Pyridoxal Phosphate - Catalytic Mechanism

Catalytic Mechanism

The pyridoxal-5′-phosphate-dependent enzymes (PLP enzymes) catalyze a myriad of biochemical reactions. Although the scope of PLP-catalyzed reactions initially appears to be immensely diverse, there is a simple unifying principle: In the resting state, the cofactor (PLP) is covalently bonded to the amino group of an active site lysine, forming an internal aldimine. Once the amino substrate interacts with the active site, a new Schiff base is generated, commonly referred to as the external aldimine. Only after this step, the mechanistic pathway for each PLP-catalyzed reaction diverges. Density functional methods have been applied to investigate the transimination reaction, and the results have shown that the reaction involves three sequential steps: (i) formation of a tetrahedral intermediate with the active site lysine and the amino substrate bonded to the PLP cofactor; (ii) nondirect proton transfer between the amino substrate and the lysine residue; and (iii) formation of the external aldimine after the dissociation of the lysine residue. The overall reaction is exothermic (−12.0 kcal/mol), and the rate-limiting step is the second one with 12.6 kcal/mol for the activation energy