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[[Image:2c3y.jpg|left|200px]]
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{{STRUCTURE_2c3y|  PDB=2c3y  |  SCENE=  }}
'''CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS'''


==CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus==
<StructureSection load='2c3y' size='340' side='right'caption='[[2c3y]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</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/c3/2c3y_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=2c3y 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>
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].
</div>
<div class="pdbe-citations 2c3y" 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 21:12:46 2008''

Latest revision as of 17:04, 13 December 2023

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

Structural highlights

2c3y is a 2 chain structure with sequence from Desulfocurvibacter africanus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.93Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Pieulle L, Guigliarelli B, Asso M, Dole F, Bernadac A, Hatchikian EC. Isolation and characterization of the pyruvate-ferredoxin oxidoreductase from the sulfate-reducing bacterium Desulfovibrio africanus. Biochim Biophys Acta. 1995 Jul 3;1250(1):49-59. doi:, 10.1016/0167-4838(95)00029-t. PMID:7612653 doi:http://dx.doi.org/10.1016/0167-4838(95)00029-t
  2. ↑ Cavazza C, Contreras-Martel C, Pieulle L, Chabriere E, Hatchikian EC, Fontecilla-Camps JC. Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate. Structure. 2006 Feb;14(2):217-24. PMID:16472741 doi:10.1016/j.str.2005.10.013

2c3y, resolution 1.93Å

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