3agn: Difference between revisions

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-[[Image:3agn.png|left|200px]]
-{{STRUCTURE_3agn|  PDB=3agn  |  SCENE=  }}
+==Crystal Structure of Ustilago sphaerogena Ribonuclease U2 Complexed with adenosine 3'-monophosphate==
+<StructureSection load='3agn' size='340' side='right'caption='[[3agn]], [[Resolution|resolution]] 0.96&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3agn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ustilago_sphaerogena Ustilago sphaerogena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AGN 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]] 0.96&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=3agn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3agn OCA], [https://pdbe.org/3agn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3agn RCSB], [https://www.ebi.ac.uk/pdbsum/3agn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3agn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNU2_USTSP RNU2_USTSP]
+== 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/ag/3agn_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=3agn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aspartates in proteins are isomerized non-enzymatically to isoaspartate via succinimide in vitro and in vivo. In order to elucidate the mechanism of isoaspartate formation within the Asp45-Glu46 sequence of Ustilago sphaerogena ribonuclease U2 based on three-dimensional structure, crystal structures of ribonuclease U2 complexed with adenosine 3'-monophosphate have been solved at 0.96 and 0.99 A resolution. The crystal structures revealed that the C(gamma) atom of Asp45 is located just beside the main-chain N atom of Glu46 and that the conformation which is suitable for succinimide formation is stabilized by a hydrogen-bond network mediated by water molecules 190, 219 and 220. These water molecules are suggested to promote the formation of isoaspartate via succinimide: in the succinimide-formation reaction water 219 receives a proton from the N atom of Glu46 as a general base and waters 190 and 220 stabilize the tetrahedral intermediate, and in the succinimide-hydrolysis reaction water 219 provides a proton for the N atom of Glu46 as a general acid. The purine-base recognition scheme of ribonuclease U2 is also discussed.
-===Crystal Structure of Ustilago sphaerogena Ribonuclease U2 Complexed with adenosine 3'-monophosphate===
+Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate.,Noguchi S Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):843-9. Epub 2010 Jun 19. PMID:20606265<ref>PMID:20606265</ref>
-{{ABSTRACT_PUBMED_20606265}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3agn" style="background-color:#fffaf0;"></div>
-[[3agn]] is a 1 chain structure of [[Ribonuclease]] with sequence from [http://en.wikipedia.org/wiki/Ustilago_sphaerogena Ustilago sphaerogena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AGN OCA].
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020606265</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Ustilago sphaerogena]]
-[[Category: Noguchi, S.]]
+[[Category: Noguchi S]]
-[[Category: Hydrolase]]
-[[Category: Purine-specific endo-ribonuclease]]