Biotin-dependent carboxylation

Most biotin-dependent carboxylations (Table 18.5) use bicarbonate as the carboxylating agent and transfer the carboxyl group to a substrate earbanion. Bicarbonate is plentiful in biological fluids, but it is a poor electrophile at carbon and must be activated for attack by the substrate earbanion. 

FIGURE 18.32 Biotin is covalently linked to a protein via the e-amino group of a lysine residue. The biotin ring is thus tethered to the protein by a 10-atom chain. It functions by carrying carboxyl groups between distant sites on biotin-dependent enzymes. 

Fatty acids with odd numbers of carbon atoms are rare in mammals, but fairly common in plants and marine organisms. Humans and animals whose diets include these food sources metabolize odd-carbon fatty acids via the /3-oxida-tion pathway. The final product of /3-oxidation in this case is the 3-carbon pro-pionyl-CoA instead of acetyl-CoA. Three specialized enzymes then carry out the reactions that convert propionyl-CoA to succinyl-CoA, a TCA cycle intermediate. (Because propionyl-CoA is a degradation product of methionine, valine, and isoleucine, this sequence of reactions is also important in amino acid catabolism, as we shall see in Chapter 26.) The pathway involves an initial carboxylation at the a-carbon of propionyl-CoA to produce D-methylmalonyl-CoA (Figure 24.19). The reaction is catalyzed by a biotin-dependent enzyme, propionyl-CoA carboxylase. The mechanism involves ATP-driven carboxylation of biotin at Nj, followed by nucleophilic attack by the a-carbanion of propi-onyl-CoA in a stereo-specific manner. 

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). 

O Pyruvate undergoes a biotin-dependent carboxylation on the methyl group to give oxaloacetate... 

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). 

Certain enzymes catalyze their reactions by way of a multisite mechanism in which the covalently linked intermediate is attached to a long arm that swings from one subsite to another subsite within the enzyme. In some cases, the covalently tethered intermediate can actually be transferred between subunits that form the active site. An example is Propionibacterium shermanii transcarboxylase an enzyme that catalyzes the biotin-dependent conversion of methylmalonyl-CoA and pyruvate to propionyl-CoA and oxaloacetate. Carboxylated biotin allows the two catalytic subsites to operate on the same reaction intermediate. 

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). 

When pyruvate with a chiral methyl group is carboxylated by pyruvate carboxylase the configuration at C-3 is retained. The carboxyl enters from the 2-si side, the same side from which the proton (marked H ) was removed to form the enolate anion (Eq. 14-12). Comparable stereochemistry has been established for other biotin-dependent enzymes.64 65... 

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. 

In this cycle, one molecule of acetyl-CoA is formed from two molecules of bicarbonate (Figure 3.5). The key carboxylating enzyme is the bifunctional biotin-dependent acetyl-CoA/propionyl-CoA carboxylase. In Bacteria and Eukarya, acetyl-CoA carboxylase catalyzes the first step of fatty acid biosynthesis. However, Archaea do not contain fatty acids in their lipids, and acetyl-CoA carboxylase cannot serve as the key enzyme of fatty acid synthesis rather, it is responsible for autotrophy. 

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. 

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. 

Figure 29.6 MECHANISM Mechanism of step 3 in Figure 29.5, the biotin-dependent carboxylation of acetyl CoA to yield malonyl CoA.

How is oxaloacetate replenished Mammals lack the enzymes for the net conversion of acetyl CoA into oxaloacetate or any other citric acid cycle intermediate. Rather, oxaloacetate is formed by the carboxylation of pyruvate, in a reaction catalyzed by the biotin-dependent enzyme pyruvate carboxylase. 

FIGURE 9,32 Structure of biotin. Biotin is used as the carrier of carboxyl groups in carboxyialion reactions. In an ATl -dcpendcnt reaction, bicarbonate is transferred to biotin, generating carboxy-biotin. The carboxyl group is bound to the I -nitrogpn. The second half of biotin-dependent carboxylation reactions involves transfer of the carboxyl group to the substrate. 

STEP 1 P3mivate undergoes biotin-dependent carboxylation to give oxaloacetate. 

Chemical and catalytic mechanisms of carboxyl transfer in biotin-dependent enzymes 02ACR113. 

Biotin (Fig. 8.40) is essential, a normal constituent of the diet, and required for four biotin-dependent carboxylation reactions. Eating raw egg white can induce a deficiency. 

The committed (rate-controlling) step is the biotin-dependent carboxylation of acetyl-CoA by acetyl-CoA carboxylase. Important allosteric effectors are citrate (positive) and long-chain acyl-CoA derivatives (negative). 

Acetyl-CoA carboxylase is a biotin-dependent enzyme. It has been purified from microorganisms, yeast, plants, and animals. In animal cells, it exists as an inactive pro-tomer (M.W. 400,000) and as an active polymer (M.W. 4-8 million). The protomer contains the activity of biotin carboxylase, biotin carboxyl carrier protein (BCCP), transcarboxylase, and a regulatory allosteric site. Each protomer contains a biotinyl group bound in amide linkage to the e-amino group of a lysyl residue. 

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