2c3o: Difference between revisions

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-[[Image:2c3o.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2c3o", creates the "Structure Box" on the page.
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-{{STRUCTURE_2c3o|  PDB=2c3o  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS'''
+==CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus==
+<StructureSection load='2c3o' size='340' side='right'caption='[[2c3o]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2c3o]] 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=2C3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C3O 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]] 2.7&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=2c3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c3o OCA], [https://pdbe.org/2c3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c3o RCSB], [https://www.ebi.ac.uk/pdbsum/2c3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c3o 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/c3/2c3o_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=2c3o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pyruvate-ferredoxin oxidoreductases (PFOR) are unique among thiamine pyrophosphate (ThDP)-containing enzymes in giving rise to a rather stable cofactor-based free-radical species upon the decarboxylation of their first substrate, pyruvate. We have obtained snapshots of unreacted and partially reacted (probably as a tetrahedral intermediate) pyruvate-PFOR complexes at different time intervals. We conclude that pyruvate decarboxylation involves very limited substrate-to-product movements but a significant displacement of the thiazolium moiety of ThDP. In this respect, PFOR seems to differ substantially from other ThDP-containing enzymes, such as transketolase and pyruvate decarboxylase. In addition, exposure of PFOR to oxygen in the presence of pyruvate results in significant inhibition of catalytic activity, both in solution and in the crystals. Examination of the crystal structure of inhibited PFOR suggests that the loss of activity results from oxime formation at the 4' amino substituent of the pyrimidine moiety of ThDP.
-==Overview==
+Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate.,Cavazza C, Contreras-Martel C, Pieulle L, Chabriere E, Hatchikian EC, Fontecilla-Camps JC Structure. 2006 Feb;14(2):217-24. PMID:16472741<ref>PMID:16472741</ref>
-Pyruvate-ferredoxin oxidoreductases (PFOR) are unique among thiamine pyrophosphate (ThDP)-containing enzymes in giving rise to a rather stable cofactor-based free-radical species upon the decarboxylation of their first substrate, pyruvate. We have obtained snapshots of unreacted and partially reacted (probably as a tetrahedral intermediate) pyruvate-PFOR complexes at different time intervals. We conclude that pyruvate decarboxylation involves very limited substrate-to-product movements but a significant displacement of the thiazolium moiety of ThDP. In this respect, PFOR seems to differ substantially from other ThDP-containing enzymes, such as transketolase and pyruvate decarboxylase. In addition, exposure of PFOR to oxygen in the presence of pyruvate results in significant inhibition of catalytic activity, both in solution and in the crystals. Examination of the crystal structure of inhibited PFOR suggests that the loss of activity results from oxime formation at the 4' amino substituent of the pyrimidine moiety of ThDP.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-C3O is a [[Single protein]] structure of 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=2C3O OCA].
+</div>
+<div class="pdbe-citations 2c3o" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate., Cavazza C, Contreras-Martel C, Pieulle L, Chabriere E, Hatchikian EC, Fontecilla-Camps JC, Structure. 2006 Feb;14(2):217-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16472741 16472741]
+*[[Pyruvate-ferredoxin oxidoreductase|Pyruvate-ferredoxin oxidoreductase]]
-[[Category: Desulfovibrio africanus]]
+== References ==
-[[Category: Pyruvate synthase]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Cavazza, C.]]
+</StructureSection>
-[[Category: Chabriere, E.]]
+[[Category: Desulfocurvibacter africanus]]
-[[Category: Contreras-Martel, C.]]
+[[Category: Large Structures]]
-[[Category: Fontecilla-Camps, J C.]]
+[[Category: Cavazza C]]
-[[Category: Hatchikian, E C.]]
+[[Category: Chabriere E]]
-[[Category: Pieulle, L.]]
+[[Category: Contreras-Martel C]]
-[[Category: 4fe-4]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Electron transport]]
+[[Category: Hatchikian EC]]
-[[Category: Iron]]
+[[Category: Pieulle L]]
-[[Category: Iron-sulfur]]
-[[Category: Iron-sulfur cluster]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Pyruvate catabolism]]
-[[Category: Tpp-dependent enzyme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 21:12:16 2008''