Monovalent ions aid catalysis of two-metal-ion dependent RNA editors

The cleavage and formation of phosphodiester bonds in nucleic acids is performed by diverse cellular machineries ranging from small protein enzymes to large complexes composed of proteins and/or RNA strands. While it has long been believed that these processes depend solely on a two-metal-ion mechanism, comparative structural analyses revealed that some complexes also contain highly conserved second-shell monovalent cations. The two-Mg 2+ -aided catalytic mechanism, in which both ions function as Lewis acids, with one metal activating the nucleophile (water or ribose hydroxyl) for the scissile phosphate group attack and the other stabilizing the leaving group, is well-established. In contrast, the function of monovalent ions has been largely overlooked, yielding divergent results across different catalytic settings. Nevertheless, recent evidence points to monovalent ions assisting catalysis beyond their roles in RNA folding and assembly. Here, building on recent computational studies on two-metal-ion dependent ribozymes, we showcase how divalent and monovalent ions finely tune the catalytic site arrangements and dynamics, affecting the kinetic and thermodynamic properties of RNA cleavage reactions. We discuss optimal catalytic mechanisms depending on nucleophile type and illuminate strategies adopted by second-shell monovalent ions to optimize catalytic geometries, which enable efficient proton transfer from nucleophile to the leaving group, a key event for effective catalysis. This review expands understanding of nucleic acid-processing machinery, providing key knowledge for potentially designing innovative gene-modulating tools and therapeutic strategies.