2g8r
From Proteopedia
(Difference between revisions)
(New page: 200px<br /><applet load="2g8r" size="450" color="white" frame="true" align="right" spinBox="true" caption="2g8r, resolution 1.70Å" /> '''The crystal structur...) |
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| - | [[Image:2g8r.gif|left|200px]]<br /><applet load="2g8r" size="450" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="2g8r, resolution 1.70Å" /> | ||
| - | '''The crystal structure of the RNase A- 3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine complex'''<br /> | ||
| - | == | + | ==The crystal structure of the RNase A- 3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine complex== |
| - | The binding of a moderate inhibitor, 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine, to ribonuclease A has | + | <StructureSection load='2g8r' size='340' side='right'caption='[[2g8r]], [[Resolution|resolution]] 1.70Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2g8r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G8R 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]] 1.7Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=N3E:1-[3-(4-CARBOXYPIPERIDIN-1-YL)-3-DEOXY-BETA-D-ARABINOFURANOSYL]PYRIMIDINE-2,4(1H,3H)-DIONE'>N3E</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=2g8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g8r OCA], [https://pdbe.org/2g8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g8r RCSB], [https://www.ebi.ac.uk/pdbsum/2g8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g8r ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g8/2g8r_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2g8r ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The binding of a moderate inhibitor, 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine, to ribonuclease A has been studied by X-ray crystallography at 1.7A resolution. Two inhibitor molecules are bound in the central RNA binding cavity of RNase A exploiting interactions with residues from peripheral binding sites rather than from the active site of the enzyme. The uracyl moiety of the first inhibitor molecule occupies the purine-preferring site of RNase A, while the rest of the molecule projects to the solvent. The second inhibitor molecule binds with the carboxyl group at the pyrimidine recognition site and the uridine moiety exploits interactions with RNase A residues Lys66, His119 and Asp121. Comparative structural analysis of the 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine complex with other RNase A-ligand complexes provides a structural explanation of its potency. The crystal structure of the RNase A-3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine complex provides evidence of a novel ligand-binding pattern in RNase A for 3'-N-aminonucleosides that was not anticipated by modelling studies, while it also suggests ways to improve the efficiency and selectivity of such compounds to develop pharmaceuticals against pathologies associated with RNase A homologues. | ||
| - | + | The binding of 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine to ribonuclease A in the crystal.,Leonidas DD, Maiti TK, Samanta A, Dasgupta S, Pathak T, Zographos SE, Oikonomakos NG Bioorg Med Chem. 2006 Sep 1;14(17):6055-64. Epub 2006 May 30. PMID:16730994<ref>PMID:16730994</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2g8r" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Bos taurus]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Leonidas DD]] | ||
| + | [[Category: Oikonomakos NG]] | ||
| + | [[Category: Zographos SE]] | ||
Current revision
The crystal structure of the RNase A- 3-N-piperidine-4-carboxyl-3-deoxy-ara-uridine complex
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