1dve: Difference between revisions

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 ==CRYSTAL STRUCTURE OF RAT HEME OXYGENASE-1 IN COMPLEX WITH HEME==
-<StructureSection load='1dve' size='340' side='right' caption='[[1dve]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1dve' size='340' side='right'caption='[[1dve]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1dve]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DVE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1dve]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qq8|1qq8]], [[1dvg|1dvg]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heme_oxygenase Heme oxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.99.3 1.14.99.3] </span></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=1dve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dve OCA], [https://pdbe.org/1dve PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dve RCSB], [https://www.ebi.ac.uk/pdbsum/1dve PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dve ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dve FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dve OCA], [http://pdbe.org/1dve PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dve RCSB], [http://www.ebi.ac.uk/pdbsum/1dve PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dve ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HMOX1_RAT HMOX1_RAT]] Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
+[https://www.uniprot.org/uniprot/HMOX1_RAT HMOX1_RAT] Heme oxygenase cleaves the heme ring at the alpha methene bridge to form biliverdin. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. Under physiological conditions, the activity of heme oxygenase is highest in the spleen, where senescent erythrocytes are sequestrated and destroyed.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1dve ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Heme oxygenase catalyzes the oxidative cleavage of protoheme to biliverdin, the first step of heme metabolism utilizing O(2) and NADPH. We determined the crystal structures of rat heme oxygenase-1 (HO-1)-heme and selenomethionyl HO-1-heme complexes. Heme is sandwiched between two helices with the delta-meso edge of the heme being exposed to the surface. Gly143N forms a hydrogen bond to the distal ligand of heme, OH(-). The distance between Gly143N and the ligand is shorter than that in the human HO-1-heme complex. This difference may be related to a pH-dependent change of the distal ligand of heme. Flexibility of the distal helix may control the stability of the coordination of the distal ligand to heme iron. The possible role of Gly143 in the heme oxygenase reaction is discussed.
-Crystal structure of rat heme oxygenase-1 in complex with heme.,Sugishima M, Omata Y, Kakuta Y, Sakamoto H, Noguchi M, Fukuyama K FEBS Lett. 2000 Apr 7;471(1):61-6. PMID:10760513<ref>PMID:10760513</ref>
+==See Also==
+*[[Heme oxygenase 3D structures|Heme oxygenase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1dve" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
+[[Category: Large Structures]]
-[[Category: Heme oxygenase]]
+[[Category: Rattus norvegicus]]
-[[Category: Fukuyama, K]]
+[[Category: Fukuyama K]]
-[[Category: Kakuta, Y]]
+[[Category: Kakuta Y]]
-[[Category: Noguchi, M]]
+[[Category: Noguchi M]]
-[[Category: Omata, Y]]
+[[Category: Omata Y]]
-[[Category: Sakamoto, H]]
+[[Category: Sakamoto H]]
-[[Category: Sugishima, M]]
+[[Category: Sugishima M]]
-[[Category: All alpha]]
-[[Category: Oxidoreductase]]
-[[Category: Protein-substrate complex]]