Coenzyme formation

Addition to NAD+ and NADPh Many nucleophilic reagents add reversibly at the para (or 4) position (Eq. 15-17) to form adducts having structures resembling those of the reduced coenzymes. Formation of... 

Each subunit is made up of two unequal domains. The active site is at the bottom of a hydrophobic pocket, about 25 A from the protein surface. The non-catalytic zinc, some 25 A away, is near the surface, but is not exposed to solvent. Both sites are on the larger domain, while the smaller domain provides the site for the coenzyme. Formation of the enzyme-NAD(H) complex induces major conformational changes,543 in which there is a rotation of the catalytic domain resulting in a narrowing of the active-site cleft. 

Early evidence for the sequential mechanism proposed by Theorell and Chance 332) has been reviewed in a previous chapter on LADH (1). The requirements of this mechanism are satisfied under certain conditions for primary alcohols and aldehydes but not for secondary alcohols 295,322,333-336). Thus, the first step is the binding of the coenzyme and the last and rate limiting step dissociation of the coenzyme. Formation of the productive ternary complexes E NAD Alc and E NADH Ald have been demonstrated 333,334,337-339). The interconversion of these complexes are not kinetically important for the above-mentioned conditions as required by the mechanism. It has been suggested, however, that this step is rate limiting during different conditions 324,336). Substrate dissociation constants for the ternary complexes have been estimated 340). 

SH is the substrate, PH the product, XH2 the vitamin Bi2 coenzyme, and I XHs an intermediate complex derived from the substrate and coenzyme. Formation of the intermediate may involve the breaking of the carbon-cobalt bond and the formation of 5 -deoxyadenosine from the adenosyl moiety of the coenzyme. One of the methyl hydrogens of 5 -deoxyadenosine is one of the C-1 hydrogens of the substrate. 

Since the coenzyme from vitamin is required in two distinct enzyme reactions, i.e., remethylation of homocystine and catabolism of methylmalonic acid, the fundamental defect must involve a step in converting to its coenzymes. Formation of both deoxyadenosyl B and methyl B requires a prior reductive step catalyzed by cobalamin reductase, which appears to be the defective enzyme in this variant (Hogervorst et al., 2002) (Fig. 20.4). 

Further results showed a certain, but again limited, parallelism between the rate of carbon dioxide evolution from phosphoglyceric acid and the rate of production of coenzyme II (1). Carbon dioxide evolution was increased by magnesium and manganese salts, as also was the quantity of coenzyme II produced. Arsenite strongly inhibited the coenzyme formation in this system also, either with or without the manganous and magnesium ions, but in the former case carbon dioxide evolution was accelerated, and in the latter case it was inhibited. 

Although a variety of oxidizing agents are available for this transformation it occurs so readily that thiols are slowly converted to disulfides by the oxygen m the air Dithiols give cyclic disulfides by intramolecular sulfur-sulfur bond formation An example of a cyclic disulfide is the coenzyme a lipoic acid The last step m the laboratory synthesis of a lipoic acid IS an iron(III) catalyzed oxidation of the dithiol shown... 

Many biological reactions involve initial binding of a carbonyl compound to an enzyme or coenzyme via mine formation The boxed essay Imines in Biological Chemistry gives some important examples... 

Formation of malonyl coenzyme A is followed by a nucleophilic acyl substitution which transfers the malonyl group to the acyl carrier protein as a thioester... 

The four carbon atoms of the butanoyl group originate m two molecules of acetyl coenzyme A Carbon dioxide assists the reaction but is not incorporated into the prod uct The same carbon dioxide that is used to convert one molecule of acetyl coenzyme A to malonyl coenzyme A is regenerated m the decarboxylation step that accompanies carbon-carbon bond formation... 

Carbon-carbon bond formation then occurs between the ketone carbonyl of acetoacetyl coenzyme A and the a carbon of a molecule of acetyl coenzyme A... 

Ammonia reacts with the ketone carbonyl group to give an mine (C=NH) which is then reduced to the amine function of the a ammo acid Both mine formation and reduc tion are enzyme catalyzed The reduced form of nicotinamide adenine diphosphonu cleotide (NADPH) is a coenzyme and acts as a reducing agent The step m which the mine is reduced is the one m which the chirality center is introduced and gives only L glutamic acid... 

Subsequent knowledge of the stmcture, function, and biosynthesis of the foHc acid coenzyme gradually allowed a picture to be formed regarding the step in this pathway that is inhibited by sulfonamides. The biosynthetic scheme for foHc acid is shown in Figure 1. Sulfonamides compete in the step where condensation of PABA with pteridine pyrophosphate takes place to form dihydropteroate (32). The amino acids, purines, and pyrimidines that are able to replace or spare PABA are those with a formation that requkes one-carbon transfer catalyzed by foHc acid coenzymes (5). 

Chelation is a feature of much research on the development and mechanism of action of catalysts. For example, enzyme chemistry is aided by the study of reactions of simpler chelates that are models of enzyme reactions. Certain enzymes, coenzymes, and vitamins possess chelate stmctures that must be involved in the mechanism of their action. The activation of many enzymes by metal ions most likely involves chelation, probably bridging the enzyme and substrate through the metal atom. Enzyme inhibition may often result from the formation by the inhibitor of a chelate with a greater stabiUty constant than that of the substrate or the enzyme for a necessary metal ion. 

In oiological systems, the most frequent mechanism of oxidation is the remov of hydrogen, and conversely, the addition of hydrogen is the common method of reduc tion. Nicotinamide-adenine dinucleotide (NAD) and nicotinamide-adenine dinucleotide phosphate (NADP) are two coenzymes that assist in oxidation and reduction. These cofactors can shuttle between biochemical reac tions so that one drives another, or their oxidation can be coupled to the formation of ATP. However, stepwise release or consumption of energy requires driving forces and losses at each step such that overall efficiency suffers. 

The fonn in which acetate is used in most of its important biochemical reactions is acetyl coenzyme A (Figure 26.1a). Acetyl coenzyme A is a thioester (Section 20.13). Its formation from pyruvate involves several steps and is summarized in the overall equation ... 

We can describe the major elements of fatty acid biosynthesis by considering the formation of butanoic acid from two molecules of acetyl coenzyme A. The machinery responsible for accomplishing this conversion is a complex of enzymes known as fatty acid synthetase. Certain portions of this complex, refened to as acyl carrier protein (ACP), bear a side chain that is structurally similar to coenzyme A. An important early step in fatty acid biosynthesis is the transfer of the acetyl group from a molecule of acetyl coenzyme A to the sulfhydryl group of acyl canier protein. 

As we have seen, the metabolic energy from oxidation of food materials—sugars, fats, and amino acids—is funneled into formation of reduced coenzymes (NADH) and reduced flavoproteins ([FADHg]). The electron transport chain reoxidizes the coenzymes, and channels the free energy obtained from these reactions into the synthesis of ATP. This reoxidation process involves the removal of both protons and electrons from the coenzymes. Electrons move from NADH and [FADHg] to molecular oxygen, Og, which is the terminal acceptor of electrons in the chain. The reoxidation of NADH,... 

Formation of tire active coenzyme 5 -deoxyadeno.sylcobalamin from inactive vitamin Bjg i-s initiated by die action of flavoprotein reducta.se.s. The re.sulting Co. specie.s, dubbed a. supernucleophile, attacks the 5 -carbon of ATP in an unusual adeno.syl transfer. 

Methyl-coenzyme M reductase participates in the conversion of CO2 to CH4 and contains 6-coordinate nickel(II) in a highly hydrogenated and highly flexible porphyrin system. This flexibility is believed to allow sufficient distortion of the octahedral ligand field to produce low-spin Ni" (Fig. 27.7) which facilitates the formation of a Ni -CHs intermediate. 

This thiol-disulfide interconversion is a key part of numerous biological processes. WeTJ see in Chapter 26, for instance, that disulfide formation is involved in defining the structure and three-dimensional conformations of proteins, where disulfide "bridges" often form cross-links between q steine amino acid units in the protein chains. Disulfide formation is also involved in the process by which cells protect themselves from oxidative degradation. A cellular component called glutathione removes potentially harmful oxidants and is itself oxidized to glutathione disulfide in the process. Reduction back to the thiol requires the coenzyme flavin adenine dinucleotide (reduced), abbreviated FADH2. 

Figure 21.9 Formation of the thioester acetyl CoA by nucleophilic acyl substitution reaction of coenzyme A (CoA with acetyl adenylate.

Lactate, a product of glucose catabolism in oxygen-starved muscles, can be converted into pyruvate by oxidation. What coenzyme do you think is needed Write the equation in the normal biochemical format using a curved arrow. 

The sharp flash in the firefly bioluminescence reaction (Fig. 1.6) is due to the formation of a strongly inhibitory byproduct in the reaction. The inhibitor formed is dehydroluciferyl adenylate, having the structure shown below at left. In the presence of coenzyme A (CoA), however, this inhibitory adenylate is converted into dehydroluciferyl-CoA, a compound only weakly inhibitory to luminescence. Thus, an addition of CoA in the reaction medium results in a long-lasting, high level of luminescence (Airth et al., 1958 McElroy and Seliger, 1966 Ford et al., 1995 Fontes et al., 1997, 1998). 

Pyridoxal phosphate mainly serves as coenzyme in the amino acid metabolism and is covalently bound to its enzyme via a Schiff base. In the enzymatic reaction, the amino group of the substrate and the aldehyde group of PLP form a Schiff base, too. The subsequent reactions can take place at the a-, (3-, or y-carbon of the respective substrate. Common types of reactions are decarboxylations (formation of biogenic amines), transaminations (transfer of the amino nitrogen of one amino acid to the keto analog of another amino acid), and eliminations. 

Vitamin B6-coenzyme is involved in a variety of reactions, e.g., in the immune system, gluconeogenesis, erythrocyte fimction, niacin formation, nervous system, lipid metabolism, and in hormone modulation/gene expression [1, 2]. 

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