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1y5i

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(New page: 200px<br /><applet load="1y5i" size="450" color="white" frame="true" align="right" spinBox="true" caption="1y5i, resolution 1.90&Aring;" /> '''The crystal structur...)
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[[Image:1y5i.gif|left|200px]]<br /><applet load="1y5i" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1y5i, resolution 1.90&Aring;" />
 
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'''The crystal structure of the NarGHI mutant NarI-K86A'''<br />
 
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==Overview==
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==The crystal structure of the NarGHI mutant NarI-K86A==
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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.
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<StructureSection load='1y5i' size='340' side='right'caption='[[1y5i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1y5i]] 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=1Y5I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y5I 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]] 1.9&#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=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=F3S:FE3-S4+CLUSTER'>F3S</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=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1y5i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5i OCA], [https://pdbe.org/1y5i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y5i RCSB], [https://www.ebi.ac.uk/pdbsum/1y5i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5i ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NARG_ECOLI NARG_ECOLI] The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The alpha chain is the actual site of nitrate reduction.
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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/y5/1y5i_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1y5i 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 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.
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==About this Structure==
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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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1Y5I is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MD1, 6MO, HEM, SF4, F3S, AGA and 3PH as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nitrate_reductase Nitrate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.99.4 1.7.99.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Y5I 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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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15615728 15615728]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 1y5i" style="background-color:#fffaf0;"></div>
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[[Category: Nitrate reductase]]
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[[Category: Protein complex]]
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[[Category: Bertero, M.G.]]
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[[Category: Blasco, F.]]
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[[Category: Boroumand, N.]]
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[[Category: Ginet, N.]]
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[[Category: Palak, M.]]
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[[Category: Rothery, R.A.]]
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[[Category: Strynadka, N.C.J.]]
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[[Category: Weiner, J.H.]]
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[[Category: 3PH]]
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[[Category: 6MO]]
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[[Category: AGA]]
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[[Category: F3S]]
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[[Category: HEM]]
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[[Category: MD1]]
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[[Category: SF4]]
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[[Category: electron transfer]]
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[[Category: membrane protein]]
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[[Category: nitrate reduction]]
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[[Category: q-site]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:34:53 2007''
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==See Also==
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*[[Nitrate reductase|Nitrate reductase]]
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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: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Bertero MG]]
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[[Category: Blasco F]]
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[[Category: Boroumand N]]
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[[Category: Ginet N]]
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[[Category: Palak M]]
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[[Category: Rothery RA]]
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[[Category: Strynadka NCJ]]
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[[Category: Weiner JH]]

Current revision

The crystal structure of the NarGHI mutant NarI-K86A

PDB ID 1y5i

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