2p7d: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2p7d.png|left|200px]]
-{{STRUCTURE_2p7d|  PDB=2p7d  |  SCENE=  }}
+==A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution==
+<StructureSection load='2p7d' size='340' side='right'caption='[[2p7d]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2p7d]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P7D 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]] 2.25&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</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=2p7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p7d OCA], [https://pdbe.org/2p7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p7d RCSB], [https://www.ebi.ac.uk/pdbsum/2p7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p7d ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.
-===A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution===
+A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.,Torelli AT, Krucinska J, Wedekind JE RNA. 2007 Jul;13(7):1052-70. Epub 2007 May 8. PMID:17488874<ref>PMID:17488874</ref>
-{{ABSTRACT_PUBMED_17488874}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2p7d" style="background-color:#fffaf0;"></div>
-[[2p7d]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P7D OCA].
 ==See Also==
-*[[Ribozyme|Ribozyme]]
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017488874</ref><ref group="xtra">PMID:016411744</ref><ref group="xtra">PMID:016262240</ref><references group="xtra"/>
+__TOC__
-[[Category: Krucinska, J.]]
+</StructureSection>
-[[Category: Torelli, A T.]]
+[[Category: Large Structures]]
-[[Category: Wedekind, J E.]]
+[[Category: Krucinska J]]
-[[Category: Active site water]]
+[[Category: Torelli AT]]
-[[Category: Hairpin ribozyme]]
+[[Category: Wedekind JE]]
-[[Category: Induced fit]]
-[[Category: Product mimic]]
-[[Category: Rna]]
-[[Category: Transition-state stabilization]]