1pd2: Difference between revisions

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-[[Image:1pd2.gif|left|200px]]<br /><applet load="1pd2" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1pd2, resolution 2.3&Aring;" />
-'''CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE==
-Hematopoietic prostaglandin (PG) D synthase is the key enzyme for, production of the D and J series of prostanoids in the immune system and, mast cells. We isolated a cDNA for the rat enzyme, crystallized the, recombinant enzyme, and determined the three-dimensional structure of the, enzyme complexed with glutathione at 2.3 A resolution. The enzyme is the, first member of the sigma class glutathione S-transferase (GST) from, vertebrates and possesses a prominent cleft as the active site, which is, never seen among other members of the GST family. The unique 3-D, architecture of the cleft leads to the putative substrate binding mode and, its catalytic mechanism, responsible for the specific isomerization from, PGH2 to PGD2.
+<StructureSection load='1pd2' size='340' side='right'caption='[[1pd2]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1pd2]] is a 2 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=1PD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PD2 FirstGlance]. <br>
+</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=GSH:GLUTATHIONE'>GSH</scene></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=1pd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pd2 OCA], [https://pdbe.org/1pd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pd2 RCSB], [https://www.ebi.ac.uk/pdbsum/1pd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pd2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HPGDS_RAT HPGDS_RAT] Bifunctional enzyme which catalyzes both the conversion of PGH2 to PGD2, a prostaglandin involved in smooth muscle contraction/relaxation and a potent inhibitor of platelet aggregation, and the conjugation of glutathione with a wide range of aryl halides and organic isothiocyanates. Also exhibits low glutathione-peroxidase activity towards cumene hydroperoxide.<ref>PMID:10871602</ref> <ref>PMID:11672424</ref> <ref>PMID:16547010</ref> <ref>PMID:9323136</ref>
+== 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/pd/1pd2_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=1pd2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hematopoietic prostaglandin (PG) D synthase is the key enzyme for production of the D and J series of prostanoids in the immune system and mast cells. We isolated a cDNA for the rat enzyme, crystallized the recombinant enzyme, and determined the three-dimensional structure of the enzyme complexed with glutathione at 2.3 A resolution. The enzyme is the first member of the sigma class glutathione S-transferase (GST) from vertebrates and possesses a prominent cleft as the active site, which is never seen among other members of the GST family. The unique 3-D architecture of the cleft leads to the putative substrate binding mode and its catalytic mechanism, responsible for the specific isomerization from PGH2 to PGD2.
-==About this Structure==
+Cloning and crystal structure of hematopoietic prostaglandin D synthase.,Kanaoka Y, Ago H, Inagaki E, Nanayama T, Miyano M, Kikuno R, Fujii Y, Eguchi N, Toh H, Urade Y, Hayaishi O Cell. 1997 Sep 19;90(6):1085-95. PMID:9323136<ref>PMID:9323136</ref>
-PD2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with GTT as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Prostaglandin-D_synthase Prostaglandin-D synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.2 5.3.99.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PD2 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Cloning and crystal structure of hematopoietic prostaglandin D synthase., Kanaoka Y, Ago H, Inagaki E, Nanayama T, Miyano M, Kikuno R, Fujii Y, Eguchi N, Toh H, Urade Y, Hayaishi O, Cell. 1997 Sep 19;90(6):1085-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9323136 9323136]
+</div>
-[[Category: Prostaglandin-D synthase]]
+<div class="pdbe-citations 1pd2" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glutathione S-transferase 3D structures|Glutathione S-transferase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Ago H]]
-[[Category: Ago, H.]]
+[[Category: Miyano M]]
-[[Category: Miyano, M.]]
-[[Category: GTT]]
-[[Category: gst]]
-[[Category: hematopoietic prostaglandin d synthase]]
-[[Category: pgds]]
-[[Category: sigma-class gst]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:42:11 2007''