Structural and mechanistic insights into Helicobacter pylori NikR function

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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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.

(2010) Nucleic Acids Res 38: 3106

  • DOI: https://doi.org/10.1093/nar/gkp1216
  • Primary Citation of Related Structures:  
    2WVB, 2WVC, 2WVD, 2WVE, 2WVF

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
148Helicobacter pylori 26695Mutation(s): 1 
Find proteins for O25896 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25896 
Go to UniProtKB:  O25896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO25896
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
G [auth B]
H [auth B]
J [auth C]
L [auth D]
E [auth A],
G [auth B],
H [auth B],
J [auth C],
L [auth D],
M [auth D]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
I [auth B]
K [auth C]
N [auth D]
O [auth D]
F [auth A],
I [auth B],
K [auth C],
N [auth D],
O [auth D],
P [auth D]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.97α = 90
b = 116.98β = 90
c = 123.95γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description