Extraordinary rates of transition metal ion-mediated ribozyme catalysis

In pre-steady-state, fast-quench kinetic analysis, the tertiary-stabilized hammerhead ribozyme RzB'' cleaves its substrate RNA with maximal measured k(obs) values of similar to 3000 min(-1) in 1 mM Mn2+ and similar to 780 min(-1) in 1 mM Mg2+ at 37 degrees C (pH 7.4). Apparent pKa for the catalytic general base is similar to 7.8-8.5, independent of the corresponding metal hydrate pKa, suggesting potential involvement of a nucleobase as general base as suggested previously from nucleobase substitution studies. The pH-rate profile is bell-shaped for Cd2+, for which the general catalytic acid has a pKa of 7.3 +/- 0.1. Simulations of the pH-rate relation suggest a pKa for the general catalytic acid to be similar to 9.5 in Mn2+ and > 9.5 in Mg2+. The acid pKa's follow the trend in the pKa of the hydrated metal ions but are displaced by similar to 1-2 pH units in the presence of Cd2+ and Mn2+. One possible explanation for this trend is direct metal ion coordination with a nucleobase, which then acts as general acid.