1zfv

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[[Image:1zfv.png|left|200px]]
 
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==The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site==
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The line below this paragraph, containing "STRUCTURE_1zfv", creates the "Structure Box" on the page.
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<StructureSection load='1zfv' size='340' side='right'caption='[[1zfv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1zfv]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZFV FirstGlance]. <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]] 2.4&#8491;</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=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_1zfv| PDB=1zfv | SCENE= }}
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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=1zfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfv OCA], [https://pdbe.org/1zfv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zfv RCSB], [https://www.ebi.ac.uk/pdbsum/1zfv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zfv ProSAT]</span></td></tr>
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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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===The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site===
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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 class="pdbe-citations 1zfv" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 16411744 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16411744}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFV OCA].
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[[Category: Wedekind JE]]
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/16411744 16411744]
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[[Category: Wedekind, J E.]]
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[[Category: All-rna]]
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[[Category: Catalytic rna]]
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[[Category: Cobalt hexaamine]]
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[[Category: E-loop]]
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[[Category: Hairpin ribozyme]]
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[[Category: Junctionless]]
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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: S-turn]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:32:21 2008''
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Current revision

The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site

PDB ID 1zfv

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