2cad

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[[Image:2cad.gif|left|200px]]<br /><applet load="2cad" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2cad, resolution 2.30&Aring;" />
 
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'''NIKR FROM HELICOBACTER PYLORI IN CLOSED TRANS-CONFORMATION AND NICKEL BOUND TO 2F, 2X AND 2I SITES.'''<br />
 
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==Overview==
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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 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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<StructureSection load='2cad' size='340' side='right'caption='[[2cad]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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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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2CAD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori] with NI, CIT, FMT and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=AC1:Ni Binding Site For Chain B'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CAD OCA].
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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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==Reference==
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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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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=16872629 16872629]
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</table>
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[[Category: Helicobacter pylori]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY] Transcriptional regulator (Potential).
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[[Category: Dian, C.]]
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== Evolutionary Conservation ==
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[[Category: Kapp, U.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Labigne, A.]]
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Check<jmol>
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[[Category: Mcsweeney, S.M.]]
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<jmolCheckbox>
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[[Category: Schauer, K.]]
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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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[[Category: Terradot, L.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: CIT]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: FMT]]
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</jmolCheckbox>
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[[Category: GOL]]
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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: NI]]
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<div style="clear:both"></div>
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[[Category: acidic-adaptive response]]
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__TOC__
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[[Category: dna-binding]]
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</StructureSection>
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[[Category: hypothetical protein]]
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[[Category: Helicobacter pylori 26695]]
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[[Category: metal-binding]]
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[[Category: Large Structures]]
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[[Category: nickel]]
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[[Category: Dian C]]
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[[Category: nickel uptake]]
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[[Category: Kapp U]]
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[[Category: ribbon-helix-helix]]
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[[Category: Labigne A]]
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[[Category: transcription regulator]]
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[[Category: McSweeney SM]]
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[[Category: transcriptional regulation]]
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[[Category: Schauer K]]
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[[Category: Terradot L]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 19:15:59 2007''
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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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