3cqs: Difference between revisions

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-[[Image:3cqs.png|left|200px]]
-{{STRUCTURE_3cqs|  PDB=3cqs  |  SCENE=  }}
+==A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases==
+<StructureSection load='3cqs' size='340' side='right'caption='[[3cqs]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3cqs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CQS FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cqs OCA], [https://pdbe.org/3cqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cqs RCSB], [https://www.ebi.ac.uk/pdbsum/3cqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cqs ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Reaction-intermediate analogs have been used to understand how phosphoryl transfer enzymes promote catalysis. Herein we report the first structure of a small ribozyme crystallized with a 3'-OH, 2',5'-linkage in lieu of the normal phosphodiester substrate. The new structure shares features of the reaction coordinate exhibited in prior ribozyme structures including a vanadate complex that mimicked the oxyphosphorane transition state. As such, the structure exhibits reaction-intermediate traits that allow direct comparison of stabilizing interactions to the 3'-OH, 2',5'-linkage contributed by the RNA enzyme and its protein counterpart, ribonuclease. Clear similarities are observed between the respective structures including hydrogen bonds to the non-bridging oxygens of the scissile phosphate. Other commonalities include carefully poised water molecules that may alleviate charge build-up in the transition state and placement of a positive charge near the leaving group. The advantages of 2',5'-linkages to investigate phosphoryl-transfer reactions are discussed, and argue for their expanded use in structural studies.
-===A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases===
+Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.,Torelli AT, Spitale RC, Krucinska J, Wedekind JE Biochem Biophys Res Commun. 2008 Jun 20;371(1):154-8. Epub 2008 Apr 16. PMID:18423397<ref>PMID:18423397</ref>
-{{ABSTRACT_PUBMED_18423397}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3cqs" style="background-color:#fffaf0;"></div>
-[[3cqs]] is a 3 chain structure of [[Ribozyme]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQS OCA].
 ==See Also==
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018423397</ref><references group="xtra"/>
+__TOC__
-[[Category: Krucinska, J.]]
+</StructureSection>
-[[Category: Spitale, R C.]]
+[[Category: Large Structures]]
-[[Category: Torelli, A T.]]
+[[Category: Krucinska J]]
-[[Category: Wedekind, J E.]]
+[[Category: Spitale RC]]
-[[Category: 2s']]
+[[Category: Torelli AT]]
-[[Category: 5' phosphodiester]]
+[[Category: Wedekind JE]]
-[[Category: Hairpin ribozyme]]
-[[Category: Phosphoryl-transfer]]
-[[Category: Reaction-intermediate]]
-[[Category: Ribonuclease]]
-[[Category: Rna]]
-[[Category: Transition-state stabilization]]