2c42: Difference between revisions

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-{{Seed}}
-[[Image:2c42.png|left|200px]]
-<!--
+==Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus==
-The line below this paragraph, containing "STRUCTURE_2c42", creates the "Structure Box" on the page.
+<StructureSection load='2c42' size='340' side='right'caption='[[2c42]], [[Resolution|resolution]] 1.78&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'>[[2c42]] 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=2C42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C42 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]] 1.78&#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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-{{STRUCTURE_2c42|  PDB=2c42  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2c42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c42 OCA], [https://pdbe.org/2c42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c42 RCSB], [https://www.ebi.ac.uk/pdbsum/2c42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c42 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/c4/2c42_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=2c42 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.
-===CRYSTAL STRUCTURE OF PYRUVATE-FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2c42" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16472741}}, adds the Publication Abstract to the page
+*[[Pyruvate-ferredoxin oxidoreductase|Pyruvate-ferredoxin oxidoreductase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16472741 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16472741}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Desulfocurvibacter africanus]]
-C42 is a 2 chains structure of sequences 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=2C42 OCA].
+[[Category: Large Structures]]
+[[Category: Cavazza C]]
-==Reference==
+[[Category: Chabriere E]]
-<ref group="xtra">PMID:16472741</ref><references group="xtra"/>
+[[Category: Contreras-Martel C]]
-[[Category: Desulfovibrio africanus]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Pyruvate synthase]]
+[[Category: Hatchikian EC]]
-[[Category: Cavazza, C.]]
+[[Category: Pieulle L]]
-[[Category: Chabriere, E.]]
-[[Category: Contreras-Martel, C.]]
-[[Category: Fontecilla-Camps, J C.]]
-[[Category: Hatchikian, E C.]]
-[[Category: Pieulle, L.]]
-[[Category: 4fe-4]]
-[[Category: Electron transport]]
-[[Category: Iron]]
-[[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 Sun Mar 22 11:34:26 2009''