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| | ==The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage site== | | ==The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage site== |
| - | <StructureSection load='1zft' size='340' side='right' caption='[[1zft]], [[Resolution|resolution]] 2.33Å' scene=''> | + | <StructureSection load='1zft' size='340' side='right'caption='[[1zft]], [[Resolution|resolution]] 2.33Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1zft]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZFT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1zft]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZFT 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=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]] 2.33Å</td></tr> |
| - | <tr id='NonStdRes'><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>, <scene name='pdbligand=I:INOSINIC+ACID'>I</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x9c|1x9c]], [[1x9k|1x9k]], [[1zfr|1zfr]], [[1zfv|1zfv]], [[1zfx|1zfx]]</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=1zft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zft OCA], [https://pdbe.org/1zft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zft RCSB], [https://www.ebi.ac.uk/pdbsum/1zft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zft ProSAT]</span></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=1zft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zft OCA], [http://pdbe.org/1zft PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zft RCSB], [http://www.ebi.ac.uk/pdbsum/1zft PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zft ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Wedekind, J E]] | + | [[Category: Large Structures]] |
| - | [[Category: 2'-ome]] | + | [[Category: Wedekind JE]] |
| - | [[Category: All-rna]]
| + | |
| - | [[Category: Catalytic rna]]
| + | |
| - | [[Category: Cobalt hexaamine]]
| + | |
| - | [[Category: E-loop]]
| + | |
| - | [[Category: Hairpin ribozyme]]
| + | |
| - | [[Category: Inosine]]
| + | |
| - | [[Category: Junctionless]]
| + | |
| - | [[Category: Low salt]]
| + | |
| - | [[Category: Mutation]]
| + | |
| - | [[Category: Ribose zipper]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: S-turn]]
| + | |
| - | [[Category: U39c]]
| + | |
| Structural highlights
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE. Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer. Biochemistry. 2006 Jan 24;45(3):686-700. PMID:16411744 doi:10.1021/bi051887k
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