3i2r: Difference between revisions
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New page: '''Unreleased structure''' The entry 3i2r is ON HOLD Authors: Wedekind, J.E., Spitale, R.C., Krucinska, J. Description: Crystal structure of the hairpin ribozyme with a 2',5'-linked su... |
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==Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9== | |||
<StructureSection load='3i2r' size='340' side='right'caption='[[3i2r]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3i2r]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I2R 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]] 2.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1DP:N1-DEAZA-ADENOSINE-5-MONOPHOSPHATE'>1DP</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=3i2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i2r OCA], [https://pdbe.org/3i2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i2r RCSB], [https://www.ebi.ac.uk/pdbsum/3i2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i2r ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The hairpin ribozyme cleaves a phosphodiester bond within a cognate substrate. Structural and biochemical data indicate the conserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalysis. To investigate these residues, we replaced the imino moiety of each base with N1-deazaadenosine. This single-atom change resulted in an 8-fold loss in k(obs) for A9 and displacement of the base from the active site; no effects were observed for A10. We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA. | |||
Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.,Spitale RC, Volpini R, Mungillo MV, Krucinska J, Cristalli G, Wedekind JE Biochemistry. 2009 Aug 25;48(33):7777-9. PMID:19634899<ref>PMID:19634899</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3i2r" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribozyme 3D structures|Ribozyme 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Krucinska J]] | |||
[[Category: Spitale RC]] | |||
[[Category: Wedekind JE]] | |||
Latest revision as of 10:36, 6 September 2023
Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9
Structural highlights
Publication Abstract from PubMedThe hairpin ribozyme cleaves a phosphodiester bond within a cognate substrate. Structural and biochemical data indicate the conserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalysis. To investigate these residues, we replaced the imino moiety of each base with N1-deazaadenosine. This single-atom change resulted in an 8-fold loss in k(obs) for A9 and displacement of the base from the active site; no effects were observed for A10. We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA. Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.,Spitale RC, Volpini R, Mungillo MV, Krucinska J, Cristalli G, Wedekind JE Biochemistry. 2009 Aug 25;48(33):7777-9. PMID:19634899[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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