The Enzyme Database

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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 2.1.3.10     
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 cofactor 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, PDB
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. [DOI]
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 2.3.1.39     
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 cofactor; that from malonate decarboxylase also contains pantetheine-4′-phosphate but in the form of a 2′-(5-triphosphoribosyl)-3′-dephospho-CoA cofactor.
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. [DOI]
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [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. [DOI] [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. [DOI] [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 2.3.1.41     
Accepted name: β-ketoacyl-[acyl-carrier-protein] synthase I
Reaction: an acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a 3-oxoacyl-[acyl-carrier protein] + CO2 + an [acyl-carrier protein]
Glossary: acyl-[acyl-carrier protein] = R-CO-[acyl-carrier protein]
malonyl-[acyl-carrier protein] = HOOC-CH2-CO-[acyl-carrier protein]
3-oxoacyl-[acyl-carrier protein] = R-CO-CH2-CO-[acyl-carrier protein]
Other name(s): β-ketoacyl-ACP synthase I; β-ketoacyl synthetase; β-ketoacyl-ACP synthetase; β-ketoacyl-acyl carrier protein synthetase; β-ketoacyl-[acyl carrier protein] synthase; β-ketoacylsynthase; condensing enzyme (ambiguous); 3-ketoacyl-acyl carrier protein synthase; fatty acid condensing enzyme; acyl-malonyl(acyl-carrier-protein)-condensing enzyme; acyl-malonyl acyl carrier protein-condensing enzyme; β-ketoacyl acyl carrier protein synthase; 3-oxoacyl-[acyl-carrier-protein] synthase; 3-oxoacyl:ACP synthase I; KASI; KAS I; FabF1; FabB; acyl-[acyl-carrier-protein]:malonyl-[acyl-carrier-protein] C-acyltransferase (decarboxylating)
Systematic name: acyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)
Comments: This enzyme is responsible for the chain-elongation step of dissociated (type II) fatty-acid biosynthesis, i.e. the addition of two C atoms to the fatty-acid chain. Escherichia coli mutants that lack this enzyme are deficient in unsaturated fatty acids. The enzyme can use fatty acyl thioesters of ACP (C2 to C16) as substrates, as well as fatty acyl thioesters of Co-A (C4 to C16) [4]. The substrate specificity is very similar to that of EC 2.3.1.179, β-ketoacyl-ACP synthase II, with the exception that the latter enzyme is far more active with palmitoleoyl-ACP (C16Δ9) as substrate, allowing the organism to regulate its fatty-acid composition with changes in temperature [4,5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9077-10-5
References:
1.  Alberts, A.W., Majerus, P.W. and Vagelos, P.R. Acetyl-CoA acyl carrier protein transacylase. Methods Enzymol. 14 (1969) 50–53. [DOI]
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [PMID: 4561013]
3.  Toomey, R.E. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVI. Preparation and general properties of acyl-malonyl acyl carrier protein-condensing enzyme from Escherichia coli. J. Biol. Chem. 241 (1966) 1159–1165. [PMID: 5327099]
4.  D'Agnolo, G., Rosenfeld, I.S. and Vagelos, P.R. Multiple forms of β-ketoacyl-acyl carrier protein synthetase in Escherichia coli. J. Biol. Chem. 250 (1975) 5289–5294. [PMID: 237914]
5.  Garwin, J.L., Klages, A.L. and Cronan, J.E., Jr.. Structural, enzymatic, and genetic studies of β-ketoacyl-acyl carrier protein synthases I and II of Escherichia coli. J. Biol. Chem. 255 (1980) 11949–11956. [PMID: 7002930]
6.  Wang, H. and Cronan, J.E. Functional replacement of the FabA and FabB proteins of Escherichia coli fatty acid synthesis by Enterococcus faecalis FabZ and FabF homologues. J. Biol. Chem. 279 (2004) 34489–34495. [DOI] [PMID: 15194690]
7.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
[EC 2.3.1.41 created 1972, modified 2006]
 
 
EC 2.3.1.179     
Accepted name: β-ketoacyl-[acyl-carrier-protein] synthase II
Reaction: a (Z)-hexadec-9-enoyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a (Z)-3-oxooctadec-11-enoyl-[acyl-carrier protein] + CO2 + an [acyl-carrier protein]
Glossary: palmitoleoyl-[acyl-carrier protein] = (Z)-hexadec-9-enoyl-[acyl-carrier protein]
cis-vaccenoyl-[acyl-carrier protein] = (Z)-octadec-11-enoyl-[acyl-carrier protein]
Other name(s): KASII; KAS II; FabF; 3-oxoacyl-acyl carrier protein synthase II; β-ketoacyl-ACP synthase II
Systematic name: (Z)-hexadec-9-enoyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)
Comments: Involved in the dissociated (or type II) fatty acid biosynthesis system that occurs in plants and bacteria. While the substrate specificity of this enzyme is very similar to that of EC 2.3.1.41, β-ketoacyl-[acyl-carrier-protein] synthase I, it differs in that palmitoleoyl-[acyl-carrier protein] is not a good substrate of EC 2.3.1.41 but is an excellent substrate of this enzyme [1,2]. The fatty-acid composition of Escherichia coli changes as a function of growth temperature, with the proportion of unsaturated fatty acids increasing with lower growth temperature. This enzyme controls the temperature-dependent regulation of fatty-acid composition, with mutants lacking this acivity being deficient in the elongation of palmitoleate to cis-vaccenate at low temperatures [3,4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1048648-42-5
References:
1.  D'Agnolo, G., Rosenfeld, I.S. and Vagelos, P.R. Multiple forms of β-ketoacyl-acyl carrier protein synthetase in Escherichia coli. J. Biol. Chem. 250 (1975) 5289–5294. [PMID: 237914]
2.  Garwin, J.L., Klages, A.L. and Cronan, J.E., Jr.. Structural, enzymatic, and genetic studies of β-ketoacyl-acyl carrier protein synthases I and II of Escherichia coli. J. Biol. Chem. 255 (1980) 11949–11956. [PMID: 7002930]
3.  Price, A.C., Rock, C.O. and White, S.W. The 1.3-Angstrom-resolution crystal structure of β-ketoacyl-acyl carrier protein synthase II from Streptococcus pneumoniae. J. Bacteriol. 185 (2003) 4136–4143. [DOI] [PMID: 12837788]
4.  Garwin, J.L., Klages, A.L. and Cronan, J.E., Jr. β-Ketoacyl-acyl carrier protein synthase II of Escherichia coli. Evidence for function in the thermal regulation of fatty acid synthesis. J. Biol. Chem. 255 (1980) 3263–3265. [PMID: 6988423]
5.  Magnuson, K., Carey, M.R. and Cronan, J.E., Jr. The putative fabJ gene of Escherichia coli fatty acid synthesis is the fabF gene. J. Bacteriol. 177 (1995) 3593–3595. [DOI] [PMID: 7768872]
6.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
[EC 2.3.1.179 created 2006, modified 2020]
 
 
EC 2.3.1.180     
Accepted name: β-ketoacyl-[acyl-carrier-protein] synthase III
Reaction: acetyl-CoA + a malonyl-[acyl-carrier protein] = an acetoacetyl-[acyl-carrier protein] + CoA + CO2
Other name(s): 3-oxoacyl:ACP synthase III; 3-ketoacyl-acyl carrier protein synthase III; KASIII; KAS III; FabH; β-ketoacyl-acyl carrier protein synthase III; β-ketoacyl-ACP synthase III; β-ketoacyl (acyl carrier protein) synthase III; acetyl-CoA:malonyl-[acyl-carrier-protein] C-acyltransferase
Systematic name: acetyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme is responsible for initiating straight-chain fatty acid biosynthesis by the dissociated (or type II) fatty-acid biosynthesis system that occurs in plants and bacteria. In contrast to EC 2.3.1.41, β-ketoacyl-[acyl-carrier-protein] synthase I, and EC 2.3.1.179, β-ketoacyl-[acyl-carrier-protein] synthase II, this enzyme specifically uses short-chain acyl-CoA thioesters (preferably acetyl-CoA) rather than acyl-[acp] as its substrate [1]. The enzyme can also catalyse the reaction of EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, but to a much lesser extent [1]. The enzymes from some organisms (e.g. the Gram-positive bacterium Streptococcus pneumoniae) can accept branched-chain acyl-CoAs in addition to acetyl-CoA [5] (cf. EC 2.3.1.300, branched-chain β-ketoacyl-[acyl-carrier-protein] synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1048646-78-1
References:
1.  Tsay, J.T., Oh, W., Larson, T.J., Jackowski, S. and Rock, C.O. Isolation and characterization of the β-ketoacyl-acyl carrier protein synthase III gene (fabH) from Escherichia coli K-12. J. Biol. Chem. 267 (1992) 6807–6814. [PMID: 1551888]
2.  Cronan, J.E., Jr. and Rock, C.O. Biosynthesis of membrane lipids. In: Neidhardt, F.C. (Ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, vol. 1, ASM Press, Washington, DC, 1996, pp. 612–636.
3.  Han, L., Lobo, S. and Reynolds, K.A. Characterization of β-ketoacyl-acyl carrier protein synthase III from Streptomyces glaucescens and its role in initiation of fatty acid biosynthesis. J. Bacteriol. 180 (1998) 4481–4486. [DOI] [PMID: 9721286]
4.  Choi, K.H., Kremer, L., Besra, G.S. and Rock, C.O. Identification and substrate specificity of β-ketoacyl (acyl carrier protein) synthase III (mtFabH) from Mycobacterium tuberculosis. J. Biol. Chem. 275 (2000) 28201–28207. [DOI] [PMID: 10840036]
5.  Khandekar, S.S., Gentry, D.R., Van Aller, G.S., Warren, P., Xiang, H., Silverman, C., Doyle, M.L., Chambers, P.A., Konstantinidis, A.K., Brandt, M., Daines, R.A. and Lonsdale, J.T. Identification, substrate specificity, and inhibition of the Streptococcus pneumoniae β-ketoacyl-acyl carrier protein synthase III (FabH). J. Biol. Chem. 276 (2001) 30024–30030. [DOI] [PMID: 11375394]
6.  Qiu, X., Choudhry, A.E., Janson, C.A., Grooms, M., Daines, R.A., Lonsdale, J.T. and Khandekar, S.S. Crystal structure and substrate specificity of the β-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus. Protein Sci. 14 (2005) 2087–2094. [DOI] [PMID: 15987898]
7.  Li, Y., Florova, G. and Reynolds, K.A. Alteration of the fatty acid profile of Streptomyces coelicolor by replacement of the initiation enzyme 3-ketoacyl acyl carrier protein synthase III (FabH). J. Bacteriol. 187 (2005) 3795–3799. [DOI] [PMID: 15901703]
[EC 2.3.1.180 created 2006, modified 2021]
 
 
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 2.3.1.207     
Accepted name: β-ketodecanoyl-[acyl-carrier-protein] synthase
Reaction: octanoyl-CoA + a malonyl-[acyl-carrier protein] = a 3-oxodecanoyl-[acyl-carrier protein] + CoA + CO2
Glossary: [acyl-carrier protein] = [acp]
Systematic name: octanoyl-CoA:malonyl-[acyl-carrier protein] C-heptanoylltransferase (decarboxylating, CoA-forming)
Comments: This enzyme, which has been characterized from the bacterium Pseudomonas aeruginosa PAO1, catalyses the condensation of octanoyl-CoA, obtained from exogenously supplied fatty acids via β-oxidation, with malonyl-[acp], forming 3-oxodecanoyl-[acp], an intermediate of the fatty acid elongation cycle. The enzyme provides a shunt for β-oxidation degradation intermediates into de novo fatty acid biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Yuan, Y., Leeds, J.A. and Meredith, T.C. Pseudomonas aeruginosa directly shunts β-oxidation degradation intermediates into de novo fatty acid biosynthesis. J. Bacteriol. 194 (2012) 5185–5196. [DOI] [PMID: 22753057]
[EC 2.3.1.207 created 2012]
 
 
EC 2.3.1.293     
Accepted name: meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I
Reaction: an ultra-long-chain mono-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain mono-unsaturated 3-oxo-fatty acyl-[acyl-carrier protein] + CO2 + a holo-[acyl-carrier protein]
Other name(s): kasA (gene name); β-ketoacyl-acyl carrier protein synthase KasA
Systematic name: ultra-long-chain mono-unsaturated fattyl acyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)
Comments: The enzyme is part of the fatty acid synthase (FAS) II system of mycobacteria, which extends modified products of the FAS I system, eventually forming meromycolic acids that are incorporated into mycolic acids. Meromycolic acids consist of a long chain, typically 50-60 carbons, which is functionalized by different groups.Two 3-oxoacyl-(acyl carrier protein) synthases function within the FAS II system, encoded by the kasA and kasB genes. The two enzymes share some sequence identity but function independently on separate sets of substrates. KasA differs from KasB [EC 2.3.1.294, meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase II], by preferring shorter (C-22 to C-36) and more saturated (only one double bond) substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Schaeffer, M.L., Agnihotri, G., Volker, C., Kallender, H., Brennan, P.J. and Lonsdale, J.T. Purification and biochemical characterization of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthases KasA and KasB. J. Biol. Chem. 276 (2001) 47029–47037. [PMID: 11600501]
2.  Bhatt, A., Kremer, L., Dai, A.Z., Sacchettini, J.C. and Jacobs, W.R., Jr. Conditional depletion of KasA, a key enzyme of mycolic acid biosynthesis, leads to mycobacterial cell lysis. J. Bacteriol. 187 (2005) 7596–7606. [PMID: 16267284]
3.  Luckner, S.R., Machutta, C.A., Tonge, P.J. and Kisker, C. Crystal structures of Mycobacterium tuberculosis KasA show mode of action within cell wall biosynthesis and its inhibition by thiolactomycin. Structure 17 (2009) 1004–1013. [PMID: 19604480]
[EC 2.3.1.293 created 2019]
 
 
EC 2.3.1.294     
Accepted name: meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase II
Reaction: an ultra-long-chain di-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain di-unsaturated 3-oxo-fatty acyl-[acyl-carrier protein] + CO2 + a holo-[acyl-carrier protein]
Other name(s): kasB (gene name); β-ketoacyl-acyl carrier protein synthase KasB
Systematic name: ultra-long-chain di-unsaturated fattyl acyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)
Comments: The enzyme is part of the fatty acid synthase (FAS) II system of mycobacteria, which extends modified products of the FAS I system, eventually forming meromycolic acids that are incorporated into mycolic acids. Meromycolic acids consist of a long chain, typically 50-60 carbons, which is functionalized by different groups.Two 3-oxoacyl-(acyl carrier protein) synthases function within the FAS II system, encoded by the kasA and kasB genes. The two enzymes share some sequence identity but function independently on separate sets of substrates. KasB differs from KasA (EC 2.3.1.293, meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I), by preferring longer substrates (closer to the upper limit), which also contain two double bonds.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Schaeffer, M.L., Agnihotri, G., Volker, C., Kallender, H., Brennan, P.J. and Lonsdale, J.T. Purification and biochemical characterization of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthases KasA and KasB. J. Biol. Chem. 276 (2001) 47029–47037. [PMID: 11600501]
2.  Gao, L.Y., Laval, F., Lawson, E.H., Groger, R.K., Woodruff, A., Morisaki, J.H., Cox, J.S., Daffe, M. and Brown, E.J. Requirement for kasB in Mycobacterium mycolic acid biosynthesis, cell wall impermeability and intracellular survival: implications for therapy. Mol. Microbiol. 49 (2003) 1547–1563. [PMID: 12950920]
3.  Molle, V., Brown, A.K., Besra, G.S., Cozzone, A.J. and Kremer, L. The condensing activities of the Mycobacterium tuberculosis type II fatty acid synthase are differentially regulated by phosphorylation. J. Biol. Chem. 281 (2006) 30094–30103. [PMID: 16873379]
4.  Bhatt, A., Fujiwara, N., Bhatt, K., Gurcha, S.S., Kremer, L., Chen, B., Chan, J., Porcelli, S.A., Kobayashi, K., Besra, G.S. and Jacobs, W.R., Jr. Deletion of kasB in Mycobacterium tuberculosis causes loss of acid-fastness and subclinical latent tuberculosis in immunocompetent mice. Proc. Natl. Acad. Sci. USA 104 (2007) 5157–5162. [PMID: 17360388]
5.  Yamada, H., Bhatt, A., Danev, R., Fujiwara, N., Maeda, S., Mitarai, S., Chikamatsu, K., Aono, A., Nitta, K., Jacobs, W.R., Jr. and Nagayama, K. Non-acid-fastness in Mycobacterium tuberculosis Δ kasB mutant correlates with the cell envelope electron density. Tuberculosis (Edinb) 92 (2012) 351–357. [PMID: 22516756]
6.  Vilcheze, C., Molle, V., Carrere-Kremer, S., Leiba, J., Mourey, L., Shenai, S., Baronian, G., Tufariello, J., Hartman, T., Veyron-Churlet, R., Trivelli, X., Tiwari, S., Weinrick, B., Alland, D., Guerardel, Y., Jacobs, W.R., Jr. and Kremer, L. Phosphorylation of KasB regulates virulence and acid-fastness in Mycobacterium tuberculosis. PLoS Pathog. 10:e1004115 (2014). [PMID: 24809459]
[EC 2.3.1.294 created 2019]
 
 
EC 2.3.1.300     
Accepted name: branched-chain β-ketoacyl-[acyl-carrier-protein] synthase
Reaction: (1) 3-methylbutanoyl-CoA + a malonyl-[acyl-carrier protein] = a 5-methyl-3-oxohexanoyl-[acyl-carrier-protein] + CoA + CO2
(2) 2-methylpropanoyl-CoA + a malonyl-[acyl-carrier protein] = a 4-methyl-3-oxopentanoyl-[acyl-carrier-protein] + CoA + CO2
(3) (2S)-2-methylbutanoyl-CoA + a malonyl-[acyl-carrier protein] = a (4S)-4-methyl-3-oxohexanoyl-[acyl-carrier-protein] + CoA + CO2
Glossary: 3-methylbutanoyl-CoA = isovaleryl-CoA
2-methylpropanoyl-CoA = isobutanoyl-CoA = isobutyryl-CoA
Systematic name: 3-methylbutanoyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme is responsible for initiating branched-chain fatty acid biosynthesis by the dissociated (or type II) fatty-acid biosynthesis system (FAS-II) in some bacteria, using molecules derived from degradation of the branched-chain amino acids L-leucine, L-valine, and L-isoleucine to form the starting molecules for elongation by the FAS-II system. In some organisms the enzyme is also able to use acetyl-CoA, leading to production of a mix of branched-chain and straight-chain fatty acids [3] (cf. EC 2.3.1.180, β-ketoacyl-[acyl-carrier-protein] synthase III).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Han, L., Lobo, S. and Reynolds, K.A. Characterization of β-ketoacyl-acyl carrier protein synthase III from Streptomyces glaucescens and its role in initiation of fatty acid biosynthesis. J. Bacteriol. 180 (1998) 4481–4486. [DOI] [PMID: 9721286]
2.  Choi, K.H., Heath, R.J. and Rock, C.O. β-ketoacyl-acyl carrier protein synthase III (FabH) is a determining factor in branched-chain fatty acid biosynthesis. J. Bacteriol. 182 (2000) 365–370. [DOI] [PMID: 10629181]
3.  Khandekar, S.S., Gentry, D.R., Van Aller, G.S., Warren, P., Xiang, H., Silverman, C., Doyle, M.L., Chambers, P.A., Konstantinidis, A.K., Brandt, M., Daines, R.A. and Lonsdale, J.T. Identification, substrate specificity, and inhibition of the Streptococcus pneumoniae β-ketoacyl-acyl carrier protein synthase III (FabH). J. Biol. Chem. 276 (2001) 30024–30030. [DOI] [PMID: 11375394]
4.  Singh, A.K., Zhang, Y.M., Zhu, K., Subramanian, C., Li, Z., Jayaswal, R.K., Gatto, C., Rock, C.O. and Wilkinson, B.J. FabH selectivity for anteiso branched-chain fatty acid precursors in low-temperature adaptation in Listeria monocytogenes. FEMS Microbiol. Lett. 301 (2009) 188–192. [DOI] [PMID: 19863661]
5.  Yu, Y.H., Hu, Z., Dong, H.J., Ma, J.C. and Wang, H.H. Xanthomonas campestris FabH is required for branched-chain fatty acid and DSF-family quorum sensing signal biosynthesis. Sci. Rep. 6:32811 (2016). [DOI] [PMID: 27595587]
[EC 2.3.1.300 created 2021]
 
 
EC 2.3.1.301     
Accepted name: mycobacterial β-ketoacyl-[acyl carrier protein] synthase III
Reaction: dodecanoyl-CoA + a malonyl-[acyl-carrier protein] = a 3-oxotetradecanoyl-[acyl-carrier protein] + CoA + CO2
Glossary: dodecanoyl-CoA = lauroyl-CoA
Other name(s): fabH (gene name) (ambiguous); mycobacterial 3-oxoacyl-[acyl carrier protein] synthase III
Systematic name: dodecanoyl-CoA:malonyl-[acyl-carrier protein] C-acyltransferase
Comments: The enzyme, characterized from mycobacteria, provides a link between the type I and type II fatty acid synthase systems (FAS-I and FAS-II, respectively) found in these organisms. The enzyme acts on medium- and long-chain acyl-CoAs (C12-C16) produced by the FAS-I system, condensing them with malonyl-[acyl-carrier protein] (malonyl-AcpM) and forming starter molecules for the FAS-II system, which elongates them into meromycolic acids. The enzyme has no activity with short-chain acyl-CoAs (e.g. acetyl-CoA), which are used by EC 2.3.1.180, β-ketoacyl-[acyl-carrier-protein] synthase III, or branched-chain acyl-CoAs, which are used by EC 2.3.1.300, branched-chain β-ketoacyl-[acyl-carrier-protein] synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Scarsdale, J.N., Kazanina, G., He, X., Reynolds, K.A. and Wright, H.T. Crystal structure of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III. J. Biol. Chem. 276 (2001) 20516–20522. [DOI] [PMID: 11278743]
2.  Musayev, F., Sachdeva, S., Scarsdale, J.N., Reynolds, K.A. and Wright, H.T. Crystal structure of a substrate complex of Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III (FabH) with lauroyl-coenzyme A. J. Mol. Biol. 346 (2005) 1313–1321. [DOI] [PMID: 15713483]
3.  Brown, A.K., Sridharan, S., Kremer, L., Lindenberg, S., Dover, L.G., Sacchettini, J.C. and Besra, G.S. Probing the mechanism of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthase III mtFabH: factors influencing catalysis and substrate specificity. J. Biol. Chem. 280 (2005) 32539–32547. [DOI] [PMID: 16040614]
4.  Sachdeva, S., Musayev, F.N., Alhamadsheh, M.M., Scarsdale, J.N., Wright, H.T. and Reynolds, K.A. Separate entrance and exit portals for ligand traffic in Mycobacterium tuberculosis FabH. Chem. Biol. 15 (2008) 402–412. [DOI] [PMID: 18420147]
[EC 2.3.1.301 created 2021]
 
 
EC 4.1.1.124     
Accepted name: malonyl-[acp] decarboxylase
Reaction: malonyl-[acp] = acetyl-[acp] + CO2
Other name(s): decarboxylative ketosynthase; bryQ (gene name); mupG (gene name); pksF (gene name); curC (gene name); jamG (gene name); pedM (gene name)
Systematic name: malonyl-[acyl-carrier protein] carboxy-lyase
Comments: This family of enzymes participates in a process that introduces a methyl branch into nascent polyketide products. The process begins with EC 4.1.1.124, malonyl-[acp] decarboxylase, which converts the common extender unit malonyl-[acp] to acetyl-[acp]. The enzyme is a mutated form of a ketosynthase enzyme, in which a Cys residue in the active site is modified to a Ser residue, leaving the decarboxylase function intact, but nulifying the ability of the enzyme to form a carbon-carbon bond. Next, EC 2.3.3.22, 3-carboxymethyl-3-hydroxy-acyl-[acp] synthase, utilizes the acetyl group to introduce the branch at the β position of 3-oxoacyl intermediates attached to a polyketide synthase, forming a 3-hydroxy-3-carboxymethyl intermediate. This is followed by dehydration catalysed by EC 4.2.1.181, 3-carboxymethyl-3-hydroxy-acyl-[acp] dehydratase (often referred to as an ECH1 domain), leaving a 3-carboxymethyl group and forming a double bond between the α and β carbons. The process concludes with decarboxylation catalysed by EC 4.1.1.125, 4-carboxy-3-alkylbut-2-enoyl-[acp] decarboxylase (often referred to as an ECH2 domain), leaving a methyl branch at the β carbon. The enzymes are usually encoded by a cluster of genes referred to as an "HMGS cassette", based on the similarity of the key enzyme to EC 2.3.3.10, hydroxymethylglutaryl-CoA synthase. cf. EC 4.1.1.87, malonyl-[malonate decarboxylase] decarboxylase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Simunovic, V. and Muller, R. 3-hydroxy-3-methylglutaryl-CoA-like synthases direct the formation of methyl and ethyl side groups in the biosynthesis of the antibiotic myxovirescin A. Chembiochem 8 (2007) 497–500. [DOI] [PMID: 17330904]
2.  Wu, J., Hothersall, J., Mazzetti, C., O'Connell, Y., Shields, J.A., Rahman, A.S., Cox, R.J., Crosby, J., Simpson, T.J., Thomas, C.M. and Willis, C.L. In vivo mutational analysis of the mupirocin gene cluster reveals labile points in the biosynthetic pathway: the "leaky hosepipe" mechanism. Chembiochem 9 (2008) 1500–1508. [DOI] [PMID: 18465759]
3.  Buchholz, T.J., Rath, C.M., Lopanik, N.B., Gardner, N.P., Hakansson, K. and Sherman, D.H. Polyketide β-branching in bryostatin biosynthesis: identification of surrogate acetyl-ACP donors for BryR, an HMG-ACP synthase. Chem. Biol. 17 (2010) 1092–1100. [DOI] [PMID: 21035732]
[EC 4.1.1.124 created 2023]
 
 


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