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[[Image:1y5i.gif|left|200px]]
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{{STRUCTURE_1y5i|  PDB=1y5i  |  SCENE=  }}
'''The crystal structure of the NarGHI mutant NarI-K86A'''


==The crystal structure of the NarGHI mutant NarI-K86A==
<StructureSection load='1y5i' size='340' side='right'caption='[[1y5i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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></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=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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NARI_ECOLI NARI_ECOLI] The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The gamma chain is a membrane-embedded heme-iron unit resembling cytochrome b, which transfers electrons from quinones to the beta 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/y5/1y5i_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=1y5i 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.


==Overview==
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>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1Y5I 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=1Y5I OCA].
</div>
<div class="pdbe-citations 1y5i" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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://www.ncbi.nlm.nih.gov/pubmed/15615728 15615728]
*[[Nitrate reductase|Nitrate reductase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Nitrate reductase]]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Bertero MG]]
[[Category: Bertero, M G.]]
[[Category: Blasco F]]
[[Category: Blasco, F.]]
[[Category: Boroumand N]]
[[Category: Boroumand, N.]]
[[Category: Ginet N]]
[[Category: Ginet, N.]]
[[Category: Palak M]]
[[Category: Palak, M.]]
[[Category: Rothery RA]]
[[Category: Rothery, R A.]]
[[Category: Strynadka NCJ]]
[[Category: Strynadka, N C.J.]]
[[Category: Weiner JH]]
[[Category: Weiner, J H.]]
[[Category: Electron transfer]]
[[Category: Membrane protein]]
[[Category: Nitrate reduction]]
[[Category: Q-site]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 15:54:03 2008''
Retrieved from "https://proteopedia.org/1y5i"