A general two-metal-ion mechanism for catalytic RNA.

TLDR

RNA splicing and RNase P reactions are thought to employ a symmetric two‑metal‑ion catalytic site that aligns with the mechanisms of group I and II introns, the spliceosome, and RNase P, with RNA positioning the metals and substrates. This study proposes a unified two‑metal‑ion mechanism for the RNA‑catalyzed reactions of RNA splicing and RNase P hydrolysis of precursor tRNA. The mechanism posits two divalent metal ions 3.9 Å apart that activate the attacking nucleophile and stabilize the leaving group, acting as Lewis acids to stabilize the pentacovalent transition state, mirroring phosphoryl‑transfer enzymes.

Abstract

A mechanism is proposed for the RNA-catalyzed reactions involved in RNA splicing and RNase P hydrolysis of precursor tRNA. The mechanism postulates that chemical catalysis is facilitated by two divalent metal ions 3.9 A apart, as in phosphoryl transfer reactions catalyzed by protein enzymes, such as the 3',5'-exonuclease of Escherichia coli DNA polymerase I. One metal ion activates the attacking water or sugar hydroxyl, while the other coordinates and stabilizes the oxyanion leaving group. Both ions act as Lewis acids and stabilize the expected pentacovalent transition state. The symmetry of a two-metal-ion catalytic site fits well with the known reaction pathway of group I self-splicing introns and can also be reconciled with emerging data on group II self-splicing introns, the spliceosome, and RNase P. The role of the RNA is to position the two catalytic metal ions and properly orient the substrates via three specific binding sites.