MetaCyc Pathway: malonate degradation II (biotin-dependent)
Traceable author statement to experimental supportInferred from experiment

Pathway diagram: malonate degradation II (biotin-dependent)

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/AssimilationCarboxylates DegradationMalonate Degradation

Some taxa known to possess this pathway include : Malonomonas rubra

Expected Taxonomic Range: Bacteria

General Background

Malonate is found in small amounts in plants [Bentley52] and is produced by some bacteria [Vogels76]. Most of the malonate in the environment, however, comes from industrial production. The dimethyl and diethyl forms, in particularly, are produced at more than 12,000 tons per year (1995) [Dimroth97].

Several strains of bacteria are able to utilize malonate as sole source of carbon and energy. The key reaction in the pathway is the decarboxylation of malonate to acetate. Malonate is a rather inert compound, and its decarboxylation under physiological conditions requires an activation step, in which malonate forms a thioester derivative.

Two types of malonate decarboxylases have been described. The first type (described here), which has been characterized in the anaerobe Malonomonas rubra, is EC, biotin-dependent malonate decarboxylase, an enzyme complex that also functions as a Na+-translocating pump. In this enzyme the carboxylate group is first transferred to a biotin carrier protein that shuttles it to the membrane-bound decarboxylase subunit (see malonate degradation II (biotin-dependent)).

The second type (described in malonate degradation I (biotin-independent)) is EC, biotin-independent malonate decarboxylase, a cytosolic enzyme copmplex that releases the carboxylate group directly to the cytosol [Koo99].

About This Pathway

Unlike the biotin-independent malonate decarboxylase from Klebsiella pneumoniae, the biotin-dependent malonate decarboxylase from Malonomonas rubra comprises water-soluble cytoplasmic and membrane components that are not assembled into a single enzyme complex [Hilbi92].

Prior to decarboxylation, malonate needs to be activated by binding to an acyl-carrier protein [acp] subunit, encoded by the madE gene. There are several steps that need to take place prior to this activation reaction. First, the [acp] subunit needs to be pre-activated by binding a unique 2'-(5''-triphospho-α-D-ribosyl)-3'-dephospho-CoA cofactor, which is also used by the citrate lyase enzyme complex (see malonate decarboxylase activation). Following this pre-activation, the [acp] subunit binds an acetyl group in a reaction catalyzed by EC, ACP-SH:acetate ligase (encoded by the madH gene), forming an acetyl-[holo malonate decarboxylase acyl-carrier protein]. Finally, this acetylated form can exchange the acetyl group for malonate in a reaction catalyzed by EC, acetyl-S-ACP:malonate ACP transferase (encoded by the madA gene).

Once activated and bound to the [acp] subunit as a malonyl-[holo malonate decarboxylase acyl-carrier protein], the malonyl group becomes the substrate for the EC, malonyl-S-ACP:biotin-protein carboxyltransferase (encoded by the madC and madD genes), which transfers a carboxylate moiety group from the bound-malonyl group to a biotin-carrier protein, encoded by the madF gene. The carboxylated biotin-carrier protein travels to carboxybiotin decarboxylase, the membrane bound component of the malonate decarboxylase complex, which releases the carboxyl group. The enzyme couples this exergonic reaction to Na+ ion pumping across the membrane, building up a gradient. After transfering the carboxylate group to the biotin-carrier protein, the [acp] subunit returns to its acetylated form, and is ready to bind a new malonate molecule. Thus, the enzyme catalyzes a continous turnover of malonate to acetate and CO2 [Dimroth97].

An operon that encodes all of the components that are involved in this pathway has been sequenced [Berg97].

The overall process is described by EC, biotin-dependent malonate decarboxylase: malonate + H+ = acetate + CO2

Variants: malonate degradation I (biotin-independent)

Created 30-Sep-2008 by Caspi R, SRI International
Revised 01-Oct-2013 by Caspi R, SRI International


Bentley52: Bentley, L.E. (1952). "Occurrence of malonic acid in plants." Nature 170(4333);847-8. PMID: 13013230

Berg97: Berg M, Hilbi H, Dimroth P (1997). "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(1);103-15. PMID: 9128730

Dimroth97: Dimroth P, Hilbi H (1997). "Enzymic and genetic basis for bacterial growth on malonate." Mol Microbiol 25(1);3-10. PMID: 11902724

Hilbi92: Hilbi H, Dehning I, Schink B, Dimroth P (1992). "Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme." Eur J Biochem 207(1);117-23. PMID: 1628643

Koo99: Koo JH, Kim YS (1999). "Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus." Eur J Biochem 266(2);683-90. PMID: 10561613

Vogels76: Vogels GD, Van der Drift C (1976). "Degradation of purines and pyrimidines by microorganisms." Bacteriol Rev 40(2);403-68. PMID: 786256

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Berg96: Berg M, Hilbi H, Dimroth P (1996). "The acyl carrier protein of malonate decarboxylase of Malonomonas rubra contains 2'-(5"-phosphoribosyl)-3'-dephosphocoenzyme A as a prosthetic group." Biochemistry 35(15);4689-96. PMID: 8664258

Hilbi94: Hilbi H, Dimroth P (1994). "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(1-2);48-56. PMID: 18251085

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Schmid96: Schmid M, Berg M, Hilbi H, Dimroth P (1996). "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(1);221-8. PMID: 8620876

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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