Biotin cycle

Figure 12-4. The biotin cycle shows the actions of biotin holocarboxylase synthetase in biotinylating carboxylases and of biotinidase in cleaving biocytin, thereby recycling biotin.

Lipoic acid exists as a mixture of two structures a closed-ring disulfide form and an open-chain reduced form (Figure 18.33). Oxidation-reduction cycles interconvert these two species. As is the case for biotin, lipoic acid does not often occur free in nature, but rather is covalently attached in amide linkage with lysine residues on enzymes. The enzyme that catalyzes the formation of the lipoamide nk.2Lg c requires ATP and produces lipoamide-enzyme conjugates, AMP, and pyrophosphate as products of the reaction. 

Pyruvate carboxylase is the most important of the anaplerotie reactions. It exists in the mitochondria of animal cells but not in plants, and it provides a direct link between glycolysis and the TCA cycle. The enzyme is tetrameric and contains covalently bound biotin and an Mg site on each subunit. (It is examined in greater detail in our discussion of gluconeogenesis in Chapter 23.) Pyruvate carboxylase has an absolute allosteric requirement for acetyl-CoA. Thus, when acetyl-CoA levels exceed the oxaloacetate supply, allosteric activation of pyruvate carboxylase by acetyl-CoA raises oxaloacetate levels, so that the excess acetyl-CoA can enter the TCA cycle. 

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. 

Biotin also has a role in regulation of the cell cycle, acting to biotinylate key nuclear proteins. 

Carboxylation of propionyl-CoA is accomplished by propionyl-CoA carboxylase (biotin, which is the carboxyl group carrier, serves as a coenzyme for this enzyme) the presence of ATP is also required. The methylmalonyl-CoA formed is converted by methylmalonyl-CoA mutase (whose coenzyme, deoxyadenosylcobalamin, is a derivative of vitamin B]2) to succinyl-CoA the latter enters the Krebs cycle. 

Figure 12.6 Free-energy cycle associated with the binding of biotin and fluorobiotin analogs to avidin. What issues arise in choosing a force field for explicit simulation of these systems What methods are better suited to computing the vertical legs of the cycle and what methods the horizontal ones ...

The formal transfer of an oxygen atom is one way of describing the function of the Mo site in molybdoenzymes.5 The formation of dinuclear reduction products is a complication that causes difficulty in trying to model the mononuclear site.5,165 This difficulty can be overcome by the use of sterically demanding ligands that prevent the formation of the dinuclear complex,73 79,125 176 177 For example, the cycle shown in Scheme 3 can be effected without dimerization. Further, in this case DMSO and the enzyme substrate biotin sulfoxide, can serve as the oxo donor to form the Movl dioxo complex during the catalytic cycle.79,177 The Movl complex involved is discussed structurally above (Figure 7). 

The reaction involves biotin as a carrier of activated HCO3 (Fig. 14-18). The reaction mechanism is shown in Figure 16-16. Pyruvate carboxylase is the first regulatory enzyme in the gluconeogenic pathway, requiring acetyl-CoA as a positive effector. (Acetyl-CoA is produced by fatty acid oxidation (Chapter 17), and its accumulation signals the availability of fatty acids as fuel.) As we shall see in Chapter 16 (see Fig. 16-15), the pyruvate carboxylase reaction can replenish intermediates in another central metabolic pathway, the citric acid cycle. 

When intermediates are shunted from the citric acid cycle to other pathways, they are replenished by several anaplerotic reactions, which produce four-carbon intermediates by carboxylation of three-carbon compounds these reactions are catalyzed by pyruvate carboxylase, PEP carboxykinase, PEP carboxylase, and malic enzyme. Enzymes that catalyze carboxylations commonly employ biotin to activate C02 and... 

Propionyl-CoA is first carboxylated to form the d stereoisomer of methylmalonyl-CoA (Pig. 17—11) by propionyl-CoA carboxylase, which contains the cofactor biotin. In this enzymatic reaction, as in the pyruvate carboxylase reaction (see Pig. 16-16), C02 (or its hydrated ion, HCO ) is activated by attachment to biotin before its transfer to the substrate, in this case the propionate moiety. Formation of the carboxybiotin intermediate requires energy, which is provided by the cleavage of ATP to ADP and Pi- The D-methylmalonyl-CoA thus formed is enzymatically epimerized to its l stereoisomer by methylmalonyl-CoA epimerase (Pig. 17-11). The L-methylmal onyl -CoA then undergoes an intramolecular rearrangement to form succinyl-CoA, which can enter the citric acid cycle. This rearrangement is catalyzed by methylmalonyl-CoA mutase, which requires as its coenzyme 5 -deoxyadenosyl-cobalamin, or coenzyme Bi2, which is derived from vitamin B12 (cobalamin). Box 17—2 describes the role of coenzyme B12 in this remarkable exchange reaction. 

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). 

To replace losses, oxaloacetate can be synthesized from pyruvate and C02 in a reaction that uses ATP as an energy source. This is indicated by the heavy gray line leading downward to the right from pyruvate in Fig. 10-1 and at the top center of Fig. 10-6. This reaction depends upon yet another coenzyme, a bound form of the vitamin biotin. Pyruvate is formed from breakdown of carbohydrates such as glucose, and the need for oxaloacetate in the citric acid cycle makes the oxidation of fats in the human body dependent on the concurrent metabolism of carbohydrates. 

Biotin enzymes are believed to function primarily in reversible carboxvlahon-decarboxylation reactions. For example, a biotin enzyme mediates the carboxylation of propionic acid to methylmalonic add, which is subsequently converted to succinic acid, a dtric acid cycle intermediate. A vitamin Bl2 coenzyme and coenzyme A are also essential to this overall reaction, again pointing out the interdependence of the B vitamin coenzymes. Another biotin enzyme-mediated reaction is the formation of malonyl-CoA by carboxylation of acetyl-CoA ( active acetate ). Malonyl-CoA is believed lo be a key intermediate in fatly add synthesis. 

Vitamin Influences. The involvement of NAD and NADP in many carbohydrate reactions explains the importance of nicotinamide in carbohydrate melaholism. Thiamine, in the form or thiamine pyrophosphate (cocarboxylase), is the cofaclor necessary in the decarboxylation of pyruvic acid, in the iraru-kelolase-calalyzed reactions of the pentose phosphaie cycle, and in the decarboxylation of alpha-keloglutaric acid in the citric acid cycle, among other reactions. Biotin is a hound cofaclor in the fixation of carbon dioxide to form nxalacetic acid from pyruvic acid. Pantothenic acid is a part of the C oA molecule. There are separate alphabetical entries in this volume on the various specific vitamins as well as a review entry on Vitamin. 

RNA catalysis and in vitro selection are ever increasing in scope, and the method presented in Section 8.3.6.1 is by no means the only alternative for separating reacted/active- catalyst complexes. Most research groups have used this type of partitioning procedure, based on some type of biotin-product capture by streptaviclin. Other partitioning methods are possible and this step in the overall RNA catalysis selection cycle is where many new innovations need to occur to advance the field. 

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. 

Thus pyruvate carboxylase generates oxaloacetate for gluconeogenesis but also must maintain oxaloacetate levels for citric acid cycle function. For the latter reason, the activity of pyruvate carboxylase depends absolutely on the presence of acetyl CoA the biotin prosthetic group of the enzyme cannot be carboxy-lated unless acetyl CoA is bound to the enzyme. This allosteric activation by acetyl CoA ensures that more oxaloacetate is made when excess acetyl CoA is present. In this role of maintaining the level of citric acid cycle intermediates, the pyruvate carboxylase reaction is said to be anaplerotic, that is filling up. ... 

The pathway The first committed step in fatty acid biosynthesis is the carboxylation of acetyl CoA to form malonyl CoA which is catalyzed by the biotin-containing enzyme acetyl CoA carboxylase. Acetyl CoA and malonyl CoA are then converted into their ACP derivatives. The elongation cycle in fatty acid synthesis involves four reactions condensation of acetyl-ACP and malonyl-ACP to form acetoacetyl-ACP releasing free ACP and C02, then reduction by NADPH to form D-3-hydroxybutyryl-ACP, followed by dehydration to crotonyl-ACP, and finally reduction by NADPH to form butyryl-ACP. Further rounds of elongation add more two-carbon units from malonyl-ACP on to the growing hydrocarbon chain, until the C16 palmitate is formed. Further elongation of fatty acids takes place on the cytosolic surface of the smooth endoplasmic reticulum (SER). 

In the first five cycles of in-vitro selection, very little (0.1-0.2%) of the total RNA reacted with biotin, predominantly because of the uncatalyzed background reaction. Several potential cofactors, for example Lewis acids, metal ions, a dipeptide compound, and a dipyridyl compound, were present in the reaction mixture. From cycle 6 onwards significant acceleration of the reaction was observed. As a consequence, in the following cycles the selection pressure was increased by shortening the reaction time and reducing the concentration of maleimide. Compared with the starting library a 6500-fold acceleration of the reaction was observed for the enriched pool after cycle 10. 

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. 

PC requires biotin for activity. Biotin is bound to the enzyme via a peptide-like linkage involving e-NH2 groups of certain lysine residues. This type of biotin complex is biocytin (see Chapter 6). Another compound necessary for PC activity is acetyl-CoA, a positive effector. PC is activated as cellular levels of acetyl-CoA increase, as when extensive lipolysis takes place. Acetyl-CoA is produced in large amounts from fatty acids via the /8-oxidation reaction (see Chapter 19). PC can also be considered an anaplerotic reaction, those reactions that replenish crucial intermediates for metabolic pathways. In this case, oxaloacetate, an important intermediate in the Krebs cycle, is replenished by a reaction catalyzed by PC. 

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