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2cad

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[[Image:2cad.gif|left|200px]]
 
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==NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 2F, 2X and 2I sites.==
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The line below this paragraph, containing "STRUCTURE_2cad", creates the "Structure Box" on the page.
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<StructureSection load='2cad' size='340' side='right'caption='[[2cad]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2cad]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CAD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.3&#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=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
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{{STRUCTURE_2cad| PDB=2cad | SCENE= }}
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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=2cad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cad OCA], [https://pdbe.org/2cad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cad RCSB], [https://www.ebi.ac.uk/pdbsum/2cad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cad ProSAT]</span></td></tr>
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</table>
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'''NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 2F, 2X AND 2I SITES.'''
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== Function ==
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[https://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY] Transcriptional regulator (Potential).
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The survival of Helicobacter pylori in the human stomach critically relies on the availability and use of nickel, an absolute cofactor of the important virulence determinant urease. Nickel-responsive gene regulation is mediated by HpNikR, a protein belonging to the ribbon-helix-helix family of transcriptional regulators. Unlike its homologues, HpNikR acts as both a repressor and an activator within an acid adaptation cascade. We report the crystal structure of the full-length HpNikR in a nickel-free conformation and two nickel-bound structures obtained in different conditions: Ni1-HpNikR and Ni2-HpNikR. Apo-HpNikR shows the same global fold as its bacterial homologues although with an unusual closed trans-conformation and asymmetrical quaternary arrangement. The structure of Ni1-HpNikR in the presence of nickel has two different sides, one showing nickel binding similar to that of known NikRs and the other reflecting an intermediate state. The structure of Ni2-HpNikR obtained using a shorter exposure to nickel provides another snapshot of the nickel incorporation. Altogether, the three structures have allowed us to determine the route for nickel within HpNikR and reveal the cooperativity between the tetramerization domain and the DNA-binding domain. Experiments using point mutations of HpnikR residues involved in nickel internalisation confirm that these residues are critical for HpNikR functions in vivo.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/2cad_consurf.spt"</scriptWhenChecked>
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2CAD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CAD OCA].
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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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==Reference==
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</jmolCheckbox>
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Structural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel-bound states., Dian C, Schauer K, Kapp U, McSweeney SM, Labigne A, Terradot L, J Mol Biol. 2006 Aug 25;361(4):715-30. Epub 2006 Jul 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16872629 16872629]
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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=2cad ConSurf].
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[[Category: Helicobacter pylori]]
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<div style="clear:both"></div>
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[[Category: Single protein]]
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__TOC__
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[[Category: Dian, C.]]
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</StructureSection>
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[[Category: Kapp, U.]]
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[[Category: Helicobacter pylori 26695]]
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[[Category: Labigne, A.]]
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[[Category: Large Structures]]
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[[Category: Mcsweeney, S M.]]
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[[Category: Dian C]]
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[[Category: Schauer, K.]]
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[[Category: Kapp U]]
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[[Category: Terradot, L.]]
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[[Category: Labigne A]]
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[[Category: Acidic-adaptive response]]
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[[Category: McSweeney SM]]
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[[Category: Dna-binding]]
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[[Category: Schauer K]]
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[[Category: Hypothetical protein]]
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[[Category: Terradot L]]
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[[Category: Metal-binding]]
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[[Category: Nickel]]
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[[Category: Nickel uptake]]
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[[Category: Ribbon-helix-helix]]
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[[Category: Transcription regulator]]
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[[Category: Transcriptional regulation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 21:34:23 2008''
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Current revision

NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 2F, 2X and 2I sites.

PDB ID 2cad

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