The Enzyme Database

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EC 1.14.14.46     
Accepted name: pimeloyl-[acyl-carrier protein] synthase
Reaction: a long-chain acyl-[acyl-carrier protein] + 2 reduced flavodoxin + 3 O2 = pimeloyl-[acyl-carrier protein] + an n-alkanal + 2 oxidized flavodoxin + 3 H2O (overall reaction)
(1a) a long-chain acyl-[acyl-carrier protein] + reduced flavodoxin + O2 = a (7S)-7-hydroxy-long-chain-acyl-[acyl-carrier protein] + oxidized flavodoxin + H2O
(1b) a (7S)-7-hydroxy-long-chain-acyl-[acyl-carrier protein] + reduced flavodoxin + O2 = a (7R,8R)-7,8-dihydroxy-long-chain-acyl-[acyl-carrier protein] + oxidized flavodoxin + H2O
(1c) a (7R,8R)-7,8-dihydroxy-long-chain-acyl-[acyl-carrier protein] + reduced flavodoxin + O2 = a 7-oxoheptanoyl-[acyl-carrier protein] + an n-alkanal + oxidized flavodoxin + 2 H2O
(1d) a 7-oxoheptanoyl-[acyl-carrier protein] + oxidized flavodoxin + H2O = a pimeloyl-[acyl-carrier protein] + reduced flavodoxin + H+
Glossary: a long-chain acyl-[acyl-carrier protein] = an acyl-[acyl-carrier protein] thioester where the acyl chain contains 13 to 22 carbon atoms.
palmitoyl-[acyl-carrier protein] = hexadecanoyl-[acyl-carrier protein]
pimeloyl-[acyl-carrier protein] = 6-carboxyhexanoyl-[acyl-carrier protein]
Other name(s): bioI (gene name); P450BioI; CYP107H1
Systematic name: acyl-[acyl-carrier protein],reduced-flavodoxin:oxygen oxidoreductase (pimeloyl-[acyl-carrier protein]-forming)
Comments: A cytochrome P-450 (heme-thiolate) protein. The enzyme catalyses an oxidative C-C bond cleavage of long-chain acyl-[acyl-carrier protein]s of various lengths to generate pimeloyl-[acyl-carrier protein], an intermediate in the biosynthesis of biotin. The preferred substrate of the enzyme from the bacterium Bacillus subtilis is palmitoyl-[acyl-carrier protein] which then gives heptanal as the alkanal. The mechanism is similar to EC 1.14.15.6, cholesterol monooxygenase (side-chain-cleaving), followed by a hydroxylation step, which may occur spontaneously [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Stok, J.E. and De Voss, J. Expression, purification, and characterization of BioI: a carbon-carbon bond cleaving cytochrome P450 involved in biotin biosynthesis in Bacillus subtilis. Arch. Biochem. Biophys. 384 (2000) 351–360. [DOI] [PMID: 11368323]
2.  Cryle, M.J. and De Voss, J.J. Carbon-carbon bond cleavage by cytochrome p450(BioI)(CYP107H1). Chem. Commun. (Camb.) (2004) 86–87. [DOI] [PMID: 14737344]
3.  Cryle, M.J. and Schlichting, I. Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex. Proc. Natl. Acad. Sci. USA 105 (2008) 15696–15701. [DOI] [PMID: 18838690]
4.  Cryle, M.J. Selectivity in a barren landscape: the P450(BioI)-ACP complex. Biochem. Soc. Trans. 38 (2010) 934–939. [DOI] [PMID: 20658980]
[EC 1.14.14.46 created 2013 as EC 1.14.15.12, transferred 2017 to EC 1.14.14.46]
 
 
EC 1.14.15.12      
Transferred entry: pimeloyl-[acyl-carrier protein] synthase. Now EC 1.14.14.46, pimeloyl-[acyl-carrier protein] synthase
[EC 1.14.15.12 created 2013, deleted 2017]
 
 
EC 2.1.1.197     
Accepted name: malonyl-[acyl-carrier protein] O-methyltransferase
Reaction: S-adenosyl-L-methionine + malonyl-[acyl-carrier protein] = S-adenosyl-L-homocysteine + malonyl-[acyl-carrier protein] methyl ester
Other name(s): BioC
Systematic name: S-adenosyl-L-methionine:malonyl-[acyl-carrier protein] O-methyltransferase
Comments: Involved in an early step of biotin biosynthesis in Gram-negative bacteria. This enzyme catalyses the transfer of a methyl group to the ω-carboxyl group of malonyl-[acyl-carrier protein] forming a methyl ester. The methyl ester is recognized by the fatty acid synthetic enzymes, which process it via the fatty acid elongation cycle to give pimelyl-[acyl-carrier-protein] methyl ester [5]. While the enzyme can also accept malonyl-CoA, it has a much higher activity with malonyl-[acyl-carrier protein] [6]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Del Campillo-Campbell, A., Kayajanian, G., Campbell, A. and Adhya, S. Biotin-requiring mutants of Escherichia coli K-12. J. Bacteriol. 94 (1967) 2065–2066. [PMID: 4864413]
2.  Rolfe, B. and Eisenberg, M.A. Genetic and biochemical analysis of the biotin loci of Escherichia coli K-12. J. Bacteriol. 96 (1968) 515–524. [PMID: 4877129]
3.  Otsuka, A.J., Buoncristiani, M.R., Howard, P.K., Flamm, J., Johnson, C., Yamamoto, R., Uchida, K., Cook, C., Ruppert, J. and Matsuzaki, J. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. J. Biol. Chem. 263 (1988) 19577–19585. [PMID: 3058702]
4.  Cleary, P.P. and Campbell, A. Deletion and complementation analysis of biotin gene cluster of Escherichia coli. J. Bacteriol. 112 (1972) 830–839. [PMID: 4563978]
5.  Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. 6 (2010) 682–688. [DOI] [PMID: 20693992]
6.  Lin, S. and Cronan, J.E. The BioC O-methyltransferase catalyzes methyl esterification of malonyl-acyl carrier protein, an essential step in biotin synthesis. J. Biol. Chem. 287 (2012) 37010–37020. [DOI] [PMID: 22965231]
[EC 2.1.1.197 created 2010, modified 2013]
 
 
EC 2.1.3.1     
Accepted name: methylmalonyl-CoA carboxytransferase
Reaction: (S)-methylmalonyl-CoA + pyruvate = propanoyl-CoA + oxaloacetate
Other name(s): transcarboxylase; methylmalonyl coenzyme A carboxyltransferase; methylmalonyl-CoA transcarboxylase; oxalacetic transcarboxylase; methylmalonyl-CoA carboxyltransferase; (S)-2-methyl-3-oxopropanoyl-CoA:pyruvate carboxyltransferase; (S)-2-methyl-3-oxopropanoyl-CoA:pyruvate carboxytransferase carboxytransferase [incorrect]
Systematic name: (S)-methylmalonyl-CoA:pyruvate carboxytransferase
Comments: A biotinyl-protein, containing cobalt and zinc. The enzyme, described from the bacterium Propionibacterium shermanii, is unique among the biotin-dependent enzymes in that it catalyses carboxyl transfer between two organic molecules, utilizing two separate carboxyltransferase domains. The enzyme is a very large complex, consisting of a hexameric central core of 12S subunits surrounded by six 5S subunit dimers, each connected to the central core by twelve 1.3S biotin carrier subunits.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 9029-86-1
References:
1.  Swick, R.W. and Wood, H.G. The role of transcarboxylation in propionic acid fermentation. Proc. Natl. Acad. Sci. USA 46 (1960) 28–41. [DOI] [PMID: 16590594]
2.  Wood, H.G. and Kumar, G.K. Transcarboxylase: its quaternary structure and the role of the biotinyl subunit in the assembly of the enzyme and in catalysis. Ann. N.Y. Acad. Sci. 447 (1985) 1–22. [DOI] [PMID: 3893281]
3.  Peikert, C., Seeger, K., Bhat, R.K. and Berger, S. Determination of the binding specificity of the 12S subunit of the transcarboxylase by saturation transfer difference NMR. Org. Biomol. Chem. 2 (2004) 1777–1781. [DOI] [PMID: 15188046]
4.  Kumar Bhat, R. and Berger, S. New and easy strategy for cloning, expression, purification, and characterization of the 5S subunit of transcarboxylase from Propionibacterium f. shermanii. Prep. Biochem. Biotechnol. 37 (2007) 13–26. [DOI] [PMID: 17134979]
5.  Carey, P.R., Sonnichsen, F.D. and Yee, V.C. Transcarboxylase: one of nature’s early nanomachines. IUBMB Life 56 (2004) 575–583. [DOI] [PMID: 15814455]
[EC 2.1.3.1 created 1961]
 
 
EC 2.1.3.10     
Accepted name: malonyl-S-ACP:biotin-protein carboxyltransferase
Reaction: a malonyl-[acyl-carrier protein] + a biotinyl-[protein] = an acetyl-[acyl-carrier protein] + a carboxybiotinyl-[protein]
For diagram of malonate decarboxylase, click here
Other name(s): malonyl-S-acyl-carrier protein:biotin-protein carboxyltransferase; MadC/MadD; MadC,D; malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxyltransferase
Systematic name: malonyl-[acyl-carrier protein]:biotinyl-[protein] carboxytransferase
Comments: Derived from the components MadC and MadD of the anaerobic bacterium Malonomonas rubra, this enzyme is a component of EC 7.2.4.4, biotin-dependent malonate decarboxylase. The carboxy group is transferred from malonate to the prosthetic group of the biotin protein (MadF) with retention of configuration [2]. Similar to EC 4.1.1.87, malonyl-S-ACP decarboxylase, which forms part of the biotin-independent malonate decarboxylase (EC 4.1.1.88), this enzyme also follows on from EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase, and results in the regeneration of the acetyl-[acyl-carrier protein] [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [DOI] [PMID: 9128730]
2.  Micklefield, J., Harris, K.J., Gröger, S., Mocek, U., Hilbi, H., Dimroth, P. and Floss, H.G. Stereochemical course of malonate decarboxylase in Malonomonas rubra has biotin decarboxylation with retention. J. Am. Chem. Soc. 117 (1995) 1153–1154.
3.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 2.1.3.10 created 2008, modified 2018]
 
 
EC 2.1.3.15     
Accepted name: acetyl-CoA carboxytransferase
Reaction: [biotin carboxyl-carrier protein]-N6-carboxybiotinyl-L-lysine + acetyl-CoA = [biotin carboxyl-carrier protein]-N6-biotinyl-L-lysine + malonyl-CoA
Other name(s): accAD (gene names)
Systematic name: [biotin carboxyl-carrier protein]-N6-carboxybiotinyl-L-lysine:acetyl-CoA:carboxytransferase
Comments: The enzyme catalyses the transfer of a carboxyl group carried on a biotinylated biotin carboxyl carrier protein (BCCP) to acetyl-CoA, forming malonyl-CoA. In some organisms this activity is part of a multi-domain polypeptide that includes the carrier protein and EC 6.3.4.14, biotin carboxylase (see EC 6.4.1.2, acetyl-CoA carboxylase). Some enzymes can also carboxylate propanonyl-CoA and butanoyl-CoA (cf. EC 6.4.1.3, propionyl-CoA carboxylase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-93-2
References:
1.  Bilder, P., Lightle, S., Bainbridge, G., Ohren, J., Finzel, B., Sun, F., Holley, S., Al-Kassim, L., Spessard, C., Melnick, M., Newcomer, M. and Waldrop, G.L. The structure of the carboxyltransferase component of acetyl-coA carboxylase reveals a zinc-binding motif unique to the bacterial enzyme. Biochemistry 45 (2006) 1712–1722. [DOI] [PMID: 16460018]
2.  Chuakrut, S., Arai, H., Ishii, M. and Igarashi, Y. Characterization of a bifunctional archaeal acyl coenzyme A carboxylase. J. Bacteriol. 185 (2003) 938–947. [DOI] [PMID: 12533469]
[EC 2.1.3.15 created 2017]
 
 
EC 2.3.1.39     
Accepted name: [acyl-carrier-protein] S-malonyltransferase
Reaction: malonyl-CoA + an [acyl-carrier protein] = CoA + a malonyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): [acyl carrier protein]malonyltransferase; FabD; malonyl coenzyme A-acyl carrier protein transacylase; malonyl transacylase; malonyl transferase; malonyl-CoA-acyl carrier protein transacylase; malonyl-CoA:[acyl-carrier-protein] S-malonyltransferase; malonyl-CoA:ACP transacylase; malonyl-CoA:ACP-SH transacylase; malonyl-CoA:AcpM transacylase; malonyl-CoA:acyl carrier protein transacylase; malonyl-CoA:acyl-carrier-protein transacylase; malonyl-CoA/dephospho-CoA acyltransferase; MAT; MCAT; MdcH
Systematic name: malonyl-CoA:[acyl-carrier protein] S-malonyltransferase
Comments: This enzyme, along with EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, is essential for the initiation of fatty-acid biosynthesis in bacteria. This enzyme also provides the malonyl groups for polyketide biosynthesis [7]. The product of the reaction, malonyl-ACP, is an elongation substrate in fatty-acid biosynthesis. In Mycobacterium tuberculosis, holo-ACP (the product of EC 2.7.8.7, holo-[acyl-carrier-protein] synthase) is the preferred substrate [5]. This enzyme also forms part of the multienzyme complexes EC 4.1.1.88, biotin-independent malonate decarboxylase and EC 7.2.4.4, biotin-dependent malonate decarboxylase. Malonylation of ACP is immediately followed by decarboxylation within the malonate-decarboxylase complex to yield acetyl-ACP, the catalytically active species of the decarboxylase [12]. In the enzyme from Klebsiella pneumoniae, methylmalonyl-CoA can also act as a substrate but acetyl-CoA cannot [10] whereas the enzyme from Pseudomonas putida can use both as substrates [11]. The ACP subunit found in fatty-acid biosynthesis contains a pantetheine-4′-phosphate prosthetic group; that from malonate decarboxylase also contains pantetheine-4′-phosphate but in the form of a 2′-(5-triphosphoribosyl)-3′-dephospho-CoA prosthetic group.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37257-17-3
References:
1.  Alberts, A.W., Majerus, P.W. and Vagelos, P.R. Acetyl-CoA acyl carrier protein transacylase. Methods Enzymol. 14 (1969) 50–53.
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [PMID: 4561013]
3.  Williamson, I.P. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVII. Preparation and general properties of acetyl coenzyme A and malonyl coenzyme A-acyl carrier protein transacylases. J. Biol. Chem. 241 (1966) 2326–2332. [PMID: 5330116]
4.  Joshi, V.C. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XXVI. Purification and properties of malonyl-coenzyme A--acyl carrier protein transacylase of Escherichia coli. Arch. Biochem. Biophys. 143 (1971) 493–505. [DOI] [PMID: 4934182]
5.  Kremer, L., Nampoothiri, K.M., Lesjean, S., Dover, L.G., Graham, S., Betts, J., Brennan, P.J., Minnikin, D.E., Locht, C. and Besra, G.S. Biochemical characterization of acyl carrier protein (AcpM) and malonyl-CoA:AcpM transacylase (mtFabD), two major components of Mycobacterium tuberculosis fatty acid synthase II. J. Biol. Chem. 276 (2001) 27967–27974. [DOI] [PMID: 11373295]
6.  Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J., O'Connell, J.D., 3rd, Khosla, C. and Stroud, R.M. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 11 (2003) 147–154. [DOI] [PMID: 12575934]
7.  Szafranska, A.E., Hitchman, T.S., Cox, R.J., Crosby, J. and Simpson, T.J. Kinetic and mechanistic analysis of the malonyl CoA:ACP transacylase from Streptomyces coelicolor indicates a single catalytically competent serine nucleophile at the active site. Biochemistry 41 (2002) 1421–1427. [DOI] [PMID: 11814333]
8.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [DOI] [PMID: 9208947]
9.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [DOI] [PMID: 10561613]
10.  Hoenke, S. and Dimroth, P. Formation of catalytically active acetyl-S-malonate decarboxylase requires malonyl-coenzyme A:acyl carrier protein transacylase as auxiliary enzyme. Eur. J. Biochem. 259 (1999) 181–187. [PMID: 9914491]
11.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [DOI] [PMID: 9851033]
12.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 2.3.1.39 created 1972, modified 2006, modified 2008]
 
 
EC 2.3.1.47     
Accepted name: 8-amino-7-oxononanoate synthase
Reaction: pimeloyl-[acyl-carrier protein] + L-alanine = 8-amino-7-oxononanoate + CO2 + holo-[acyl-carrier protein]
Glossary: pimeloyl-[acyl-carrier protein] = 6-carboxyhexanoyl-[acyl-carrier protein]
Other name(s): 7-keto-8-aminopelargonic acid synthetase; 7-keto-8-aminopelargonic synthetase; 8-amino-7-oxopelargonate synthase; bioF (gene name)
Systematic name: 6-carboxyhexanoyl-[acyl-carrier protein]:L-alanine C-carboxyhexanoyltransferase (decarboxylating)
Comments: A pyridoxal-phosphate protein. The enzyme catalyses the decarboxylative condensation of L-alanine and pimeloyl-[acyl-carrier protein], a key step in the pathway for biotin biosynthesis. Pimeloyl-CoA can be used with lower efficiency [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-61-0
References:
1.  Eisenberg, M.A. and Star, C. Synthesis of 7-oxo-8-aminopelargonic acid, a biotin vitamer, in cell-free extracts of Escherichia coli biotin auxotrophs. J. Bacteriol. 96 (1968) 1291–1297. [PMID: 4879561]
2.  Alexeev, D., Alexeeva, M., Baxter, R.L., Campopiano, D.J., Webster, S.P. and Sawyer, L. The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme. J. Mol. Biol. 284 (1998) 401–419. [DOI] [PMID: 9813126]
3.  Ploux, O., Breyne, O., Carillon, S. and Marquet, A. Slow-binding and competitive inhibition of 8-amino-7-oxopelargonate synthase, a pyridoxal-5′-phosphate-dependent enzyme involved in biotin biosynthesis, by substrate and intermediate analogs. Kinetic and binding studies. Eur. J. Biochem. 259 (1999) 63–70. [PMID: 9914476]
4.  Webster, S.P. , Alexeev. D., Campopiano, D.J., Watt, R.M., Alexeeva, M., Sawyer, L. and Baxter, R. Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies. Biochemistry 39 (2000) 516–528. [DOI] [PMID: 10642176]
5.  Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. 6 (2010) 682–688. [DOI] [PMID: 20693992]
[EC 2.3.1.47 created 1976, modified 2013]
 
 
EC 2.3.1.187     
Accepted name: acetyl-S-ACP:malonate ACP transferase
Reaction: an acetyl-[acyl-carrier protein] + malonate = a malonyl-[acyl-carrier protein] + acetate
For diagram of malonate decarboxylase, click here
Other name(s): acetyl-S-ACP:malonate ACP-SH transferase; acetyl-S-acyl-carrier protein:malonate acyl-carrier-protein-transferase; MdcA; MadA; ACP transferase; malonate/acetyl-CoA transferase; malonate:ACP transferase; acetyl-S-acyl carrier protein:malonate acyl carrier protein-SH transferase
Systematic name: acetyl-[acyl-carrier-protein]:malonate S-[acyl-carrier-protein]transferase
Comments: This is the first step in the catalysis of malonate decarboxylation and involves the exchange of an acetyl thioester residue bound to the activated acyl-carrier protein (ACP) subunit of the malonate decarboxylase complex for a malonyl thioester residue [2]. This enzyme forms the α subunit of the multienzyme complexes biotin-independent malonate decarboxylase (EC 4.1.1.88) and biotin-dependent malonate decarboxylase (EC 7.2.4.4). The enzyme can also use acetyl-CoA as a substrate but more slowly [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hilbi, H. and Dimroth, P. Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase. Arch. Microbiol. 162 (1994) 48–56. [PMID: 18251085]
2.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [DOI] [PMID: 9208947]
3.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [DOI] [PMID: 10561613]
4.  Chohnan, S., Akagi, K. and Takamura, Y. Functions of malonate decarboxylase subunits from Pseudomonas putida. Biosci. Biotechnol. Biochem. 67 (2003) 214–217. [DOI] [PMID: 12619701]
5.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 2.3.1.187 created 2008, modified 2018]
 
 
EC 2.6.1.62     
Accepted name: adenosylmethionine—8-amino-7-oxononanoate transaminase
Reaction: S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-(methylsulfanyl)-2-oxobutanoate + 7,8-diaminononanoate
Other name(s): 7,8-diaminonanoate transaminase; 7,8-diaminononanoate transaminase; DAPA transaminase (ambiguous); 7,8-diaminopelargonic acid aminotransferase; DAPA aminotransferase (ambiguous); 7-keto-8-aminopelargonic acid; diaminopelargonate synthase; 7-keto-8-aminopelargonic acid aminotransferase
Systematic name: S-adenosyl-L-methionine:8-amino-7-oxononanoate aminotransferase
Comments: A pyridoxal 5′-phosphate enzyme. S-adenosylhomocysteine can also act as donor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37259-71-5
References:
1.  Izumi, Y., Sato, K., Tani, Y. and Ogata, K. Purification of 7-keto-8-aminopelargonic acid-7,8-diaminopelargonic acid aminotransferase, an enzyme involved in biotin synthesis, from Brevibacterium divaricatum. Agric. Biol. Chem. 37 (1973) 2683–2684.
2.  Izumi, Y., Sato, K., Tani, Y. and Ogata, K. 7,8-Diaminopelargonic acid aminotransferase, an enzyme involved in biotin synthesis by microorganisms. Agric. Biol. Chem. 39 (1975) 175–181.
3.  Stoner, G.L. and Eisenberg, M.A. Purification and properties of 7,8-diaminopelargonic acid aminotransferase. An enzyme in the biotin biosynthetic pathway. J. Biol. Chem. 250 (1973) 4029–4036. [PMID: 1092681]
[EC 2.6.1.62 created 1983]
 
 
EC 2.6.1.105     
Accepted name: lysine—8-amino-7-oxononanoate transaminase
Reaction: L-lysine + 8-amino-7-oxononanoate = (S)-2-amino-6-oxohexanoate + 7,8-diaminononanoate
Glossary: (S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine
Other name(s): DAPA aminotransferase (ambiguous); bioA (gene name) (ambiguous); bioK (gene name)
Systematic name: L-lysine:8-amino-7-oxononanoate aminotransferase
Comments: A pyridoxal 5′-phosphate enzyme [2]. Participates in the pathway for biotin biosynthesis. The enzyme from the bacterium Bacillus subtilis cannot use S-adenosyl-L-methionine as amino donor and catalyses an alternative reaction for the conversion of 8-amino-7-oxononanoate to 7,8-diaminononanoate (cf. EC 2.6.1.62, adenosylmethionine—8-amino-7-oxononanoate transaminase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Van Arsdell, S.W., Perkins, J.B., Yocum, R.R., Luan, L., Howitt, C.L., Chatterjee, N.P. and Pero, J.G. Removing a bottleneck in the Bacillus subtilis biotin pathway: bioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction. Biotechnol. Bioeng. 91 (2005) 75–83. [DOI] [PMID: 15880481]
2.  Dey, S., Lane, J.M., Lee, R.E., Rubin, E.J. and Sacchettini, J.C. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase. Biochemistry 49 (2010) 6746–6760. [DOI] [PMID: 20565114]
[EC 2.6.1.105 created 2014]
 
 
EC 2.8.1.6     
Accepted name: biotin synthase
Reaction: dethiobiotin + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + 2 reduced [2Fe-2S] ferredoxin = biotin + (sulfur carrier) + 2 L-methionine + 2 5′-deoxyadenosine + 2 oxidized [2Fe-2S] ferredoxin
Glossary: biotin = 5[(3aS,4S,6aR)-2-oxohexahydro(4H-thieno[4,5-d]imidazol-4-yl)]pentanoate
4,5-secobiotin = 6-[(4R,5R)-2-oxo-5-(sulfanylmethyl)imidazolidin-4-yl]hexanoate = 9-mercaptodethiobiotin
Other name(s): dethiobiotin:sulfur sulfurtransferase
Systematic name: dethiobiotin:sulfur-(sulfur carrier) sulfurtransferase
Comments: The enzyme binds a [4Fe-4S] and a [2Fe-2S] cluster. In every reaction cycle, the enzyme consumes two molecules of AdoMet. The first reaction produces 5′-deoxyadenosine and 4,5-secobiotin. Reaction with another equivalent of AdoMet results in abstraction of the C-6 methylene pro-S hydrogen atom from 4,5-secobiotin, and the resulting carbon radical is quenched via formation of an intramolecular C-S bond, thus closing the biotin tetrahydrothiophene ring. The sulfur donor is believed to be the [2Fe-2S] cluster, which is sacrificed in the process, so that in vitro the reaction is a single turnover. In vivo, the [2Fe-2S] cluster can be reassembled by the Isc or Suf iron-sulfur cluster assembly systems, to allow further catalysis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 80146-93-6
References:
1.  Trainor, D.A., Parry, R.J. and Gitterman, A. Biotin biosynthesis. 2. Stereochemistry of sulfur introduction at C-4 of dethiobiotin. J. Am. Chem. Soc. 102 (1980) 1467–1468.
2.  Shiuan, D. and Campbell, A. Transcriptional regulation and gene arrangement of Escherichia coli, Citrobacter freundii and Salmonella typhimurium biotin operons. Gene 67 (1988) 203–211. [DOI] [PMID: 2971595]
3.  Zhang, S., Sanyal, I., Bulboaca, G.H., Rich, A. and Flint, D.H. The gene for biotin synthase from Saccharomyces cerevisiae: cloning, sequencing, and complementation of Escherichia coli strains lacking biotin synthase. Arch. Biochem. Biophys. 309 (1994) 29–35. [DOI] [PMID: 8117110]
4.  Ugulava, N.B., Gibney, B.R. and Jarrett, J.T. Biotin synthase contains two distinct iron-sulfur cluster binding sites: chemical and spectroelectrochemical analysis of iron-sulfur cluster interconversions. Biochemistry 40 (2001) 8343–8351. [DOI] [PMID: 11444981]
5.  Berkovitch, F., Nicolet, Y., Wan, J.T., Jarrett, J.T. and Drennan, C.L. Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science 303 (2004) 76–79. [DOI] [PMID: 14704425]
6.  Lotierzo, M., Tse Sum Bui, B., Florentin, D., Escalettes, F. and Marquet, A. Biotin synthase mechanism: an overview. Biochem. Soc. Trans. 33 (2005) 820–823. [DOI] [PMID: 16042606]
7.  Taylor, A.M., Farrar, C.E. and Jarrett, J.T. 9-Mercaptodethiobiotin is formed as a competent catalytic intermediate by Escherichia coli biotin synthase. Biochemistry 47 (2008) 9309–9317. [DOI] [PMID: 18690713]
8.  Reyda, M.R., Fugate, C.J. and Jarrett, J.T. A complex between biotin synthase and the iron-sulfur cluster assembly chaperone HscA that enhances in vivo cluster assembly. Biochemistry 48 (2009) 10782–10792. [DOI] [PMID: 19821612]
[EC 2.8.1.6 created 1999, modified 2006, modified 2011, modified 2014]
 
 
EC 2.8.1.7     
Accepted name: cysteine desulfurase
Reaction: L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor (overall reaction)
(1a) L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine
(1b) [enzyme]-S-sulfanylcysteine + acceptor = [enzyme]-cysteine + S-sulfanyl-acceptor
For diagram of MoCo biosynthesis, click here
Other name(s): IscS; NIFS; NifS; SufS; cysteine desulfurylase
Systematic name: L-cysteine:acceptor sulfurtransferase
Comments: A pyridoxal-phosphate protein. The sulfur from free L-cysteine is first transferred to a cysteine residue in the active site, and then passed on to various other acceptors. The enzyme is involved in the biosynthesis of iron-sulfur clusters, thio-nucleosides in tRNA, thiamine, biotin, lipoate and pyranopterin (molybdopterin) [2]. In Azotobacter vinelandii, this sulfur provides the inorganic sulfide required for nitrogenous metallocluster formation [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 149371-08-4
References:
1.  Zheng, L.M., White, R.H., Cash, V.L., Jack, R.F. and Dean, D.R. Cysteine desulfurase activity indicates a role for NIFS in metallocluster biosynthesis. Proc. Natl. Acad. Sci. USA 90 (1993) 2754–2758. [DOI] [PMID: 8464885]
2.  Mihara, H. and Esaki, N. Bacterial cysteine desulfurases: Their function and mechanisms. Appl. Microbiol. Biotechnol. 60 (2002) 12–23. [DOI] [PMID: 12382038]
3.  Frazzon, J. and Dean, D.R. Formation of iron-sulfur clusters in bacteria: An emerging field in bioinorganic chemistry. Curr. Opin. Chem. Biol. 7 (2003) 166–173. [DOI] [PMID: 12714048]
[EC 2.8.1.7 created 2003, modified 2011]
 
 
EC 3.1.1.85     
Accepted name: pimelyl-[acyl-carrier protein] methyl ester esterase
Reaction: pimeloyl-[acyl-carrier protein] methyl ester + H2O = pimeloyl-[acyl-carrier protein] + methanol
Other name(s): BioH
Systematic name: pimeloyl-[acyl-carrier protein] methyl ester hydrolase
Comments: Involved in biotin biosynthesis in Gram-negative bacteria. The enzyme exhibits carboxylesterase activity, particularly toward substrates with short acyl chains [1,2]. Even though the enzyme can interact with coenzyme A thioesters [3], the in vivo role of the enzyme is to hydrolyse the methyl ester of pimeloyl-[acyl carrier protein], terminating the part of the biotin biosynthesis pathway that is catalysed by the fatty acid elongation enzymes [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sanishvili, R., Yakunin, A.F., Laskowski, R.A., Skarina, T., Evdokimova, E., Doherty-Kirby, A., Lajoie, G.A., Thornton, J.M., Arrowsmith, C.H., Savchenko, A., Joachimiak, A. and Edwards, A.M. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J. Biol. Chem. 278 (2003) 26039–26045. [DOI] [PMID: 12732651]
2.  Lemoine, Y., Wach, A. and Jeltsch, J.M. To be free or not: the fate of pimelate in Bacillus sphaericus and in Escherichia coli. Mol. Microbiol. 19 (1996) 645–647. [DOI] [PMID: 8830257]
3.  Tomczyk, N.H., Nettleship, J.E., Baxter, R.L., Crichton, H.J., Webster, S.P. and Campopiano, D.J. Purification and characterisation of the BIOH protein from the biotin biosynthetic pathway. FEBS Lett. 513 (2002) 299–304. [DOI] [PMID: 11904168]
4.  Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. 6 (2010) 682–688. [DOI] [PMID: 20693992]
[EC 3.1.1.85 created 2011]
 
 
EC 3.2.2.9     
Accepted name: adenosylhomocysteine nucleosidase
Reaction: (1) S-adenosyl-L-homocysteine + H2O = S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
(2) 5′-deoxyadenosine + H2O = 5-deoxy-D-ribose + adenine
(3) S-methyl-5′-thioadenosine + H2O = 5-(methylsulfanyl)-D-ribose + adenine
For diagram of autoinducer AI-2 biosynthesis, click here and for diagram of the methionine-salvage pathway, click here
Other name(s): S-adenosylhomocysteine hydrolase (ambiguous); S-adenosylhomocysteine nucleosidase; 5′-methyladenosine nucleosidase; S-adenosylhomocysteine/5′-methylthioadenosine nucleosidase; AdoHcy/MTA nucleosidase; MTN2 (gene name); mtnN (gene name)
Systematic name: S-adenosyl-L-homocysteine homocysteinylribohydrolase
Comments: This enzyme, found in bacteria and plants, acts on three different substrates. It is involved in the S-adenosyl-L-methionine (SAM, AdoMet) cycle, which recycles S-adenosyl-L-homocysteine back to SAM, and in salvage pathways for 5′-deoxyadenosine and S-methyl-5′-thioadenosine, which are produced from SAM during the action of many enzymes. cf. the plant enzyme EC 3.2.2.16, methylthioadenosine nucleosidase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9055-10-1
References:
1.  Duerre, J.A. A hydrolytic nucleosidase acting on S-adenosylhomocysteine and on 5-methylthioadenosine. J. Biol. Chem. 237 (1962) 3737–3741.
2.  Ferro, A.J., Barrett, A. and Shapiro, S.K. Kinetic properties and the effect of substrate analogues on 5′-methylthioadenosine nucleosidase from Escherichia coli. Biochim. Biophys. Acta 438 (1976) 487–494. [DOI] [PMID: 782530]
3.  Cornell, K.A., Swarts, W.E., Barry, R.D. and Riscoe, M.K. Characterization of recombinant Eschericha coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase: analysis of enzymatic activity and substrate specificity. Biochem. Biophys. Res. Commun. 228 (1996) 724–732. [PMID: 8941345]
4.  Park, E.Y., Choi, W.S., Oh, S.I., Kim, K.N., Shin, J.S. and Song, H.K. Biochemical and structural characterization of 5′-methylthioadenosine nucleosidases from Arabidopsis thaliana. Biochem. Biophys. Res. Commun. 381 (2009) 619–624. [PMID: 19249293]
5.  Farrar, C.E., Siu, K.K., Howell, P.L. and Jarrett, J.T. Biotin synthase exhibits burst kinetics and multiple turnovers in the absence of inhibition by products and product-related biomolecules. Biochemistry 49 (2010) 9985–9996. [PMID: 20961145]
6.  North, J.A., Wildenthal, J.A., Erb, T.J., Evans, B.S., Byerly, K.M., Gerlt, J.A. and Tabita, F.R. A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli. Mol. Microbiol. (2020) . [PMID: 31950558]
[EC 3.2.2.9 created 1972, modified 2004, modified 2020]
 
 
EC 3.5.1.12     
Accepted name: biotinidase
Reaction: biotin amide + H2O = biotin + NH3
Other name(s): amidohydrolase biotinidase
Systematic name: biotin-amide amidohydrolase
Comments: Also acts on biotin esters.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9025-15-4
References:
1.  Knappe, J., Brümer, W. and Biederbick, K. Reinigung und Eigenschaften der Biotinidase aus Schweinenieren und Lactobacillus casei. Biochem. Z. 338 (1963) 599–613. [PMID: 14087327]
2.  Thoma, R.W. and Peterson, W.H. The enzymatic degradation of soluble bound biotin. J. Biol. Chem. 210 (1954) 569–579. [PMID: 13211594]
[EC 3.5.1.12 created 1961]
 
 
EC 4.1.1.3      
Transferred entry: oxaloacetate decarboxylase. Now recognized to be two enzymes EC 7.2.4.2 [oxaloacetate decarboxylase (Na+ extruding)] and EC 4.1.1.112 (oxaloacetate decarboxylase).
[EC 4.1.1.3 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, deleted 2018]
 
 
EC 4.1.1.41      
Transferred entry: (S)-methylmalonyl-CoA decarboxylase. Now EC 7.2.4.3, (S)-methylmalonyl-CoA decarboxylase
[EC 4.1.1.41 created 1972, modified 1983, modified 1986, deleted 2018]
 
 
EC 4.1.1.70      
Transferred entry: glutaconyl-CoA decarboxylase. Now EC 7.2.4.5, glutaconyl-CoA decarboxylase
[EC 4.1.1.70 created 1986, modified 2003, deleted 2019]
 
 
EC 4.1.1.87     
Accepted name: malonyl-S-ACP decarboxylase
Reaction: a malonyl-[acyl-carrier protein] + H+ = an acetyl-[acyl-carrier protein] + CO2
For diagram of malonate decarboxylase, click here
Other name(s): malonyl-S-acyl-carrier protein decarboxylase; MdcD/MdcE; MdcD,E
Systematic name: malonyl-[acyl-carrier-protein] carboxy-lyase
Comments: This enzyme comprises the β and γ subunits of EC 4.1.1.88, biotin-independent malonate decarboxylase but is not present in EC 7.2.4.4, biotin-dependent malonate decarboxylase. It follows on from EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase, and results in the regeneration of the acetylated form of the acyl-carrier-protein subunit of malonate decarboxylase [5]. The carboxy group is lost with retention of configuration [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schmid, M., Berg, M., Hilbi, H. and Dimroth, P. Malonate decarboxylase of Klebsiella pneumoniae catalyses the turnover of acetyl and malonyl thioester residues on a coenzyme-A-like prosthetic group. Eur. J. Biochem. 237 (1996) 221–228. [DOI] [PMID: 8620876]
2.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [DOI] [PMID: 10561613]
3.  Handa, S., Koo, J.H., Kim, Y.S. and Floss, H.G. Stereochemical course of biotin-independent malonate decarboxylase catalysis. Arch. Biochem. Biophys. 370 (1999) 93–96. [DOI] [PMID: 10496981]
4.  Chohnan, S., Akagi, K. and Takamura, Y. Functions of malonate decarboxylase subunits from Pseudomonas putida. Biosci. Biotechnol. Biochem. 67 (2003) 214–217. [DOI] [PMID: 12619701]
5.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 4.1.1.87 created 2008]
 
 
EC 4.1.1.88     
Accepted name: biotin-independent malonate decarboxylase
Reaction: malonate + H+ = acetate + CO2
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): malonate decarboxylase (without biotin); malonate decarboxylase (ambiguous); MDC
Systematic name: malonate carboxy-lyase (biotin-independent)
Comments: Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. This enzyme is a cytosolic protein that is biotin-independent. The other type is a biotin-dependent, Na+-translocating enzyme that includes both soluble and membrane-bound components (cf. EC 7.2.4.4, biotin-dependent malonate decarboxylase). As free malonate is chemically rather inert, it has to be activated prior to decarboxylation. In both enzymes, this is achieved by exchanging malonate with an acetyl group bound to an acyl-carrier protiein (ACP), to form malonyl-ACP and acetate, with subsequent decarboxylation regenerating the acetyl-ACP. The ACP subunit of both enzymes differs from that found in fatty-acid biosynthesis by having phosphopantethine attached to a serine side-chain as 2-(5-triphosphoribosyl)-3-dephospho-CoA rather than as phosphopantetheine 4′-phosphate. The individual enzymes involved in carrying out the reaction of this enzyme complex are EC 2.3.1.187 (acetyl-S-ACP:malonate ACP transferase), EC 2.3.1.39 ([acyl-carrier-protein] S-malonyltransferase) and EC 4.1.1.87 (malonyl-S-ACP decarboxylase). The carboxy group is lost with retention of configuration [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schmid, M., Berg, M., Hilbi, H. and Dimroth, P. Malonate decarboxylase of Klebsiella pneumoniae catalyses the turnover of acetyl and malonyl thioester residues on a coenzyme-A-like prosthetic group. Eur. J. Biochem. 237 (1996) 221–228. [DOI] [PMID: 8620876]
2.  Byun, H.S. and Kim, Y.S. Subunit organization of bacterial malonate decarboxylases: the smallest δ subunit as an acyl-carrier protein. J. Biochem. Mol. Biol. 30 (1997) 132–137.
3.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [DOI] [PMID: 9208947]
4.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [DOI] [PMID: 9851033]
5.  Hoenke, S., Schmid, M. and Dimroth, P. Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases. Biochemistry 39 (2000) 13233–13240. [DOI] [PMID: 11052676]
6.  Handa, S., Koo, J.H., Kim, Y.S. and Floss, H.G. Stereochemical course of biotin-independent malonate decarboxylase catalysis. Arch. Biochem. Biophys. 370 (1999) 93–96. [DOI] [PMID: 10496981]
7.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [DOI] [PMID: 10561613]
8.  Kim, Y.S. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application. J. Biochem. Mol. Biol. 35 (2002) 443–451. [PMID: 12359084]
9.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 4.1.1.88 created 2008, modified 2018]
 
 
EC 4.1.1.89      
Transferred entry: biotin-dependent malonate decarboxylase. Now EC 7.2.4.4, biotin-dependent malonate decarboxylase
[EC 4.1.1.89 created 2008, deleted 2018]
 
 
EC 4.3.99.2      
Transferred entry: carboxybiotin decarboxylase. Now EC 7.2.4.1, carboxybiotin decarboxylase
[EC 4.3.99.2 created 2008, deleted 2018]
 
 
EC 5.3.3.3     
Accepted name: vinylacetyl-CoA Δ-isomerase
Reaction: vinylacetyl-CoA = (E)-but-2-enoyl-CoA
Glossary: (E)-but-2-enoyl-CoA = crotonyl-CoA
Other name(s): vinylacetyl coenzyme A Δ-isomerase; vinylacetyl coenzyme A isomerase; Δ3-cis2-trans-enoyl-CoA isomerase
Systematic name: vinylacetyl-CoA Δ32-isomerase
Comments: Also acts on 3-methyl-vinylacetyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-73-8
References:
1.  Lynen, F., Knappe, J., Lorch, E., Jütting, G. and Ringelmann, E. Die biochemische Funktion des Biotins. Angew. Chem. 71 (1959) 481–486.
2.  Rilling, H.C. and Coon, M.J. The enzymatic isomerization of α-methylvinylacetyl coenzyme A and the specificity of a bacterial α-methylcrotonyl coenzyme A carboxylase. J. Biol. Chem. 235 (1960) 3087–3092. [PMID: 13741692]
[EC 5.3.3.3 created 1961, modified 2011]
 
 
EC 6.2.1.11     
Accepted name: biotin—CoA ligase
Reaction: ATP + biotin + CoA = AMP + diphosphate + biotinyl-CoA
Other name(s): biotinyl-CoA synthetase; biotin CoA synthetase; biotinyl coenzyme A synthetase
Systematic name: biotin:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37318-60-8
References:
1.  Christner, J.E., Schlesinger, M.J. and Coon, M.J. Enzymatic activation of biotin. Biotinyl adenylate formation. J. Biol. Chem. 239 (1964) 3997–4005. [PMID: 14257635]
[EC 6.2.1.11 created 1972]
 
 
EC 6.2.1.14     
Accepted name: 6-carboxyhexanoate—CoA ligase
Reaction: ATP + 6-carboxyhexanoate + CoA = AMP + diphosphate + 6-carboxyhexanoyl-CoA
Other name(s): 6-carboxyhexanoyl-CoA synthetase; pimelyl-CoA synthetase
Systematic name: 6-carboxyhexanoate:CoA ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 55467-50-0
References:
1.  Izumi, Y., Morita, H., Sato, K., Tani, Y. and Ogata, K. Synthesis of biotin-vitamers from pimelic acid and coenzyme A by cell-free extracts of various bacteria. Biochim. Biophys. Acta 264 (1972) 210–213. [DOI] [PMID: 4623286]
2.  Izumi, Y., Morita, H., Tani, Y. and Ogata, K. The pimelyl-CoA synthetase responsible for the first step in biotin biosynthesis by microorganisms. Agric. Biol. Chem. 38 (1974) 2257–2262.
[EC 6.2.1.14 created 1983]
 
 
EC 6.2.1.35     
Accepted name: acetate—[acyl-carrier protein] ligase
Reaction: ATP + acetate + an [acyl-carrier protein] = AMP + diphosphate + an acetyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): HS-acyl-carrier protein:acetate ligase; [acyl-carrier protein]:acetate ligase; MadH; ACP-SH:acetate ligase
Systematic name: acetate:[acyl-carrier-protein] ligase (AMP-forming)
Comments: This enzyme, from the anaerobic bacterium Malonomonas rubra, is a component of the multienzyme complex EC 7.2.4.4, biotin-dependent malonate decarboxylase. The enzyme uses the energy from hydrolysis of ATP to convert the thiol group of the acyl-carrier-protein-bound 2′-(5-phosphoribosyl)-3′-dephospho-CoA prosthetic group into its acetyl thioester [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hilbi, H., Dehning, I., Schink, B. and Dimroth, P. Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme. Eur. J. Biochem. 207 (1992) 117–123. [DOI] [PMID: 1628643]
2.  Berg, M., Hilbi, H. and Dimroth, P. The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2′-(5"-phosphoribosyl)-3′-dephosphocoenzyme A as a prosthetic group. Biochemistry 35 (1996) 4689–4696. [DOI] [PMID: 8664258]
3.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [DOI] [PMID: 9128730]
4.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 6.2.1.35 created 2008, modified 2018]
 
 
EC 6.3.3.3     
Accepted name: dethiobiotin synthase
Reaction: ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
Other name(s): desthiobiotin synthase
Systematic name: 7,8-diaminononanoate:carbon-dioxide cyclo-ligase (ADP-forming)
Comments: CTP has half the activity of ATP.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37259-75-9
References:
1.  Krell, K. and Eisenberg, M.A. The purification and properties of dethiobiotin synthetase. J. Biol. Chem. 245 (1970) 6558–6566. [PMID: 4921568]
2.  Yang, H.-C., Tani, Y. and Ogata, K. Synthesis of biotin vitamers from biotin diaminocarboxylic acid or 7,8-diaminopelargonic acid by a purified enzyme of Pseudomonas graveolens. Agric. Biol. Chem. 34 (1970) 1748–1750.
[EC 6.3.3.3 created 1976]
 
 
EC 6.3.4.6     
Accepted name: urea carboxylase
Reaction: ATP + urea + HCO3- = ADP + phosphate + urea-1-carboxylate
Glossary: urea-1-carboxylate = allophanate
Other name(s): urease (ATP-hydrolysing); urea carboxylase (hydrolysing); ATP—urea amidolyase; urea amidolyase; UALase; UCA
Systematic name: urea:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein. The yeast enzyme (but not that from green algae) also catalyses the reaction of EC 3.5.1.54 allophanate hydrolase, thus bringing about the hydrolysis of urea to CO2 and NH3. Previously also listed as EC 3.5.1.45. The enzyme from the prokaryotic bacterium Oleomonas sagaranensis can also use acetamide and formamide as substrates [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9058-98-4
References:
1.  Roon, R.J. and Levenberg, B. ATP-Urea amidolyase (ADP) (Candida utilis). Methods Enzymol. 17A (1970) 317–324.
2.  Roon, R.J. and Levenberg, B. Urea amidolyase. I. Properties of the enzyme from Candida utilis. J. Biol. Chem. 247 (1972) 4107–4113. [PMID: 4556303]
3.  Sumrada, R.A. and Cooper, T.G. Urea carboxylase and allophanate hydrolase are components of a multifunctional protein in yeast. J. Biol. Chem. 257 (1982) 9119–9127. [PMID: 6124544]
4.  Kanamori, T., Kanou, N., Atomi, H. and Imanaka, T. Enzymatic characterization of a prokaryotic urea carboxylase. J. Bacteriol. 186 (2004) 2532–2539. [DOI] [PMID: 15090492]
[EC 6.3.4.6 created 1972, modified 1986 (EC 3.5.1.45 created 1978, incorporated 1986)]
 
 
EC 6.3.4.9     
Accepted name: biotin—[methylmalonyl-CoA-carboxytransferase] ligase
Reaction: ATP + biotin + apo-[methylmalonyl-CoA:pyruvate carboxytransferase] = AMP + diphosphate + [methylmalonyl-CoA:pyruvate carboxytransferase]
Other name(s): biotin-[methylmalonyl-CoA-carboxyltransferase] synthetase; biotin-methylmalonyl coenzyme A carboxyltransferase synthetase; biotin-transcarboxylase synthetase; methylmalonyl coenzyme A holotranscarboxylase synthetase; biotin—[methylmalonyl-CoA-carboxyltransferase] ligase; biotin:apo[methylmalonyl-CoA:pyruvate carboxyltransferase] ligase (AMP-forming)
Systematic name: biotin:apo[methylmalonyl-CoA:pyruvate carboxytransferase] ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37318-66-4
References:
1.  Lane, M.D., Young, D.L. and Lynen, F. The enzymatic synthesis of holotranscarboxylase from apotranscarboxylase and (+)-biotin. I. Purification of the apoenzyme and synthetase; characteristics of the reaction. J. Biol. Chem. 239 (1964) 2858–2864. [PMID: 14216436]
[EC 6.3.4.9 created 1972]
 
 
EC 6.3.4.10     
Accepted name: biotin—[propionyl-CoA-carboxylase (ATP-hydrolysing)] ligase
Reaction: ATP + biotin + apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [propionyl-CoA:carbon-dioxide ligase (ADP-forming)]
Other name(s): biotin-[propionyl-CoA-carboxylase (ATP-hydrolysing)] synthetase; biotin-propionyl coenzyme A carboxylase synthetase; propionyl coenzyme A holocarboxylase synthetase
Systematic name: biotin:apo-[propanoyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37318-67-5
References:
1.  Siegel, L., Foote, J.L. and Coon, M.J. The enzymatic synthesis of propionyl coenzyme A holocarboxylase from d-biotinyl 5′-adenylate and the apocarboxylase. J. Biol. Chem. 240 (1965) 1025–1031. [PMID: 14284697]
[EC 6.3.4.10 created 1972]
 
 
EC 6.3.4.11     
Accepted name: biotin—[methylcrotonoyl-CoA-carboxylase] ligase
Reaction: ATP + biotin + apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] = AMP + diphosphate + [3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)]
Other name(s): biotin-[methylcrotonoyl-CoA-carboxylase] synthetase; biotin-β-methylcrotonyl coenzyme A carboxylase synthetase; β-methylcrotonyl coenzyme A holocarboxylase synthetase; holocarboxylase-synthetase
Systematic name: biotin:apo-[3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37318-68-6
References:
1.  Höpner, T. and Knappe, J. Einbau von Biotin in β-methylcrotonyl-CoA-carboxylase urch Holocarboxylase-synthetase. Biochem. Z. 342 (1965) 190–206. [PMID: 5867144]
[EC 6.3.4.11 created 1972]
 
 
EC 6.3.4.14     
Accepted name: biotin carboxylase
Reaction: ATP + [biotin carboxyl-carrier protein]-biotin-N6-L-lysine + hydrogencarbonate- = ADP + phosphate + [biotin carboxyl-carrier protein]-carboxybiotin-N6-L-lysine
Other name(s): accC (gene name); biotin-carboxyl-carrier-protein:carbon-dioxide ligase (ADP-forming)
Systematic name: [biotin carboxyl-carrier protein]-biotin-N6-L-lysine:hydrogencarbonate ligase (ADP-forming)
Comments: This enzyme, part of an acetyl-CoA carboxylase complex, acts on a biotin carboxyl-carrier protein (BCCP) that has been biotinylated by EC 6.3.4.15, biotin—[biotin carboxyl-carrier protein] ligase. In some organisms the enzyme is part of a multi-domain polypeptide that also includes the carrier protein (e.g. mycobacteria). Yet in other organisms (e.g. mammals) this activity is included in a single polypeptide that also catalyses the transfer of the carboxyl group from biotin to acetyl-CoA (see EC 6.4.1.2, acetyl-CoA carboxylase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9075-71-2
References:
1.  Dimroth, P., Guchhait, R.B., Stoll, E. and Lane, M.D. Enzymatic carboxylation of biotin: molecular and catalytic properties of a component enzyme of acetyl CoA carboxylase. Proc. Natl. Acad. Sci. USA 67 (1970) 1353–1360. [DOI] [PMID: 4922289]
2.  Norman, E., De Smet, K.A., Stoker, N.G., Ratledge, C., Wheeler, P.R. and Dale, J.W. Lipid synthesis in mycobacteria: characterization of the biotin carboxyl carrier protein genes from Mycobacterium leprae and M. tuberculosis. J. Bacteriol. 176 (1994) 2525–2531. [DOI] [PMID: 7909542]
3.  Janiyani, K., Bordelon, T., Waldrop, G.L. and Cronan, J.E., Jr. Function of Escherichia coli biotin carboxylase requires catalytic activity of both subunits of the homodimer. J. Biol. Chem. 276 (2001) 29864–29870. [DOI] [PMID: 11390406]
4.  Chou, C.Y., Yu, L.P. and Tong, L. Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism. J. Biol. Chem. 284 (2009) 11690–11697. [DOI] [PMID: 19213731]
5.  Broussard, T.C., Pakhomova, S., Neau, D.B., Bonnot, R. and Waldrop, G.L. Structural analysis of substrate, reaction intermediate, and product binding in Haemophilus influenzae biotin carboxylase. Biochemistry 54 (2015) 3860–3870. [DOI] [PMID: 26020841]
[EC 6.3.4.14 created 1976, modified 2014, modified 2018]
 
 
EC 6.3.4.15     
Accepted name: biotin—[biotin carboxyl-carrier protein] ligase
Reaction: ATP + biotin + [biotin carboxyl-carrier protein]-L-lysine = AMP + diphosphate + [biotin carboxyl-carrier protein]-N6-biotinyl-L-lysine
Other name(s): birA (gene name); HLCS (gene name); HCS1 (gene name); biotin-[acetyl-CoA carboxylase] synthetase; biotin-[acetyl coenzyme A carboxylase] synthetase; acetyl coenzyme A holocarboxylase synthetase; acetyl CoA holocarboxylase synthetase; biotin:apocarboxylase ligase; Biotin holoenzyme synthetase; biotin:apo-[acetyl-CoA:carbon-dioxide ligase (ADP-forming)] ligase (AMP-forming); biotin—[acetyl-CoA-carboxylase] ligase
Systematic name: biotin:apo-[carboxyl-carrier protein] ligase (AMP-forming)
Comments: The enzyme biotinylates a biotin carboxyl-carrier protein that is part of an acetyl-CoA carboxylase complex, enabling its subsequent carboxylation by EC 6.3.4.14, biotin carboxylase. The carboxyl group is eventually transferred to acetyl-CoA by EC 2.1.3.15, acetyl-CoA carboxytransferase. In some organisms the carrier protein is part of EC 6.4.1.2, acetyl-CoA carboxylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37340-95-7
References:
1.  Landman, A.D. and Dakshinamurti, K. Acetyl-Coenzyme A carboxylase. Role of the prosthetic group in enzyme polymerization. Biochem. J. 145 (1975) 545–548. [PMID: 239688]
2.  Wilson, K.P., Shewchuk, L.M., Brennan, R.G., Otsuka, A.J. and Matthews, B.W. Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc. Natl. Acad. Sci. USA 89 (1992) 9257–9261. [DOI] [PMID: 1409631]
3.  Nenortas, E. and Beckett, D. Purification and characterization of intact and truncated forms of the Escherichia coli biotin carboxyl carrier subunit of acetyl-CoA carboxylase. J. Biol. Chem. 271 (1996) 7559–7567. [DOI] [PMID: 8631788]
[EC 6.3.4.15 created 1978, modified 2018]
 
 
EC 6.4.1.1     
Accepted name: pyruvate carboxylase
Reaction: ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate
Other name(s): pyruvic carboxylase
Systematic name: pyruvate:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein containing manganese (animal tissues) or zinc (yeast). The animal enzyme requires acetyl-CoA.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-19-1
References:
1.  McClure, W.R., Lardy, H.A. and Kneifel, H.P. Rat liver pyruvate carboxylase. I. Preparation, properties, and cation specificity. J. Biol. Chem. 246 (1971) 3569–3578. [PMID: 5578910]
2.  Scrutton, M.C., Young, M.R. and Utter, M.F. Pyruvate carboxylase from baker's yeast. The presence of bound zinc. J. Biol. Chem. 245 (1970) 6220–6227. [PMID: 5484476]
3.  Seubert, W. and Remberger, U. Renigung und Wirkungsweise der Pyruvatcarboxylase aus Pseudomonas citronellolis. Biochem. Z. 334 (1961) 401–414. [PMID: 13750403]
4.  Utter, M.F. and Keech, D.B. Pyruvate carboxylase. I. Nature of the reaction. J. Biol. Chem. 238 (1963) 2603–2608. [PMID: 14063279]
[EC 6.4.1.1 created 1961]
 
 
EC 6.4.1.2     
Accepted name: acetyl-CoA carboxylase
Reaction: ATP + acetyl-CoA + hydrogencarbonate = ADP + phosphate + malonyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here and for diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here
Other name(s): HFA1 (gene name); ACC1 (gene name); acetyl coenzyme A carboxylase; acetyl-CoA:carbon-dioxide ligase (ADP-forming)
Systematic name: acetyl-CoA:hydrogencarbonate ligase (ADP-forming)
Comments: This enzyme is a multi-domain polypeptide that catalyses three different activities - a biotin carboxyl-carrier protein (BCCP), a biotin carboxylase that catalyses the transfer of a carboxyl group from hydrogencarbonate to the biotin molecule carried by the carrier protein, and the transfer of the carboxyl group from biotin to acetyl-CoA, forming malonyl-CoA. In some organisms these activities are catalysed by separate enzymes (see EC 6.3.4.14, biotin carboxylase, and EC 2.1.3.15, acetyl-CoA carboxytransferase). The carboxylation of the carrier protein requires ATP, while the transfer of the carboxyl group to acetyl-CoA does not.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-93-2
References:
1.  Wakil, S.J. A malonic acid derivative as an intermediate in fatty acid synthesis. J. Am. Chem. Soc. 80 (1958) 6465.
2.  Hatch, M.D. and Stumpf, P.K. Fat metabolism in higher plants. XVI. Acetyl coenzyme A carboxylase and acyl coenzyme A-malonyl coenzyme A transcarboxylase from wheat germ. J. Biol. Chem. 236 (1961) 2879–2885. [PMID: 13905314]
3.  Matsuhashi, M., Matsuhashi, S., Numa, S. and Lynen, F. Zur Biosynthese der Fettsäuren. IV Acetyl CoA Carboxylase aus Hefe. Biochem. Z. 340 (1964) 243–262. [PMID: 14317957]
4.  Matsuhashi, M., Matsuhashi, S. and Lynen, F. Zur Biosynthese der Fettsäuren. V. Die Acetyl-CoA Carboxylase aus Rattenleber und ihre Aktivierung durch Citronsäure. Biochem. Z. 340 (1964) 263–289. [PMID: 14317958]
5.  Vagelos, P. Regulation of fatty acid biosynthesis. Curr. Top. Cell. Regul. 4 (1971) 119–166.
6.  Trumble, G.E., Smith, M.A. and Winder, W.W. Purification and characterization of rat skeletal muscle acetyl-CoA carboxylase. Eur. J. Biochem. 231 (1995) 192–198. [DOI] [PMID: 7628470]
7.  Cheng, D., Chu, C.H., Chen, L., Feder, J.N., Mintier, G.A., Wu, Y., Cook, J.W., Harpel, M.R., Locke, G.A., An, Y. and Tamura, J.K. Expression, purification, and characterization of human and rat acetyl coenzyme A carboxylase (ACC) isozymes. Protein Expr. Purif. 51 (2007) 11–21. [DOI] [PMID: 16854592]
8.  Kim, K.W., Yamane, H., Zondlo, J., Busby, J. and Wang, M. Expression, purification, and characterization of human acetyl-CoA carboxylase 2. Protein Expr. Purif. 53 (2007) 16–23. [DOI] [PMID: 17223360]
[EC 6.4.1.2 created 1961, modified 2018]
 
 
EC 6.4.1.3     
Accepted name: propionyl-CoA carboxylase
Reaction: ATP + propanoyl-CoA + HCO3- = ADP + phosphate + (S)-methylmalonyl-CoA
For diagram of the 3-hydroxypropanoate cycle, click here
Other name(s): propionyl coenzyme A carboxylase
Systematic name: propanoyl-CoA:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein. Also carboxylates butanoyl-CoA and catalyses transcarboxylation.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9023-94-3
References:
1.  Kaziro, Y., Ochoa, S., Warner, R.C. and Chen, J.-Y. Metabolism of propionic acid in animal tissues. VIII. Crystalline propionyl carboxylase. J. Biol. Chem. 236 (1961) 1917–1923. [PMID: 13752080]
2.  Lane, M.D., Halenz, D.R., Kosow, D.P. and Hegre, C.S. Further studies on mitochondrial propionyl carboxylase. J. Biol. Chem. 235 (1960) 3082–3086. [PMID: 13758723]
3.  Meyer, H., Nevaldine, B. and Meyer, F. Acyl-coenzyme A carboxylase of the free-living nematode Turbatrix aceti. 1. Its isolation and molecular characteristics. Biochemistry 17 (1978) 1822–1827. [PMID: 656363]
4.  Moss, J. and Lane, M.D. The biotin-dependent enzymes. Adv. Enzymol. Relat. Areas Mol. Biol. 35 (1971) 321–442. [PMID: 4150153]
5.  Vagelos, P. Regulation of fatty acid biosynthesis. Curr. Top. Cell. Regul. 4 (1971) 119–166.
[EC 6.4.1.3 created 1961, modified 1983]
 
 
EC 6.4.1.4     
Accepted name: methylcrotonoyl-CoA carboxylase
Reaction: ATP + 3-methylcrotonoyl-CoA + HCO3- = ADP + phosphate + 3-methylglutaconyl-CoA
Other name(s): methylcrotonyl coenzyme A carboxylase; β-methylcrotonyl coenzyme A carboxylase; β-methylcrotonyl CoA carboxylase; methylcrotonyl-CoA carboxylase
Systematic name: 3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9023-95-4
References:
1.  Knappe, J., Schlegel, H.-G. and Lynen, F. Zur biochemischen Funktion des Biotins. I. Die Beteilligung der β-Methyl-crotonyl-Carboxylase an der Bildung von β-Hydroxy-β-methyl-glutaryl-CoA from β-Hydroxy-isovaleryl-CoA. Biochem. Z. 335 (1961) 101–122. [PMID: 14457200]
2.  Lynen, F., Knappe, J., Lorch, E., Jütting, G., Ringelmann, E. and Lachance, J.-P. Zur biochemischen Funktion des Biotins. II. Reinigung und Wirkungsweise der β-Methyl-crotonyl-Carboxlase. Biochem. Z. 335 (1961) 123–166. [PMID: 14467590]
3.  Rilling, H.C. and Coon, M.J. The enzymatic isomerization of α-methylvinylacetyl coenzyme A and the specificity of a bacterial α-methylcrotonyl coenzyme A carboxylase. J. Biol. Chem. 235 (1960) 3087–3092. [PMID: 13741692]
4.  Vagelos, P. Regulation of fatty acid biosynthesis. Curr. Top. Cell. Regul. 4 (1971) 119–166.
[EC 6.4.1.4 created 1961]
 
 
EC 6.4.1.5     
Accepted name: geranoyl-CoA carboxylase
Reaction: ATP + geranoyl-CoA + HCO3- = ADP + phosphate + 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA
Other name(s): geranoyl coenzyme A carboxylase; geranyl-CoA carboxylase
Systematic name: geranoyl-CoA:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein. Also carboxylates dimethylpropenoyl-CoA and farnesoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, UM-BBD, CAS registry number: 37324-35-9
References:
1.  Seubert, W., Fass, E. and Remberger, U. Untersuchungen über den bakteriellen Abbau von Isoprenoiden. III. Reinigung und Eigenschaften der Geranylcarboxylase. Biochem. Z. 338 (1963) 265–275. [PMID: 14087299]
[EC 6.4.1.5 created 1972]
 
 
EC 6.4.1.7     
Accepted name: 2-oxoglutarate carboxylase
Reaction: ATP + 2-oxoglutarate + HCO3- = ADP + phosphate + oxalosuccinate
For diagram of reaction, click here
Glossary: oxalosuccinate = 1-oxopropane-1,2,3-tricarboxylate
Other name(s): oxalosuccinate synthetase; carboxylating factor for ICDH (incorrect); CFI; OGC
Comments: A biotin-containing enzyme that requires Mg2+ for activity. It was originally thought [1] that this enzyme was a promoting factor for the carboxylation of 2-oxoglutarate by EC 1.1.1.41, isocitrate dehydrogenase (NAD+), but this has since been disproved [2]. The product of the reaction is unstable and is quickly converted into isocitrate by the action of EC 1.1.1.41 [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 60382-75-4
References:
1.  Aoshima, M., Ishii, M. and Igarashi, Y. A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 51 (2004) 791–798. [DOI] [PMID: 14731279]
2.  Aoshima, M. and Igarashi, Y. A novel oxalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 62 (2006) 748–759. [DOI] [PMID: 17076668]
[EC 6.4.1.7 created 2006]
 
 
EC 7.2.4.1     
Accepted name: carboxybiotin decarboxylase
Reaction: a carboxybiotinyl-[protein] + n Na+[side 1] + H+[side 2] = CO2 + a biotinyl-[protein] + n Na+[side 2] (n = 1–2)
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): MadB; carboxybiotin protein decarboxylase
Systematic name: carboxybiotinyl-[protein] carboxy-lyase
Comments: The integral membrane protein MadB from the anaerobic bacterium Malonomonas rubra is a component of the multienzyme complex EC 4.1.1.89, biotin-dependent malonate decarboxylase. The free energy of the decarboxylation reaction is used to pump Na+ out of the cell. The enzyme is a member of the Na+-translocating decarboxylase family, other members of which include EC 7.2.4.2 [oxaloacetate decarboxylase (Na+ extruding)] and EC 7.2.4.3 [(S)-methylmalonyl-CoA decarboxylase (sodium-transporting)] [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [DOI] [PMID: 9128730]
2.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 7.2.4.1 created 2008 as EC 4.3.99.2, transferred 2018 to EC 7.2.4.1]
 
 
EC 7.2.4.2     
Accepted name: oxaloacetate decarboxylase (Na+ extruding)
Reaction: oxaloacetate + 2 Na+[side 1] = pyruvate + CO2 + 2 Na+[side 2]
Other name(s): oxaloacetate β-decarboxylase (ambiguous); oxalacetic acid decarboxylase (ambiguous); oxalate β-decarboxylase (ambiguous); oxaloacetate carboxy-lyase (ambiguous)
Systematic name: oxaloacetate carboxy-lyase (pyruvate-forming; Na+-extruding)
Comments: The enzyme from the bacterium Klebsiella aerogenes is a biotinyl protein and also decarboxylates glutaconyl-CoA and methylmalonyl-CoA. The process is accompanied by the extrusion of two sodium ions from cells. Some animal enzymes require Mn2+. Differs from EC 4.1.1.112 (oxaloacetate decarboxylase) for which there is no evidence for involvement in Na+ transport.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-98-0
References:
1.  Dimroth, P. Characterization of a membrane-bound biotin-containing enzyme: oxaloacetate decarboxylase from Klebsiella aerogenes. Eur. J. Biochem. 115 (1981) 353–358. [DOI] [PMID: 7016536]
2.  Dimroth, P. The role of biotin and sodium in the decarboxylation of oxaloacetate by the membrane-bound oxaloacetate decarboxylase from Klebsiella aerogenes. Eur. J. Biochem. 121 (1982) 435–441. [DOI] [PMID: 7037395]
[EC 7.2.4.2 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, transferred 2018 to EC 7.2.4.2]
 
 
EC 7.2.4.3     
Accepted name: (S)-methylmalonyl-CoA decarboxylase (sodium-transporting)
Reaction: (S)-methylmalonyl-CoA + Na+[side 1] + H+[side 2] = propanoyl-CoA + CO2 + Na+[side 2]
Other name(s): methylmalonyl-coenzyme A decarboxylase (ambiguous); (S)-2-methyl-3-oxopropanoyl-CoA carboxy-lyase (incorrect); (S)-methylmalonyl-CoA carboxy-lyase (ambiguous)
Systematic name: (S)-methylmalonyl-CoA carboxy-lyase (propanoyl-CoA-forming, sodium-transporting)
Comments: This bacterial enzyme couples the decarboxylation of (S)-methylmalonyl-CoA to propanoyl-CoA to the vectorial transport of Na+ across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis. It is a membrane-associated biotin protein and is strictly dependent on sodium ions for activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37289-44-4
References:
1.  Galivan, J.H. and Allen, S.H.G. Methylmalonyl coenzyme A decarboxylase. Its role in succinate decarboxylation by Micrococcus lactilyticus. J. Biol. Chem. 243 (1968) 1253–1261. [PMID: 5646172]
2.  Hilpert, W. and Dimroth, P. Conversion of the chemical energy of methylmalonyl-CoA decarboxylation into a Na+ gradient. Nature 296 (1982) 584–585. [PMID: 7070502]
3.  Hoffmann, A., Hilpert, W. and Dimroth, P. The carboxyltransferase activity of the sodium-ion-translocating methylmalonyl-CoA decarboxylase of Veillonella alcalescens. Eur. J. Biochem. 179 (1989) 645–650. [DOI] [PMID: 2920730]
4.  Huder, J.B. and Dimroth, P. Expression of the sodium ion pump methylmalonyl-coenzyme A-decarboxylase from Veillonella parvula and of mutated enzyme specimens in Escherichia coli. J. Bacteriol. 177 (1995) 3623–3630. [PMID: 7601825]
5.  Bott, M., Pfister, K., Burda, P., Kalbermatter, O., Woehlke, G. and Dimroth, P. Methylmalonyl-CoA decarboxylase from Propionigenium modestum--cloning and sequencing of the structural genes and purification of the enzyme complex. Eur. J. Biochem. 250 (1997) 590–599. [PMID: 9428714]
[EC 7.2.4.3 created 1972 as EC 4.1.1.41, modified 1983, modified 1986, transferred 2018 to EC 7.2.4.3]
 
 
EC 7.2.4.4     
Accepted name: biotin-dependent malonate decarboxylase
Reaction: malonate + H+ + Na+[side 1] = acetate + CO2 + Na+[side 2]
For diagram of the reactions involved in the multienzyme complex malonate decarboxylase, click here
Other name(s): malonate decarboxylase (with biotin); malonate decarboxylase (ambiguous)
Systematic name: malonate carboxy-lyase (biotin-dependent)
Comments: Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. The enzyme described here is a membrane-bound biotin-dependent, Na+-translocating enzyme [6]. The other type is a biotin-independent cytosolic protein (cf. EC 4.1.1.88, biotin-independent malonate decarboxylase). As free malonate is chemically rather inert, it has to be activated prior to decarboxylation. Both enzymes achieve this by exchanging malonate with an acetyl group bound to an acyl-carrier protiein (ACP), to form malonyl-ACP and acetate, with subsequent decarboxylation regenerating the acetyl-bound form of the enzyme. The ACP subunit of both enzymes differs from that found in fatty-acid biosynthesis by having phosphopantethine attached to a serine side-chain as 2-(5-triphosphoribosyl)-3-dephospho-CoA rather than as phosphopantetheine 4′-phosphate. In the anaerobic bacterium Malonomonas rubra, the components of the multienzyme complex/enzymes involved in carrying out the reactions of this enzyme are as follows: MadA (EC 2.3.1.187, acetyl-S-ACP:malonate ACP transferase), MadB (EC 7.2.4.1, carboxybiotin decarboxylase), MadC/MadD (EC 2.1.3.10, malonyl-S-ACP:biotin-protein carboxyltransferase) and MadH (EC 6.2.1.35, acetate—[acyl-carrier protein] ligase). Two other components that are involved are MadE, the acyl-carrier protein and MadF, the biotin protein. The carboxy group is lost with retention of configuration [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hilbi, H., Dehning, I., Schink, B. and Dimroth, P. Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme. Eur. J. Biochem. 207 (1992) 117–123. [DOI] [PMID: 1628643]
2.  Hilbi, H. and Dimroth, P. Purification and characterization of a cytoplasmic enzyme component of the Na+-activated malonate decarboxylase system of Malonomonas rubra: acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase. Arch. Microbiol. 162 (1994) 48–56. [PMID: 18251085]
3.  Berg, M., Hilbi, H. and Dimroth, P. The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2′-(5"-phosphoribosyl)-3′-dephosphocoenzyme A as a prosthetic group. Biochemistry 35 (1996) 4689–4696. [DOI] [PMID: 8664258]
4.  Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103–115. [DOI] [PMID: 9128730]
5.  Micklefield, J., Harris, K.J., Gröger, S., Mocek, U., Hilbi, H., Dimroth, P. and Floss, H.G. Stereochemical course of malonate decarboxylase in Malonomonas rubra has biotin decarboxylation with retention. J. Am. Chem. Soc. 117 (1995) 1153–1154.
6.  Kim, Y.S. Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application. J. Biochem. Mol. Biol. 35 (2002) 443–451. [PMID: 12359084]
7.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 7.2.4.4 created 2008 as EC 4.1.1.89, transferred 2018 to EC 7.2.4.4]
 
 
EC 7.2.4.5     
Accepted name: glutaconyl-CoA decarboxylase
Reaction: (2E)-4-carboxybut-2-enoyl-CoA + Na+[side 1] = (2E)-but-2-enoyl-CoA + CO2 + Na+[side 2]
Glossary: (E)-glutaconyl-CoA = (2E)-4-carboxybut-2-enoyl-CoA
Other name(s): glutaconyl coenzyme A decarboxylase; pent-2-enoyl-CoA carboxy-lyase; 4-carboxybut-2-enoyl-CoA carboxy-lyase
Systematic name: (2E)-4-carboxybut-2-enoyl-CoA carboxy-lyase [(2E)-but-2-enoyl-CoA-forming]
Comments: The enzyme from the bacterium Acidaminococcus fermentans is a biotinyl-protein, requires Na+, and acts as a sodium pump. Prior to the Na+-dependent decarboxylation, the carboxylate is transferred to biotin in a Na+-independent manner. The conserved lysine, to which biotin forms an amide bond, is located 34 amino acids before the C-terminus, flanked on both sides by two methionine residues, which are conserved in every biotin-dependent enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 84399-93-9
References:
1.  Buckel, W.S. and Semmler, R. Purification, characterisation and reconstitution of glutaconyl-CoA decarboxylase, a biotin-dependent sodium pump from anaerobic bacteria. Eur. J. Biochem. 136 (1983) 427–434. [DOI] [PMID: 6628393]
2.  Buckel, W. Sodium ion-translocating decarboxylases. Biochim. Biophys. Acta 1505 (2001) 15–27. [DOI] [PMID: 11248185]
[EC 7.2.4.5 created 1986 as EC 4.1.1.70, modified 2003, transferred 2019 to EC 7.2.4.5]
 
 


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