On the Importance of Preserving Active Induced-Fit Conformations during Enzyme-Catalyzed Reactions: a Case Study of CARNMT1

Considerable efforts have been made to understand how precise orientations of catalytic groups/substrate in enzyme-substrate complexes are generated for catalysis, leading to the proposals of lock-and-key, induced-fit and conformational selection models as well as their extensions. By contrast, little attention has been paid to the importance of preserving such active conformations during enzyme-catalyzed reactions to allow catalytic residues to exert their effects during catalysis, including transition state stabilization. Here MD and free energy simulations based on QM/MM potentials are carried out for CARNMT1, a histidine methyltransferase, to determine the importance and requirements for preservation of catalytic competent induced-fit conformations during methylation. We examine interplay of certain anchor residues that occupy similar positions before and after substrate binding (Asp316, Tyr386 and Tyr396) with the latch residue (His347) that is responsible for generating the active induced-fit conformation. For wild type, the catalytic competent orientations can be preserved well after the reaction passes TS allowing the active site residues to exert the effects. For the Tyr386Ala and Tyr396Asp mutants, the induced-fit conformation can be formed in the mutant-substrate complex but collapses in the early stage of reaction well before it can reach TS. Such pre-mature collapse of the active conformations as a result of the mutations is likely to be responsible for the significant reduction of catalytic efficiency. His347Phe also fails to preserve the active induced-fit conformation, and the active induced-fit conformation cannot be formed in the Asp316Ala-substrate complex. The results demonstrate the importance of preserving the active induced-fit conformation during enzyme-catalyzed reaction. They also show that generation of active induced-fit conformations of enzyme-substrate complexes may be a necessary but not sufficient condition for efficient catalysis. Interestingly, the catalytic efficiency seems to be correlated with the ability of the enzyme/mutant to preserve the active induced-fit conformation during catalysis.