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

    Gene ID: 947995, updated on 3-Dec-2024

    Summary

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    Official Symbol
    nikR
    Official Full Name
    DNA-binding transcriptional repressor NikR
    Primary source
    ECOCYC:EG11519
    Locus tag
    b3481
    See related
    ASAP:ABE-0011366
    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. NikR-operator complex structure and the mechanism of repressor activation by metal ions. Schreiter ER, et al. Proc Natl Acad Sci U S A, 2006 Sep 12. PMID 16945905, Free PMC Article
    2. Regulation of high affinity nickel uptake in bacteria. Ni2+-Dependent interaction of NikR with wild-type and mutant operator sites. Chivers PT, et al. J Biol Chem, 2000 Jun 30. PMID 10787413
    3. NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA. Chivers PT, et al. Chem Biol, 2002 Oct. PMID 12401498
    4. Crystal structure of the nickel-responsive transcription factor NikR. Schreiter ER, et al. Nat Struct Biol, 2003 Oct. PMID 12970756
    5. Selectivity of metal binding and metal-induced stability of Escherichia coli NikR. Wang SC, et al. Biochemistry, 2004 Aug 10. PMID 15287729

    See all (37) 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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    Homology

    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
      Conserved Domains (1) summary
      PRK02967
      Location:1 → 133
      PRK02967; nickel-responsive transcriptional regulator NikR
    Nucleotide Protein
    Heading Accession and Version

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