1yq4

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[[Image:1yq4.gif|left|200px]]<br /><applet load="1yq4" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yq4, resolution 2.33&Aring;" />
 
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'''Avian respiratory complex ii with 3-nitropropionate and ubiquinone'''<br />
 
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==Overview==
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==Avian respiratory complex ii with 3-nitropropionate and ubiquinone==
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<StructureSection load='1yq4' size='340' side='right'caption='[[1yq4]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yq4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YQ4 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]] 2.33&#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=3NP:3-NITROPROPANOIC+ACID'>3NP</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=JZR:HEXYL+BETA-D-GLUCOPYRANOSIDE'>JZR</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=UQ:COENZYME+Q10,+(2Z,6E,10Z,14E,18E,22E,26Z)-ISOMER'>UQ</scene></td></tr>
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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=1yq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yq4 OCA], [https://pdbe.org/1yq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yq4 RCSB], [https://www.ebi.ac.uk/pdbsum/1yq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yq4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/D0VWW3_CHICK D0VWW3_CHICK]
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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/yq/1yq4_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=1yq4 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 ==
We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg(297) as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg(297). The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg(297) to be increased by 83 Da and to have the potential of losing 44 Da, consistent with decarboxylation, during fragmentation.
We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 A resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg(297) as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator of succinate dehydrogenase, forms a covalent adduct with the side chain of Arg(297). The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg(297) to be increased by 83 Da and to have the potential of losing 44 Da, consistent with decarboxylation, during fragmentation.
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==About this Structure==
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3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.,Huang LS, Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE, Berry EA J Biol Chem. 2006 Mar 3;281(9):5965-72. Epub 2005 Dec 21. PMID:16371358<ref>PMID:16371358</ref>
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1YQ4 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with <scene name='pdbligand=BHG:'>BHG</scene>, <scene name='pdbligand=FAD:'>FAD</scene>, <scene name='pdbligand=FES:'>FES</scene>, <scene name='pdbligand=SF4:'>SF4</scene>, <scene name='pdbligand=F3S:'>F3S</scene>, <scene name='pdbligand=HEM:'>HEM</scene>, <scene name='pdbligand=3NP:'>3NP</scene>, <scene name='pdbligand=UQ:'>UQ</scene>, <scene name='pdbligand=PEE:'>PEE</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Succinate_dehydrogenase_(ubiquinone) Succinate dehydrogenase (ubiquinone)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.5.1 1.3.5.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YQ4 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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3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme., Huang LS, Sun G, Cobessi D, Wang AC, Shen JT, Tung EY, Anderson VE, Berry EA, J Biol Chem. 2006 Mar 3;281(9):5965-72. Epub 2005 Dec 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16371358 16371358]
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</div>
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[[Category: Gallus gallus]]
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<div class="pdbe-citations 1yq4" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Succinate dehydrogenase (ubiquinone)]]
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[[Category: Anderson, V E.]]
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[[Category: Berry, E A.]]
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[[Category: Cobessi, D.]]
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[[Category: Huang, L.]]
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[[Category: Shen, J T.]]
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[[Category: Sun, G.]]
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[[Category: Tung, E Y.]]
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[[Category: Wang, A.]]
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[[Category: 3NP]]
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[[Category: BHG]]
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[[Category: F3S]]
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[[Category: FAD]]
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[[Category: FES]]
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[[Category: GOL]]
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[[Category: HEM]]
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[[Category: PEE]]
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[[Category: SF4]]
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[[Category: UQ]]
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[[Category: complex ii]]
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[[Category: cytochrome b]]
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[[Category: heme protein]]
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[[Category: iron sulfur protein]]
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[[Category: membrane protein]]
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[[Category: oxaloacetate nitropropionate ubiquinone]]
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[[Category: oxidoreductase]]
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[[Category: redox enzyme]]
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[[Category: respiratory chain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:07:55 2008''
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==See Also==
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*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
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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: Gallus gallus]]
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[[Category: Large Structures]]
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[[Category: Anderson VE]]
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[[Category: Berry EA]]
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[[Category: Cobessi D]]
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[[Category: Huang L]]
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[[Category: Shen JT]]
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[[Category: Sun G]]
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[[Category: Tung EY]]
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[[Category: Wang A]]

Current revision

Avian respiratory complex ii with 3-nitropropionate and ubiquinone

PDB ID 1yq4

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