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Crucial Roles of Two Hydrated Mg 2+ Ions in Reaction Catalysis of the Pistol Ribozyme
Author(s) -
Teplova Marianna,
Falschlunger Christoph,
Krasheninina Olga,
Egger Michaela,
Ren Aiming,
Patel Dinshaw J.,
Micura Ronald
Publication year - 2020
Publication title -
angewandte chemie
Language(s) - English
Resource type - Journals
eISSN - 1521-3757
pISSN - 0044-8249
DOI - 10.1002/ange.201912522
Subject(s) - ribozyme , phosphodiester bond , chemistry , catalysis , cleavage (geology) , vanadate , transition state , stereochemistry , hydrogen bond , hairpin ribozyme , crystallography , inorganic chemistry , molecule , rna , organic chemistry , materials science , biochemistry , fracture (geology) , composite material , gene
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 Mg 2+ 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 Mg 2+ 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 Mg 2+ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme‐catalyzed backbone cleavage.