2WVC
Structural and mechanistic insights into Helicobacter pylori NikR function
Summary for 2WVC
| Entry DOI | 10.2210/pdb2wvc/pdb |
| Related | 2CA9 2CAD 2CAJ 2WVB 2WVD 2WVE 2WVF |
| Descriptor | PUTATIVE NICKEL-RESPONSIVE REGULATOR, GLYCEROL, SULFATE ION, ... (5 entities in total) |
| Functional Keywords | transcription factor, transcription regulation, rhh, dna-binding, transcription, metal-binding, metalloregulator |
| Biological source | HELICOBACTER PYLORI |
| Total number of polymer chains | 2 |
| Total formula weight | 34998.96 |
| Authors | Dian, C.,Bahlawane, C.,Muller, C.,Round, A.,Delay, C.,Fauquant, C.,Schauer, K.,de Reuse, H.,Michaud-Soret, I.,Terradot, L. (deposition date: 2009-10-16, release date: 2010-01-19, Last modification date: 2023-12-20) |
| Primary citation | Bahlawane, C.,Dian, C.,Muller, C.,Round, A.,Fauquant, C.,Schauer, K.,De Reuse, H.,Terradot, L.,Michaud-Soret, I. Structural and Mechanistic Insights Into Helicobacter Pylori Nikr Activation. Nucleic Acids Res., 38:3106-, 2010 Cited by 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. PubMed: 20089510DOI: 10.1093/NAR/GKP1216 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
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