1y5i: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1y5i.gif|left|200px]]


{{Structure
==The crystal structure of the NarGHI mutant NarI-K86A==
|PDB= 1y5i |SIZE=350|CAPTION= <scene name='initialview01'>1y5i</scene>, resolution 1.90&Aring;
<StructureSection load='1y5i' size='340' side='right'caption='[[1y5i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <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=6MO:MOLYBDENUM(VI)+ION'>6MO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=AGA:(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL+OCTANOATE'>AGA</scene> and <scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</scene>
<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>
|ACTIVITY= [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]  
</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>
|GENE= narG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), narH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), narI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<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.


'''The crystal structure of the NarGHI mutant NarI-K86A'''
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>


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


==Overview==
==See Also==
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.
*[[Nitrate reductase|Nitrate reductase]]
 
== References ==
==About this Structure==
<references/>
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].
__TOC__
 
</StructureSection>
==Reference==
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]
[[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: 3PH]]
[[Category: 6MO]]
[[Category: AGA]]
[[Category: F3S]]
[[Category: HEM]]
[[Category: MD1]]
[[Category: SF4]]
[[Category: electron transfer]]
[[Category: membrane protein]]
[[Category: nitrate reduction]]
[[Category: q-site]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:18:40 2008''
Retrieved from "https://proteopedia.org/1y5i"