From cofactor to enzymes. The molecular evolution of pyridoxal‐5′‐phosphate‐dependent enzymes

Abstract The pyridoxal‐5′‐phosphate (vitamin B 6 )‐dependent enzymes that act on amino acid substrates have multiple evolutionary origins. Thus, the common mechanistic features of B 6 enzymes are not accidental historical traits but reflect evolutionary or chemical necessities. The B 6 enzymes belong to four independent evolutionary lineages of paralogous proteins, of which the α family (with aspartate aminotransferase as the prototype enzyme) is by far the largest and most diverse. The considerably smaller β family (tryptophan synthase β as the prototype enzyme) is structurally and functionally more homogenous. Both the D ‐alanine aminotransferase family and the alanine racemase family consist of only a few enzymes. The primordial pyridoxal‐5′‐phosphate‐dependent protein catalysts apparently first diverged into reaction‐specific protoenzymes, which then diverged further by specializing for substrate specificity. Aminotransferases as well as amino acid decarboxylases are found in two different evolutionary lineages, providing examples of convergent enzyme evolution. The functional specialization of most B 6 enzymes seems to have already occurred in the universal ancestor cell before the divergence of eukaryotes, archebacteria, and eubacteria 1500 million years ago. Pyridoxal‐5′‐phosphate must have emerged very early in biological evolution; conceivably, metal ions and organic cofactors were the first biological catalysts. To simulate particular steps of molecular evolution, both the substrate and reaction specificity of existent B 6 enzymes were changed by substitution of active‐site residues, and monoclonal pyridoxal‐5′‐phosphate‐dependent catalytic antibodies were produced with selection criteria that might have been operative in the evolution of protein‐assisted pyridoxal catalysis. © 2001 John Wiley & Sons, Inc. and The Japan Chemical Journal Forum Chem Rec 1:436–447, 2001