Unraveling the Critical Role Played by Ado762′OH in the Post-Transfer Editing by Archaeal Threonyl-tRNA Synthetase

Archaeal threonyl-tRNA synthetase (ThrRS) possesses an editing active site wherein tRNA(Thr) that has been misaminoacylated with serine (i.e., Ser-tRNA(Thr)) is hydrolytically cleaved to serine and tRNA(Thr). It has been suggested that the free ribose sugar hydroxyl of Ado76 of the tRNA(Thr) ((Ado76)2'OH) is the mechanistic base, promoting hydrolysis by orienting a nucleophilic water near the scissile Ser-tRNA(Thr) ester bond. We have performed a computational study, involving molecular dynamics (MD) and hybrid ONIOM quantum mechanics/molecular mechanics (QM/MM) methods, considering all possible editing mechanisms to gain an understanding of the role played by (Ado76)2'OH group. More specifically, a range of concerted or stepwise mechanisms involving four-, six-, or eight-membered transition structures (total of seven mechanisms) were considered. In addition, these seven mechanisms were fully optimized using three different DFT functionals, namely, B3LYP, M06-2X, and M06-HF. The M06-HF functional gave the most feasible energy barriers followed by the M06-2X functional. The most favorable mechanism proceeds stepwise through two six-membered ring transition states in which the (Ado76)2'OH group participates, overall, as a shuttle for the proton transfer from the nucleophilic H2O to the bridging oxygen ((Ado76)3'O) of the substrate. More specifically, in the first step, which has a barrier of 25.9 kcal/mol, the (Ado76)2'-OH group accepts a proton from the attacking nucleophilic water while concomitantly transferring its proton onto the substrates C-O-carb center. Then, in the second step, which also proceeds with a barrier of 25.9 kcal/mol, the (Ado76)2'-OH group transfers its proton on the adjacent (Ado76)3'-oxygen, cleaving the scissile C-carb-O3'(Ado76) bond, while concomitantly accepting a proton from the previously formed C-OcarbH group.