Pyridoxal phosphate racemases

This enzyme [EC 5.1.1.15], also referred to as 2-amino-hexano-6-lactam racemase, catalyzes the reversible interconversion of the L- and D-stereoisomers of 2-amino-hexano-6-lactam. The enzyme, which utilizes pyridoxal phosphate, will also catalyze the interconversion of 2-aminopentano-5-lactam and 2-amino-3-mercaptohex-ano-6-lactam. The enzyme exhibits a minor aminotransferase activity with certain a-amino acids. 

Inhibition of pyridoxal phosphate enzymes by fluoroalanines has been widely studied. Among the numerous examples, alanine racemase, tyrosine phenol... 

Due to the absence of a hydrogen atom on the a-carbon, the a-fluoroalkyl amino acids (except, of course, the fluoroalanines, vide supra) cannot undergo an elimination of HR Consequently, they are more stable than fluoroalanines and other jS-fluoro amino acids previously described. On the other hand, similar to proteogenic amino acids, jS-fluoro amino acids and a-fluoroalkyl amino acids are generally substrates of pyridoxal phosphate depending on enzymes such as racemases and decarboxylases. When an amino acid is a substrate of such enzymes, the enzyme induces the development of a negative charge on the a-carbon, which can initiate a /(-elimination process. This reaction affords an electrophilic species (Michael acceptor type), which is able to add a nucleophilic residue of the enzyme. This notion of mechanism-based inhibitor is detailed in Chapter 7. 

Among the numerous enzymes that utilize pyridoxal phosphate (PLP) as cofactor, the amino acid racemases, amino acid decarboxylases (e.g., aromatic amino acids, ornithine, glutamic acid), aminotransferases (y-aminobutyrate transaminase), and a-oxamine synthases, have been the main targets in the search for fluorinated mechanism-based inhibitors. Pharmaceutical companies have played a very active role in this promising research (control of the metabolism of amino acids and neuroamines is very important at the physiological level). 

T Although D-amino acids do not generally occur in proteins, they do serve some special functions in the structure of bacterial cell walls and peptide antibiotics. Bacterial peptidoglycans (see Fig. 20-23) contain both D-alanine and D-glutamate. D-Amino acids arise directly from the l isomers by the action of amino acid racemases, which have pyridoxal phosphate as cofactor (see Fig. 18-6). Amino acid racemization is uniquely important to bacterial metabolism, and enzymes such as... 

A number of other racemases and epimerases may function by similar mechanisms. While some amino acid racemases depend upon pyridoxal phosphate (Chapter 14), several others function without this coenzyme. These include racemases for aspartate,113 glutamate,114-1153 proline, phenylalanine,116 and diamino-pimelate epimerase.117 Some spiders are able to interconvert d and l forms of amino acid residues in intact polypeptide chains.118119... 

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). 

Besides a lysine 5,6-aminomutase, Clostridium sticklandii also has a D-ornithine 4,5-aminomutase (EC 5.4.3.5) [78, 79], D-Ornithine is generated from L-ornithine by ornithine racemase [80], The two genes encoding D-ornithine 4,5-aminomutase have been cloned, sequenced, and expressed in E. coli [81]. The enzyme is an a2/ 2-heterotetramer, consisting of 12 800 Da and 82 900 Da subunits. The protein requires Bn and pyridoxal phosphate as cofactors. Similar to the lysine 5,6-aminomutase, a conserved base-ofi)/histidine-on cobalamin binding motif is present in the 82 900 Da protein. 

Like modular PKSs, peptide synthetases also epimerize some substrates and/or intermediates. For example, the starter substrate amino acid of cyclosporin A is D-Ala. Racemization of alanine is not catalyzed by an integrated subunit of cyclosporin A synthetase, but by alanine racemase. This is a separate, pyridoxal phosphate-dependent enzyme [ 193]. In contrast, Grsl and Tycl covalently activate L-Phe as a thioester and subsequently epimerize the amino acid [194]. D-Phe is the only epimer accepted as a substrate for dipeptide formation by Grs2 and Tyc2 [195, 196]. No racemization activity is detected in a pantetheine-deficient mutant of Grsl [197]. Deletion mutagenesis pointed to the requirement of the COOH-terminal part of the module for epimerizing L-Phe to D-Phe [180]. In contrast, the biosynthesis of actinomycin D, a bicyclic chromo-pentapeptide lactone (Fig. 10), involves formation of the dipeptide 6-MHA (methylanthranilic acid)-L-Thr-L-Val prior to epimerization of the L-Val exten-... 

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. 

Pyridoxal phosphate is actually a catalyst for a number of transformations of amino adds that do not involve transamination. It is the catalyst in amino acid racemases, for... 

Racemases are enzymes capable of interconverting D- to L-amino acids. Pyridoxal phosphate has been claimed to play a role as a cofactor in bacterial racemases for alanine, glutamic acid, and methionine, but not in others. It has also been claimed that in mammals the administration of pyridoxine facilitates the use of D-amino acids. 

Except in the case of racemases, pyridoxal phosphate enzymes are stereospecific. This has been illustrated dramatically in experiments with glutamic decarboxylase." The mechanism for decarboxylation postulated earlier involves only electron shifts about the a-carbon, while the a-hydrogen remains fixed. This mechanism was supported when it was found that the a-hydrogen does not exchange with D2O during enzymatic decarboxylation. The resulting mono-D-7-aminobutyric acid was found to... 

Chloroalanine has been found to be an irreversible inhibitor of the pyridoxal phosphate-linked yS-aspartate decarboxylase/ aspartate aminotransferase/ and alanine racemase. The mechanism of inhibition is shown above by Eq. (7) (the sulfate reacts in the same manner) amino-ethane sulfonate irreversibly inhibits pyridoxal phosphate-linked GABA transaminase and L-serine-O-sulfate irreversibly inhibits aspartate aminotransferase. ... 

The existence of enzymes in microorganisms which catalyze the interconversion of D- and L-amino acids is of considerable interest, since the intramolecular transfer of an amino group is apparently involved. The term racemase has been proposed for such enzymes. Two racemases have been reported. Alanine racemase has been shown to be present in a large number of microorganisms and has been partially purified from extracts of S. faecalis. Glutamic acid racemase has been demonstrated in acetone powders of Lactobacillus arabinosus. Both enzymes catalyze the interconversion of the n- and l- forms of their respective substrates. Alanine racemase requires pyridoxal phosphate as coenzyme. Pyri-doxamine phosphate under the conditions employed was not active. Glutamic acid racemase was found not to be affected by the addition of pyridoxal phosphate. However, further studies with purified preparations are necessary before pyridoxal phosphate can be excluded as cofactor for the glutamic acid racemase. Examination of animal tissues under conditions favorable for the demonstration of bacterial alanine racemase failed to reveal any activity. 

In certain bacteria there is a specific nutritional requirement for D-amino acids which are found as components of cell structures or antimetabolites. Bacteria normally meet this need by the conversion of L-amino acids to D-amino acids and in the case of alanine, methionine and tryptophan the evidence suggests that these reactions are directly catalysed by amino acid racemases which have a cofactor requirement for pyridoxal phosphate . An oxidation-reduction cofactor may also be a general feature of racemases of this class. However, the mode of epimerisation of L-phenylalanine to D-phenylalanine necessary for the synthesis of some peptide antibiotics, proceeds in an entirely different way, which as yet has only been partially resolved. 

Racemases are enzymes that catalyze the inversion of the chiral center by deprotonation of the C , followed by reprotonation on the opposite face of the planar carban-ionic transition-state species [13,14], In order to overcome the high energetic barrier of racemization, for example, on a-amino acids, some racemases employ pyridoxal phosphate (PLP) as a cofactor to use the resonance-stabilized amino acid complex as an electron sink because the estimated pK values for the C of amino acids are high, in the range 21-32 [14,15]. The formation of an imine PLP-substrate covalent bond makes the pK value of a-hydrogen of amino acids low. The second class of enzymes includes proline, aspartate, and glutamate racemases and diaminopimelate epimer-ase, with a cofactor-independent two-base mechanism [14],... 

M. Pietzsch, C. Syldatk, and F. Wagner, Isolation and characterization of a new, non pyridoxal-5 -phosphate dependent hydantoin racemase, DECHEMA Biotechnol. Conf. 1990, 4, 259-262. 

A variety of amino acid racemases have been identified in bacteria, archaea, and eukaryotes. They are dassified into two groups pyridoxal 5 -phosphate (PLP) -dependent and -independent enzymes. Therefore, racemization can be achieved via two mechanisms through a chiraUy unstable Schiff base intermediate with an aromatic aldehyde serving as co-factor PLP (Scheme 13.22a) and by a two-base mechanism without co-factor (Scheme 13.22b). 

Perhaps the best characterized organic cofactor-dependent racemase is alanine racemase, which employs pyridoxal 5 -phosphate (PLP) (Table 7.1). o-alanine is necessary for the synthesis of the peptidoglycan layer of bacterial cell walls in Gram negative and positive bacteria [1]. Alanine racemase is thus a ubiquitous enzyme in bacteria and an excellent drug target [2]. Both its crystal structure and mechanism have been well investigated. PLP reacts with amino acids to produce... 

Pyridoxal 5 -phosphate-dependent Amino Acid Racemases and Epimerases... 

Alanine racemase is a bacterial enzyme that catalyzes racemization of l- and d-alanine, and requires pyridoxal 5 -phosphate (PLP) as a cofactor. The enzyme plays an important role in the bacterial growth by providing D-alanine, a central molecule in the peptidoglycan assembly and cross-linking, and has been purified from various sources15 161. The enzyme has been used for the production of stereospecifically deuterated NADH and various D-amino acids by combination of L-alanine dehydrogenase (E. C. 1.4.1.1), D-amino acid aminotransferase (E. C. 2.6.1.21), and formate dehydrogenase (E.C. 1.2.1.2)I17, 18. ... 

Rudnick and Abeles purified proline racemase to 95% homogeneity from Clostridium sticklandii, and characterized it 92. The enzyme is composed of two identical subunits with a molecular weight of about 38000, and is independent of any cofactors or metals. Most amino acid racemases require pyridoxal 5 -phosphate, which labilizes the bond between the a-hydrogen and the chiral center by aldimine formation with the a-amino group of the substrate. However, PLP is not involved in the reaction of proline racemase acting on an a-imino acid. The enzyme also acts on 2-hydroxy-L-proline and 2-allo-hydroxy-D-proline although slowly they are epimer-ized at a rate of 2 and 5% of the rate of L-proline racemization, respectively. L-Proline and D-proline showed Km values of 2.9 and 2.5 mti, respectively1119. ... 

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