The catalytic diversity of RNAs

Top Cited Papers
Publisher Website
Google Scholar
Abstract
Small self-cleaving ribozymes catalyse the same reversible phosphodiester-cleavage reaction, but can adopt different structures and use distinct catalytic strategies. These catalytic RNAs do not require metal-cation cofactors and instead use active-site nucleotide bases for their catalytic chemistry. Structural and biochemical studies of the hepatitis delta virus ribozyme are consistent with models in which an active-site cytosine activates the nucleophile through general base catalysis, whereas a metal-bound water protonates the leaving group. In an alternative model, these roles are reversed and the metal-bound water accepts a proton to activate the nucleophile, whereas cytosine mediates general acid catalysis to stabilize the leaving group. Structural studies of the hairpin ribozyme place two active-site nucleobases near the reactive phosphate where hydrogen-bonding interactions provide electrostatic stabilization to the transition state. The nucleobase that interacts with the bridging 5′ oxygen might also mediate general acid–base catalysis. Biochemical studies support a three-metal model for group-I intron splicing, in which catalytic metal cations activate nucleophiles, stabilize leaving groups and position reactants in the appropriate geometry. Structural studies have so far identified only two active-site metals. The catalytic chemistry that is mediated by ribosomal RNA in the peptidyl-transferase centre of the ribosome focuses on peptide release, whereas the 2′ hydroxyl of the P-site tRNA is important for peptide-bond formation.