2wdr: Difference between revisions

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{{Seed}}
[[Image:2wdr.png|left|200px]]


<!--
==E. coli succinate:quinone oxidoreductase (SQR) with pentachlorophenol bound==
The line below this paragraph, containing "STRUCTURE_2wdr", creates the "Structure Box" on the page.
<StructureSection load='2wdr' size='340' side='right'caption='[[2wdr]], [[Resolution|resolution]] 3.20&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'>[[2wdr]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WDR 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]] 3.2&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCI:PENTACHLOROPHENOL'>PCI</scene>, <scene name='pdbligand=TEO:MALATE+LIKE+INTERMEDIATE'>TEO</scene></td></tr>
{{STRUCTURE_2wdr|  PDB=2wdr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wdr OCA], [https://pdbe.org/2wdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wdr RCSB], [https://www.ebi.ac.uk/pdbsum/2wdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wdr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SDHA_ECOLI SDHA_ECOLI] Two distinct, membrane-bound, FAD-containing enzymes are responsible for the catalysis of fumarate and succinate interconversion; the fumarate reductase is used in anaerobic growth, and the succinate dehydrogenase is used in aerobic growth.<ref>PMID:24374335</ref> <ref>PMID:12560550</ref> <ref>PMID:16407191</ref> <ref>PMID:19710024</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/wd/2wdr_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=2wdr ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Three new structures of Escherichia coli succinate-quinone oxidoreductase (SQR) have been solved. One with the specific quinone-binding site (Q-site) inhibitor carboxin present has been solved at 2.4 A resolution and reveals how carboxin inhibits the Q-site. The other new structures are with the Q-site inhibitor pentachlorophenol and with an empty Q-site. These structures reveal important details unresolved in earlier structures. Comparison of the new SQR structures shows how subtle rearrangements of the quinone-binding site accommodate the different inhibitors. The position of conserved water molecules near the quinone binding pocket leads to a reassessment of possible water-mediated proton uptake networks that complete reduction of ubiquinone. The dicarboxylate-binding site in the soluble domain of SQR is highly similar to that seen in high resolution structures of avian SQR (PDB 2H88) and soluble flavocytochrome c (PDB 1QJD) showing mechanistically significant structural features conserved across prokaryotic and eukaryotic SQRs.


===E. COLI SUCCINATE:QUINONE OXIDOREDUCTASE (SQR) WITH PENTACHLOROPHENOL BOUND===
Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.,Ruprecht J, Yankovskaya V, Maklashina E, Iwata S, Cecchini G J Biol Chem. 2009 Oct 23;284(43):29836-46. Epub 2009 Aug 25. PMID:19710024<ref>PMID:19710024</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2wdr" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19710024}}, adds the Publication Abstract to the page
*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19710024 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19710024}}
__TOC__
 
</StructureSection>
==About this Structure==
2WDR is a 12 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WDR OCA].
 
==Reference==
<ref group="xtra">PMID:19710024</ref><references group="xtra"/>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Cecchini, G.]]
[[Category: Large Structures]]
[[Category: Iwata, S.]]
[[Category: Cecchini G]]
[[Category: Maklashina, E.]]
[[Category: Iwata S]]
[[Category: Ruprecht, J.]]
[[Category: Maklashina E]]
[[Category: Yankovskaya, V.]]
[[Category: Ruprecht J]]
[[Category: 2fe-2]]
[[Category: Yankovskaya V]]
[[Category: 3fe-4]]
[[Category: 4fe-4]]
[[Category: Acetylation]]
[[Category: Cell inner membrane]]
[[Category: Cell membrane]]
[[Category: Electron transport]]
[[Category: Fad]]
[[Category: Flavoprotein]]
[[Category: Heme]]
[[Category: Iron]]
[[Category: Iron-sulfur]]
[[Category: Metal-binding]]
[[Category: Oxidoreductase]]
[[Category: Succinate dehydrogenase activity]]
[[Category: Transmembrane]]
[[Category: Transport]]
[[Category: Tricarboxylic acid cycle]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep  9 08:44:26 2009''

Latest revision as of 17:34, 8 September 2026

E. coli succinate:quinone oxidoreductase (SQR) with pentachlorophenol bound

2wdr, resolution 3.20Å

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