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| - | [[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="2oue, resolution 2.05Å" /> | |
| - | '''Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution'''<br /> | |
| | | | |
| - | ==Overview== | + | ==Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution== |
| - | 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.
| + | <StructureSection load='2oue' size='340' side='right'caption='[[2oue]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | + | == Structural highlights == |
| | + | <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> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> |
| | + | <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> |
| | + | <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> |
| | + | </table> |
| | | | |
| - | ==About this Structure== | + | ==See Also== |
| - | 2OUE is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1ZFR. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA].
| + | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
| - | | + | __TOC__ |
| - | ==Reference==
| + | </StructureSection> |
| - | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16411744 16411744]
| + | [[Category: Large Structures]] |
| - | [[Category: Protein complex]] | + | [[Category: Wedekind JE]] |
| - | [[Category: Wedekind, J E.]] | + | |
| - | [[Category: NCO]]
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| - | [[Category: SO4]]
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| - | [[Category: all-rna]]
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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]]
| + | |
| - | [[Category: mutation]]
| + | |
| - | [[Category: ribose zipper]]
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| - | [[Category: rna]]
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| - | [[Category: s-turn]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:22:35 2008''
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