Chemical feasibility of the general acid/base mechanism of glmS ribozyme self‐cleavage

In numerous Gram‐positive bacteria, the glmS ribozyme or catalytic riboswitch regulates the expression of glucosamine‐6‐phosphate (GlcN6P) synthase via site‐specific cleavage of its sugar‐phosphate backbone in response to GlcN6P ligand binding. Biochemical data have suggested a crucial catalytic role for an active site guanine (G40 in Thermoanaerobacter tengcongensis, G33 in Bacillus anthracis). We used hybrid quantum chemical/molecular mechanical (QM/MM) calculations to probe the mechanism where G40 is deprotonated and acts as a general base. The calculations suggest that the deprotonated guanine G40 − is sufficiently reactive to overcome the thermodynamic penalty arising from its rare protonation state, and thus is able to activate the A‐1(2′‐OH) group toward nucleophilic attack on the adjacent backbone. Furthermore, deprotonation of A‐1(2′‐OH) and nucleophilic attack are predicted to occur as separate steps, where activation of A‐1(2′‐OH) precedes nucleophilic attack. Conversely, the transition state associated with the rate‐determining step corresponds to concurrent nucleophilic attack and protonation of the G1(O5′) leaving group by the ammonium moiety of the GlcN6P cofactor. Overall, our calculations help to explain the crucial roles of G40 (as a general base) and GlcN6P (as a general acid) during glmS ribozyme self‐cleavage. In addition, we show that the QM/MM description of the glmS ribozyme self‐cleavage reaction is significantly more sensitive to the size of the QM region and the quality of the QM‐MM coupling than that of other small ribozymes. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 550–562, 2015.