This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2wdr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:04, 6 April 2022) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
{{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/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <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=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TEO:MALATE+LIKE+INTERMEDIATE'>TEO</scene></td></tr>
-
-->
+
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nek|1nek]], [[1nen|1nen]], [[2acz|2acz]], [[2wdq|2wdq]], [[2wdv|2wdv]]</div></td></tr>
-
{{STRUCTURE_2wdr| PDB=2wdr | SCENE= }}
+
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate_dehydrogenase_(quinone) Succinate dehydrogenase (quinone)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.5.1 1.3.5.1] </span></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=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/DHSD_ECOLI DHSD_ECOLI]] Membrane-anchoring subunit of succinate dehydrogenase (SDH). [[https://www.uniprot.org/uniprot/DHSA_ECOLI DHSA_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. [[https://www.uniprot.org/uniprot/DHSC_ECOLI DHSC_ECOLI]] Membrane-anchoring subunit of succinate dehydrogenase (SDH). [[https://www.uniprot.org/uniprot/DHSB_ECOLI DHSB_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.
 +
== 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/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=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==
+
[[Category: Bacillus coli migula 1895]]
-
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].
+
[[Category: Large Structures]]
-
 
+
[[Category: Cecchini, G]]
-
==Reference==
+
[[Category: Iwata, S]]
-
<ref group="xtra">PMID:19710024</ref><references group="xtra"/>
+
[[Category: Maklashina, E]]
-
[[Category: Escherichia coli]]
+
[[Category: Ruprecht, J]]
-
[[Category: Cecchini, G.]]
+
[[Category: Yankovskaya, V]]
-
[[Category: Iwata, S.]]
+
-
[[Category: Maklashina, E.]]
+
-
[[Category: Ruprecht, J.]]
+
-
[[Category: Yankovskaya, V.]]
+
-
[[Category: 2fe-2]]
+
-
[[Category: 3fe-4]]
+
-
[[Category: 4fe-4]]
+
-
[[Category: Acetylation]]
+
[[Category: Cell inner membrane]]
[[Category: Cell inner membrane]]
[[Category: Cell membrane]]
[[Category: Cell membrane]]
Line 48: Line 58:
[[Category: Transport]]
[[Category: Transport]]
[[Category: Tricarboxylic acid cycle]]
[[Category: Tricarboxylic acid cycle]]
- 
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 9 08:44:26 2009''
 

Current revision

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

PDB ID 2wdr

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wdr"
Personal tools