Enzymes may not only generate catalytic competent conformations for enzyme-substrate complexes but also be able to preserve the reactive conformations to the stage when the reactions reach TS to allow catalytic residues to exert their effects. Such property could be lost for some mutants, leading to diminished TS stabilization and significant reduction of catalytic efficiency. Blue: enzyme; Yellow: substrate; Orange: the altered structure of substrate in TS.

Abstract

Determining strategies used by enzymes to achieve enormous rate enhancements has been a central goal in biochemical research. The abilities to form catalytic competent reactive conformations for enzyme-substrate complexes with well-positioned residues and to lower activation barriers through transition state (TS) stabilization are two accepted mechanisms. Enzymes might have evolved to possess other unrecognized strategies to achieve rate enhancements, and identification of such strategies is of fundamental importance. Here we perform a quantum mechanical/molecular mechanical study of carnosine N-methyltransferase 1 and its mutants, and results indicate that enzymes may possess the ability to preserve reactive conformations and prevent their premature distortions into less active forms during reactions. For wild-type, the reactive conformation can be formed in the enzyme-substrate complex and be preserved to the stage when the reaction reaches TS. For Tyr386Ala, Tyr396Asp, and Tyr398Ala, the wild-type-like reactive conformations can be formed in the mutant-substrate complexes but undergo distortions into less active conformations in the early stage of the reaction before TS. Such premature distortions of the wild-type-like reactive conformations in the mutant complexes prevent residues from fully exerting catalytic effects. Thus, the ability to preserve reactive conformations may be an important feature for some enzymes and can make important contributions to catalytic efficiency.