ArticleJournal of the American Chemical Society2010
Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel-binding sites.
Article in Journal of the American Chemical Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- 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
- The Electronic Structure of the Metal Active Site Determines the Geometric Structure and Function of the Metalloregulator NikR.Biochemistry · 2019Article
- Nickel Metalloregulators and Chaperones.Inorganics · 2019Article
- Metallochaperones and metalloregulation in bacteria.Essays in biochemistry · 2017Review
- 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
- Mechanistic insights into small molecule activation induced by ligand cooperativity in PCcarbeneP nickel pincer complexes: a quantum chemistry study.Journal of molecular modeling · 2015Article
- Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria.Molecules (Basel, Switzerland) · 2015Review
- Transcription factor-based biosensors enlightened by the analyte.Frontiers in microbiology · 2015Review
- Crosstalk between the HpArsRS two-component system and HpNikR is necessary for maximal activation of urease transcription.Frontiers in microbiology · 2015Article
- Nickel trafficking system responsible for urease maturation in Helicobacter pylori.World journal of gastroenterology · 2013Review
- The C-terminal domain of the virulence factor MgtC is a divergent ACT domain.Journal of bacteriology · 2012Article
- Specific metal recognition in nickel trafficking.Biochemistry · 2012Review
- Ni(II) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Metal site occupancy and allosteric switching in bacterial metal sensor proteins.Archives of biochemistry and biophysics · 2012Review
- Mechanisms of nickel toxicity in microorganisms.Metallomics : integrated biometal science · 2011Review
- In vivo recognition of the fecA3 target promoter by Helicobacter pylori NikR.Journal of bacteriology · 2011Article
- Allosteric regulation of the nickel-responsive NikR transcription factor from Helicobacter pylori.The Journal of biological chemistryArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The metalloregulatory protein NikR from Helicobacter pylori (HpNikR) is a master regulator of gene expression which both activates and represses specific genes in response to nickel availability. Here, we report the first crystal structure (at 2.37 Å resolution) of Ni(II)HpNikR prepared directly from the holo protein. The protein contains four nickel ions located in two distinct coordination environments. Two nickel ions are bound to sites in a four-coordinate square-planar geometry as predicted on the basis of the structures of NikR from Escherichia coli and Pyrococcus horikoshii . The remaining two nickel ions are bound to sites with unexpected 5- or 6-coordination geometries which were previously thought to be involved in nickel incorporation into the protein. The nickel with 5-/6-coordination geometry utilizes three histidines from two separate monomeric HpNikR units along with two or three water molecules as ligands. The spatial location of the nickel in the 5-/6-coordinate site is within approximately 5 Å of the expected site if a 4-coordinate square-planar geometry occurred. Two of the histidines that participate as ligands in the 5-/6-coordinate site would also participate as ligands if the 4-coordinate site was occupied, making it impossible for both sites to be occupied simultaneously. DFT calculations show that the 5-/6-coordinate geometries are energetically favorable when the local protein environment is included in the calculations. The presence of two distinct coordination environments in HpNikR is suggested to be related to the specificity and binding affinity of this transcription factor for DNA.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.