Unraveling the Critical Role Played by 2'OH in the Post-Transfer Editing by Archaeal Threonyl-tRNA Synthetase.

Archaeal threonyl-tRNA synthetase (ThrRS) possesses an editing active site wherein tRNA that has been misaminoacylated with serine (i.e., Ser-tRNA) is hydrolytically cleaved to serine and tRNA. It has been suggested that the free ribose sugar hydroxyl of Ado76 of the tRNA (2'OH) is the mechanistic base, promoting hydrolysis by orienting a nucleophilic water near the scissile Ser-tRNA 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 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 2'OH group participates, overall, as a shuttle for the proton transfer from the nucleophilic HO to the bridging oxygen (3'O) of the substrate. More specifically, in the first step, which has a barrier of 25.9 kcal/mol, the 2'-OH group accepts a proton from the attacking nucleophilic water while concomitantly transferring its proton onto the substrates C-O center. Then, in the second step, which also proceeds with a barrier of 25.9 kcal/mol, the 2'-OH group transfers its proton on the adjacent 3'-oxygen, cleaving the scissile C-O3' bond, while concomitantly accepting a proton from the previously formed C-OH group.