6uf1: Difference between revisions

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-'''Unreleased structure'''
-The entry 6uf1 is ON HOLD  until Paper Publication
+==Pistol ribozyme transition-state analog vanadate==
+<StructureSection load='6uf1' size='340' side='right'caption='[[6uf1]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6uf1]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UF1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UF1 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=Q61:'>Q61</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uf1 OCA], [http://pdbe.org/6uf1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uf1 RCSB], [http://www.ebi.ac.uk/pdbsum/6uf1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uf1 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pistol ribozymes constitute a new class of small self-cleaving RNAs. We have solved crystal structures that provide 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 resulting architectonic framework dictates the proposed underlying chemical mechanism, which is corroborated by functional assays that involve atomic mutagenesis of the ribozyme. Importantly, a hydrated Mg2+ ion remains innersphere-coordinated to N7-G33 in all three states. This is consistent with its likely role as acid in general acid base catalysis (delta and ss catalysis), supported further by the observation of a more than 1000-fold rate reduction if its positioning is impaired by deletion of the N7 site. 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 H-bonding in the cyclophosphate product. Because this second hydrated Mg2+ ion is also close to the 6-oxygen atom of G40 (general base, gamma catalysis), its potential impact on activation of G40 has been experimentally evaluated, however, the major role of the second Mg2+ ion appears to be the stabilization of product conformation. Together, our study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage with unprecedented precision.
-Authors: Teplova, M., Falschlunger, C., Krasheninina, O., Patel, D.J., Micura, R.
+On crucial roles of two hydrated Mg2+ ions in reaction catalysis of the pistol ribozyme.,Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R Angew Chem Int Ed Engl. 2019 Dec 5. doi: 10.1002/anie.201912522. PMID:31804735<ref>PMID:31804735</ref>
-Description: Pistol ribozyme transition-state analog vanadate
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Patel, D.J]]
+<div class="pdbe-citations 6uf1" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Falschlunger, C]]
 [[Category: Krasheninina, O]]
+[[Category: Micura, R]]
+[[Category: Patel, D J]]
 [[Category: Teplova, M]]
-[[Category: Micura, R]]
+[[Category: Cyclophosphate product]]
-[[Category: Falschlunger, C]]
+[[Category: Pentavalent transition state analog]]
+[[Category: Pre-catalytic state]]
+[[Category: Rna]]
+[[Category: Self-cleaving ribozyme]]
+[[Category: Transesterification reaction]]