6UFK

Pistol ribozyme product crystal soaked in Mn2+

Summary for 6UFK

• Entry DOI: 10.2210/pdb6ufk/pdb
• Descriptor: RNA (50-MER), RNA (5'-R(*UP*CP*UP*GP*CP*UP*CP*UP*CP*(23G))-3'), RNA (5'-R(*UP*CP*CP*AP*G)-3'), ... (4 entities in total)
• Functional Keywords: self-cleaving ribozymes, transesterification reaction, pre-catalytic state, pentavalent transition state analog, cyclophosphate product, rna
• Biological source: synthetic construct; More
• Total number of polymer chains: 6
• Total formula weight: 43682.06

Authors

Teplova, M.,Falschlunger, C.,Krasheninina, O.,Patel, D.J.,Micura, R. (deposition date: 2019-09-24, release date: 2019-12-18, Last modification date: 2024-03-13)

Primary citation

Teplova, M.,Falschlunger, C.,Krasheninina, O.,Egger, M.,Ren, A.,Patel, D.J.,Micura, R.
Crucial Roles of Two Hydrated Mg2+Ions in Reaction Catalysis of the Pistol Ribozyme.
Angew.Chem.Int.Ed.Engl., 59:2837-2843, 2020

PubMed 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 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.

PubMed: 31804735
DOI: 10.1002/anie.201912522

Experimental method

X-RAY DIFFRACTION (3.2 Å)