ArticleProceedings of the National Academy of Sciences of the United States of America2012
Ni(II) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking.Chemical reviews · 2024Review
- MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV-visible spectroscopy combined with size-exclusion chromatography.Biophysics and physicobiology · 2023Article
- Mechanistic insights into the nickel-dependent allosteric response of the Helicobacter pylori NikR transcription factor.The Journal of biological chemistry · 2023Article
- Insights into the Orchestration of Gene Transcription Regulators inInternational journal of molecular sciences · 2022Review
- Allosteric control of metal-responsive transcriptional regulators in bacteria.The Journal of biological chemistry · 2020Review
- Nickel Metalloregulators and Chaperones.Inorganics · 2019Article
- Tuning site-specific dynamics to drive allosteric activation in a pneumococcal zinc uptake regulator.eLife · 2018Article
- Metallochaperones and metalloregulation in bacteria.Essays in biochemistry · 2017Review
- Protein Arginine Methyltransferase 8: Tetrameric Structure and Protein Substrate Specificity.Biochemistry · 2015Article
- On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.Biophysical journal · 2015Article
- Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria.Molecules (Basel, Switzerland) · 2015Review
- Crosstalk between the HpArsRS two-component system and HpNikR is necessary for maximal activation of urease transcription.Frontiers in microbiology · 2015Article
- Structural basis of the pH-dependent assembly of a botulinum neurotoxin complex.Journal of molecular biology · 2014Article
- Architectures of whole-module and bimodular proteins from the 6-deoxyerythronolide B synthase.Journal of molecular biology · 2014Article
- Nickel trafficking system responsible for urease maturation in Helicobacter pylori.World journal of gastroenterology · 2013Review
- Helicobacter hepaticus NikR controls urease and hydrogenase activities via the NikABDE and HH0418 putative nickel import proteins.Microbiology (Reading, England) · 2013Article
- Structure of the arginine methyltransferase PRMT5-MEP50 reveals a mechanism for substrate specificity.PloS one · 2013Article
- Specific metal recognition in nickel trafficking.Biochemistry · 2012Review
- Allosteric regulation of the nickel-responsive NikR transcription factor from Helicobacter pylori.The Journal of biological chemistryArticle
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Helicobacter pylori NikR (HpNikR) is a nickel-dependent transcription factor that regulates multiple genes in the H. pylori pathogen. There are conflicting data regarding the locations of the Ni(II) sites and the role of Ni(II) coordination in DNA recognition. Herein, we report crystal structures of (i) the metal-binding domain (MBD) of HpNikR (3.08 Å) and (ii) a mutant, H74A (2.04 Å), designed to disrupt native Ni(II) coordination. In the MBD structure, four nickel ions are coordinated to two different types of nickel sites (4-coordinate, square planar, and 5/6-coordinate, square pyramidal/octahedral). In the H74A structure, all four nickel ions are coordinated to 4-coordinate square-planar sites. DNA-binding studies reveal tighter binding for target DNA sequences for holo-HpNikR compared with the affinities of Ni(II) reconstituted apo-HpNikR and H74A for these same DNA targets, supporting a role for Ni(II) coordination to 5/6 sites in DNA recognition. Small-angle X-ray scattering studies of holo-HpNikR and H74A reveal a high degree of conformational flexibility centered at the DNA-binding domains of H74A, which is consistent with disorder observed in the crystal structure of the protein. A model of DNA recognition by HpNikR is proposed in which Ni(II) coordination to specific sites in the MBD have a long-range effect on the flexibility of the DNA-binding domains and, consequently, the DNA recognition properties.
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