2wvd

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{{Seed}}
 
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[[Image:2wvd.png|left|200px]]
 
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==Structural and mechanistic insights into Helicobacter pylori NikR function==
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The line below this paragraph, containing "STRUCTURE_2wvd", creates the "Structure Box" on the page.
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<StructureSection load='2wvd' size='340' side='right'caption='[[2wvd]], [[Resolution|resolution]] 2.65&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'>[[2wvd]] is a 4 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=2WVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVD 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]] 2.65&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_2wvd| PDB=2wvd | 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=2wvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wvd OCA], [https://pdbe.org/2wvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wvd RCSB], [https://www.ebi.ac.uk/pdbsum/2wvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wvd ProSAT]</span></td></tr>
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</table>
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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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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wv/2wvd_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=2wvd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly secondary external (X) sites. We describe a biochemical characterization of HpNikR mutants that shows that the HA sites are essential but not sufficient for DNA binding, while the secondary external (X) sites and residues from the HpNikR dimer-dimer interface are important for DNA binding. We show that a second metal is necessary for HpNikR/DNA binding, but only to some promoters. Small-angle X-ray scattering shows that HpNikR adopts a defined conformation in solution, resembling the cis-conformation and suggests that nickel does not trigger large conformational changes in HpNikR. The crystal structures of selected mutants identify the effects of each mutation on HpNikR structure. This study unravels key structural features from which we derive a model for HpNikR activation where: (i) HA sites and an hydrogen bond network are required for DNA binding and (ii) metallation of a unique secondary external site (X) modulates HpNikR DNA binding to low-affinity promoters by disruption of a salt bridge.
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===STRUCTURAL AND MECHANISTIC INSIGHTS INTO HELICOBACTER PYLORI NIKR FUNCTION===
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Structural and mechanistic insights into Helicobacter pylori NikR activation.,Bahlawane C, Dian C, Muller C, Round A, Fauquant C, Schauer K, de Reuse H, Terradot L, Michaud-Soret I Nucleic Acids Res. 2010 May;38(9):3106-18. Epub 2010 Jan 19. PMID:20089510<ref>PMID:20089510</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_20089510}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2wvd" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20089510 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20089510}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Helicobacter pylori 26695]]
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2WVD is a 4 chains structure with sequences 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=2WVD OCA].
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[[Category: Large Structures]]
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[[Category: Bahlawane C]]
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==Reference==
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[[Category: Delay C]]
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<ref group="xtra">PMID:20089510</ref><references group="xtra"/>
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[[Category: Dian C]]
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[[Category: Helicobacter pylori]]
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[[Category: Fauquant C]]
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[[Category: Bahlawane, C.]]
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[[Category: Michaud-Soret I]]
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[[Category: Delay, C.]]
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[[Category: Muller C]]
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[[Category: Dian, C.]]
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[[Category: Round A]]
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[[Category: Fauquant, C.]]
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[[Category: Schauer K]]
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[[Category: Michaud-Soret, I.]]
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[[Category: Terradot L]]
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[[Category: Muller, C.]]
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[[Category: De Reuse H]]
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[[Category: Reuse, H De.]]
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[[Category: Round, A.]]
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[[Category: Schauer, K.]]
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[[Category: Terradot, L.]]
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[[Category: Metal-binding]]
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[[Category: Metalloregulator]]
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[[Category: Rhh dna-binding]]
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[[Category: Transcription]]
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[[Category: Transcription factor]]
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[[Category: Transcription regulation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 09:07:40 2010''
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Current revision

Structural and mechanistic insights into Helicobacter pylori NikR function

PDB ID 2wvd

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