Role of Induced Fit in Enzyme Specificity: A Molecular Forward/Reverse Switch

Kenneth A. Johnson

doi:10.1074/jbc.r800034200

Abstract

Enzyme structures solved with and without bound substrate often show that substrate-induced conformational changes bring catalytic residues into alignment, alter the local environment, and position the substrate for catalysis. Although the structural data are compelling, the role of conformational changes in enzyme specificity has been controversial in that specificity is a kinetic property that is not easy to predict based upon structure alone. Recent studies on DNA polymerization have illuminated the role of substrate-induced conformational changes in enzyme specificity by showing that the rate at which the enzyme opens to release the bound substrate is a key kinetic parameter. The slow release of a correct substrate commits it to the forward reaction so that specificity is determined solely by the rate of substrate binding, including the isomerization step, and not by the slower rate of the chemical reaction. In contrast, fast dissociation of an incorrect substrate favors release rather than reaction. Thus, the conformational change acts as a molecular switch to select the right substrate and to recognize and disfavor the reaction of an incorrect substrate. A conformational switch may also favor release rather than reverse reaction of the product.

Highlights

The role of induced fit in enzyme specificity has been controversial
The simple logic said that when ATP bound in the absence of glucose, the ATP must be protected from water, whereas the binding of glucose must induce a change in structure to make the ATP accessible [3]
The solution of the structure of the ribosome has revealed a “steric switch mechanism” that protects the peptidyl-tRNA from hydrolysis, whereas the binding of a cognate aa-tRNA2 induces a change in structure to allow reaction [5]

Summary

Introduction

The role of induced fit in enzyme specificity has been controversial. On the one hand, it is apparent that catalysis is facilitated by the rapid binding of a substrate to an open form of the enzyme, whereas the chemical reaction is accelerated most efficiently by the precise alignment of amino acids surrounding the substrate and by the altered reaction environment in the closed state. Kcat/Km is defined by the product of the binding constant (K1) for the substrate in the collision complex (ES) and the rate of the conformational change (k2).

Results

Conclusion