3b9j: Difference between revisions

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-{{Seed}}
-[[Image:3b9j.png|left|200px]]
-<!--
+==Structure of Xanthine Oxidase with 2-hydroxy-6-methylpurine==
-The line below this paragraph, containing "STRUCTURE_3b9j", creates the "Structure Box" on the page.
+<StructureSection load='3b9j' size='340' side='right'caption='[[3b9j]], [[Resolution|resolution]] 2.30&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'>[[3b9j]] is a 6 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=3B9J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B9J 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=290:6-METHYL-3,9-DIHYDRO-2H-PURIN-2-ONE'>290</scene>, <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=MOS:DIOXOTHIOMOLYBDENUM(VI)+ION'>MOS</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></td></tr>
-{{STRUCTURE_3b9j|  PDB=3b9j  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b9j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9j OCA], [https://pdbe.org/3b9j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b9j RCSB], [https://www.ebi.ac.uk/pdbsum/3b9j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b9j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XDH_BOVIN XDH_BOVIN] Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species.
+== 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/b9/3b9j_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=3b9j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Xanthine oxidoreductase catalyzes the final two steps of purine catabolism and is involved in a variety of pathological states ranging from hyperuricemia to ischemia-reperfusion injury. The human enzyme is expressed primarily in its dehydrogenase form utilizing NAD+ as the final electron acceptor from the enzyme's flavin site but can exist as an oxidase that utilizes O2 for this purpose. Central to an understanding of the enzyme's function is knowledge of purine substrate orientation in the enzyme's molybdenum-containing active site. We report here the crystal structure of xanthine oxidase, trapped at the stage of a critical intermediate in the course of reaction with the slow substrate 2-hydroxy-6-methylpurine at 2.3A. This is the first crystal structure of a reaction intermediate with a purine substrate that is hydroxylated at its C8 position as is xanthine and confirms the structure predicted to occur in the course of the presently favored reaction mechanism. The structure also corroborates recent work suggesting that 2-hydroxy-6-methylpurine orients in the active site with its C2 carbonyl group interacting with Arg-880 and extends our hypothesis that xanthine binds opposite this orientation, with its C6 carbonyl positioned to interact with Arg-880 in stabilizing the MoV transition state.
-===Structure of Xanthine Oxidase with 2-hydroxy-6-methylpurine===
+Substrate orientation in xanthine oxidase: crystal structure of enzyme in reaction with 2-hydroxy-6-methylpurine.,Pauff JM, Zhang J, Bell CE, Hille R J Biol Chem. 2008 Feb 22;283(8):4818-24. Epub 2007 Dec 6. PMID:18063585<ref>PMID:18063585</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3b9j" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18063585}}, adds the Publication Abstract to the page
+*[[Xanthine dehydrogenase 3D structures|Xanthine dehydrogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18063585 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18063585}}
+__TOC__
+</StructureSection>
-==About this Structure==
-B9J is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9J OCA].
-==Reference==
-<ref group="xtra">PMID:18063585</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Xanthine oxidase]]
+[[Category: Large Structures]]
-[[Category: Bell, C E.]]
+[[Category: Bell CE]]
-[[Category: Hille, R.]]
+[[Category: Hille R]]
-[[Category: Pauff, J M.]]
+[[Category: Pauff JM]]
-[[Category: Zhang, J.]]
+[[Category: Zhang J]]
-[[Category: Catalysis]]
-[[Category: Intermediate]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxisome]]
-[[Category: Substrate orientation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 15 09:21:27 2009''