IUBMB Enzyme Nomenclature


Accepted name: biotin-independent malonate decarboxylase

Reaction: malonate + H+ = acetate + CO2

For diagram of the reaction 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, 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 (acetyl-S-ACP:malonate ACP transferase), EC ([acyl-carrier-protein] S-malonyltransferase) and EC (malonyl-S-ACP decarboxylase). The carboxy group is lost with retention of configuration [6].

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:


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. [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. [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. [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. [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. [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. [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. [PMID: 11902724]

[EC created 2008, modified 2018]

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