3ld4: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3ld4.png|left|200px]]
-<!--
+==Urate oxidase complexed with 8-nitro xanthine==
-The line below this paragraph, containing "STRUCTURE_3ld4", creates the "Structure Box" on the page.
+<StructureSection load='3ld4' size='340' side='right'caption='[[3ld4]], [[Resolution|resolution]] 1.35&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'>[[3ld4]] is a 1 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=3LD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LD4 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]] 1.35&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8NX:8-NITRO-3,7-DIHYDRO-1H-PURINE-2,6-DIONE'>8NX</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_3ld4|  PDB=3ld4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ld4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ld4 OCA], [https://pdbe.org/3ld4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ld4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ld4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ld4 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/ld/3ld4_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=3ld4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Urate oxidase (uricase; EC 1.7.3.3; UOX) from Aspergillus flavus catalyzes the oxidation of uric acid in the presence of molecular oxygen to 5-hydroxyisourate in the degradation cascade of purines; intriguingly, catalysis proceeds using neither a metal ion (Fe, Cu etc.) nor a redox cofactor. UOX is a tetrameric enzyme with four active sites located at the interface of two subunits; its structure was refined at atomic resolution (1 A) using new crystal data in the presence of xanthine and at near-atomic resolution (1.3-1.7 A) in complexes with the natural substrate (urate) and two inhibitors: 8-nitroxanthine and 8-thiouric acid. Three new features of the structural and mechanistic behaviour of the enzyme were addressed. Firstly, the high resolution of the UOX-xanthine structure allowed the solution of an old structural problem at a contact zone within the tetramer; secondly, the protonation state of the substrate was determined from both a halochromic inhibitor complex (UOX-8-nitroxanthine) and from the H-atom distribution in the active site, using the structures of the UOX-xanthine and the UOX-uric acid complexes; and thirdly, it was possible to extend the general base system, characterized by the conserved catalytic triad Thr-Lys-His, to a large water network that is able to buffer and shuttle protons back and forth between the substrate and the peroxo hole along the reaction pathway.
-===Urate oxidase complexed with 8-nitro xanthine===
+Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand.,Gabison L, Chiadmi M, El Hajji M, Castro B, Colloc'h N, Prange T Acta Crystallogr D Biol Crystallogr. 2010 Jun;66(Pt 6):714-24. Epub 2010 May 15. PMID:20516624<ref>PMID:20516624</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20516624}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3ld4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20516624 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_20516624}}
-==About this Structure==
-[[3ld4]] is a 1 chain structure of [[Urate Oxidase]] 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=3LD4 OCA].
 ==See Also==
-*[[Urate Oxidase|Urate Oxidase]]
+*[[Urate oxidase 3D structures|Urate oxidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020516624</ref><references group="xtra"/>
+__TOC__
-[[Category: Aspergillus flavus]]
+</StructureSection>
-[[Category: Urate oxidase]]
-[[Category: Gabison, L.]]
-[[Category: H, N Colloc.]]
-[[Category: Prange, T.]]
 [[Category: Aspergillus flavus]]
-[[Category: Nitroxanthine]]
+[[Category: Large Structures]]
-[[Category: Oxidoreductase]]
+[[Category: Colloc'h N]]
-[[Category: Peroxisome]]
+[[Category: Gabison L]]
-[[Category: Protonation]]
+[[Category: Prange T]]
-[[Category: Purine metabolism]]
-[[Category: Thioxanthine]]
-[[Category: Urate oxidase]]
-[[Category: Xanthine]]