View source for 2fgp


==Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6==
<StructureSection load='2fgp' size='340' side='right'caption='[[2fgp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2fgp]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FGP FirstGlance]. <br>
</td></tr><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></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=N6G:((2R,3S,4R,5S)-5-(2,6-DIAMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL+DIHYDROGEN+PHOSPHATE'>N6G</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zfr|1zfr]], [[1zft|1zft]], [[2bcz|2bcz]], [[1zfv|1zfv]], [[1zfx|1zfx]], [[2bcy|2bcy]]</div></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=2fgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fgp OCA], [https://pdbe.org/2fgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fgp RCSB], [https://www.ebi.ac.uk/pdbsum/2fgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fgp ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== 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<ref>PMID:16411744</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2fgp" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribozyme|Ribozyme]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Salter, J D]]
[[Category: Wedekind, J E]]
[[Category: Diaminopurine]]
[[Category: G8]]
[[Category: In-line geometry]]
[[Category: Mutant]]
[[Category: Ribozyme]]
[[Category: Rna]]