Crucial Roles of Two Hydrated Mg Ions in Reaction Catalysis of the Pistol Ribozyme.

Publication Type:

Journal Article


Angew Chem Int Ed Engl (2019)


<p>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 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 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 ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage.</p>

6UEY for pistol ribozyme TS analog vanadate, 6UFJ for its 2′,3′ cyclophosphate product complex, 6UF1 for TS analog vanadate crystals soaked in Mn2+, and 6UFK for the 2′,3′ cyclophosphate product crystals soaked in Mn2+.