Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactions

Abstract

We have studied the stereospecificities of various pyridoxal 5'-phosphate dependent enzymes for the hydrogen transfer between the C-4' of a bound coenzyme and the C-2 of a substrate in the transamination catalyzed by the enzymes. Prior to our studies, pyridoxal enzymes so far studied were reported to catalyze the hydrogen transfer only on the si-face of the planar imine intermediate formed from substrate and coenzyme. This finding had been considered as the evidence that pyridoxal enzymes have evolved divergently from a common ancestral protein, because identity in the stereospecificity reflects the similarity in the active-site structure, in particular in the geometrical relationship between the coenzyme and the active site base participating in the hydrogen transfer. However, we found that D-amino acid aminotransferase, branched-chain L-amino acid aminotransferase, and 4-amino-4-deoxychorismate lyase catalyze the re-face specific hydrogen transfer, and that amino acid racemases catalyze the nonstereospecific hydrogen transfer. These findings suggest the convergent evolution of pyridoxal enzymes. Crystallographical studies have shown that the stereospecificity reflects the active-site structure of the enzymes, and that the enzymes with the same fold exhibit the same stereospecificity. The active site structure with the catalytic base being situated on the specific face of the cofactor has been conserved during the evolution among the pyridoxal enzymes of the same family.

Cofactors of serine racemase that physiologically stimulate the synthesis of the N -methyl- d -aspartate (NMDA) receptor coagonist d -serine

“…Occurrence of racemization in the course of dehydration͞deamination reaction has not been observed for any other enzyme. This activity can be explained by the numerous transformations of amino acids that are carried out by pyridoxal 5Ј-phosphate enzymes; the specific reaction depends on the microenvironment of the catalytic site (20). The bifunctional role of SR explains our previous finding that SR generates pyruvate from L-serine O-sulfate, an artificial L-serine analog and inhibitor of D-serine synthesis by SR (6).…”

Broad Substrate Stereospecificity of the Mycobacterium tuberculosis 7-Keto-8-aminopelargonic Acid Synthase

“…The utilization of both L-and D-alanine as substrates by the M. tuberculosis KAPA synthase demonstrates its broad substrate stereospecificity. PLP-dependent enzymes exhibit stereospecificity at the level of the exchange of ␣-protons of their amino acid substrates by catalyzing this reaction either on the si-(sinister) or the re-(rectus) face of the planar external aldimine intermediate (29,32). The ability of the M. tuberculosis KAPA synthase to exchange ␣-protons of both L-and D-enantiomers on both the si-and the re-faces as reported in case of the PLPdependent amino acid racemases (32) may give rise to its broad stereospecificity.…”

Conserved Pyridoxal Protein That Regulates Ile and Val Metabolism

“…This was not surprising, because they lack the residue that is approached from the si side of PLP. Generally, the racemization of an amino acid requires ␣-proton abstraction and subsequent reprotonation at the opposite face where ␣-proton abstraction occurs (22). To achieve this, PLP-dependent amino acid racemases, such as AR and eukaryotic serine racemase (SR), are equipped with 2 catalytic residues that are situated at the re and si faces of the PLP plane, respectively.…”