Simulation of the charge relay structure in ribonuclease A.

Abstract

X-ray diffraction analysis shows that RNase A is an enzyme which changes its conformation upon substrate binding. Amino acids were rotated to simulate the coupling movements of the amino acid side chains, water molecule and the substrate. From the study of the movements of amino acids and the quantum chemical calculations, a charge relay structure composed of Asp 121, His 119 and a water molecule was simulated in the active site of the RNase A. The water is located in the position where the OH group of the water molecule can attack the P of the substrate in the 2nd step of the hydrolysis. Lys 7 and Lys 41 may participate in the enzymatic reaction.