Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism

A recent crystal structure of the precleaved HDV ribozyme along with biochemical data support a mechanism for phosphodiester bond self-cleavage in which C75 acts as a general acid and bound Mg²⁺ ion acts as a Lewis acid. Herein this precleaved crystal structure is used as the basis for quantum mechanical/molecular mechanical calculations. These calculations indicate that the self-cleavage reaction is concerted with a phosphorane-like transition state when a divalent ion, Mg²⁺ or Ca²⁺, is bound at the catalytic site but is sequential with a phosphorane intermediate when a monovalent ion, such as Na⁺, is at this site. Electrostatic potential calculations suggest that the divalent metal ion at the catalytic site lowers the pK_a of C75, leading to the concerted mechanism in which the proton is partially transferred to the leaving group in the phosphorane-like transition state. These observations are consistent with experimental data, including pK_a measurements, reaction kinetics, and proton inventories with divalent and monovalent ions.