3cqs: Difference between revisions

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{{Seed}}
[[Image:3cqs.png|left|200px]]


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==A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases==
The line below this paragraph, containing "STRUCTURE_3cqs", creates the "Structure Box" on the page.
<StructureSection load='3cqs' size='340' side='right'caption='[[3cqs]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3cqs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CQS FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#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=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene></td></tr>
{{STRUCTURE_3cqs|  PDB=3cqs  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cqs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cqs OCA], [https://pdbe.org/3cqs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cqs RCSB], [https://www.ebi.ac.uk/pdbsum/3cqs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cqs ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Reaction-intermediate analogs have been used to understand how phosphoryl transfer enzymes promote catalysis. Herein we report the first structure of a small ribozyme crystallized with a 3'-OH, 2',5'-linkage in lieu of the normal phosphodiester substrate. The new structure shares features of the reaction coordinate exhibited in prior ribozyme structures including a vanadate complex that mimicked the oxyphosphorane transition state. As such, the structure exhibits reaction-intermediate traits that allow direct comparison of stabilizing interactions to the 3'-OH, 2',5'-linkage contributed by the RNA enzyme and its protein counterpart, ribonuclease. Clear similarities are observed between the respective structures including hydrogen bonds to the non-bridging oxygens of the scissile phosphate. Other commonalities include carefully poised water molecules that may alleviate charge build-up in the transition state and placement of a positive charge near the leaving group. The advantages of 2',5'-linkages to investigate phosphoryl-transfer reactions are discussed, and argue for their expanded use in structural studies.


===A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases===
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.,Torelli AT, Spitale RC, Krucinska J, Wedekind JE Biochem Biophys Res Commun. 2008 Jun 20;371(1):154-8. Epub 2008 Apr 16. PMID:18423397<ref>PMID:18423397</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3cqs" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18423397}}, adds the Publication Abstract to the page
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18423397 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_18423397}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3CQS is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQS OCA].
[[Category: Krucinska J]]
 
[[Category: Spitale RC]]
==Reference==
[[Category: Torelli AT]]
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme., Torelli AT, Spitale RC, Krucinska J, Wedekind JE, Biochem Biophys Res Commun. 2008 Jun 20;371(1):154-8. Epub 2008 Apr 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18423397 18423397]
[[Category: Wedekind JE]]
[[Category: Protein complex]]
[[Category: Krucinska, J.]]
[[Category: Spitale, R C.]]
[[Category: Torelli, A T.]]
[[Category: Wedekind, J E.]]
[[Category: 2s']]
[[Category: 5' phosphodiester]]
[[Category: Hairpin ribozyme]]
[[Category: Phosphoryl-transfer]]
[[Category: Reaction-intermediate]]
[[Category: Ribonuclease]]
[[Category: Rna]]
[[Category: Transition-state stabilization]]
 
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Retrieved from "https://proteopedia.org/3cqs"