Biotin carboxylation reactions

Biotin — Enzyme-bound biotin Carboxylation reactions i... 

Biotin Carboxylation reactions in carbohydrate and lipid metabolism Sections 18.2, 21.6... 

FIGURE 25.2 (a) The acetyl-CoA carboxylase reaction produces malonyl-CoA for fatty acid synthesis, (b) A mechanism for the acetyl-CoA carboxylase reaction. Bicarbonate is activated for carboxylation reactions by formation of N-carboxybiotin. ATP drives the reaction forward, with transient formation of a carbonylphosphate intermediate (Step 1). In a typical biotin-dependent reaction, nncleophilic attack by the acetyl-CoA carbanion on the carboxyl carbon of N-carboxybiotin—a transcarboxylation—yields the carboxylated product (Step 2). 

Bicarbonate as a source of CO2 is required in the initial reaction for the carboxylation of acetyl-CoA to mal-onyl-CoA in the presence of ATP and acetyl-CoA carboxylase. Acetyl-CoA carboxylase has a requirement for the vitamin biotin (Figure 21-1). The enzyme is a multienzyme protein containing a variable number of identical subunits, each containing biotin, biotin carboxylase, biotin carboxyl carrier protein, and transcarboxylase, as well as a regulatory allosteric site. The reaction takes place in two steps (1) carboxylation of biotin involving ATP and (2) transfer of the carboxyl to acetyl-CoA to form malonyl-CoA. 

H Biotin Coenzyme in carboxylation reactions in gluco-neogenesis and fatty acid synthesis Impaired fat and carbohydrate metabolism, dermatitis... 

Biotin functions to transfer carbon dioxide in a small number of carboxylation reactions. A holocarboxylase synthetase acts on a lysine residue of the apoenzymes of acetyl-CoA carboxylase, pymvate carboxylase, propi-onyl-CoA carboxylase, or methylcrotonyl-CoA carboxylase to react with free biotin to form the biocytin residue of the holoenzyme. The reactive intermediate is 1-7V-carboxybiocytin, formed from bicarbonate in an ATP-dependent reaction. The carboxyl group is then transferred to the substrate for carboxylation (Figure 21—1). 

However, if we can design some sophisticated routes to generate carbanion equivalents in the active site of the enzyme, carboxylation reaction might be possible. In fact, acetyl-CoA is carboxylated with the aid of biotin in the biosynthetic pathway of long-chain fatty acids. 

However, a more favourable pathway is used, employing a more reactive nucleophile. Rather than using the enolate anion derived from acetyl-CoA, nature uses the enolate anion derived from malonyl-CoA. Malonyl-CoA is obtained from acetyl-CoA by means of an enzymic carboxylation reaction, incorporating CO2 (usually from the soluble form bicarbonate). Now CO2 is a particularly unreactive material, so this reaction requires the input of energy (from ATP) and the presence of a suitable coenzyme, biotin, as the carrier of CO2 (see Section 15.9). The... 

We have briefly noted the role of biotin when we considered the biosynthesis of fatty acids (see Section 15.5). Biotin is a carrier of carbon dioxide and involved in carboxylation reactions. In fatty acid biosynthesis, we noted how acetyl-CoA was... 

Vitamin H (biotin) is present in liver, egg yolk, and other foods it is also synthesized by the intestinal flora. In the body, biotin is covalently attached via a lysine side chain to enzymes that catalyze carboxylation reactions. Biotin-dependent carboxylases include pyruvate carboxylase (see p. 154) and acetyl-CoA carboxylase (see p. 162). CO2 binds, using up ATP, to one of the two N atoms of biotin, from which it is transferred to the acceptor (see p. 108). 

Biotin Tight Biotin Intermediate carrier of CO2 in carboxylation reactions... 

The chemistry of a fourth coenzyme was at least partially elucidated in the period under discussion. F. Lynen and coworkers treated P-methylcrotonyl coenzyme A (CoA) carboxylase with bicarbonate labelled with 14C, and discovered that one atom of radiocarbon was incorporated per molecule of enzyme. They postulated that an intermediate was formed between the enzyme and C02, in which the biotin of the enzyme had become car-boxylated. The carboxylated enzyme could transfer its radiolabelled carbon dioxide to methylcrotonyl CoA more interestingly, they found that the enzyme-COz compound would also transfer radiolabelled carbon dioxide to free biotin. The resulting compound, carboxybiotin [4], was quite unstable, but could be stabilized by treatment with diazomethane to yield the methyl ester of N-carboxymethylbiotin (7) (Lynen et al., 1959). The identification of this radiolabelled compound demonstrated that the unstable material is N-carboxybiotin itself, which readily decarboxylates esterification prevents this reaction, and allows the isolation and identification of the product. Lynen et al. then postulated that the structure of the enzyme-C02 compound was essentially the same as that of the product they had isolated from the reaction with free biotin, but where the carbon dioxide was inserted into the bound biotin of the enzyme (Lynen et al., 1961). Although these discoveries still leave significant questions to be answered as to the detailed mechanism of the carboxylation reactions in which biotin participates as coenzyme, they provide a start toward elucidating the way in which the coenzyme functions. 

Carboxyl groups are activated in a reaction that splits ATP and joins C02 to enzyme-bound biotin. This activated C02 is then passed to an acceptor (pyruvate in this case) in a carboxylation reaction. 

MECHANISM FIGURE 16-16 The role of biotin in the reaction catalyzed by pyruvate carboxylase. Biotin is attached to the enzyme through an amide bond with the e-amino group of a Lys residue, forming biotinyl-enzyme. Biotin-mediated carboxylation reactions occur in two phases, generally catalyzed by separate active sites on the enzyme as exemplified by the pyruvate carboxylase reaction. In the first phase (steps to ), bicarbonate is converted to the more activated C02, and then used to carboxylate biotin. The bicarbonate is first activated by reaction with ATP to form carboxyphosphate (step ), which breaks down to carbon dioxide (step ). In effect, the... 

Carboxylation of pyruvate to oxaloacetate (OAA) by pyruvate carboxylase is a biotin-dependent reaction (see Figure 8.24). This reaction is important because it replenishes the citric acid cycle intermediates, and provides substrate for gluconeogenesis (see p. 116). 

Biotin is active when covalently attached to a carboxylase, participating in carboxylation reactions. A deficiency of biotin is rare, and it has no known toxicity. 

Biotin acts as a carboxyl group carrier in a series of carboxylation reactions, a function originally suggested by the fact that aspartate partially replaces biotin in promoting the growth of the yeast Torula cremonis. Aspartate was known to arise by transamination from oxaloacetate, which in turn could be formed by carboxylation of pyruvate. Subsequent studies showed that biotin was needed for an enzymatic ATP-dependent reaction of pyruvate with bicarbonate ion to form oxaloacetate (Eq. 14-3). This is a (3 carboxylation coupled to the hydrolysis of ATP. 

In the degradation of isoleucine, (3 oxidation proceeds to completion in the normal way with generation of acetyl-CoA and propionyl-CoA. However, in the catabolism of leucine after the initial dehydrogenation in the (3-oxidation sequence, carbon dioxide is added using a biotin enzyme (Chapter 14). The double bond conjugated with the carbonyl of the thioester makes this carboxylation analogous to a standard (3-carboxylation reaction. Why add the extra C02 ... 

Biotin is the essential coenzyme for carboxylation reactions involving bicarbonate as the carboxylating agent. Several reactions have been described in which ATP-depen-dent carboxylation occurs at carbon atoms activated for enolization by ketonic or activated acyl groups. One reaction is known in which a nitrogen atom of urea is carboxyl-ated. 

Knowles, J. R., The mechanism of biotin-dependent enzymes. Ann. Rev. Biochem. 58 195, 1989. Review of the chemical mechanism of biotin-dependent carboxylation reactions. 

Jencks and coworkers9 noted that a likely route for catalysis of carboxylation reactions (replacement of a proton by a carboxyl group) is the generation of low entropy carbon dioxide by a reaction of ATP and bicarbonate adjacent to Nl of biotin. This way of promoting carboxylation produces a situation which is precisely what is created at the stage of the initial formation of products in decarboxylation reactions. Since there is no directional momentum, the proximity of low entropy carbon dioxide and a nucleophile similarly will slow the reaction in the direction of decarboxylation. The same authors suggest that for decarboxylation reactions, nucleophilic addition to carbon dioxide in an enzyme s active site would prevent re-addition and promote the forward reaction if the addition product is itself sufficiently unstable. 

Claisen reactions involving acetyl-CoA are made even more favourable by first converting acetyl-CoA into malonyl-CoA by a carboxylation reaction with CO2 using ATP and the coenzyme biotin (Figure 2.9). ATP and CO2 (as bicarbonate, HC03-) form the mixed anhydride, which car-boxy lates the coenzyme in a biotin-enzyme complex. Fixation of carbon dioxide by biotin-enzyme complexes is not unique to acetyl-CoA, and another important example occurs in the generation of oxaloacetate from pyruvate in the synthesis of glucose from non-carbohydrate sources... 

Although the fatty acid oxidation scheme works neatly for even-numbered chain lengths, it can t work completely for fatty acids that contain an odd number of carbons. P-oxidation of these compounds leads to propionyl-CoA and acetyl-CoA, rather than to two acetyl-CoA at the final step. The propionyl-CoA is not a substrate for the TCA cycle or other simple pathways. Propionyl-CoA undergoes a carboxylation reaction to form methylmalonyl-CoA. This reaction requires biotin as a cofactor, and is similar to an essential step in fatty acid biosynthesis. Methylmalonyl-CoA is then isomerized by an epimerase and then by methylmalonyl-CoA mutase—an enzyme that uses Vitamin Bi2 as a cofactor—to form succinyl-CoA, which is a TCA-cycle intermediate. 

Vitamin B12 is essential for the methylmalonyl-CoAmutase reaction. Methylmalonyl-CoA mutase is required during the degradation of odd-chain fatty acids and of branched-chain amino acids. Odd-chained fatty acids lead to propionyl-CoA as the last step of P-oxida-tion. Methylmalonyl-CoA can be derived from propionyl-CoA by a carboxylase reaction similar to that of fatty acid biosynthesis. The cofactor for this carboxylation reaction is biotin, just as for acetyl-CoA carboxylase. The reaction of methylmalonyl-CoA mutase uses a free radical intermediate to insert the methyl group into the dicar-boxylic acid chain. The product is succinyl-CoA, a Krebs cycle intermediate. The catabolisms of branched-chain lipids and of the branched-chain amino acids also require the methylmalonyl-CoA mutase, because these pathways also generate propionyl-CoA. 

The enzymatic role of the thieno[3,4-d]imidazole derivative biotin as the coenzyme for the transfer of carbon dioxide in carboxylation reactions is well established. Strong acidic hydrolysis of biocytin, a naturally occurring complex of biotin, yields biotin and L-lysine. 

The main metabolic function of vitamin K is as the coenzyme in the carboxyla-tion ofprotein-incorporated glutamate residues to yield y -carboxyglutamate -a unique type of carboxylation reaction, clearly distinct from the biotin-dependent carboxylation reactions (Section 11.2.1). 

Biotin is the coenzyme in a small number of carboxylation reactions in mammalian metabolism and some decarboxylation and transcarboxylation reactions in bacteria. Although the biotin-dependent enzymes are cytosolic and mitochondrial, about 25% of tissue biotin is found in the nucleus, much of it bound as thioesters to histones. Biotin has two noncoenzyme functions induction of enzyme synthesis and regulation of the cell cycle. 

The role of ATP in the carboxylation of biotin is unclear. It is possible that biotin is O-phosphorylated during the carboxylation reaction. However, evidence suggests that the immediate reactive species that carboxylates biotin is carboxyphosphate, as in the (biotin-independent) reaction of carbamyl phosphate synthetase in urea and pyrimidine synthesis. 

Steady-state kinetic analysis shows that biotin-dependent reactions proceed by way of a two-site ping-pong mechanism the two-part reactions are catalyzed at distinct sites in the enzyme. These sites may be on the same or different polypeptide chains in different biotin-dependent enzymes. The e-amino linkage of lysine to the side chain of biotin in biocytin allows considerable movement of the coenzyme - the distance from C-2 of lysine to C-5 of biotin is IdA, thus allowing movement of biotin between the carboxylation and carboxyltransfer sites. 

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