The role of axial chirality in Schiff bases of pyridoxal phosphate and amino acids in the mechanism of racemase enzyme : a quantum-chemical study

In the enzymatic racemization of L and D amino acids, the coenzyme pyridoxal phosphate (PLP) forms a Schiff base with the amino acid. In the first step of the isomerization reaction, both the L and D PLP-amino acid compounds are deprotonated by a single basic site in the enzyme, which is normally assumed to occur via large conformational changes of coenzyme or enzyme. We propose a more efficient mechanism in which axial chirality is introduced into the PLP-amino acid complex by a rotation around the C4C4' bond, placing the iminium side-chain in an out-of-plane orientation. This allows optimal location of both L and D amino acids for deprotonation by one basic site in the enzyme. A combination of the calculated results with the kinetic data of Farad and Walsh (Biochemistry 27, 3267 (1988)) provides insight into the location of the catalytic base in the enzyme with respect to the coenzyme.