1yq4

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[[Image:1yq4.gif|left|200px]]
 
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{{Structure
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==Avian respiratory complex ii with 3-nitropropionate and ubiquinone==
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|PDB= 1yq4 |SIZE=350|CAPTION= <scene name='initialview01'>1yq4</scene>, resolution 2.33&Aring;
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<StructureSection load='1yq4' size='340' side='right'caption='[[1yq4]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=3NP:3-NITROPROPANOIC+ACID'>3NP</scene>, <scene name='pdbligand=BHG:2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>BHG</scene>, <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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PEE:PHOSPHATIDYLETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UQ:UBIQUINONE-10'>UQ</scene>
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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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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=[[1yq3|1YQ3]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yq4 OCA], [http://www.ebi.ac.uk/pdbsum/1yq4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yq4 RCSB]</span>
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== Function ==
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}}
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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 ==
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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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'''Avian respiratory complex ii with 3-nitropropionate and ubiquinone'''
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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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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 1yq4" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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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*[[Succinate dehydrogenase 3D structures|Succinate dehydrogenase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1YQ4 is a [[Protein complex]] structure of sequences from [http://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].
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__TOC__
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</StructureSection>
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/16371358 16371358]
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[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Succinate dehydrogenase (ubiquinone)]]
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[[Category: Anderson VE]]
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[[Category: Anderson, V E.]]
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[[Category: Berry EA]]
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[[Category: Berry, E A.]]
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[[Category: Cobessi D]]
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[[Category: Cobessi, D.]]
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[[Category: Huang L]]
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[[Category: Huang, L.]]
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[[Category: Shen JT]]
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[[Category: Shen, J T.]]
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[[Category: Sun G]]
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[[Category: Sun, G.]]
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[[Category: Tung EY]]
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[[Category: Tung, E Y.]]
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[[Category: Wang A]]
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[[Category: Wang, A.]]
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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 Mon Mar 31 01:17:33 2008''
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Current revision

Avian respiratory complex ii with 3-nitropropionate and ubiquinone

PDB ID 1yq4

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