Information on EC 4.1.1.89 - biotin-dependent malonate decarboxylase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.1.1.89
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RECOMMENDED NAME
GeneOntology No.
biotin-dependent malonate decarboxylase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
malonate + H+ = acetate + CO2
show the reaction diagram
SYSTEMATIC NAME
IUBMB Comments
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 4.1.1.88, 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 2.3.1.187, acetyl-S-ACP:malonate ACP transferase), MadB (EC 4.3.99.2, carboxybiotin decarboxylase), MadC/MadD (EC 2.1.3.10, malonyl-S-ACP:biotin-protein carboxyltransferase) and MadH (EC 6.2.1.35, 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].
CAS REGISTRY NUMBER
COMMENTARY hide
80700-20-5
multienzyme complex malonate decarboxylase
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
malonate + H+
acetate + CO2
show the reaction diagram
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?
additional information
?
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subunit acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase catalyzes the transfer of acyl carrier protein from acetyl acyl carrier protein and malonate to yield malonyl acyl carrier protein and acetate. Malonate is thus activated on the enzyme by exchange for the catalytically important enzyme-bound acetyl thioester residues
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
additional information
?
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subunit acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase catalyzes the transfer of acyl carrier protein from acetyl acyl carrier protein and malonate to yield malonyl acyl carrier protein and acetate. Malonate is thus activated on the enzyme by exchange for the catalytically important enzyme-bound acetyl thioester residues
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
biotin
additional information
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the acyl carrier protein subunit contains 2-(5'-phosphoribosyl)-3-dephosphocoenzyme A as a prosthetic group
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Avidin
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inhibition can be partially reversed with an excess of biotin
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hydroxylamine
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complete inhibition
iodoacetate
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specific reaction with subunit acyl carrier protein
Thiocyanate
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complete inhibition
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2.67
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pH 7.5, 30°C
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14000
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x * 14000, SDS-PAGE of subunit acyl carrier protein
67000
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x * 67000, SDS-PAGE, subunit acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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the genes encoding components of the malonate decarboxylase enzyme system are located within a gene cluster of about 11 kb comprizing 14 genes that have been termed madYZGBAECDHKFLMN. MadA represents the acyl-carrier-protein-transferase component, MadB is the integral membrane-bound carboxybiotin protein decarboxylase, MadC and MadD are the two subunits of the carboxyltransferase, MadE is the acyl carrier protein and MadF is the biotin protein
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
isolation of the biotinyl protein from the complex in catalytically inactive form in presence of detergent
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purification of subunit acetyl-S-acyl carrier protein: malonate acyl carrier protein-SH transferase and of whole enzyme complex
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recombinant subunit biotinyl protein MadF. Despite coexpression of biotin ligase birA, MadF is poorly biotinylated
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression of subunit biotinyl protein MadF and biotin ligase birA in Escherichia coli
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme inhibited by thiocyanate or hydroxylamine, 50-65% of the original decarboxylase activity is restored by incubation of the extract with ATP in the presence of acetate, and the extent of reactivation increases after incubation with dithioerythritol. Reactivation is also obtained by chemical acetylation with acetic anhydride
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inhibition of malonate decarboxylase complex by avidin can be partially reversed with an excess of biotin
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