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2oue

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==Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution==
==Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution==
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<StructureSection load='2oue' size='340' side='right' caption='[[2oue]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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<StructureSection load='2oue' size='340' side='right'caption='[[2oue]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2oue]] is a 4 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1zfr 1zfr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OUE FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2oue]] is a 4 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1zfr 1zfr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OUE FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zfx|1zfx]], [[1zfv|1zfv]], [[1zft|1zft]], [[2bcy|2bcy]], [[2fgp|2fgp]], [[2bcz|2bcz]], [[1x9k|1x9k]], [[1x9c|1x9c]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2oue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oue OCA], [https://pdbe.org/2oue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oue RCSB], [https://www.ebi.ac.uk/pdbsum/2oue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oue ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oue OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oue RCSB], [http://www.ebi.ac.uk/pdbsum/2oue PDBsum]</span></td></tr>
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</table>
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<table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The hairpin ribozyme requires functional group contributions from G8 to assist in phosphodiester bond cleavage. Previously, replacement of G8 by a series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on catalysis. To identify G8 features that contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were determined by X-ray crystallography in a resolution range between 2.3 and 2.7 A. For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution. The native structure revealed a scissile bond angle (tau) of 158 degrees, which is close to the requisite 180 degrees "in-line" geometry. Mutations G8(inosine), G8(diaminopurine), G8(aminopurine), G8(adenosine), and G8(uridine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees to 93 degrees) that paralleled their diminished solution activities. A superposition ensemble of all structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resulting from perturbation of the chemical environment and provided a rationale for how the exocyclic amine of nucleobase 8 promotes productive, in-line geometry. Changes at position 8 also caused variations in the A-1 sugar pucker. In this regard, variants A8 and U8 appeared to represent nonproductive ground states in which their 2'-OH groups mimicked the pro-R, nonbridging oxygen of the vanadate transition-state complex. Finally, the results indicated that ordered water molecules bind near the 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may play an important role in the reaction.
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Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.,Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE Biochemistry. 2006 Jan 24;45(3):686-700. PMID:16411744<ref>PMID:16411744</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[Ribozyme|Ribozyme]]
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Wedekind, J E.]]
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[[Category: Large Structures]]
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[[Category: All-rna]]
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[[Category: Wedekind JE]]
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[[Category: Catalytic rna]]
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[[Category: E-loop]]
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[[Category: Hairpin ribozyme]]
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[[Category: Low salt]]
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[[Category: Mutation]]
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[[Category: Ribose zipper]]
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[[Category: Rna]]
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[[Category: S-turn]]
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Current revision

Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution

PDB ID 2oue

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