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. Author manuscript; available in PMC: 2013 Jun 14.
Published in final edited form as: J Phys Chem B. 2012 Apr 11;116(23):6991–6999. doi: 10.1021/jp300845h

Figure 2. Deacylation of Ala-tRNAPro by E. faecalis ProRS INS domain via A76 as general base.

Figure 2

(A) Catalytic water (W1) is activated by the 2′-OH. (B) A proton transfer occurs from W1 to N3 of A76 via the 2′-OH and W2 to form a protonated A76 intermediate. (C) A proton is subsequently transferred to O3′ via W2 and 2′-OH to form the hydrolyzed product. The oxyanionic intermediate is stabilized by the GXXXP loop. The reaction coordinate refers to bond broken (Ala-C(O) – O3′-A76) – bond formed (Ala-C(O) – OH2). Panels A, B and C show the optimized reactant, intermediate, and products, respectively. (D) The calculated potential energy surface for this mechanism at the BP86/TZVPP//BP86/SV(P) level of theory for the QM domain.