Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis

Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2 '-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.

Automated summary

Ribonucleases and small nucleolytic ribozymes both catalyze RNA strand cleavage through 2'-O-transphosphorylation, but their mechanisms involve distinct transition states. In this study, we demonstrate that hepatitis delta virus ribozyme catalysis proceeds through a dissociative, metaphosphate-like transition state, in contrast to the associative transition states observed with other enzymes. These findings provide evidence for a unique ribozyme active site design that modulates the RNA cleavage pathway.