2w3s: Difference between revisions

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-{{Seed}}
-[[Image:2w3s.png|left|200px]]
-<!--
+==Crystal Structure of Xanthine Dehydrogenase (desulfo form) from Rhodobacter capsulatus in Complex with Xanthine==
-The line below this paragraph, containing "STRUCTURE_2w3s", creates the "Structure Box" on the page.
+<StructureSection load='2w3s' size='340' side='right'caption='[[2w3s]], [[Resolution|resolution]] 2.60&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'>[[2w3s]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W3S 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MOM:HYDROXY(DIOXO)MOLYBDENUM'>MOM</scene>, <scene name='pdbligand=MTE:PHOSPHONIC+ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER'>MTE</scene>, <scene name='pdbligand=XAN:XANTHINE'>XAN</scene></td></tr>
-{{STRUCTURE_2w3s|  PDB=2w3s  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2w3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w3s OCA], [https://pdbe.org/2w3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w3s RCSB], [https://www.ebi.ac.uk/pdbsum/2w3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w3s ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O54050_RHOCA O54050_RHOCA]
+== 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/w3/2w3s_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=2w3s ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rhodobacter capsulatus xanthine dehydrogenase (XDH) is an (alphabeta)(2) heterotetrameric cytoplasmic enzyme that resembles eukaryotic xanthine oxidoreductases in respect to both amino acid sequence and structural fold. To obtain a detailed understanding of the mechanism of substrate and inhibitor binding at the active site, we solved crystal structures of R. capsulatus XDH in the presence of its substrates hypoxanthine, xanthine, and the inhibitor pterin-6-aldehyde using either the inactive desulfo form of the enzyme or an active site mutant (E(B)232Q) to prevent substrate turnover. The hypoxanthine- and xanthine-bound structures reveal the orientation of both substrates at the active site and show the importance of residue Glu(B)-232 for substrate positioning. The oxygen atom at the C-6 position of both substrates is oriented toward Arg(B)-310 in the active site. Thus the substrates bind in an orientation opposite to the one seen in the structure of the reduced enzyme with the inhibitor oxypurinol. The tightness of the substrates in the active site suggests that the intermediate products must exit the binding pocket to allow first the attack of the C-2, followed by oxidation of the C-8 atom to form the final product uric acid. Structural studies of pterin-6-aldehyde, a potent inhibitor of R. capsulatus XDH, contribute further to the understanding of the relative positioning of inhibitors and substrates in the binding pocket. Steady state kinetics reveal a competitive inhibition pattern with a K(i) of 103.57 +/- 18.96 nm for pterin-6-aldehyde.
-===CRYSTAL STRUCTURE OF XANTHINE DEHYDROGENASE (DESULFO FORM) FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH XANTHINE===
+Mechanism of Substrate and Inhibitor Binding of Rhodobacter capsulatus Xanthine Dehydrogenase.,Dietzel U, Kuper J, Doebbler JA, Schulte A, Truglio JJ, Leimkuhler S, Kisker C J Biol Chem. 2009 Mar 27;284(13):8768-76. Epub 2008 Dec 24. PMID:19109249<ref>PMID:19109249</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2w3s" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19109249}}, adds the Publication Abstract to the page
+*[[Xanthine dehydrogenase|Xanthine dehydrogenase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19109249 is the PubMed ID number.
+*[[Xanthine dehydrogenase 3D structures|Xanthine dehydrogenase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_19109249}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-W3S is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W3S OCA].
+[[Category: Large Structures]]
-==Reference==
-Mechanism of substrate and inhibitor binding of Rhodobacter capsulatus xanthine dehydrogenase., Dietzel U, Kuper J, Doebbler JA, Schulte A, Truglio JJ, Leimkuhler S, Kisker C, J Biol Chem. 2008 Dec 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19109249 19109249]
-[[Category: Protein complex]]
 [[Category: Rhodobacter capsulatus]]
-[[Category: Xanthine dehydrogenase]]
+[[Category: Dietzel U]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Kisker C]]
-[[Category: 2fe-2]]
+[[Category: Kuper J]]
-[[Category: Gout]]
+[[Category: Leimkuhler S]]
-[[Category: Hyperuricemia]]
-[[Category: Hypoxanthine]]
-[[Category: Iron]]
-[[Category: Iron-sulfur]]
-[[Category: Metal-binding]]
-[[Category: Molybdenum cofactor]]
-[[Category: Oxidoreductase]]
-[[Category: Purine metabolism]]
-[[Category: Xanthine]]
-[[Category: Xdh]]
-[[Category: Xo]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 20:22:23 2009''