Pyridoxal phosphate as a cofactor

The active form of vitamin Be, pyridoxai phosphate, is the most important coenzyme in the amino acid metabolism (see p. 106). Almost all conversion reactions involving amino acids require pyridoxal phosphate, including transaminations, decarboxylations, dehydrogenations, etc. Glycogen phosphory-lase, the enzyme for glycogen degradation, also contains pyridoxal phosphate as a cofactor. Vitamin Be deficiency is rare. 

This enzyme [EC 4.1.1.19] uses pyridoxal phosphate as a cofactor in catalyzing the conversion of arginine to carbon dioxide and agmatine. 

This enzyme [EC 5.1.1.9] catalyzes the interconversion of L- and D-arginine. The enzyme requires pyridoxal phosphate as a cofactor. 

This enzyme [EC 4.3.1.9] catalyzes the following reaction involving pyridoxal phosphate as a cofactor D-glucosam-inate = 2-dehydro-3-deoxy-o-gluconate -f NH3. 

The principal pathways for the biogenesis and metabolism of histamine are well known. Histamine is formed by decarboxylation of the amino acid, L-histidine, a reaction catalyzed by the enzyme, histidine decarboxylase. This decarboxylase is found in both mammalian and non-mammalian species. The mammalian enzyme requires pyridoxal phosphate as a cofactor. The bacterial enzyme has a different pH optimum and utilizes pyruvate as a cofactor (26.27). 

D-Alanine is found in bacterial cell wall peptidogly-can. l-Alanine is converted to D-alanine by a racemase that contains pyridoxal phosphate as a cofactor. The racemiza-tion is followed by the formation of a D-alanyl-D-alanine dipeptide, which is accompanied by the conversion of ATP to ADP. The dipeptide is subsequently incorporated into the glycopeptide (see fig. 16.16). 

Transaminations involve moving a a-amino group from a donor a-amino acid to the keto carbon of an acceptor a-keto acid. These reversible reactions are catalyzed by a group of intracellular enzymes known as transaminases (aminotransferases), which employ covalently bound pyridoxal phosphate as a cofactor. 

Amines are produced by decarboxylation of amino acids in reactions that utilize pyridoxal phosphate as a cofactor. 

ALAS is the initial enzyme of the pathway and catalyzes the formation of ALA from succinyl-CoA and glycine. The enzyme is mitochondrial and requires pyridoxal phosphate as a cofactor, which forms a Schiff base with the amino group of glycine at the enzyme surface. The carbanion of the Schiff base displaces Co enzyme A from succinyl-CoA with the formation of a-amino-P-ketoadipic acid, which is then... 

The first step in the catabolism of most amino acids is the transfer of the o-amino group from the amino acid to a-ketoglutarate (tx-KG). This process is catalyzed by transaminase (aminotransferase) enzymes that require pyridoxal phosphate as a cofactor. The products of this reaction are glutamate (Glu) and the a-ketoacid analog of the amino acid destined for catabolic breakdown. For example, aspartate is converted to its a-keto analog, oxalo-acetate, by the action of aspartate transaminase (AST), which also produces Glu from a-KG. The transamination process is freely reversible, and the direction in which the reaction proceeds is dependent on the concentrations of the reactants and products. These reactions do not effect a net removal of amino nitrogen the amino group is only transferred from one amino acid to another. 

H) 4-Amino-4-deoxychorismate lyase (EC 4.1.3.38) PabC protein (Figure 2, 1) catalyzes the elimination of pyruvate (21) from 4-amino-4-deoxychorismate (20). The enzyme utilizes pyridoxal phosphate as a cofactor. The reaction mechanism shown in Figure 4 implies that pyridoxal phosphate forms a Schiff base (23) with the substrate, 4-amino-4-deoxychorismate. Abstraction of a proton from C-4 of the amino-4-deoxychorismate moiety is believed to result in a shift of the imine bond. Pyruvate can then be eliminated from the Schiff base form 23, and the pyridoxal phosphate moiety can be transferred back to a lysine residue (specifically, lysine 159 of coli PabC protein) under liberation of 4-amino benzoate (14) as shown by X-ray crystallography (Figure 4). ... 

ACC synthase activity which utilises AdoMet as a specific substrate and 5 -pyridoxal phosphate as a cofactor was soon detected in extracts of ripe tomato fruits [34,35] and auxin-treated stems [32,36], and later in many other ethylene producing tissues. In tissues... 

Conversion of serine to glycine. This reaction requires tetrahydrofolate as an acceptor of a methylene group from Ser and utilizes pyridoxal phosphate as a cofactor. It results in the formation of 5,10-CH PteGlu, an essential coenzyme for the synthesis of thymidylate. 

Fig. 38.5. Summary of the sources of NH4 for the urea cycle. All of the reactions are irreversible except glutamate dehydrogenase (GDH). Only the dehydratase reactions, which produce NH4 from serine and threonine, require pyridoxal phosphate as a cofactor. The reactions that are not shown occurring in the muscle or the gut can all occur in the liver, where the NH4 generated can be converted to urea. The purine nucleotide cycle of the brain and muscle is further described in Chapter 41.

The transamination of P-aminoisobutyrate to form methylmalonate semialdehyde requires pyridoxal phosphate as a cofactor. This reaction is similar to the conversion of ornithine to glutamate y-semialdehyde. Then NAD+ serves as an electron acceptor for the oxidation of methylmalonate semialdehyde to methylmalonate. The conversion of methylmalonate to methylmalonyl CoA requires coenzyme A. The final reaction, in which methylmalonyl CoA is converted to succinyl CoA, is catalyzed by methylmalonyl CoA mutase, an enzyme that contains a derivative of vitamin B12 as its coenzyme. 

In biochemical parlance, these systems are called mutases, or sometimes isomerases. When Z = OH and Y = OH or NHj, the product eliminates an aldehyde and either HjO or NH3 so that the process is irreversible. Such systems sometimes are referred to as eliminases, dehydrases or ammonia-lyases. Examples of these various types of systems are shown by the first five examples in Figure 8.3, where (CoA)—S represents coenzyme A. It should be noted that the amino mutases, such as ornithine amino mutase, also require pyridoxal phosphate as a cofactor. 

To emphasize some of the common features, these systems have been separated into three classes Class I are the mutases, such as glutamate mutase, in which a C—C bond is broken, and all exist in the base-off/hist-on form Class II are the eliminases which involve C—O or C—N bond cleavage and ribonuleotide triphosphate reductase, and are in the base-on form Class III are the amino mutases which interchange H and NH2 and require pyridoxal phosphate as a cofactor. The structure of one member of this class has b n determined and found to be in the base-off/hist-on form. The pyridoxal phosphate is covalently bonded to a lysine, Lys-NHj, of the peptide, as shown in the following reaction ... 

Model reactions of this type have been studied in which the catalyst is pyridoxal plus a metal. The enzymatic reactions all appear to use pyridoxal phosphate as a cofactor, and in the case of a bacterial system, Mn" is also required. A major difference between the enzymatic and the model reactions is the requirement for a folic acid cofactor in the former. The formation of glycine and acetaldehyde from L-threonine and L-allo-threonine has been described by Lin and Greenberg. Their partially purified enzyme, threonine aldolase, was not shown to require any cofactors, and the reaction was not reversed. This is in contrast to the results of nonenzymatic experiments in which pyridoxal and a metal catalyze the reversible cleavage of threonine. 

Siibstitution. A modification of the jS-elimination reaction may be substitution of a new group. This has been proposed as the mechanism of action of tryptophan desmolase, in which indole is substituted for the OH of serine. This reaction was found to proceed to a measurable extent in model reactions, in spite of the competing 8-elimination reactions of both serine and tryptophan and other side reactions of indole compounds. Additional substitution reactions of biological significance are the formation of cystathionine from homocysteine and serine and the formation of (Sf-methylcysteine from methyl mercaptan and serine. These reactions are catalyzed by enzymes that require pyridoxal phosphate as a cofactor. 

Phenol is formed from L-tyrosine and its derivatives in some bacterial cultures not through a stepwise degradation of the molecule but through primary fission of the side chain. The L-tyrosine inducible enzyme L-tyrosine phenol lyase has been prepared in crystalline form from cell extracts of Escherichia intermedia A-21 and a molecular weight of 170000 was estimated . The enzyme catalyses the stoichiometric conversion of L-tyrosine (5) to phenol (20), pyruvate (21) and ammonia in the presence of added pyridoxal phosphate as a cofactor. Brot, Smit and Weissbach have described... 

An amino oxidase that catalyzes the oxidation of peptidyllysine to form a-aminoadipic-6-semialdehyde (allysine) has been isolated from bovine aorta (Rucker et al., 1970) and chick aorta (Harris et al, 1974). This enzyme has been given the name lysyl oxidase to differentiate it from other amine oxidases. Lysyl oxidase contains copper and apparently requires pyridoxal phosphate as a cofactor (Chou et al., 1970). 

The transamination reaction is important biologically in amino acid metabolism. Simple aldehydes are rare in biological systems and are mostly masked as imines. Biochemists often refer to them as Schiff bases, which are a special class of aldehyde imine where the nitrogen atom is substituted by an alkyl or aryl group. The transamination reaction interconverts amino and carbonyl functionalities (Figure 14.32). The enzymes involved in the process are called transaminases, and they require pyridoxal phosphate as a cofactor. 

Tryptophanase is an enzyme which catalyzes the stoichiometric interconversion of L-tryptophan and pyruvate, ammonia and indole it requires pyridoxal phosphate as a cofactor. The enzyme from Proteus rettgeri has been isolated in a crystalline state and its catalytic properties were investigated. The enzyme catalyzes a series of oc,p-elimination, P-replacement and the reversal of oc,P-elimination reactions. 

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