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1y5n
From Proteopedia
(Difference between revisions)
(New page: 200px<br /><applet load="1y5n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1y5n, resolution 2.50Å" /> '''The crystal structur...) |
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| - | [[Image:1y5n.gif|left|200px]]<br /><applet load="1y5n" size="450" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1y5n, resolution 2.50Å" /> | ||
| - | '''The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol'''<br /> | ||
| - | == | + | ==The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol== |
| - | The crystal structure of Escherichia coli nitrate reductase A (NarGHI) in | + | <StructureSection load='1y5n' size='340' side='right'caption='[[1y5n]], [[Resolution|resolution]] 2.50Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1y5n]] is a 3 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=1Y5N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y5N FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</scene>, <scene name='pdbligand=6MO:MOLYBDENUM(VI)+ION'>6MO</scene>, <scene name='pdbligand=AGA:(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL+OCTANOATE'>AGA</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MD1:PHOSPHORIC+ACID+4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL+ESTER+GUANYLATE+ESTER'>MD1</scene>, <scene name='pdbligand=PCI:PENTACHLOROPHENOL'>PCI</scene></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=1y5n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5n OCA], [https://pdbe.org/1y5n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y5n RCSB], [https://www.ebi.ac.uk/pdbsum/1y5n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5n ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/NARH_ECOLI NARH_ECOLI] The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The beta chain is an electron transfer unit containing four cysteine clusters involved in the formation of iron-sulfur centers. Electrons are transferred from the gamma chain to the molybdenum cofactor of the alpha subunit. | ||
| + | == 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/y5/1y5n_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=1y5n ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The crystal structure of Escherichia coli nitrate reductase A (NarGHI) in complex with pentachlorophenol has been determined to 2.0 A of resolution. We have shown that pentachlorophenol is a potent inhibitor of quinol:nitrate oxidoreductase activity and that it also perturbs the EPR spectrum of one of the hemes located in the membrane anchoring subunit (NarI). This new structural information together with site-directed mutagenesis data, biochemical analyses, and molecular modeling provide the first molecular characterization of a quinol binding and oxidation site (Q-site) in NarGHI. A possible proton conduction pathway linked to electron transfer reactions has also been defined, providing fundamental atomic details of ubiquinol oxidation by NarGHI at the bacterial membrane. | ||
| - | + | Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A.,Bertero MG, Rothery RA, Boroumand N, Palak M, Blasco F, Ginet N, Weiner JH, Strynadka NC J Biol Chem. 2005 Apr 15;280(15):14836-43. Epub 2004 Dec 22. PMID:15615728<ref>PMID:15615728</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1y5n" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Nitrate reductase|Nitrate reductase]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Escherichia coli]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Bertero MG]] | ||
| + | [[Category: Blasco F]] | ||
| + | [[Category: Boroumand N]] | ||
| + | [[Category: Ginet N]] | ||
| + | [[Category: Palak M]] | ||
| + | [[Category: Rothery RA]] | ||
| + | [[Category: Strynadka NCJ]] | ||
| + | [[Category: Weiner JH]] | ||
Current revision
The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol
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