Other pyridoxal phosphate-catalyzed reactions

Common stereochemical features of pyridoxal phosphate enzymes 

Finally, the concept that the proteins of different PLP enzymes determine reaction specificity by controlling the conformations of critical bonds of the PLP- 

Work from the authors laboratories has been supported by the National Institutes of Health (Research Grant GM 18852 to H.G.F.) and by the Natural Sciences and Engineering Research Council of Canada (Grant NSERC A 0845 to J.C.V.). 

1 Jencks, W.P. (1969) Catalysis in Chemistry and Enzymology, McGraw-Hill, New York, pp. 133-146. 

4 Walsh, C. (1979) Enzymatic Reaction Mechanisms, W.H. Freeman, San Francisco, pp. 777-833. 

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The stereochemistry of pyridoxal phosphate-catalyzed reactions was last summarized comprehensively in 1971 by Dunathan [2], who outlined many of the basic concepts in this field. Aspects of PLP catalysis have been discussed in other reviews on enzyme reaction stereochemistry (e.g., [9]), and a brief review, emphasizing their own work, has recently been published by the present authors [ 10]. Much work has been done in this field during the past ten years, most of it supporting the concepts laid out in Dunathan s review, often refining the picture and sometimes modifying the original ideas. 

Transamination Reactions of Other Pyridoxal Phosphate Enzymes Inaddition to theirmainreactions, anumberofpyridoxalphosphate-dependent enzymes also catalyze the half-reaction of transamination. Such enzymes include serine hydroxymethyltransferase (Section 10.3.1.1), several decarboxylases, and kynureninase (Section 8.3.3.2). 

Effective electron sinks. Pyridoxal phosphate stabilizes carbanionic intermediates by serving as an electron sink. Which other prosthetic group catalyzes reactions in this way ... 

While metal ions catalyze the reaction in aqueous systems, they are not an absolute requirement for the reaction (875-877). The enzyme-catalyzed transamination systems [and other pyridoxal phosphate requiring enz3rme systems (87S)] involve, in all probability, a similar mechanism (874) ... 

Biotin (5) is the coenzyme of the carboxylases. Like pyridoxal phosphate, it has an amide-type bond via the carboxyl group with a lysine residue of the carboxylase. This bond is catalyzed by a specific enzyme. Using ATP, biotin reacts with hydrogen carbonate (HCOa ) to form N-carboxybiotin. From this activated form, carbon dioxide (CO2) is then transferred to other molecules, into which a carboxyl group is introduced in this way. Examples of biotindependent reactions of this type include the formation of oxaloacetic acid from pyruvate (see p. 154) and the synthesis of malonyl-CoA from acetyl-CoA (see p. 162). 

This enzyme [EC 2.3.1.37] catalyzes the reaction of suc-cinyl-CoA with glycine to yield 5-aminolevulinate, coenzyme A, and carbon dioxide. Pyridoxal phosphate is used as a cofactor in this reaction. In mammals, the enzyme isolated from erythrocytes is genetically distinct from that in other tissues. 

This pyridoxal-phosphate-dependent enzyme [EC 4.4.1.10] catalyzes the reaction cysteine with sulfite to produce cysteate and H2S. The enzyme can also catalyze the reaction of two cysteines (thereby producing lanthio-nine) as well as other alkyl thiols as substrates. 

This enzyme [EC 4.1.99.1], also known as L-tryptophan indole-lyase, catalyzes the hydrolysis of L-tryptophan to generate indole, pyruvate, and ammonia. The reaction requires pyridoxal phosphate and potassium ions. The enzyme can also catalyze the synthesis of tryptophan from indole and serine as well as catalyze 2,3-elimination and j8-replacement reactions of some indole-substituted tryptophan analogs of L-cysteine, L-serine, and other 3-substituted amino acids. 

The amino acid and nucleotide biosynthetic pathways make repeated use of the biological cofactors pyridoxal phosphate, tetrahydrofolate, and A-adenosylmethionine. Pyridoxal phosphate is required for transamination reactions involving glutamate and for other amino acid transformations. One-carbon transfers require S-adenosyhnethionine and tetrahydrofolate. Glutamine amidotransferases catalyze reactions that incorporate nitrogen derived from glutamine. 

The reactions catalyzed by transaminases are anergonic as they do not require an input of metabolic energy. They are also freely reversible, the direction of the reaction being determined by the relative concentrations of the amino acid-keto acid pairs. Pyridoxal phosphate is not just used as the coenzyme in transamination reactions, but is also the coenzyme for several other reactions involving amino acids including decarboxylations, deaminations, racemizations and aldol cleavages. 

In a number of enzymes that catalyze reactions that might be assumed to be pyridoxal phosphate-dependent, pyruvate provides the reactive carbonyl group (Section 9.8.1). Other enzymes have reactive carbonyl groups provided by a variety of quinones. One of these quinones, pyrrolidone quino-linequinone, may be a dietary essential, although no mammalian enzymes... 

A number of enzymes contain other carbonyl compounds that catalyze reactions in the same way as does pyridoxal phosphate or that catalyze redox reactions. Such compounds include pyruvate (Section 9.8.1) pyrroloquino-line quinone, which may be a dietary essential (Section 9.8.2) and a variety... 

Serine Hydroxymethyltransferase Serinehydroxymethyltrans-ferase is a pyridoxed phosphate-dependent aldolase that catalyzes the cleavage of serine to glycine and methylene-tetrahydrofolate (as shown in Figure 10.5). Serine is the major source of one-carbon substituted folates for biosynthetic reactions. At times of increeised cell proliferation, the activities of serine hydroxymethyltransferase emd the enzymes of the serine biosynthetic pathway cue increased. The other product of the reaction, glycine, is also required in increased cimounts under these conditions (for de novo synthesis of purines). 

A transferase that also has aldolase activity and has been used to prepare a number of chiral compounds is the enzyme serine hydroxymethyltransferase (SHMT) (EC 2.1.2.1). This enzyme, also known as threonine aldolase, catalyzes the physiological reaction of the interconversion of serine and glycine with pyridoxal phosphate (PLP) and tetrahydrofolate (FH4) as the shuttling cofactor of the C-1 unit. It also catalyzes a number of other reactions, some of which are independent of PLP and FH4 [72]. The SHMT-catalyzed aldolase reaction generates two stereocenters, which it does stereospecifically at the (/.-carbon, whereas it is less strict at the [l-carbon (Scheme 13). Nevertheless, this enzyme from porcine liver, Escherichia coU and Candida humicola (threonine aldolase) has been used to prepare a number of P-hydroxy-a-amino acids [73-76],... 

The glycolytic pathway includes three such reactions glucose 6-phosphate isomer-ase (1,2-proton transfer), triose phosphate isomerase (1,2-proton transfer), and eno-lase (yS-elimination/dehydration). The tricarboxylic acid cycle includes four citrate synthase (Claisen condensation), aconitase (j5-elimination/dehydration followed by yS-addition/hydration), succinate dehydrogenase (hydride transfer initiated by a-proton abstraction), and fumarase (j5-elimination/dehydration). Many more reactions are found in diverse catabolic and anabolic pathways. Some enzyme-catalyzed proton abstraction reactions are facilitated by organic cofactors, e.g., pyridoxal phosphate-dependent enzymes such as amino acid racemases and transaminases and flavin cofactor-dependent enzymes such as acyl-C-A dehydrogenases others. 

Enzymes catalyze almost every metabolic reaction in extant cells. A few tmusually facile reactions, such as cyclization of L-glutamate 7-semialdehyde to form pyrroline-5-carboxylate in the proline biosynthesis pathway and decarboxylation of 2-amino-3-oxo-4-phosphonooxybutyrate in the pyridoxal phosphate (PLP) synthesis pathway, do not require acceleration to satisfy the demands of the cell. For all other reactions, catalysis is required because the rates of nonenzymatic reactions are very slow. Modern enzymes are marvelous catalysts. They accelerate reactions by up to 20 orders of magnitude, prevent side reactions of reactive intermediates, and catalyze stereoselective and stereospecific reactions. Further, they are often exquisitely regulated by small molecule ligands. 

Schiff base formation between pyridoxal phosphate and amino acids are the basis for most enzymatic transformations of amino acids including transamination, decarboxylation, and racemization. Schiff bases formed between amino acids and pyridoxal phosphate or other heteroaromatic or aromatic aldehydes are, however, not only transformed enzymatically, but can, without enzymatic catalysis, undergo a large number of reactions, although at lower rate and/or higher temperatures than those for the corresponding enzymatic reactions. The enzymatic reactions require metal ions as cofactors and in analogy the nonenzymatic reaction are also catalyzed by metal ions, most effectively by cupric ions. 

As noted above, cystathionine formation is the other major fate of methionine. The condensation of homocysteine with serine is catalyzed by the vitamin requiring enzyme cystathionine P-synthase. In the last step of the transsulfuration sequence, cystathionine undergoes cleavage to cysteine and a-ketobutyrate in yet another enzyme reaction that requires pyridoxal phosphate. 

Extensive research work has gone into modification of proteins, not for commercial applications but for academic reasons. Thus, for instance, Frances et al. developed a new reaction that introduces single reactive ketones or aldehydes at the N-terminal groups of protein when the proteins are mixed with pyridoxal phosphate [44]. The researchers also developed a palladium-catalyzed allylic alkylation that attaches long lipid tails to proteins, a process that can be used to customize the solubihty of enzymes, antibodies, viral capsids, and other proteins. 

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. 

Support for this enzymic desulfhydration came from the work of Metzler and Snell (72), who proposed a detailed chemical mechanism of desulfhydration in model experiments in the presence of pyridoxine and a metal ion. Similar enzyme models were proposed by others (73). The enzymic aspect of this reaction is not entirely satisfactory however, ce relatively little is known of the desulfhydrase enzyme, either derived from the liver (74) or from bacteria (75). In addition several pyridoxal phosphate-protein enzymes can catalyze cysteine desulfhydration (see Section IV). 

The apoenzyme, the protein itself, has also been called a colloidal carrier. This terminology is based largely on Willstatter s idea that the molecule of an enzyme consists of a colloidal carrier and an active group with purely chemical activity. Today the concept of a colloidal carrier must be rejected, because it implies that the protein component is inactive, and we now know that it is not. For one thing, the protein component decides the substrate specificity, it determines which substances react and which do not. In many cases this same protein component also determines the direction of the reaction reaction specificity), in other words, which reaction out of the numerous possible ones is undergone by the substrate. This point becomes especially clear in cases where the same coenzyme, i.e. the same prosthetic group, catalyzes different reactions, as does, for instance, pyridoxal phosphate (see Chapt. VIII-4) or heme (see Chapt. IX-3). 

The mechanism of this enzymic reaction, catalyzed by pyridoxal phosphate, has been discussed above as pathway b (Section 4). The net result is the production of CO2 and a primary amine, whose formula can easily be derived from the amino acid which was decarboxylated. Amines of this type are called biogenic amines (Guggenheim) many of them possess a strong pharmacologic effect, and others are important as precursors of hormones and as components of coenzymes and other active substances. 

This enzyme [EC 2.7.1.35] (also known as pyridoxine kinase, pyridoxamine kinase, and vitamin kinase) catalyzes the reaction of ATP with pyridoxal to produce ADP and pyridoxal 5 -phosphate. Pyridoxine, pyridoxamine, and various other derivatives can also act as substrates. 

Tryptophanase (L-tryptophan indole-lyase (deaminating) EC 4.1.99.1) belongs to the family of the pyridoxal 5 -phosphate (PLP)-dependent enzymes. It serves in vivo to degrade L-tryptophan, is induced by L-tryptophan, and found in various bacteria, particularly in enteric species. Tryptophanase catalyzes a,/3-elimination1 and /3-replacement reactions on interaction with L-tryptophan and various other /3-substituted amino acids2 ... 

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