DSSR-PyMOL cartoon-block schematics: PDB entry 6uey

PDB-id

6uey; DSSR-derived features in text and JSON formats

Class

RNA

Method

X-ray (2.8 Å)

Summary

Pistol ribozyme transition-state analog vanadate

Reference

Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R (2020): "Crucial Roles of Two Hydrated Mg2+Ions in Reaction Catalysis of the Pistol Ribozyme." Angew.Chem.Int.Ed.Engl., 59, 2837-2843. doi: 10.1002/anie.201912522.

Abstract

Pistol ribozymes constitute a new class of small self-cleaving RNAs. Crystal structures have been solved, providing three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg₂₊ ion remains innersphere-coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg₂₊ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reach out for water-mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg₂₊ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage.