3cqs

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[[Image:3cqs.jpg|left|200px]]
 
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==A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases==
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The line below this paragraph, containing "STRUCTURE_3cqs", creates the "Structure Box" on the page.
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<StructureSection load='3cqs' size='340' side='right'caption='[[3cqs]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<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>
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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]] 2.8&#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>
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{{STRUCTURE_3cqs| PDB=3cqs | 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=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>
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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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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.
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'''A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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3CQS is a [[Protein complex]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQS OCA].
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</div>
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<div class="pdbe-citations 3cqs" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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]
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*[[Ribozyme 3D structures|Ribozyme 3D structures]]
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[[Category: Protein complex]]
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== References ==
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[[Category: Krucinska, J.]]
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<references/>
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[[Category: Spitale, R C.]]
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__TOC__
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[[Category: Torelli, A T.]]
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</StructureSection>
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[[Category: Wedekind, J E.]]
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[[Category: Large Structures]]
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[[Category: 2s']]
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[[Category: Krucinska J]]
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[[Category: 5' phosphodiester]]
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[[Category: Spitale RC]]
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[[Category: Hairpin ribozyme]]
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[[Category: Torelli AT]]
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[[Category: Phosphoryl-transfer]]
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[[Category: Wedekind JE]]
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[[Category: Reaction-intermediate]]
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[[Category: Ribonuclease]]
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[[Category: Rna]]
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[[Category: Transition-state stabilization]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 22 22:13:19 2008''
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A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases

PDB ID 3cqs

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