3gs8: Difference between revisions

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 ==An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand==
-<StructureSection load='3gs8' size='340' side='right' caption='[[3gs8]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+<StructureSection load='3gs8' size='340' side='right'caption='[[3gs8]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3gs8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GS8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GS8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3gs8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GS8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GS8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gs1|3gs1]], [[3gs5|3gs5]]</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3gs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gs8 OCA], [http://pdbe.org/3gs8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gs8 RCSB], [http://www.ebi.ac.uk/pdbsum/3gs8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gs8 ProSAT]</span></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=3gs8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gs8 OCA], [https://pdbe.org/3gs8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gs8 RCSB], [https://www.ebi.ac.uk/pdbsum/3gs8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gs8 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.
-Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme.,Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE J Am Chem Soc. 2009 Apr 8. PMID:19354216<ref>PMID:19354216</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3gs8" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Cristalli, G]]
+[[Category: Large Structures]]
-[[Category: Heller, M G]]
+[[Category: Cristalli G]]
-[[Category: Krucinska, J]]
+[[Category: Heller MG]]
-[[Category: Spitale, R C]]
+[[Category: Krucinska J]]
-[[Category: Volpini, R]]
+[[Category: Spitale RC]]
-[[Category: Wedekind, J E]]
+[[Category: Volpini R]]
-[[Category: Hairpin ribozyme]]
+[[Category: Wedekind JE]]
-[[Category: N1-deazaadenosine]]
-[[Category: Rna]]
-[[Category: Rna ribozyme]]