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 .
the holoenzyme contains four subunits having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD-MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities
malonate decarboxylation proceeds by a catalytic cycle in which the acetyl group on the active enzyme is displaced by malonate, which binds covalently to a thiol group on the enzyme and is subsequently decarboxylated
malonate decarboxylation proceeds in two steps: the acetyl residue on the acyl carrier protein is first replaced by a malonyl residue which subsequently undergoes decarboxylation thereby regenerating the acetyl-S-acyl carrier protein
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SYSTEMATIC NAME
IUBMB Comments
malonate carboxy-lyase (biotin-independent)
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].
subunit acyl carrier protein contains a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group attached via a phosphodiester to residue S25. Formation of this phosphodiester bond is catalyzed by a phosphoribosyl-dephospho-coenzyme A transferase MdcG. Site-directed mutagenesis of D134 and/or D136 of MdcG to alanine abolishes the transfer of the prosthetic group to apo acyl carrier protein
enzyme is encoded by a gene cluster consisting of the eight consecutive genes mdcABCDEFCH and the divergently oriented mdcR gene. The mdcA, C, D and E genes encode subunits alpha, beta, gamma and delta of malonate decarboxylase. MdcA represents the ACP-transferase and that MdcD and E together probably function as malonyl-S-acyl carrier protein decarboxylase. MdcC is the (apo) acyl carrier protein subunit. MdcB and MdcG are involved in the synthesis and attachment of the prosthetic group. MdcH is probably involved in the initial activation of the enzyme by malonylation. MdcF is a membrane protein that could function as a malonate carrier
enzyme complex is formed by subunits alpha, beta, gamma, delta. The mdcA gene product, the alpha subunit, is malonate/acetyl-CoA transferase and the mdcD gene product, the beta subunit, is malonyl-CoA decarboxylase. The mdcE gene product, the gamma subunit, may play a role in subunit interaction to form a stable complex or as a codecarboxylase. The mdcC gene product, the delta subunit, is an acyl-carrier protein
mdcA gene encodes the alpha subunit carrying acyl carrier protein transferase activity. The mdcD gene encodes the delta subunit, the acyl carrier protein. mdcB encodes the beta subunit, the catalytic subunit of decarboxylation of malonate. The mdcC gene encodes the gamma subunit involved in decarboxylation of the malonyl-S-acyl carrier protein
mdcA gene encodes the alpha subunit carrying acyl carrier protein transferase activity. The mdcD gene encodes the delta subunit, the acyl carrier protein. mdcB encodes the beta subunit, the catalytic subunit of decarboxylation of malonate. The mdcC gene encodes the gamma subunit involved in decarboxylation of the malonyl-S-acyl carrier protein
enzyme complex is formed by subunits alpha, beta, gamma, delta. The mdcA gene product, the alpha subunit, is malonate/acetyl-CoA transferase and the mdcD gene product, the beta subunit, is malonyl-CoA decarboxylase. The mdcE gene product, the gamma subunit, may play a role in subunit interaction to form a stable complex or as a codecarboxylase. The mdcC gene product, the delta subunit, is an acyl-carrier protein
enzyme is encoded by a gene cluster consisting of the eight consecutive genes mdcABCDEFCH and the divergently oriented mdcR gene. The mdcA, C, D and E genes encode subunits alpha, beta, gamma and delta of malonate decarboxylase. MdcA represents the ACP-transferase and that MdcD and E together probably function as malonyl-S-acyl carrier protein decarboxylase. MdcC is the (apo) acyl carrier protein subunit. MdcB and MdcG are involved in the synthesis and attachment of the prosthetic group. MdcH is probably involved in the initial activation of the enzyme by malonylation. MdcF is a membrane protein that could function as a malonate carrier
presence of two forms of the enzyme: a catalytically inactive SH-enzyme and the catalytically active acetyl-S-enzyme which is formed by post-translational acetylation of the SH-enzyme with ATP, acetate and a specific ligase. the delta subunit is the acyl carrier protein of the enzyme complex
subunit acyl carrier protein contains a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group attached via a phosphodiester to residue S25. Formation of this phosphodiester bond is catalyzed by a phosphoribosyl-dephospho-coenzyme A transferase MdcG. Site-directed mutagenesis of D134 and/or D136 of MdcG to alanine abolishes the transfer of the prosthetic group to apo acyl carrier protein
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
MdcD-MdcE subunits, sitting drop vapor diffusion method, using 0.1 M Bis-Tris (pH 5.8), 18% (w/v) PEG 3350, and 0.2 M ammonium acetate. Holoenzyme in complex with CoA and malonate, sitting drop vapor diffusion method, using 20% (w/v) PEG 3350 and 8% (w/v) tacsimate
the holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD-MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Structure of the MdcD-MdcE complex at 1.86 A resolution, and overall strcuture of the heterotetramer at 2.2 A resolution
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
reactivation of deacetyl malonate decarboxylase with malonyl-CoA to 100%, with acetyl-CoA or methylmalonyl-CoA to about 50% of initial activity, respectively
reacylation of the catalytically inactive SH-enzyme to form the catalytically active acetyl-S-enzyme can be achieved with acetic anhydride or more efficiently with malonyl-CoA
Identification of the active site of phosphoribosyl-dephospho-coenzyme A transferase and relationship of the enzyme to an ancient class of nucleotidyltransferases