View source for 2wvb


==Structural and mechanistic insights into Helicobacter pylori NikR function==
<StructureSection load='2wvb' size='340' side='right'caption='[[2wvb]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2wvb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WVB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2caj|2caj]], [[2ca9|2ca9]], [[2cad|2cad]], [[2wvd|2wvd]], [[2wve|2wve]], [[2wvf|2wvf]], [[2wvc|2wvc]]</div></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=2wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wvb OCA], [https://pdbe.org/2wvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wvb RCSB], [https://www.ebi.ac.uk/pdbsum/2wvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wvb ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/NIKR_HELPY NIKR_HELPY]] Transcriptional regulator (Potential). 
== 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/wv/2wvb_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2wvb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.

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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2wvb" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Campylobacter pylori]]
[[Category: Large Structures]]
[[Category: Bahlawane, C]]
[[Category: Delay, C]]
[[Category: Dian, C]]
[[Category: Fauquant, C]]
[[Category: Michaud-Soret, I]]
[[Category: Muller, C]]
[[Category: Reuse, H De]]
[[Category: Round, A]]
[[Category: Schauer, K]]
[[Category: Terradot, L]]
[[Category: Dna-binding]]
[[Category: Metal-binding]]
[[Category: Metalloregulator]]
[[Category: Rhh]]
[[Category: Transcription]]
[[Category: Transcription factor]]
[[Category: Transcription regulation]]