The HDV ribozyme uses both metal ion and nucleobase catalysis in its self-cleavage mechanism. Experimental and theoretical studies support a mechanism in which C75 acts as a general acid and bound Mg2+ ion acts as a Lewis acid. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction, as well as key experiments, indicate that the mechanism is concerted with a phosphorane-like transition state when a divalent ion is bound at the catalytic site but sequential with a phosphorane intermediate when a monovalent ion is at this site. Experiments and simulations probing the impact of sulfur substitution at each nonbridging oxygen of the scissile phosphate on the mechanism and rate provide further insights. The results imply that the catalytic Mg2+ ion may play three key roles: assisting in the activation of the O2’ nucleophile, acidifying the general acid C75, and stabilizing the nonbridging oxygen to prevent proton transfer to it.

Mechanistic strategies in the HDV ribozyme: Metal ion identity controls the reaction pathway

249th National Meeting (2015)

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Mechanistic strategies in the HDV ribozyme: Metal ion identity controls the reaction pathway<br />