2acz

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{{Seed}}
 
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[[Image:2acz.png|left|200px]]
 
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==Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site==
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The line below this paragraph, containing "STRUCTURE_2acz", creates the "Structure Box" on the page.
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<StructureSection load='2acz' size='340' side='right'caption='[[2acz]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2acz]] is a 4 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=2ACZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ACZ FirstGlance]. <br>
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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]] 3.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AT5:3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE'>AT5</scene>, <scene name='pdbligand=CDN:CARDIOLIPIN'>CDN</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OAA:OXALOACETATE+ION'>OAA</scene></td></tr>
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{{STRUCTURE_2acz| PDB=2acz | SCENE= }}
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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=2acz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2acz OCA], [https://pdbe.org/2acz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2acz RCSB], [https://www.ebi.ac.uk/pdbsum/2acz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2acz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ac/2acz_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2acz 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 ==
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The transfer of electrons and protons between membrane-bound respiratory complexes is facilitated by lipid-soluble redox-active quinone molecules (Q). This work presents a structural analysis of the quinone-binding site (Q-site) identified in succinate:ubiquinone oxidoreductase (SQR) from Escherichia coli. SQR, often referred to as Complex II or succinate dehydrogenase, is a functional member of the Krebs cycle and the aerobic respiratory chain and couples the oxidation of succinate to fumarate with the reduction of quinone to quinol (QH(2)). The interaction between ubiquinone and the Q-site of the protein appears to be mediated solely by hydrogen bonding between the O1 carbonyl group of the quinone and the side chain of a conserved tyrosine residue. In this work, SQR was co-crystallized with the ubiquinone binding-site inhibitor Atpenin A5 (AA5) to confirm the binding position of the inhibitor and reveal additional structural details of the Q-site. The electron density for AA5 was located within the same hydrophobic pocket as ubiquinone at, however, a different position within the pocket. AA5 was bound deeper into the site prompting further assessment using protein-ligand docking experiments in silico. The initial interpretation of the Q-site was re-evaluated in the light of the new SQR-AA5 structure and protein-ligand docking data. Two binding positions, the Q(1)-site and Q(2)-site, are proposed for the E. coli SQR quinone-binding site to explain these data. At the Q(2)-site, the side chains of a serine and histidine residue are suitably positioned to provide hydrogen bonding partners to the O4 carbonyl and methoxy groups of ubiquinone, respectively. This allows us to propose a mechanism for the reduction of ubiquinone during the catalytic turnover of the enzyme.
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===Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site===
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Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction.,Horsefield R, Yankovskaya V, Sexton G, Whittingham W, Shiomi K, Omura S, Byrne B, Cecchini G, Iwata S J Biol Chem. 2006 Mar 17;281(11):7309-16. Epub 2005 Dec 27. PMID:16407191<ref>PMID:16407191</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2acz" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16407191}}, adds the Publication Abstract to the page
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*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16407191 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16407191}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2ACZ is a [[Protein complex]] 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=2ACZ OCA].
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==Reference==
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Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction., Horsefield R, Yankovskaya V, Sexton G, Whittingham W, Shiomi K, Omura S, Byrne B, Cecchini G, Iwata S, J Biol Chem. 2006 Mar 17;281(11):7309-16. Epub 2005 Dec 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16407191 16407191]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Succinate dehydrogenase]]
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[[Category: Byrne B]]
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[[Category: Byrne, B.]]
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[[Category: Cecchini G]]
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[[Category: Cecchini, G.]]
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[[Category: Horsefield R]]
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[[Category: Horsefield, R.]]
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[[Category: Iwata S]]
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[[Category: Iwata, S.]]
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[[Category: Omura S]]
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[[Category: Omura, S.]]
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[[Category: Sexton G]]
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[[Category: Sexton, G.]]
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[[Category: Shiomi K]]
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[[Category: Shiomi, K.]]
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[[Category: Whittingham W]]
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[[Category: Whittingham, W.]]
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[[Category: Yankovskaya V]]
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[[Category: Yankovskaya, V.]]
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[[Category: Aa5]]
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[[Category: Aerobic reparatory complex ii]]
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[[Category: At5]]
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[[Category: Atpenin a5]]
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[[Category: Membrane protein]]
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[[Category: Sdh]]
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[[Category: Sqr]]
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[[Category: Succinate dehydrogenase]]
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[[Category: Succinate:ubiquinone oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:25:48 2008''
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Current revision

Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site

PDB ID 2acz

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