2c3y

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[[Image:2c3y.jpg|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus==
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|PDB= 2c3y |SIZE=350|CAPTION= <scene name='initialview01'>2c3y</scene>, resolution 1.93&Aring;
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<StructureSection load='2c3y' size='340' side='right'caption='[[2c3y]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Co2+Binding+Site+For+Chain+B'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <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>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>
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<table><tr><td colspan='2'>[[2c3y]] 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=2C3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C3Y FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_synthase Pyruvate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.7.1 1.2.7.1] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
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|GENE=
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<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>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2c3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c3y OCA], [https://pdbe.org/2c3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c3y RCSB], [https://www.ebi.ac.uk/pdbsum/2c3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c3y ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c3y OCA], [http://www.ebi.ac.uk/pdbsum/2c3y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2c3y RCSB]</span>
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== Function ==
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}}
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[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>
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== Evolutionary Conservation ==
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'''CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c3/2c3y_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2c3y ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== 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.
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.
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==About this Structure==
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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>
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2C3Y 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=2C3Y OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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]
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</div>
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[[Category: Desulfovibrio africanus]]
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<div class="pdbe-citations 2c3y" style="background-color:#fffaf0;"></div>
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[[Category: Pyruvate synthase]]
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[[Category: Single protein]]
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[[Category: Cavazza, C.]]
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[[Category: Chabriere, E.]]
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[[Category: Contreras-Martel, C.]]
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[[Category: Fontecilla-Camps, J C.]]
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[[Category: Hatchikian, E C.]]
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[[Category: Pieulle, L.]]
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[[Category: 4fe-4]]
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[[Category: electron transport]]
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[[Category: iron]]
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[[Category: iron-sulfur]]
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[[Category: iron-sulfur cluster]]
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[[Category: metal-binding]]
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[[Category: oxidoreductase]]
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[[Category: pyruvate catabolism]]
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[[Category: tpp-dependent enzyme]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:15:59 2008''
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==See Also==
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*[[Pyruvate-ferredoxin oxidoreductase|Pyruvate-ferredoxin oxidoreductase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Desulfocurvibacter africanus]]
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[[Category: Large Structures]]
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[[Category: Cavazza C]]
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[[Category: Chabriere E]]
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[[Category: Contreras-Martel C]]
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[[Category: Fontecilla-Camps JC]]
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[[Category: Hatchikian EC]]
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[[Category: Pieulle L]]

Current revision

CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

PDB ID 2c3y

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