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nikR DNA-binding transcriptional repressor NikR [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 947995, updated on 23-Nov-2023

Summary

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Gene symbol
nikR
Gene description
DNA-binding transcriptional repressor NikR
Primary source
ASAP:ABE-0011366
Locus tag
b3481
See related
ECOCYC:EG11519
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as
ECK3465; yhhG
Summary
ACT-like domain (Grant, 2006). [More information is available at EcoGene: EG11519].
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Genomic context

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Sequence:
NC_000913.3 (3618588..3618989)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene Ni(2(+)) ABC transporter membrane subunit NikB Neighboring gene Ni(2(+)) ABC transporter membrane subunit NikC Neighboring gene Ni(2(+)) ABC transporter ATP binding subunit NikD Neighboring gene Ni(2(+)) ABC transporter ATP binding subunit NikE Neighboring gene rhs element protein RhsB Neighboring gene PF15631 family protein YhhH Neighboring gene pseudo

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The Electronic Structure of the Metal Active Site Determines the Geometric Structure and Function of the Metalloregulator NikR. Ha Y, et al. Biochemistry, 2019 Aug 27. PMID 31339709, Free PMC Article
  2. Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli. Phillips CM, et al. Biochemistry, 2010 Sep 14. PMID 20704276, Free PMC Article
  3. The response of Escherichia coli NikR to nickel: a second nickel-binding site. Wang SC, et al. Biochemistry, 2010 Aug 10. PMID 20583753
  4. Potassium is critical for the Ni(II)-responsive DNA-binding activity of Escherichia coli NikR. Wang SC, et al. J Am Chem Soc, 2010 Feb 10. PMID 20088519
  5. Physical basis of metal-binding specificity in Escherichia coli NikR. Phillips CM, et al. J Am Chem Soc, 2009 Jul 29. PMID 19621966, Free PMC Article

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Both the Z(eff) of the metal ion and the donor nature of the ligands determine the electronic structure of the metal site metalloregulator NikR. This impacts the geometric structure of the metal site and thus the conformation of the protein.
    Title: The Electronic Structure of the Metal Active Site Determines the Geometric Structure and Function of the Metalloregulator NikR.
  2. Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli
    Title: Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli.
  3. localized this Ni(II) site to a region at the interface between the metal- and DNA-binding domains and identified His48 and His110 as residues that participate in the low-affinity Ni(II)-binding response
    Title: The response of Escherichia coli NikR to nickel: a second nickel-binding site.
  4. Mutagenesis and cation exchange experiments reveal that K(+) is a critical structural component for the activation of Ni(II)-responsive DNA binding by NikR.
    Title: Potassium is critical for the Ni(II)-responsive DNA-binding activity of Escherichia coli NikR.
  5. Results examine a series of residue interrelationships that describe an allosteric communication pathway between the Ni(2+)- and DNA-binding sites of NikR, which are separated by 40 A.
    Title: Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways.
  6. This data sheds light on the Ni(II)-selective conformational changes that allow NikR to bind DNA optimally and repress transcription of the nik operon.
    Title: Protease digestion analysis of Escherichia coli NikR: evidence for conformational stabilization with Ni(II).
  7. Two crystal structures of nickel-activated E. coli NikR were reported.
    Title: NikR-operator complex structure and the mechanism of repressor activation by metal ions.
  8. NikR response is specific to nickel in vivo.
    Title: Nickel-specific response in the transcriptional regulator, Escherichia coli NikR.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription repressor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables DNA-binding transcription repressor activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables core promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nickel cation binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nickel cation binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables sequence-specific DNA binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription cis-regulatory region binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables transcription cis-regulatory region binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within negative regulation of DNA-templated transcription initiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in response to nickel cation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of protein-DNA complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of protein-DNA complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA-binding transcriptional repressor NikR

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_000913.3 Reference assembly

    Range
    3618588..3618989
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_417938.1 DNA-binding transcriptional repressor NikR [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_417938.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A5B9AQ04, A0A5N8H7V5, A0A827Q5I2
    Conserved Domains (1) summary
    PRK02967
    Location:1 → 133
    PRK02967; nickel-responsive transcriptional regulator NikR
Nucleotide Protein
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Research Materials