Malonate decarboxylase

Hilbi H, R Hermann, P Dimroth (1993) The malonate decarboxylase enzyme system of Malonomonas rubra evidence for the cytoplasmic location of the biotin-containing component. Arch Microbiol 160 126-131. 

Malonate decarboxylase (EC 4.1.1.88) and citrate lyase (EC 4.1.3.6) are both large enzyme complexes that consist of multiple subunits, the smallest of which acts as an ACP. These two complexes catalyze the decarboxylation of malonate to acetate and CO2 and the Mg -dependent cleavage of citrate to acetate and oxaloacetate, respectively. Both have been shown to require a thiol-containing prosthetic group for activity. However, unlike the carrier proteins described in the previous section, the ACP subunits of these proteins are not phosphopantetheinylated by a reaction with CoA. Instead, they rely on a unique cofactor, 2 -(5"-triphosphoribosyl)-3 -dephospho-CoA (24, dePCoA-RibPPP), as source of a 2 -(5"-phosphoribosyl)-3 -dephospho-CoA prosthetic group, which is bound to a conserved serine residue of the ACP. ° ° A similar prosthetic group has been identified in citramalate lyase (EC 4.1.3.22). The proposed biosynthesis and subsequent transfer reactions of the cofactor 24 to the ACPs of these complexes are shown in Scheme 5. 

Scheme 5 Malonate decarboxylase and citrate lyase both contain a bo/o-ACP (MdcC and CitD, respectively) that has a 2 -(5"-phosphoribosyl)-3 -dephospho-CoA prosthetic group which is attached by a phosphodiester linkage to a conserved serine residue. The prosthetic group originates from the cofactor 2 -(5"-triphosphoribosyl)-3 -dephospho-CoA 24, which is biosynthesized from dephospho-CoA 11 and ATP by either MdcB or CitG. The posttranslational modification of theapo-ACP proteins is catalyzed by a complex of the enzyme MdcG with 24, or CitX, depending on the system.

Decarboxylases. Pour decarboxylases, methylmalonyl-CoA decarboxylase, oxaloacetate decarboxylase, glutaconyl-CoA decarboxylase, and malonate decarboxylase, are encountered in anaerobic procaryotes. These biotin-dependent enzymes do not require ATP, are membrane bound, and are coupled to sodium... 

Also, decarboxylations of malonate-type compounds have been confirmed to proceed with retention of configuration. Indeed, malonyl-CoA decarboxylase from uropygial gland is enantioselective to the substrate as well as the product. Only... 

Thus, decarboxylase of disubstituted malonic acid could be easily converted to racemase of the corresponding monobasic acid, in spite of the fact that decarboxylation and racemization are quite different from each other. The key for the success is the mechanistic consideration focusing on the fact that the intermediate of both reactions is the same type of enolate of monobasic carboxylic acid. 

To obtain a better understanding of the reaction mechanism, some compounds that are considered to he intermediates were subjected to the reaction. Various reaction courses can be considered as illustrated in Fig. 21. Path A a-Methyltropic acid is oxidized to a-phenyl-a-methylmalonic acid. Then, the malonate is converted to optically active a-phenylpropionate hy arylmalonate decarboxylase. In order to confirm this assumption, incubation of the malonic acid with Rhodococcus sp. was carried out. The result obtained was the total recovery of the substrate, indicating that no decarboxylase is present in this bacterium. Path B a-Methyltropic acid is converted to racemic a-phenylpropionic acid, which is deracemized to optically active propionic acid. To examine the possibility of this route, racemic a-phenylpropionic acid was subjected to the reaction to observe... 

Poelarends GJ, WH Johnson, AG Murzin, CP Whitman (2003) Mechanistic characterization of a bacterial malonate semialdehyde decarboxylase. J Biol Chem 278 48674-48683. 

The enzymatic reaction was performed at 30 °C for 2 hours in a volume of 1 ml of 250 mM phosphate buffer (pH 6.5) containing 50 mM of KOH, 32 U/ml of the enzyme, and [1- C]-substrate. The product was isolated as the methyl ester. When the (S)-enantiomer was employed as the substrate, C remained completely in the product, as confirmed by C NMR and HRMS. In addition, spin-spin coupling between and was observed in the product, and the frequency of the C-O bond-stretching vibration was down-shifted to 1690 cm" (cf. 1740 cm for C-O). On the contrary, reaction of the (R)-enantiomer resulted in the formation of (R)-monoacid containing C only within natural abundance. These results clearly indicate that the pro-R carboxyl group of malonic acid is ehminated to form (R)-phenylpropionate with inversion of configuration [28]. This is in sharp contrast to the known decarboxylation reaction by malonyl CoA decarboxylase [1] and serine hydroxymethyl transferase [2], which proceeds with retention of configuration. 

Nevertheless, malonyl-CoA is a major metabolite. It is an intermediate in fatty acid synthesis (see Fig. 17-12) and is formed in the peroxisomal P oxidation of odd chain-length dicarboxylic acids.703 Excess malonyl-CoA is decarboxylated in peroxisomes, and lack of the decarboxylase enzyme in mammals causes the lethal malonic aciduria.703 Some propionyl-CoA may also be metabolized by this pathway. The modified P oxidation sequence indicated on the left side of Fig. 17-3 is used in green plants and in many microorganisms. 3-Hydroxypropionyl-CoA is hydrolyzed to free P-hydroxypropionate, which is then oxidized to malonic semialdehyde and converted to acetyl-CoA by reactions that have not been completely described. Another possible pathway of propionate metabolism is the direct conversion to pyruvate via a oxidation into lactate, a mechanism that may be employed by some bacteria. Another route to lactate is through addition of water to acrylyl-CoA, the product of step a of Fig. 17-3. Tire water molecule adds in the "wrong way," the OH ion going to the a carbon instead of the P (Eq. 17-8). An enzyme with an active site similar to that of histidine ammonia-lyase (Eq. 14-48) could... 

Tautomerase supertamily Malonate semialdehyde decarboxylase Decarboxylation of malonate Hydration of 2-oxo-3-pentynoate 113-117... 

The decarboxylation of L-aspartic acid to L-alanine is catalysed by a pyridoxal-P-dependent j8-decarboxylase whose reaction mechanism is clearly different from that of the a-decarboxylases since the initial step probably involves C -H bond cleavage. The steric course at during the normal decarboxylation reaction has recently been shown [23b] to be inversion. In addition to this, however, the enzyme will also catalyse the decarboxylation of amino-malonic acid to glycine and Meister and coworkers [24,25] have shown that this process involves loss of the Si carboxyl group with overall retention at C . 

Many enzymes are dependent on dissociable metal ions for their activity, and the operation of most of the important metabolic systems thus requires the presence of these cofactors. For example, the list of enzymes requiring Mg is a long one and includes the oxidases and decarboxylases for the keto acids, most of the enzymes involved in phosphate metabolism, some dehydrogenases, some peptidases, phosphoglucomutase and enolase. These enzymes may be inhibited with inhibitors forming stable complexes with Mg ions. For example, malonate and other dicarboxylic compounds are able to chelate effectively with Mg" and other metal ions, and their inhibition may result from the reduction of metal ion concentration in the medium or the removal of the metal ions from the enzyme [3] ... 

Malonic aciduria is caused by a reduced activity of mitochondrial malo-nyl-CoA decarboxylase, the enzyme responsible for conversion of intramito-chondrial malonyl-CoA to acetyl-CoA. Hitherto, the disorder has been confined to nine patients. Clinical symptoms, which can develop soon after birth or in early childhood, include delayed neurological development, seizures, episodes of vomiting and anorexia, mild to severe metabolic acidosis and cardiomyopathy [12-15]. One patient died at the age of 8 days [15] the other patients are still alive, the oldest being 13 years of age. 

Biochemically, malonyl-CoA decarboxylase deficiency is characterised by the excretion of excess malonic and methylmalonic acids in urine, mostly... 

Fig. 8.1. Pathways of 2-ketoglutarate, fumarate, malonate and N-acetylaspartate metabolism and proposed pathways of D- and L-2-hydroxyglutarate metabolism. 8.1, 2-Ketoglutarate dehydrogenase complex (El or E2) 8.2, fumarase 8.3, malonyl-CoA decarboxylase 8.6, aspartoacylase...

Incorporation experiments proved that lunularin (595) and lunularic acid (598) were biosynthesized by the shikimate-malonate pathway 288, 290). The co-occurrence of (595) and (598), and the presence of a lunularic acid decarboxylase in Lunularia cruciata and Conocephalum conicum indicated that a decarboxylation step was involved in forming naturally occurring C-14 stilbenes and their dihydro products 290, 292). 

Pathways 8-10 are all thermodynamically favorable and produce 1 mol of ATP. Malonyl-CoA and malonic-semialdehyde can be derived from oxaloacetate by employing novel enzymes, with CoA-dependent oxaloacetate dehydrogenase and 2-keto acid decarboxylase activity, respectively. Malate can be converted to 3-HP using a novel enzyme with malate decarboxylase activity (Figure 14.4). These enzymes do not exist in nature and, because of this, it has been proposed that malate decarboxylase activity can be created by enzyme engineering in order to increase their specificity toward oxaloacetate and ability to produce the metabolic intermediates [33]. 

To explain the inhibition of the incorporation of malonic acid into fatty acid in intact plants by the cyclohexane-1,3-diones (Burgstahler 1985) and aryloxy-phenoxypropionic acid-herbicides (Hoppe and Zacher 1982), we suggest the action of a malonate and/or malony1-CoA decarboxylase, able to catalyze the formation of acetate/acetyl-CoA, substrates the incorporation of which into fatty acids can then be blocked by these herbicides. Our model is summarized in Figure 4. 

Decarboxylation of malonic acid derivatives is a well studied process in the biosynthesis of biomolecules such as long-chain fatty acids and polyketides. A decarboxylase that exhibits enantioselectivity for substituted malonates would be useful for producing ophcally active carboxylic acids, hi fact, malonyl-CoA decarboxylase does catalyze an enantioselective decarboxylation (Figure 3.2) [5], but malonyl-CoA is an unsuitable precursor for optically active substances. Instead, we focused on the prochiral-activated compoimd arylmalonate, an intermediate of malonic ester synthesis, to develop a method for enantioselective decarboxylation. Malonates are stable at room temperature but readily decompose to arylacetate and CO2 at high temperatures. This suggests that the decarboxylation of arylmalonate may occur naturally if arylmalonate acts as a substrate for a decarboxylase. 

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