1y5n

From Proteopedia

(Difference between revisions)

Current revision

The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol

Structural highlights

1y5n is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bertero MG, Rothery RA, Boroumand N, Palak M, Blasco F, Ginet N, Weiner JH, Strynadka NC. Structural and biochemical characterization of a quinol binding site of Escherichia coli nitrate reductase A. J Biol Chem. 2005 Apr 15;280(15):14836-43. Epub 2004 Dec 22. PMID:15615728 doi:10.1074/jbc.M410457200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1y5n"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1y5n.png|left|200px]]
-<!--
+==The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol==
-The line below this paragraph, containing "STRUCTURE_1y5n", creates the "Structure Box" on the page.
+<StructureSection load='1y5n' size='340' side='right'caption='[[1y5n]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#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>, <scene name='pdbligand=PCI:PENTACHLOROPHENOL'>PCI</scene></td></tr>
-{{STRUCTURE_1y5n|  PDB=1y5n  |  SCENE=  }}
+<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.
-===The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol===
+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 1y5n" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15615728}}, adds the Publication Abstract to the page
+*[[Nitrate reductase|Nitrate reductase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15615728 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15615728}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Y5N 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=1Y5N OCA].
-==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: 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 Mon Jul 28 15:41:31 2008''

1y5n

From Proteopedia

Current revision

The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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