EC - Biotin-dependent malonate decarboxylase

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IntEnz Enzyme Nomenclature


Accepted name:
biotin-dependent malonate decarboxylase
Other names:
malonate decarboxylase (with biotin)
malonate decarboxylase [ambiguous]
Systematic name:
malonate carboxy-lyase (biotin-dependent)



Two types of malonate decarboxylase are currently known, both of which form multienzyme complexes. The enzyme described here is a biotin-dependent, Na+-translocating enzyme that includes both soluble and membrane-bound components [6]. The other type is a biotin-independent cytosolic protein (cf. EC, 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, acetyl-S-ACP:malonate ACP transferase), MadB (EC, carboxybiotin decarboxylase), MadC/MadD (EC, malonyl-S-ACP:biotin-protein carboxyltransferase) and MadH (EC, ACP-SH:acetate 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

Enzymes and pathways: NC-IUBMB , BRENDA , DIAGRAM , ExplorEnz , ENZYME@ExPASy , KEGG , MetaCyc , UniPathway
Protein domains and families: PROSITE:PDOC50980
Structural data: CSA , EC2PDB


  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: 117-123 (1992). [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: 48-56 (1994). [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: 4689-4696 (1996). [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: 103-115 (1997). [PMID: 9128730]
  5. Kim, Y.S.
    Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application.
    J. Biochem. Mol. Biol. 35: 443-451 (2002). [PMID: 12359084]
  6. Dimroth, P. and Hilbi, H.
    Enzymic and genetic basis for bacterial growth on malonate.
    Mol. Microbiol. 25: 3-10 (1997). [PMID: 11902724]

[EC created 2008]