Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme

In the presence of magnesium ions, cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities, In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash-freezing of crystals under conditions where the ribozyme is active, provide evidence that a mu-bridging OH(-)ion is located between two Mg2+ ions close to the cleavable phosphate, Constrained simulations show further that a flip from the CS'-endo to the C2'-endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorous atom and the mu-bridging OH(-)ion, Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a mu-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH(-)ion that is able to activate the 2'-hydroxyl nucleophile after a minor and localized conformational change in the RNA.