Substrate-assisted catalysis in the aminoacyl transfer mechanism of histidyl-tRNA synthetase: a density functional theory study.

Density functional theory methods have been used to investigate possible mechanisms of the second half-reaction of aminoacylation catalyzed by histidyl-tRNA synthetase: transfer of the aminoacyl moiety from histidyl-adenylate to the terminal adenosine (A76) of tRNA. The properties of the two mechanistically important nonbridging phosphate oxygens of the histidyl-adenylate in the substrate-bound complex were first considered. It is found that the nonbridging pro-S oxygen is slightly more basic than the pro-R oxygen due to the fact that the former is involved in a weaker hydrogen bonding network than the latter. Three possible mechanisms in which the proton of the 3'-OH group of A76 transfers to the bridging phosphate oxygen and the nonbridging pro-R and -S oxygens were then investigated. When the bridging phosphate oxygen acts as the base, the reaction occurs via a four-membered ring transition structure with a considerably high barrier. When the pro-R oxygen acts as the base, a concerted mechanism was again found. However, it proceeds via a six-membered ring transition structure. In contrast, when the pro-S oxygen acts as a base, an associative stepwise mechanism was found which, furthermore, also had the lowest barrier of the three mechanisms obtained. Comparisons of these three mechanisms and reasons for the differences in barriers are also provided.