferredoxin + 2 H+
Other name(s): 2-ketoglutarate ferredoxin oxidoreductase; 2-oxoglutarate:ferredoxin oxidoreductase; KGOR; 2-oxoglutarate ferredoxin oxidoreductase; 2-oxoglutarate:ferredoxin 2-oxidoreductase (CoA-succinylating)
Systematic name: 2-oxoglutarate:ferredoxin oxidoreductase (decarboxylating)
Comments: The enzyme contains thiamine diphosphate and two [4Fe-4S] clusters. Highly specific for 2-oxoglutarate. This enzyme is a member of the 2-oxoacid oxidoreductases, a family of enzymes that oxidatively decarboxylate different 2-oxoacids to form their CoA derivatives, and are differentiated based on their substrate specificity. For examples of other members of this family, see EC 1.2.7.1, pyruvate synthase and EC 1.2.7.7, 3-methyl-2-oxobutanoate dehydrogenase (ferredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37251-05-1
References:
1.  Buchanan, B.B. and Evans, M.C.W. The synthesis of α-ketoglutarate from succinate and carbon dioxide by a subcellular preparation of a photosynthetic bacterium. Proc. Natl. Acad. Sci. USA 54 (1965) 1212–1218. [DOI] [PMID: 4286833]
2.  Gehring, U. and Arnon, D.I. Purification and properties of α-ketoglutarate synthase from a photosynthetic bacterium. J. Biol. Chem. 247 (1972) 6963–6969. [PMID: 4628267]
3.  Dorner, E. and Boll, M. Properties of 2-oxoglutarate:ferredoxin oxidoreductase from Thauera aromatica and its role in enzymatic reduction of the aromatic ring. J. Bacteriol. 184 (2002) 3975–3983. [DOI] [PMID: 12081970]
4.  Mai, X. and Adams, M.W. Characterization of a fourth type of 2-keto acid-oxidizing enzyme from a hyperthermophilic archaeon: 2-ketoglutarate ferredoxin oxidoreductase from Thermococcus litoralis. J. Bacteriol. 178 (1996) 5890–5896. [DOI] [PMID: 8830683]
5.  Schut, G.J., Menon, A.L. and Adams, M.W.W. 2-Keto acid oxidoreductases from Pyrococcus furiosus and Thermococcus litoralis. Methods Enzymol. 331 (2001) 144–158. [DOI] [PMID: 11265457]
[EC 1.2.7.3 created 1972, modified 2005]
 
 
EC 1.2.7.7     
Accepted name: 3-methyl-2-oxobutanoate dehydrogenase (ferredoxin)
Reaction: 3-methyl-2-oxobutanoate + CoA + 2 oxidized ferredoxin = S-(2-methylpropanoyl)-CoA + CO2 + 2 reduced ferredoxin + H+
Other name(s): 2-ketoisovalerate ferredoxin reductase; 3-methyl-2-oxobutanoate synthase (ferredoxin); VOR; branched-chain ketoacid ferredoxin reductase; branched-chain oxo acid ferredoxin reductase; keto-valine-ferredoxin oxidoreductase; ketoisovalerate ferredoxin reductase; 2-oxoisovalerate ferredoxin reductase
Systematic name: 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (decarboxylating; CoA-2-methylpropanoylating)
Comments: The enzyme is CoA-dependent and contains thiamine diphosphate and iron-sulfur clusters. Preferentially utilizes 2-oxo-acid derivatives of branched chain amino acids, e.g. 3-methyl-2-oxopentanoate, 4-methyl-2-oxo-pentanoate, and 2-oxobutanoate. This enzyme is a member of the 2-oxoacid oxidoreductases, a family of enzymes that reversibly catalyse the oxidative decarboxylation of different 2-oxoacids to form their CoA derivatives, and are differentiated based on their substrate specificity. For examples of other members of this family, see EC 1.2.7.1, pyruvate synthase, and EC 1.2.7.3, 2-oxoglutarate synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Buchanan, B.B. Role of ferredoxin in the synthesis of α-ketobutyrate from propionyl coenzyme A and carbon dioxide by enzymes from photosynthetic and nonphotosynthetic bacteria. J. Biol. Chem. 244 (1969) 4218–4223. [PMID: 5800441]
2.  Heider, J., Mai, X.H. and Adams, M.W.W. Characterization of 2-ketoisovalerate ferredoxin oxidoreductase, a new and reversible coenzyme A-dependent enzyme involved in peptide fermentation by hyperthermophilic archaea. J. Bacteriol. 178 (1996) 780–787. [DOI] [PMID: 8550513]
3.  Tersteegen, A., Linder, D., Thauer, R.K. and Hedderich, R. Structures and functions of four anabolic 2-oxoacid oxidoreductases in Methanobacterium thermoautotrophicum. Eur. J. Biochem. 244 (1997) 862–868. [DOI] [PMID: 9108258]
4.  Schut, G.J., Menon, A.L. and Adams, M.W.W. 2-Keto acid oxidoreductases from Pyrococcus furiosus and Thermococcus litoralis. Methods Enzymol. 331 (2001) 144–158. [DOI] [PMID: 11265457]
[EC 1.2.7.7 created 2003]
 
 
EC 1.2.7.8     
Accepted name: indolepyruvate ferredoxin oxidoreductase
Reaction: (indol-3-yl)pyruvate + CoA + 2 oxidized ferredoxin = S-2-(indol-3-yl)acetyl-CoA + CO2 + 2 reduced ferredoxin + H+
Other name(s): 3-(indol-3-yl)pyruvate synthase (ferredoxin); IOR
Systematic name: 3-(indol-3-yl)pyruvate:ferredoxin oxidoreductase (decarboxylating, CoA-indole-acetylating)
Comments: Contains thiamine diphosphate and [4Fe-4S] clusters. Preferentially utilizes the transaminated forms of aromatic amino acids and can use phenylpyruvate and p-hydroxyphenylpyruvate as substrates. This enzyme, which is found in archaea, is a member of the 2-oxoacid oxidoreductases, a family of enzymes that oxidatively decarboxylate different 2-oxoacids to form their CoA derivatives, and are differentiated based on their substrate specificity. For examples of other members of this family, see EC 1.2.7.3, 2-oxoglutarate synthase and EC 1.2.7.7, 3-methyl-2-oxobutanoate dehydrogenase (ferredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 158886-06-7
References:
1.  Mai, X.H. and Adams, M.W.W. Indolepyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus - a new enzyme involved in peptide fermentation. J. Biol. Chem. 269 (1994) 16726–16732. [PMID: 8206994]
2.  Siddiqui, M.A., Fujiwara, S. and Imanaka, T. Indolepyruvate ferredoxin oxidoreductase from Pyrococcus sp. K0d1 possesses a mosaic: Structure showing features of various oxidoreductases. Mol. Gen. Genet. 254 (1997) 433–439. [PMID: 9180697]
3.  Tersteegen, A., Linder, D., Thauer, R.K. and Hedderich, R. Structures and functions of four anabolic 2-oxoacid oxidoreductases in Methanobacterium thermoautotrophicum. Eur. J. Biochem. 244 (1997) 862–868. [DOI] [PMID: 9108258]
4.  Schut, G.J., Menon, A.L. and Adams, M.W.W. 2-Keto acid oxidoreductases from Pyrococcus furiosus and Thermococcus litoralis. Methods Enzymol. 331 (2001) 144–158. [DOI] [PMID: 11265457]
[EC 1.2.7.8 created 2003]
 
 
EC 1.2.7.10     
Accepted name: oxalate oxidoreductase
Reaction: oxalate + oxidized ferredoxin = 2 CO2 + reduced ferredoxin
Systematic name: oxalate:ferredoxin oxidoreductase
Comments: Contains thiamine diphosphate and [4Fe-4S] clusters. Acceptors include ferredoxin and the nickel-dependent carbon monoxide dehydrogenase (EC 1.2.7.4)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Daniel, S.L., Pilsl, C. and Drake, H.L. Oxalate metabolism by the acetogenic bacterium Moorella thermoacetica. FEMS Microbiol. Lett. 231 (2004) 39–43. [DOI] [PMID: 14769464]
2.  Pierce, E., Becker, D.F. and Ragsdale, S.W. Identification and characterization of oxalate oxidoreductase, a novel thiamine pyrophosphate-dependent 2-oxoacid oxidoreductase that enables anaerobic growth on oxalate. J. Biol. Chem. 285 (2010) 40515–40524. [DOI] [PMID: 20956531]
[EC 1.2.7.10 created 2011]
 
 
EC 1.2.7.11     
Accepted name: 2-oxoacid oxidoreductase (ferredoxin)
Reaction: a 2-oxocarboxylate + CoA + 2 oxidized ferredoxin = an acyl-CoA + CO2 + 2 reduced ferredoxin + 2 H+
Other name(s): OFOR
Systematic name: 2-oxocarboxylate:ferredoxin 2-oxidoreductase (decarboxylating, CoA-acylating)
Comments: Contains thiamine diphosphate and [4Fe-4S] clusters [2]. This enzyme is a member of the 2-oxoacid oxidoreductases, a family of enzymes that oxidatively decarboxylate different 2-oxoacids to form their CoA derivatives, and are differentiated based on their substrate specificity. For example, see EC 1.2.7.3, 2-oxoglutarate synthase and EC 1.2.7.7, 3-methyl-2-oxobutanoate dehydrogenase (ferredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Kerscher, L. and Oesterhelt, D. Purification and properties of two 2-oxoacid:ferredoxin oxidoreductases from Halobacterium halobium. Eur. J. Biochem. 116 (1981) 587–594. [DOI] [PMID: 6266826]
2.  Zhang, Q., Iwasaki, T., Wakagi, T. and Oshima, T. 2-oxoacid:ferredoxin oxidoreductase from the thermoacidophilic archaeon, Sulfolobus sp. strain 7. J. Biochem. 120 (1996) 587–599. [PMID: 8902625]
3.  Fukuda, E., Kino, H., Matsuzawa, H. and Wakagi, T. Role of a highly conserved YPITP motif in 2-oxoacid:ferredoxin oxidoreductase: heterologous expression of the gene from Sulfolobus sp.strain 7, and characterization of the recombinant and variant enzymes. Eur. J. Biochem. 268 (2001) 5639–5646. [DOI] [PMID: 11683888]
4.  Fukuda, E. and Wakagi, T. Substrate recognition by 2-oxoacid:ferredoxin oxidoreductase from Sulfolobus sp. strain 7. Biochim. Biophys. Acta 1597 (2002) 74–80. [DOI] [PMID: 12009405]
5.  Nishizawa, Y., Yabuki, T., Fukuda, E. and Wakagi, T. Gene expression and characterization of two 2-oxoacid:ferredoxin oxidoreductases from Aeropyrum pernix K1. FEBS Lett. 579 (2005) 2319–2322. [DOI] [PMID: 15848165]
6.  Park, Y.J., Yoo, C.B., Choi, S.Y. and Lee, H.B. Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1. J. Biochem. Mol. Biol. 39 (2006) 46–54. [PMID: 16466637]
[EC 1.2.7.11 created 2013]
 
 
EC 1.4.3.19     
Accepted name: glycine oxidase
Reaction: glycine + H2O + O2 = glyoxylate + NH3 + H2O2 (overall reaction)
(1a) glycine + O2 = 2-iminoacetate + H2O2
(1b) 2-iminoacetate + H2O = glyoxylate + NH3
For diagram of thiamine diphosphate biosynthesis, click here
Systematic name: glycine:oxygen oxidoreductase (deaminating)
Comments: A flavoenzyme containing non-covalently bound FAD. The enzyme from Bacillus subtilis is active with glycine, sarcosine, N-ethylglycine, D-alanine, D-α-aminobutyrate, D-proline, D-pipecolate and N-methyl-D-alanine. It differs from EC 1.4.3.3, D-amino-acid oxidase, due to its activity on sarcosine and D-pipecolate. The intermediate 2-iminoacetate is used directly by EC 2.8.1.10, thiazole synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 39307-16-9
References:
1.  Job, V., Marcone, G.L., Pilone, M.S. and Pollegioni, L. Glycine oxidase from Bacillus subtilis. Characterization of a new flavoprotein. J. Biol. Chem. 277 (2002) 6985–6993. [DOI] [PMID: 11744710]
2.  Nishiya, Y. and Imanaka, T. Purification and characterization of a novel glycine oxidase from Bacillus subtilis. FEBS Lett. 438 (1998) 263–266. [DOI] [PMID: 9827558]
[EC 1.4.3.19 created 2002, modified 2012]
 
 
EC 2.2.1.1     
Accepted name: transketolase
Reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
For diagram of reaction, click here, for diagram of the calvin cycle, click here, for diagram of the calvin cycle, click here, for diagram of the calvin cycle, click here and for diagram of the pentose phosphate pathway (later stages), click here
Glossary: thiamine diphosphate
Other name(s): glycolaldehydetransferase
Systematic name: sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glycolaldehydetransferase
Comments: A thiamine-diphosphate protein. Wide specificity for both reactants, e.g. converts hydroxypyruvate and R-CHO into CO2 and R-CHOH-CO-CH2OH. The enzyme from the bacterium Alcaligenes faecalis shows high activity with D-erythrose 4-phosphate as acceptor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-48-6
References:
1.  De La Haba, G., Leder, I.G and Racker, E. Crystalline transketolase from bakers' yeast: isolation and properties. J. Biol. Chem. 214 (1955) 409–426. [PMID: 14367398]
2.  Domagk, G.F. and Horecker, B.L. Fructose and erythrose metabolism in Alcaligenes faecalis. Arch. Biochem. Biophys. 109 (1965) 342–349.
3.  Horecker, B.L., Smyrniotis, P.Z. and Hurwitz, J. The role of xylulose 5-phosphate in the transketolase reaction. J. Biol. Chem. 223 (1956) 1009–1019. [PMID: 13385248]
4.  Racker, E. Transketolase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 5, Academic Press, New York, 1961, pp. 397–412.
[EC 2.2.1.1 created 1961]
 
 
EC 2.2.1.3     
Accepted name: formaldehyde transketolase
Reaction: D-xylulose 5-phosphate + formaldehyde = D-glyceraldehyde 3-phosphate + glycerone
For diagram of reaction, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): dihydroxyacetone synthase
Systematic name: D-xylulose-5-phosphate:formaldehyde glycolaldehydetransferase
Comments: A thiamine-diphosphate protein. Not identical with EC 2.2.1.1 transketolase. Also converts hydroxypyruvate and formaldehyde into glycerone and CO2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 124566-23-0
References:
1.  Bystrykh, L.V., Sokolov, A.P. and Trotsenko, Yu.A. Separation of transketolase and dihydroxyacetone synthase from methylotrophic yeasts. Dokl. Akad. Nauk S.S.S.R. 258 (1981) 499–501. [PMID: 7249920]
2.  Kato, N., Higuchi, T., Sakazawa, C., Nishizawa, T., Tani, Y. and Yamada, H. Purification and properties of a transketolase responsible for formaldehyde fixation in a methanol-utilizing yeast, Candida boidinii (Kloeckera sp.) No. 2201. Biochim. Biophys. Acta 715 (1982) 143–150. [DOI] [PMID: 7074134]
3.  Waites, M.J. and Quayle, J.R. The interrelation between transketolase and dihydroxyacetone synthase activities in the methylotrophic yeast Candida boidinii. J. Gen. Microbiol. 124 (1981) 309–316. [DOI] [PMID: 6276498]
[EC 2.2.1.3 created 1984]
 
 
EC 2.2.1.4     
Accepted name: acetoin—ribose-5-phosphate transaldolase
Reaction: 3-hydroxybutan-2-one + D-ribose 5-phosphate = acetaldehyde + 1-deoxy-D-altro-heptulose 7-phosphate
For diagram of reaction, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): 1-deoxy-D-altro-heptulose-7-phosphate synthetase; 1-deoxy-D-altro-heptulose-7-phosphate synthase; 3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase [wrong substrate name]
Systematic name: 3-hydroxybutan-2-one:D-ribose-5-phosphate aldehydetransferase
Comments: A thiamine-diphosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 87843-76-3
References:
1.  Yokota, A. and Sasajima, K. Enzymatic formation of a new monosaccharide, 1-deoxy-D-altro-heptulose phosphate, from DL-acetoin and D-ribose 5-phosphate by a transketolase mutant of Bacillus pumilus. Agric. Biol. Chem. 47 (1983) 1545–1553.
[EC 2.2.1.4 created 1989]
 
 
EC 2.2.1.5     
Accepted name: 2-hydroxy-3-oxoadipate synthase
Reaction: 2-oxoglutarate + glyoxylate = 2-hydroxy-3-oxoadipate + CO2
For diagram of reaction mechanism, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): 2-hydroxy-3-oxoadipate glyoxylate-lyase (carboxylating); α-ketoglutaric-glyoxylic carboligase; oxoglutarate: glyoxylate carboligase
Systematic name: 2-oxoglutarate:glyoxylate succinaldehydetransferase (decarboxylating)
Comments: The bacterial enzyme requires thiamine diphosphate. The product decarboxylates to 5-hydroxy-4-oxopentanoate. The enzyme can decarboxylate 2-oxoglutarate. Acetaldehyde can replace glyoxylate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9054-72-2
References:
1.  Schlossberg, M.A., Bloom, R.J., Richert, D.A. and Westerfield, W.W. Carboligase activity of α-ketoglutarate dehydrogenase. Biochemistry 9 (1970) 1148–1153. [PMID: 5418712]
2.  Schlossberg, M.A., Richert, D.A., Bloom, R.J. and Westerfield, W.W. Isolation and identification of 5-hydroxy-4-ketovaleric acid as a product of α-ketoglutarate: glyoxylate carboligase. Biochemistry 7 (1968) 333–337. [PMID: 4320439]
3.  Stewart, P.R. and Quayle, J.R. The synergistic decarboxylation of glyoxalate and 2-oxoglutarate by an enzyme system from pig-liver mitochondria. Biochem. J. 102 (1967) 885–897. [PMID: 16742506]
[EC 2.2.1.5 created 1972 as EC 4.1.3.15, transferred 2002 to EC 2.2.1.5]
 
 
EC 2.2.1.6     
Accepted name: acetolactate synthase
Reaction: 2 pyruvate = 2-acetolactate + CO2
For diagram of reaction mechanism, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): α-acetohydroxy acid synthetase; α-acetohydroxyacid synthase; α-acetolactate synthase; α-acetolactate synthetase; acetohydroxy acid synthetase; acetohydroxyacid synthase; acetolactate pyruvate-lyase (carboxylating); acetolactic synthetase
Systematic name: pyruvate:pyruvate acetaldehydetransferase (decarboxylating)
Comments: This enzyme requires thiamine diphosphate. The reaction shown is in the pathway of biosynthesis of valine; the enzyme can also transfer the acetaldehyde from pyruvate to 2-oxobutanoate, forming 2-ethyl-2-hydroxy-3-oxobutanoate, also known as 2-aceto-2-hydroxybutanoate, a reaction in the biosynthesis of isoleucine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-45-6
References:
1.  Bauerle, R.H., Freundlich, M., Størmer, F.C. and Umbarger, H.E. Control of isoleucine, valine and leucine biosynthesis. II. Endproduct inhibition by valine of acetohydroxy acid synthetase in Salmonella typhimurium. Biochim. Biophys. Acta 92 (1964) 142–149. [PMID: 14243762]
2.  Huseby, N.E., Christensen, T.B., Olsen, B.R. and Størmer, F.C. The pH 6 acetolactate-forming enzyme from Aerobacter aerogenes. Subunit structure. Eur. J. Biochem. 20 (1971) 209–214. [DOI] [PMID: 5560406]
3.  Størmer, F.C., Solberg, Y. and Hovig, T. The pH 6 acetolactate-forming enzyme from Aerobacter aerogenes. Molecular properties. Eur. J. Biochem. 10 (1969) 251–260. [DOI] [PMID: 5823101]
4.  Barak, Z., Chipman, D.M. and Gollop, N. Physiological implications of the specificity of acetohydroxy acid synthase isozymes of enteric bacteria. J. Bacteriol. 169 (1987) 3750–3756. [DOI] [PMID: 3301814]
[EC 2.2.1.6 created 1972 as EC 4.1.3.18, transferred 2002 to EC 2.2.1.6]
 
 
EC 2.2.1.7     
Accepted name: 1-deoxy-D-xylulose-5-phosphate synthase
Reaction: pyruvate + D-glyceraldehyde 3-phosphate = 1-deoxy-D-xylulose 5-phosphate + CO2
For diagram of non-mevalonate terpenoid biosynthesis, click here and for mechanism of reaction, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): 1-deoxy-D-xylulose-5-phosphate pyruvate-lyase (carboxylating); DXP-synthase
Systematic name: pyruvate:D-glyceraldehyde-3-phosphate acetaldehydetransferase (decarboxylating)
Comments: Requires thiamine diphosphate. The enzyme forms part of an alternative nonmevalonate pathway for terpenoid biosynthesis (for diagram, click here).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 202218-79-9
References:
1.  Sprenger, G.A., Schörken, U., Weigert, T., Grolle, S., deGraaf, A.A., Taylor, S.V., Begley, T.P., Bringer-Meyer, S. and Sahm, H. Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol. Proc. Natl. Acad. Sci. USA 94 (1997) 12857–12862. [DOI] [PMID: 9371765]
2.  Kuzuyama, T., Takagi, M., Takahashi, S. and Seto, H. Cloning and characterization of 1-deoxy-D-xylulose 5-phosphate synthase from Streptomyces sp. strain CL190, which uses both the mevalonate and nonmevalonate pathways for isopentenyl diphosphate biosynthesis. J. Bacteriol. 182 (2000) 891–897. [DOI] [PMID: 10648511]
[EC 2.2.1.7 created 2001 as EC 4.1.3.37 transferred 2002 to EC 2.2.1.7]
 
 
EC 2.2.1.12     
Accepted name: 3-acetyloctanal synthase
Reaction: pyruvate + (E)-oct-2-enal = (S)-3-acetyloctanal + CO2
Other name(s): pigD (gene name)
Systematic name: pyruvate:(E)-oct-2-enal acetaldehydetransferase (decarboxylating)
Comments: Requires thiamine diphosphate. The enzyme, characterized from the bacterium Serratia marcescens, participates in the biosynthesis of the antibiotic prodigiosin. The enzyme decarboxylates pyruvate, followed by attack of the resulting two-carbon fragment on (E)-oct-2-enal, resulting in a Stetter reaction. In vitro the enzyme can act on a number of α,β-unsaturated carbonyl compounds, including aldehydes and ketones, and can catalyse both 1-2 and 1-4 carboligations depending on the substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Williamson, N.R., Simonsen, H.T., Ahmed, R.A., Goldet, G., Slater, H., Woodley, L., Leeper, F.J. and Salmond, G.P. Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Mol. Microbiol. 56 (2005) 971–989. [DOI] [PMID: 15853884]
2.  Dresen, C., Richter, M., Pohl, M., Ludeke, S. and Müller, M. The enzymatic asymmetric conjugate umpolung reaction. Angew. Chem. Int. Ed. Engl. 49 (2010) 6600–6603. [DOI] [PMID: 20669204]
3.  Kasparyan, E., Richter, M., Dresen, C., Walter, L.S., Fuchs, G., Leeper, F.J., Wacker, T., Andrade, S.L., Kolter, G., Pohl, M. and Müller, M. Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes. Appl. Microbiol. Biotechnol. 98 (2014) 9681–9690. [DOI] [PMID: 24957249]
[EC 2.2.1.12 created 2014]
 
 
EC 2.3.1.190     
Accepted name: acetoin dehydrogenase system
Reaction: acetoin + CoA + NAD+ = acetaldehyde + acetyl-CoA + NADH + H+
Other name(s): acetoin dehydrogenase complex; acetoin dehydrogenase enzyme system; AoDH ES; acetoin dehydrogenase
Systematic name: acetyl-CoA:acetoin O-acetyltransferase
Comments: Requires thiamine diphosphate. It belongs to the 2-oxoacid dehydrogenase system family, which also includes EC 1.2.1.104, pyruvate dehydrogenase system, EC 1.2.1.105, 2-oxoglutarate dehydrogenase system, EC 1.2.1.25, branched-chain α-keto acid dehydrogenase system, and EC 1.4.1.27, glycine cleavage system. With the exception of the glycine cleavage system, which contains 4 components, the 2-oxoacid dehydrogenase systems share a common structure, consisting of three main components, namely a 2-oxoacid dehydrogenase (E1), a dihydrolipoamide acyltransferase (E2), and dihydrolipoamide dehydrogenase (E3).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Priefert, H., Hein, S., Kruger, N., Zeh, K., Schmidt, B. and Steinbuchel, A. Identification and molecular characterization of the Alcaligenes eutrophus H16 aco operon genes involved in acetoin catabolism. J. Bacteriol. 173 (1991) 4056–4071. [DOI] [PMID: 2061286]
2.  Oppermann, F.B. and Steinbuchel, A. Identification and molecular characterization of the aco genes encoding the Pelobacter carbinolicus acetoin dehydrogenase enzyme system. J. Bacteriol. 176 (1994) 469–485. [DOI] [PMID: 8110297]
3.  Kruger, N., Oppermann, F.B., Lorenzl, H. and Steinbuchel, A. Biochemical and molecular characterization of the Clostridium magnum acetoin dehydrogenase enzyme system. J. Bacteriol. 176 (1994) 3614–3630. [DOI] [PMID: 8206840]
4.  Huang, M., Oppermann, F.B. and Steinbuchel, A. Molecular characterization of the Pseudomonas putida 2,3-butanediol catabolic pathway. FEMS Microbiol. Lett. 124 (1994) 141–150. [DOI] [PMID: 7813883]
5.  Huang, M., Oppermann-Sanio, F.B. and Steinbuchel, A. Biochemical and molecular characterization of the Bacillus subtilis acetoin catabolic pathway. J. Bacteriol. 181 (1999) 3837–3841. [DOI] [PMID: 10368162]
[EC 2.3.1.190 created 2010, modified 2020]
 
 
EC 2.5.1.3     
Accepted name: thiamine phosphate synthase
Reaction: (1) 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate = diphosphate + thiamine phosphate + CO2
(2) 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate = diphosphate + thiamine phosphate + CO2
(3) 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-5-(2-phosphooxyethyl)thiazole = diphosphate + thiamine phosphate
For diagram of thiamine diphosphate biosynthesis, click here
Other name(s): thiamine phosphate pyrophosphorylase; thiamine monophosphate pyrophosphorylase; TMP-PPase; thiamine-phosphate diphosphorylase; thiE (gene name); TH1 (gene name); THI6 (gene name); 2-methyl-4-amino-5-hydroxymethylpyrimidine-diphosphate:4-methyl-5-(2-phosphoethyl)thiazole 2-methyl-4-aminopyrimidine-5-methenyltransferase; 4-amino-2-methyl-5-diphosphomethylpyrimidine:2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate 4-amino-2-methylpyrimidine-5-methenyltransferase (decarboxylating)
Systematic name: 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine:2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate 4-amino-2-methylpyrimidine-5-methenyltransferase (decarboxylating)
Comments: The enzyme catalyses the penultimate reaction in thiamine de novo biosynthesis, condensing the pyrimidine and thiazole components. The enzyme is thought to accept the product of EC 2.8.1.10, thiazole synthase, as its substrate. However, it has been shown that in some bacteria, such as Bacillus subtilis, an additional enzyme, thiazole tautomerase (EC 5.3.99.10) converts that compound into its tautomer 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate, and that it is the latter that serves as the substrate for the synthase. In addition to this activity, the enzyme participates in a salvage pathway, acting on 4-methyl-5-(2-phosphooxyethyl)thiazole, which is produced from thiamine degradation products. In yeast this activity is found in a bifunctional enzyme (THI6) and in the plant Arabidopsis thaliana the activity is part of a trifunctional enzyme (TH1).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9030-30-2
References:
1.  Camiener, G.W. and Brown, G.M. The biosynthesis of thiamine. 2. Fractionation of enzyme system and identification of thiazole monophosphate and thiamine monophosphate as intermediates. J. Biol. Chem. 235 (1960) 2411–2417. [PMID: 13807175]
2.  Leder, I.G. The enzymatic synthesis of thiamine monophosphate. J. Biol. Chem. 236 (1961) 3066–3071. [PMID: 14463407]
3.  Kawasaki, Y. Copurification of hydroxyethylthiazole kinase and thiamine-phosphate pyrophosphorylase of Saccharomyces cerevisiae: characterization of hydroxyethylthiazole kinase as a bifunctional enzyme in the thiamine biosynthetic pathway. J. Bacteriol. 175 (1993) 5153–5158. [DOI] [PMID: 8394314]
4.  Backstrom, A.D., McMordie, R.A.S. and Begley, T.P. Biosynthesis of thiamin I: the function of the thiE gene product. J. Am. Chem. Soc. 117 (1995) 2351–2352.
5.  Chiu, H.J., Reddick, J.J., Begley, T.P. and Ealick, S.E. Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 Å resolution. Biochemistry 38 (1999) 6460–6470. [DOI] [PMID: 10350464]
6.  Ajjawi, I., Tsegaye, Y. and Shintani, D. Determination of the genetic, molecular, and biochemical basis of the Arabidopsis thaliana thiamin auxotroph th1. Arch. Biochem. Biophys. 459 (2007) 107–114. [DOI] [PMID: 17174261]
[EC 2.5.1.3 created 1965, modified 2015]
 
 
EC 2.5.1.64      
Transferred entry: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. The reaction that was attributed to this enzyme is now known to be catalysed by two separate enzymes: EC 2.2.1.9 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase) and EC 4.2.99.20 (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase)
[EC 2.5.1.64 created 2003, deleted 2008]
 
 
EC 2.5.1.66     
Accepted name: N2-(2-carboxyethyl)arginine synthase
Reaction: D-glyceraldehyde 3-phosphate + L-arginine = N2-(2-carboxyethyl)-L-arginine + phosphate
For diagram of clavulanate biosynthesis, click here
Other name(s): CEAS; N2-(2-carboxyethyl)arginine synthetase; CEA synthetase; glyceraldehyde-3-phosphate:L-arginine 2-N-(2-hydroxy-3-oxopropyl) transferase (2-carboxyethyl-forming)
Systematic name: glyceraldehyde-3-phosphate:L-arginine N2-(2-hydroxy-3-oxopropyl) transferase (2-carboxyethyl-forming)
Comments: The enzyme requires thiamine diphosphate and catalyses the first step in the clavulanic-acid-biosynthesis pathway. The 2-hydroxy-3-oxo group transferred from glyceraldehyde 3-phosphate is isomerized during transfer to form the 2-carboxyethyl group.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 250207-48-8
References:
1.  Caines, M.E.C., Elkins, J.M., Hewitson, K.S. and Schofield, C.J. Crystal structure and mechanistic implications of N2-(2-carboxyethyl)arginine synthase, the first enzymes in the clavulanic acid biosynthesis pathway. J. Biol. Chem. 279 (2004) 5685–5692. [DOI] [PMID: 14623876]
2.  Khaleeli, N., Li, R. and Townsend, C.A. Origin of the β-lactam carbons in clavulanic acid from an unusual thiamine pyrophosphate-mediated reaction. J. Am. Chem. Soc. 121 (1999) 9223–9224.
[EC 2.5.1.66 created 2004]
 
 
EC 2.7.4.7     
Accepted name: phosphooxymethylpyrimidine kinase
Reaction: ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
For diagram of thiamine diphosphate biosynthesis, click here
Glossary: 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = (4-amino-2-methylpyrimidin-5-yl)methyl dihydrogen phosphate
Other name(s): hydroxymethylpyrimidine phosphokinase; ATP:4-amino-2-methyl-5-phosphooxymethylpyrimidine phosphotransferase; ATP:(4-amino-2-methylpyrimidin-5-yl)methyl-phosphate phosphotransferase; phosphomethylpyrimidine kinase
Systematic name: ATP:4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine phosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37278-18-5
References:
1.  Lewin, L.M. and Brown, G.M. The biosynthesis of thiamine. III. Mechanism of enzymatic formation of the pyrophosphate ester of 2-methyl-4-amino-5-hydroxymethylpyrimidine. J. Biol. Chem. 236 (1961) 2768–2771.
[EC 2.7.4.7 created 1965, modified 2016]
 
 
EC 2.7.4.15     
Accepted name: thiamine-diphosphate kinase
Reaction: ATP + thiamine diphosphate = ADP + thiamine triphosphate
For diagram of thiamine diphosphate biosynthesis, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): ATP:thiamin-diphosphate phosphotransferase; TDP kinase; thiamin diphosphate kinase; thiamin diphosphate phosphotransferase; thiamin pyrophosphate kinase; thiamine diphosphate kinase; protein bound thiamin diphosphate:ATP phosphoryltransferase
Systematic name: ATP:thiamine-diphosphate phosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9075-79-0
References:
1.  Itokawa, Y. and Cooper, J.R. The enzymatic synthesis of triphosphothiamin. Biochim. Biophys. Acta 158 (1968) 180–182. [DOI] [PMID: 5661031]
2.  Kikuchi, M. and Ikawa, T. Presence of an enzyme mediating transfer of phosphate from thiamine triphosphate to ADP in germinating maize. Bot. Mag. (Tokyo) 97 (1984) 193–205.
[EC 2.7.4.15 created 1972]
 
 
EC 2.7.4.16     
Accepted name: thiamine-phosphate kinase
Reaction: ATP + thiamine phosphate = ADP + thiamine diphosphate
For diagram of thiamine diphosphate biosynthesis, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): thiamin-monophosphate kinase; thiamin monophosphatase; thiamin monophosphokinase
Systematic name: ATP:thiamine-phosphate phosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9068-23-9
References:
1.  Nishino, H. Biogenesis of cocarboxylase in Escherichia coli. Partial purification and some properties of thiamine monophosphate kinase. J. Biochem. (Tokyo) 72 (1972) 1093–1100. [PMID: 4567662]
[EC 2.7.4.16 created 1976]
 
 
EC 2.7.6.2     
Accepted name: thiamine diphosphokinase
Reaction: ATP + thiamine = AMP + thiamine diphosphate
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): thiamin kinase; thiamine pyrophosphokinase; ATP:thiamin pyrophosphotransferase; thiamin pyrophosphokinase; thiamin pyrophosphotransferase; thiaminokinase; thiamin:ATP pyrophosphotransferase; TPTase
Systematic name: ATP:thiamine diphosphotransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9026-24-8
References:
1.  Leuthardt, F. and Nielsen, H. Phosphorylation biologique de la thiamine. Helv. Chim. Acta 35 (1952) 1196–1209.
2.  Shimazono, N., Mano, Y., Tanaka, R. and Kajiro, Y. Mechanism of transpyrophosphorylation with thiamine pyrophosphokinase. J. Biochem. (Tokyo) 46 (1959) 959–961.
3.  Steyn-Parvé, E.P. Partial purification and properties of thiaminokinase from yeast. Biochim. Biophys. Acta 8 (1952) 310–324. [DOI] [PMID: 14934742]
[EC 2.7.6.2 created 1961]
 
 
EC 2.8.1.10     
Accepted name: thiazole synthase
Reaction: 1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-[sulfur-carrier protein ThiS] = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate + [sulfur-carrier protein ThiS] + 2 H2O
For diagram of thiamine diphosphate biosynthesis, click here
Glossary: cThz*-P = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate
Other name(s): thiG (gene name)
Systematic name: 1-deoxy-D-xylulose 5-phosphate:thiol sulfurtransferase
Comments: H2S can provide the sulfur in vitro. Part of the pathway for thiamine biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Park, J.H., Dorrestein, P.C., Zhai, H., Kinsland, C., McLafferty, F.W. and Begley, T.P. Biosynthesis of the thiazole moiety of thiamin pyrophosphate (vitamin B1). Biochemistry 42 (2003) 12430–12438. [DOI] [PMID: 14567704]
2.  Dorrestein, P.C., Zhai, H., McLafferty, F.W. and Begley, T.P. The biosynthesis of the thiazole phosphate moiety of thiamin: the sulfur transfer mediated by the sulfur carrier protein ThiS. Chem. Biol. 11 (2004) 1373–1381. [DOI] [PMID: 15489164]
3.  Dorrestein, P.C., Zhai, H., Taylor, S.V., McLafferty, F.W. and Begley, T.P. The biosynthesis of the thiazole phosphate moiety of thiamin (vitamin B1): the early steps catalyzed by thiazole synthase. J. Am. Chem. Soc. 126 (2004) 3091–3096. [DOI] [PMID: 15012138]
4.  Settembre, E.C., Dorrestein, P.C., Zhai, H., Chatterjee, A., McLafferty, F.W., Begley, T.P. and Ealick, S.E. Thiamin biosynthesis in Bacillus subtilis: structure of the thiazole synthase/sulfur carrier protein complex. Biochemistry 43 (2004) 11647–11657. [DOI] [PMID: 15362849]
5.  Hazra, A., Chatterjee, A. and Begley, T.P. Biosynthesis of the thiamin thiazole in Bacillus subtilis: identification of the product of the thiazole synthase-catalyzed reaction. J. Am. Chem. Soc. 131 (2009) 3225–3229. [DOI] [PMID: 19216519]
6.  Hazra, A.B., Han, Y., Chatterjee, A., Zhang, Y., Lai, R.Y., Ealick, S.E. and Begley, T.P. A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase. J. Am. Chem. Soc. 133 (2011) 9311–9319. [DOI] [PMID: 21534620]
[EC 2.8.1.10 created 2011, modified 2016]
 
 
EC 3.1.3.100     
Accepted name: thiamine phosphate phosphatase
Reaction: thiamine phosphate + H2O = thiamine + phosphate
Systematic name: thiamine phosphate phosphohydrolase
Comments: The enzyme participates in the thiamine biosynthesis pathway in eukaryotes and a few prokaryotes. These organisms lack EC 2.7.4.16, thiamine-phosphate kinase, and need to convert thiamine phosphate to thiamine diphosphate, the active form of the vitamin, by first removing the phosphate group, followed by diphosphorylation by EC 2.7.6.2, thiamine diphosphokinase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sanemori, H., Egi, Y. and Kawasaki, T. Pathway of thiamine pyrophosphate synthesis in Micrococcus denitrificans. J. Bacteriol. 126 (1976) 1030–1036. [PMID: 181359]
2.  Komeda, Y., Tanaka, M. and Nishimune, T. A th-1 mutant of Arabidopsis thaliana is defective for a thiamin-phosphate-synthesizing enzyme: thiamin phosphate pyrophosphorylase. Plant Physiol. 88 (1988) 248–250. [PMID: 16666289]
3.  Schweingruber, A.M., Dlugonski, J., Edenharter, E. and Schweingruber, M.E. Thiamine in Schizosaccharomyces pombe: dephosphorylation, intracellular pool, biosynthesis and transport. Curr. Genet. 19 (1991) 249–254. [PMID: 1868574]
4.  Muller, I.B., Bergmann, B., Groves, M.R., Couto, I., Amaral, L., Begley, T.P., Walter, R.D. and Wrenger, C. The vitamin B1 metabolism of Staphylococcus aureus is controlled at enzymatic and transcriptional levels. PLoS One 4:e7656 (2009). [DOI] [PMID: 19888457]
5.  Kolos, I.K. and Makarchikov, A.F. [Identification of thiamine monophosphate hydrolyzing enzymes in chicken liver] Ukr. Biochem. J. 86 (2014) 39–49. [PMID: 25816604] (in Russian)
6.  Mimura, M., Zallot, R., Niehaus, T.D., Hasnain, G., Gidda, S.K., Nguyen, T.N., Anderson, E.M., Mullen, R.T., Brown, G., Yakunin, A.F., de Crecy-Lagard, V., Gregory, J.F., 3rd, McCarty, D.R. and Hanson, A.D. Arabidopsis TH2 encodes the orphan enzyme thiamin monophosphate phosphatase. Plant Cell 28 (2016) 2683–2696. [DOI] [PMID: 27677881]
[EC 3.1.3.100 created 2016]
 
 
EC 3.5.1.28     
Accepted name: N-acetylmuramoyl-L-alanine amidase
Reaction: Hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): acetylmuramyl-L-alanine amidase; N-acetylmuramyl-L-alanine amidase; N-acylmuramyl-L-alanine amidase; acetylmuramoyl-alanine amidase; N-acetylmuramic acid L-alanine amidase; acetylmuramyl-alanine amidase; N-acetylmuramylalanine amidase; murein hydrolase; N-acetylmuramoyl-L-alanine amidase type I; N-acetylmuramoyl-L-alanine amidase type II
Systematic name: peptidoglycan amidohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9013-25-6
References:
1.  Ghuysen, J.-M., Dierickx, L., Coyette, J., Leyh-Bouille, M., Guinand, M. and Campbell, J.N. An improved technique for the preparation of Streptomyces peptidases and N-acetylmuramyl-L-alanine amidase active on bacterial wall peptidoglycans. Biochemistry 8 (1969) 213–222. [PMID: 5777325]
2.  Herbold, D.R. and Glaser, L. Interaction of N-acetylmuramic acid L-alanine amidase with cell wall polymers. J Biol Chem 250 (1975) 7231–7238. [PMID: 809432]
3.  Herbold, D.R. and Glaser, L. Bacillus subtilis N-acetylmuramic acid L-alanine amidase. J. Biol. Chem. 250 (1975) 1676–1682. [PMID: 803507]
4.  Ward, J.B., Curtis, C.A.M., Taylor, C. and Buxton, R.S. Purification and characterization of two phage PBSX-induced lytic enzymes of Bacillus subtilis 168: an N-acetylmuramoyl-L-alanine amidase and an N-acetylmuramidase. J. Gen. Microbiol. 128 (1982) 1171–1178. [DOI] [PMID: 6126517]
[EC 3.5.1.28 created 1972 (EC 3.4.19.10 created 1992, incorporated 1997)]
 
 
EC 3.6.1.15     
Accepted name: nucleoside-triphosphate phosphatase
Reaction: a nucleoside triphosphate + H2O = a nucleoside diphosphate + phosphate
Other name(s): nucleoside-triphosphatase; nucleoside triphosphate phosphohydrolase; nucleoside-5-triphosphate phosphohydrolase; nucleoside 5-triphosphatase; unspecific diphosphate phosphohydrolase
Systematic name: nucleoside-triphosphate phosphohydrolase
Comments: The enzyme is found in eukaryotes and thermophilic bacteria, but appears to be absent from mesophilic bacteria. Also hydrolyses nucleoside diphosphates, thiamine diphosphate and FAD. The enzyme from the plant Pisum sativum (garden pea) is regulated by calmodulin [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-51-8
References:
1.  Brightwell, R. and Tappel, A.L. Lysosomal acid pyrophosphatase and acid phosphatase. Arch. Biochem. Biophys. 124 (1968) 333–343. [DOI] [PMID: 5661608]
2.  Lewis, M. and Weissman, S. Properties of a soluble nucleoside triphosphatase activity in mammalian liver. Arch. Biochem. Biophys. 109 (1965) 490–498. [DOI] [PMID: 14320490]
3.  Matsushita, S. and Raacke, I.D. Purification of nucleoside triphosphatases from pea seedling ribosomes. Biochim. Biophys. Acta 166 (1968) 707–710. [DOI] [PMID: 4301913]
4.  Tong, C.G., Dauwalder, M., Clawson, G.A., Hatem, C.L. and Roux, S.J. The major nucleoside triphosphatase in pea (Pisum sativum L.) nuclei and in rat liver nuclei share common epitopes also present in nuclear lamins. Plant Physiol. 101 (1993) 1005–1011. [PMID: 7508630]
5.  Hsieh, H.L., Tong, C.G., Thomas, C. and Roux, S.J. Light-modulated abundance of an mRNA encoding a calmodulin-regulated, chromatin-associated NTPase in pea. Plant Mol. Biol. 30 (1996) 135–147. [PMID: 8616230]
6.  Klinger, C., Rossbach, M., Howe, R. and Kaufmann, M. Thermophile-specific proteins: the gene product of aq_1292 from Aquifex aeolicus is an NTPase. BMC Biochem. 4:12 (2003). [DOI] [PMID: 14503925]
7.  Placzek, W.J., Almeida, M.S. and Wuthrich, K. NMR structure and functional characterization of a human cancer-related nucleoside triphosphatase. J. Mol. Biol. 367 (2007) 788–801. [DOI] [PMID: 17291528]
[EC 3.6.1.15 created 1972]
 
 
EC 3.6.1.28     
Accepted name: thiamine-triphosphatase
Reaction: thiamine triphosphate + H2O = thiamine diphosphate + phosphate
For diagram of thiamine diphosphate biosynthesis, click here
Systematic name: thiamine-triphosphate phosphohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9068-47-7
References:
1.  Hashitani, Y. and Cooper, J.R. The partial purification of thiamine triphosphatase from rat brain. J. Biol. Chem. 247 (1972) 2117–2199. [PMID: 4335862]
[EC 3.6.1.28 created 1978]
 
 
EC 4.1.1.1     
Accepted name: pyruvate decarboxylase
Reaction: a 2-oxo carboxylate = an aldehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): α-carboxylase (ambiguous); pyruvic decarboxylase; α-ketoacid carboxylase; 2-oxo-acid carboxy-lyase
Systematic name: 2-oxo-acid carboxy-lyase (aldehyde-forming)
Comments: A thiamine-diphosphate protein. Also catalyses acyloin formation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9001-04-1
References:
1.  Singer, T.P. and Pensky, J. Isolation and properties of the α-carboxylase of wheat germ. J. Biol. Chem. 196 (1952) 375–388. [PMID: 12980978]
[EC 4.1.1.1 created 1961]
 
 
EC 4.1.1.7     
Accepted name: benzoylformate decarboxylase
Reaction: phenylglyoxylate = benzaldehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
phenylglyoxylate = benzoylformate = 2-oxo-2-phenylacetate
Other name(s): phenylglyoxylate decarboxylase; benzoylformate carboxy-lyase; benzoylformate carboxy-lyase (benzaldehyde-forming)
Systematic name: phenylglyoxylate carboxy-lyase (benzaldehyde-forming)
Comments: A thiamine-diphosphate protein.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9025-00-7
References:
1.  Gunsalus, C.F., Stanier, R.Y. and Gunsalus, I.C. The enzymatic conversion of mandelic acid to benzoic acid. III. Fractionation and properties of the soluble enzymes. J. Bacteriol. 66 (1953) 548–553. [PMID: 13108854]
[EC 4.1.1.7 created 1961]
 
 
EC 4.1.1.8     
Accepted name: oxalyl-CoA decarboxylase
Reaction: oxalyl-CoA = formyl-CoA + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): oxalyl coenzyme A decarboxylase; oxalyl-CoA carboxy-lyase
Systematic name: oxalyl-CoA carboxy-lyase (formyl-CoA-forming)
Comments: A thiamine-diphosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-96-8
References:
1.  Quayle, J.R. Carbon assimilation by Pseudomonas oxalaticus (OX1). 7. Decarboxylation of oxalyl-coenzyme A to formyl-coenzyme A. Biochem. J. 89 (1963) 492–503. [PMID: 14101969]
[EC 4.1.1.8 created 1961]
 
 
EC 4.1.1.71     
Accepted name: 2-oxoglutarate decarboxylase
Reaction: 2-oxoglutarate = succinate semialdehyde + CO2
For diagram of the citric acid cycle, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): oxoglutarate decarboxylase; α-ketoglutarate decarboxylase; α-ketoglutaric decarboxylase; pre-2-oxoglutarate decarboxylase; 2-oxoglutarate carboxy-lyase
Systematic name: 2-oxoglutarate carboxy-lyase (succinate-semialdehyde-forming)
Comments: Requires thiamine diphosphate. Highly specific.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37205-42-8
References:
1.  Shigeoka, S., Onishi, T., Maeda, K., Nakano, Y. and Kitaoka, S. Occurrence of thiamin pyrophosphate-dependent 2-oxoglutarate decarboxylase in mitochondria of Euglena gracilis. FEBS Lett. 195 (1986) 43–47.
[EC 4.1.1.71 created 1989]
 
 
EC 4.1.1.74     
Accepted name: indolepyruvate decarboxylase
Reaction: 3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): indol-3-yl-pyruvate carboxy-lyase; 3-(indol-3-yl)pyruvate carboxy-lyase
Systematic name: 3-(indol-3-yl)pyruvate carboxy-lyase [(2-indol-3-yl)acetaldehyde-forming]
Comments: Thiamine diphosphate- and Mg2+-dependent. More specific than EC 4.1.1.1 pyruvate decarboxylase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9074-92-4
References:
1.  Koga, J. Structure and function of indolepyruvate decarboxylase, a key enzyme in indole-3-pyruvic acid biosynthesis. Biochim. Biophys. Acta 1249 (1995) 1–13. [DOI] [PMID: 7766676]
[EC 4.1.1.74 created 1999]
 
 
EC 4.1.1.75     
Accepted name: 5-guanidino-2-oxopentanoate decarboxylase
Reaction: 5-guanidino-2-oxopentanoate = 4-guanidinobutanal + CO2
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): α-ketoarginine decarboxylase; 2-oxo-5-guanidinopentanoate carboxy-lyase
Systematic name: 5-guanidino-2-oxopentanoate carboxy-lyase (4-guanidinobutanal-forming)
Comments: Enzyme activity is dependent on the presence of thiamine diphosphate and a divalent cation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 56831-67-5
References:
1.  Vanderbilt, A.S., Gaby, N.S., Rodwell, V.W. Intermediates and enzymes between α-ketoarginine and γ-guanidinobutyrate in the L-arginine catabolic pathway of Pseudomonas putida. J. Biol. Chem. 250 (1975) 5322–5329. [PMID: 237915]
[EC 4.1.1.75 created 1999]
 
 
EC 4.1.1.79     
Accepted name: sulfopyruvate decarboxylase
Reaction: 3-sulfopyruvate = 2-sulfoacetaldehyde + CO2
For diagram of coenzyme-M biosynthesis, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
2-sulfoacetaldehyde = 2-oxoethanesulfonate
Other name(s): sulfopyruvate carboxy-lyase
Systematic name: 3-sulfopyruvate carboxy-lyase (2-sulfoacetaldehyde-forming)
Comments: Requires thiamine diphosphate. Does not decarboxylate pyruvate or phosphonopyruvate. The enzyme appears to be oxygen-sensitive.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 303155-97-7
References:
1.  Graupner, M., Xu, H. and White, R.H. Identification of the gene encoding sulfopyruvate decarboxylase, an enzyme involved in biosynthesis of coenzyme M. J. Bacteriol. 182 (2000) 4862–4867. [DOI] [PMID: 10940029]
[EC 4.1.1.79 created 2002]
 
 
EC 4.1.1.82     
Accepted name: phosphonopyruvate decarboxylase
Reaction: 3-phosphonopyruvate = 2-phosphonoacetaldehyde + CO2
For diagram of phosphonate metabolism, click here
Other name(s): 3-phosphonopyruvate carboxy-lyase
Systematic name: 3-phosphonopyruvate carboxy-lyase (2-phosphonoacetaldehyde-forming)
Comments: The enzyme catalyses a step in the biosynthetic pathway of 2-aminoethylphosphonate, a component of the capsular polysaccharide complex of Bacteroides fragilis. Requires thiamine diphosphate and Mg2+ as cofactors. The enzyme is activated by the divalent cations Mg2+, Ca2+ and Mn2+. Pyruvate and sulfopyruvate can also act as substrates, but more slowly. This enzyme drives the reaction catalysed by EC 5.4.2.9, phosphoenolpyruvate mutase, in the thermodynamically unfavourable direction of 3-phosphonopyruvate formation [2]. It is the initial step in all of the major biosynthetic pathways of phosphonate natural products [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 151662-34-9
References:
1.  Zhang, G., Dai, J., Lu, Z. and Dunaway-Mariano, D. The phosphonopyruvate decarboxylase from Bacteroides fragilis. J. Biol. Chem. 278 (2003) 41302–41308. [DOI] [PMID: 12904299]
2.  Seidel, H.M. and Knowles, J.R. Interaction of inhibitors with phosphoenolpyruvate mutase: implications for the reaction mechanism and the nature of the active site. Biochemistry 33 (1994) 5641–5646. [PMID: 8180189]
3.  Nakashita, H., Watanabe, K., Hara, O., Hidaka, T. and Seto, H. Studies on the biosynthesis of bialaphos. Biochemical mechanism of C-P bond formation: discovery of phosphonopyruvate decarboxylase which catalyzes the formation of phosphonoacetaldehyde from phosphonopyruvate. J. Antibiot. (Tokyo) 50 (1997) 212–219. [PMID: 9127192]
[EC 4.1.1.82 created 2005]
 
 
EC 4.1.2.9     
Accepted name: phosphoketolase
Reaction: D-xylulose 5-phosphate + phosphate = acetyl phosphate + D-glyceraldehyde 3-phosphate + H2O
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): D-xylulose-5-phosphate D-glyceraldehyde-3-phosphate-lyase (phosphate-acetylating)
Systematic name: D-xylulose-5-phosphate D-glyceraldehyde-3-phosphate-lyase (adding phosphate; acetyl-phosphate-forming)
Comments: A thiamine-diphosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9031-75-8
References:
1.  Heath, E.C., Hurwitz, J., Horecker, B.L. and Ginsburg, A. Pentose fermentation by Lactobacillus plantarum. I. The cleavage of xylulose 5-phosphate by phosphoketolase. J. Biol. Chem. 231 (1958) 1009–1029. [PMID: 13539033]
2.  Schramm, M., Klybas, V. and Racker, E. Phospholytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum. J. Biol. Chem. 233 (1958) 1283–1288. [PMID: 13610828]
[EC 4.1.2.9 created 1961]
 
 
EC 4.1.2.38     
Accepted name: benzoin aldolase
Reaction: 2-hydroxy-1,2-diphenylethanone = 2 benzaldehyde
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
benzoin = 2-hydroxy-1,2-diphenylethanone
Other name(s): benzaldehyde lyase; 2-hydroxy-1,2-diphenylethanone benzaldehyde-lyase
Systematic name: 2-hydroxy-1,2-diphenylethanone benzaldehyde-lyase (benzaldehyde-forming)
Comments: A thiamine-diphosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 122097-01-2
References:
1.  González, B. and Vicuñna, R. Benzaldehyde lyase, a novel thiamine PPi-requiring enzyme, from Pseudomonas fluorescens biovar I. J. Bacteriol. 171 (1989) 2401–2405. [DOI] [PMID: 2496105]
[EC 4.1.2.38 created 1992]
 
 
EC 4.1.2.63     
Accepted name: 2-hydroxyacyl-CoA lyase
Reaction: (1) a 2-hydroxy-3-methyl-Cn-fatty-acyl-CoA = a 2-methyl-branched Cn-1-fatty aldehyde + formyl-CoA
(2) a (2R)-2-hydroxy-Cn-long-chain fatty acyl-CoA = a Cn-1-long-chain fatty aldehyde + formyl-CoA
Other name(s): HACL1 (gene name); 2-hydroxyphytanoyl-CoA lyase; 2-HPCL
Systematic name: 2-hydroxy-3-methyl fatty-CoA formyl-CoA lyase (2-methyl branched fatty aldehyde-forming)
Comments: Requires Mg2+ and thiamine diphosphate. This peroxisomal enzyme, found in animals, is involved in the α-oxidation of 3-methyl-branched fatty acids like phytanic acid and the shortening of 2-hydroxy long-chain fatty acids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Foulon, V., Antonenkov, V.D., Croes, K., Waelkens, E., Mannaerts, G.P., Van Veldhoven, P.P. and Casteels, M. Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during α-oxidation of 3-methyl-branched fatty acids. Proc. Natl. Acad. Sci. USA 96 (1999) 10039–10044. [DOI] [PMID: 10468558]
2.  Foulon, V., Sniekers, M., Huysmans, E., Asselberghs, S., Mahieu, V., Mannaerts, G.P., Van Veldhoven, P.P. and Casteels, M. Breakdown of 2-hydroxylated straight chain fatty acids via peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the α-oxidation of straight chain fatty acids. J. Biol. Chem. 280 (2005) 9802–9812. [DOI] [PMID: 15644336]
3.  Casteels, M., Sniekers, M., Fraccascia, P., Mannaerts, G.P. and Van Veldhoven, P.P. The role of 2-hydroxyacyl-CoA lyase, a thiamin pyrophosphate-dependent enzyme, in the peroxisomal metabolism of 3-methyl-branched fatty acids and 2-hydroxy straight-chain fatty acids. Biochem Soc Trans. 35 (2007) 876–880. [DOI] [PMID: 17956236]
[EC 4.1.2.63 created 2021]
 
 
EC 4.1.99.17     
Accepted name: phosphomethylpyrimidine synthase
Reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5′-deoxyadenosine + L-methionine + formate + CO
For diagram of thiamine diphosphate biosynthesis, click here
Other name(s): thiC (gene name)
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole formate-lyase (decarboxylating, 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine-forming)
Comments: Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5′-deoxyadenosin-5′-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Chatterjee, A., Li, Y., Zhang, Y., Grove, T.L., Lee, M., Krebs, C., Booker, S.J., Begley, T.P. and Ealick, S.E. Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat. Chem. Biol. 4 (2008) 758–765. [DOI] [PMID: 18953358]
2.  Martinez-Gomez, N.C., Poyner, R.R., Mansoorabadi, S.O., Reed, G.H. and Downs, D.M. Reaction of AdoMet with ThiC generates a backbone free radical. Biochemistry 48 (2009) 217–219. [DOI] [PMID: 19113839]
3.  Chatterjee, A., Hazra, A.B., Abdelwahed, S., Hilmey, D.G. and Begley, T.P. A "radical dance" in thiamin biosynthesis: mechanistic analysis of the bacterial hydroxymethylpyrimidine phosphate synthase. Angew. Chem. Int. Ed. Engl. 49 (2010) 8653–8656. [DOI] [PMID: 20886485]
[EC 4.1.99.17 created 2011]
 
 
EC 4.1.99.19     
Accepted name: 2-iminoacetate synthase
Reaction: L-tyrosine + S-adenosyl-L-methionine + NADPH = 2-iminoacetate + 4-methylphenol + 5′-deoxyadenosine + L-methionine + NADP+ + H+
For diagram of thiamine diphosphate biosynthesis, click here
Glossary: 4-methylphenol = 4-cresol = p-cresol
Other name(s): thiH (gene name)
Systematic name: L-tyrosine 4-methylphenol-lyase (2-iminoacetate-forming)
Comments: Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce methionine and a 5-deoxyadenosin-5-yl radical that is crucial for the conversion of the substrate. The reductant is assumed to be NADPH, which is provided by a flavoprotein:NADPH oxidoreductase system [4]. Part of the pathway for thiamine biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Leonardi, R., Fairhurst, S.A., Kriek, M., Lowe, D.J. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex. FEBS Lett. 539 (2003) 95–99. [DOI] [PMID: 12650933]
2.  Kriek, M., Martins, F., Challand, M.R., Croft, A. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: identification of the intermediate and by-product derived from tyrosine. Angew. Chem. Int. Ed. Engl. 46 (2007) 9223–9226. [DOI] [PMID: 17969213]
3.  Kriek, M., Martins, F., Leonardi, R., Fairhurst, S.A., Lowe, D.J. and Roach, P.L. Thiazole synthase from Escherichia coli: an investigation of the substrates and purified proteins required for activity in vitro. J. Biol. Chem. 282 (2007) 17413–17423. [DOI] [PMID: 17403671]
4.  Challand, M.R., Martins, F.T. and Roach, P.L. Catalytic activity of the anaerobic tyrosine lyase required for thiamine biosynthesis in Escherichia coli. J. Biol. Chem. 285 (2010) 5240–5248. [DOI] [PMID: 19923213]
[EC 4.1.99.19 created 2011, modified 2014]
 
 
EC 5.3.99.10     
Accepted name: thiazole tautomerase
Reaction: 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate = 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate
For diagram of thiamine diphosphate biosynthesis, click here
Glossary: cThz*-P = 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate
cThz-P = 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate = 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylate
Other name(s): tenI (gene name)
Systematic name: 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate isomerase
Comments: The enzyme catalyses the irreversible aromatization of the thiazole moiety of 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Hazra, A.B., Han, Y., Chatterjee, A., Zhang, Y., Lai, R.Y., Ealick, S.E. and Begley, T.P. A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase. J. Am. Chem. Soc. 133 (2011) 9311–9319. [DOI] [PMID: 21534620]
[EC 5.3.99.10 created 2012]
 
 
EC 7.6.2.15     
Accepted name: ABC-type thiamine transporter
Reaction: ATP + H2O + thiamine-[thiamine-binding protein][side 1] = ADP + phosphate + thiamine[side 2] + [thiamine-binding protein][side 1]
Other name(s): thiamin transporting ATPase; thiamine ABC transporter; thiamin ABC transporter; thiamine transporting ATPase; thiBPQ (gene names)
Systematic name: ATP phosphohydrolase (ABC-type, thiamine-importing)
Comments: ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. The enzyme, characterized from the bacterium Salmonella typhimurium, is a heterodimeric complex that interacts with an extracytoplasmic substrate binding protein and functions to import thiamine, thiamine monophosphate and thiamine diphosphate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Webb, E., Claas, K. and Downs, D. thiBPQ encodes an ABC transporter required for transport of thiamine and thiamine pyrophosphate in Salmonella typhimurium. J. Biol. Chem. 273 (1998) 8946–8950. [PMID: 9535878]
[EC 7.6.2.15 created 2019]
 
 


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