Lyases;
Carbon-carbon lyases;
Carboxy-lyases
BRITE hierarchy

malonate carboxy-lyase (biotin-independent)

malonate + H+ = acetate + CO2 [RN:R09483]

R09483
Reaction

malonate [CPD:C00383];
H+ [CPD:C00080]

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].

EC 4.1.1.88 created 2008, modified 2018

1  [PMID:8620876]

Schmid M, Berg M, Hilbi H, 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 237:221-8 (1996)
DOI:10.1111/j.1432-1033.1996.0221n.x

2

Byun, H.S. and Kim, Y.S.

Subunit organization of bacterial malonate decarboxylases: the smallest delta subunit as an acyl-carrier protein.

J Biochem Mol Biol 30:132-137 (1997)

3  [PMID:9208947]

Hoenke S, Schmid M, Dimroth P

Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli.

Eur J Biochem 246:530-8 (1997)
DOI:10.1111/j.1432-1033.1997.00530.x

4  [PMID:9851033]

Chohnan S, Fujio T, Takaki T, Yonekura M, Nishihara H, Takamura Y

Malonate decarboxylase of Pseudomonas putida is composed of five subunits.

FEMS Microbiol Lett 169:37-43 (1998)
DOI:10.1111/j.1574-6968.1998.tb13296.x

5  [PMID:11052676]

Hoenke S, Schmid M, 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 39:13233-40 (2000)
DOI:10.1021/bi001154u

6  [PMID:10496981]

Handa S, Koo JH, Kim YS, Floss HG

Stereochemical course of biotin-independent malonate decarboxylase catalysis.

Arch Biochem Biophys 370:93-6 (1999)
DOI:10.1006/abbi.1999.1369

7  [PMID:10561613]

Koo JH, Kim YS

Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus.

Eur J Biochem 266:683-90 (1999)
DOI:10.1046/j.1432-1327.1999.00924.x

8  [PMID:12359084]

Kim YS

Malonate metabolism: biochemistry, molecular biology, physiology, and industrial application.

J Biochem Mol Biol 35:443-51 (2002)
DOI:10.5483/bmbrep.2002.35.5.443

9  [PMID:11902724]

Dimroth P, Hilbi H

Enzymic and genetic basis for bacterial growth on malonate.

Mol Microbiol 25:3-10 (1997)
DOI:10.1046/j.1365-2958.1997.4611824.x