1ws3: Difference between revisions

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-[[Image:1ws3.png|left|200px]]
-<!--
+==Urate oxidase from aspergillus flavus complexed with uracil==
-The line below this paragraph, containing "STRUCTURE_1ws3", creates the "Structure Box" on the page.
+<StructureSection load='1ws3' size='340' side='right'caption='[[1ws3]], [[Resolution|resolution]] 3.20&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'>[[1ws3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WS3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WS3 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]] 3.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAC:N-ACETYL-SERINE'>SAC</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
-{{STRUCTURE_1ws3|  PDB=1ws3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ws3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ws3 OCA], [https://pdbe.org/1ws3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ws3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ws3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ws3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/URIC_ASPFL URIC_ASPFL] Catalyzes the oxidation of uric acid to 5-hydroxyisourate, which is further processed to form (S)-allantoin.
+== 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/ws/1ws3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1ws3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Urate oxidase from Aspergillus flavus (uricase or Uox; EC 1.7.3.3) is a 135 kDa homotetramer with a subunit consisting of 301 amino acids. It catalyses the first step of the degradation of uric acid into allantoin. The structure of the extracted enzyme complexed with a purine-type inhibitor (8-azaxanthin) had been solved from high-resolution X-ray diffraction of I222 crystals. Expression of the recombinant enzyme in Saccharomyces cerevisiae followed by a new purification procedure allowed the crystallization of both unliganded and liganded enzymes utilizing the same conditions but in various crystal forms. Here, four different crystal forms of Uox are analyzed. The diversity of the Uox crystal forms appears to depend strongly on the chemicals used as inhibitors. In the presence of uracil and 5,6-diaminouracil crystals usually belong to the trigonal space group P3(1)21, the asymmetric unit (AU) of which contains one tetramer of Uox (four subunits). Chemical oxidation of 5,6-diaminouracil within the protein may occur, leading to the canonical (I222) packing with one subunit per AU. Coexistence of two crystal forms, P2(1) with two tetramers per AU and I222, was found in the same crystallization drop containing another inhibitor, guanine. Finally, a fourth form, P2(1)2(1)2 with one tetramer per AU, resulted fortuitously in the presence of cymelarsan, an additive. Of all the reported forms, the I222 crystal forms present by far the best X-ray diffraction resolution (approximately 1.6 angstroms resolution compared with 2.3-3.2 angstroms for the other forms). The various structures and contacts in all crystalline lattices are compared. The backbones are essentially conserved except for the region near the active site. Its location at the dimer interface is thus likely to be at the origin of the crystal contact changes as a response to the various bound inhibitors.
-===Urate oxidase from aspergillus flavus complexed with uracil===
+Urate oxidase from Aspergillus flavus: new crystal-packing contacts in relation to the content of the active site.,Retailleau P, Colloc'h N, Vivares D, Bonnete F, Castro B, El Hajji M, Prange T Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):218-29. Epub 2005, Feb 24. PMID:15735331<ref>PMID:15735331</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ws3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15735331}}, adds the Publication Abstract to the page
+*[[Urate oxidase 3D structures|Urate oxidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15735331 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15735331}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[1ws3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WS3 OCA].
-==Reference==
-<ref group="xtra">PMID:15735331</ref><ref group="xtra">PMID:9360612</ref><references group="xtra"/>
 [[Category: Aspergillus flavus]]
-[[Category: Urate oxidase]]
+[[Category: Large Structures]]
-[[Category: Bonnete, F.]]
+[[Category: Bonnete F]]
-[[Category: Castro, B.]]
+[[Category: Castro B]]
-[[Category: H, N Colloc.]]
+[[Category: Colloc'h N]]
-[[Category: Hajji, M El.]]
+[[Category: El Hajji M]]
-[[Category: Prange, T.]]
+[[Category: Prange T]]
-[[Category: Retailleau, P.]]
+[[Category: Retailleau P]]
-[[Category: Vivares, D.]]
+[[Category: Vivares D]]
-[[Category: Dimeric barrel]]
-[[Category: Oxidoreductase]]
-[[Category: Tunnel-shaped protein]]
-[[Category: Uric acid degradation]]