2oue

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2oue" size="450" color="white" frame="true" align="right" spinBox="true" caption="2oue, resolution 2.05&Aring;" /> '''Crystal structure of...)
Current revision (09:06, 21 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2oue, resolution 2.05&Aring;" />
 
-
'''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]] 2.05&Aring;' 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]] 2.05&#8491;</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 SO4 and NCO as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1ZFR. Full crystallographic information is available from [http://ispc.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]]
+
-
[[Category: SO4]]
+
-
[[Category: all-rna]]
+
-
[[Category: catalytic rna]]
+
-
[[Category: e-loop]]
+
-
[[Category: hairpin ribozyme]]
+
-
[[Category: low salt]]
+
-
[[Category: mutation]]
+
-
[[Category: ribose zipper]]
+
-
[[Category: rna]]
+
-
[[Category: s-turn]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 08:53:01 2007''
+

Current revision

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

PDB ID 2oue

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2oue"
Personal tools