1kek: Difference between revisions

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-[[Image:1kek.png|left|200px]]
-{{STRUCTURE_1kek|  PDB=1kek  |  SCENE=  }}
+==Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase==
+<StructureSection load='1kek' size='340' side='right'caption='[[1kek]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kek]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfocurvibacter_africanus Desulfocurvibacter africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEK 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]] 1.9&#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=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=HTL:2-ACETYL-THIAMINE+DIPHOSPHATE'>HTL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1kek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kek OCA], [https://pdbe.org/1kek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kek RCSB], [https://www.ebi.ac.uk/pdbsum/1kek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kek ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PFOR_DESAF PFOR_DESAF] Catalyzes the ferredoxin-dependent oxidative decarboxylation of pyruvate. Required for the transfer of electrons from pyruvate to ferredoxin (PubMed:9294422, PubMed:7612653). Ferredoxin I and ferredoxin II, which are single 4Fe-4S cluster ferredoxins are the most effective electron carriers of POR (PubMed:7612653).<ref>PMID:7612653</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/ke/1kek_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=1kek ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In anaerobic organisms, the decarboxylation of pyruvate, a crucial component of intermediary metabolism, is catalyzed by the metalloenzyme pyruvate: ferredoxin oxidoreductase (PFOR) resulting in the generation of low potential electrons and the subsequent acetylation of coenzyme A (CoA). PFOR is the only enzyme for which a stable acetyl thiamine diphosphate (ThDP)-based free radical reaction intermediate has been identified. The 1.87 A-resolution structure of the radical form of PFOR from Desulfovibrio africanus shows that, despite currently accepted ideas, the thiazole ring of the ThDP cofactor is markedly bent, indicating a drastic reduction of its aromaticity. In addition, the bond connecting the acetyl group to ThDP is unusually long, probably of the one-electron type already described for several cation radicals but not yet found in a biological system. Taken together, our data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA-based) radicals.
-===Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase===
+Crystal structure of the free radical intermediate of pyruvate:ferredoxin oxidoreductase.,Chabriere E, Vernede X, Guigliarelli B, Charon MH, Hatchikian EC, Fontecilla-Camps JC Science. 2001 Dec 21;294(5551):2559-63. PMID:11752578<ref>PMID:11752578</ref>
-{{ABSTRACT_PUBMED_11752578}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1kek" style="background-color:#fffaf0;"></div>
-[[1kek]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEK OCA].
 ==See Also==
 *[[Pyruvate-ferredoxin oxidoreductase|Pyruvate-ferredoxin oxidoreductase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:011752578</ref><ref group="xtra">PMID:012651851</ref><references group="xtra"/>
+__TOC__
-[[Category: Desulfovibrio africanus]]
+</StructureSection>
-[[Category: Pyruvate synthase]]
+[[Category: Desulfocurvibacter africanus]]
-[[Category: Chabriere, E.]]
+[[Category: Large Structures]]
-[[Category: Charon, M H.]]
+[[Category: Chabriere E]]
-[[Category: Fontecilla-Camps, J C.]]
+[[Category: Charon M-H]]
-[[Category: Guigliarelli, B.]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Hatchikian, E C.]]
+[[Category: Guigliarelli B]]
-[[Category: Vernede, X.]]
+[[Category: Hatchikian EC]]
-[[Category: 7 domain]]
+[[Category: Vernede X]]
-[[Category: Homodimer]]
-[[Category: Oxidoreductase]]