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    nikA Ni(2(+)) ABC transporter periplasmic binding protein [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947981, updated on 3-Dec-2024

    Summary

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    Official Symbol
    nikA
    Official Full Name
    Ni(2(+)) ABC transporter periplasmic binding protein
    Primary source
    ECOCYC:EG12075
    Locus tag
    b3476
    See related
    ASAP:ABE-0011354
    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
    ECK3460; hydC; hydD
    Summary
    NikA binds hemin and protoporphyrin IX (Shepherd, 2007). [More information is available at EcoGene: EG12075]. NikA is the periplasmic binding component of the nickel ABC transporter in Escherichia coli. [More information is available at EcoCyc: EG12075].
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    Genomic context

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    Sequence:
    NC_000913.3 (3613667..3615241)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene putative transporter YhhT Neighboring gene holo-[acyl carrier protein] synthase 2 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

    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. Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography. Addy C, et al. Acta Crystallogr D Biol Crystallogr, 2007 Feb. PMID 17242515
    2. Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli. Heddle J, et al. J Biol Chem, 2003 Dec 12. PMID 12960164
    3. Backbone 1H, 13C, and 15N assignments of a 56 kDa E. coli nickel binding protein NikA. Rajesh S, et al. J Biomol NMR, 2005 Jun. PMID 16034673
    4. Specific binding of the NikA protein to one arm of 17-base-pair inverted repeat sequences within the oriT region of plasmid R64. Furuya N, et al. J Bacteriol, 1995 Jan. PMID 7798148, Free PMC Article
    5. Nickel deficiency gives rise to the defective hydrogenase phenotype of hydC and fnr mutants in Escherichia coli. Wu LF, et al. Mol Microbiol, 1989 Dec. PMID 2695744

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Six "NikA/iron complex" hybrids have been characterized by X-ray crystallography, and their interactions and solution properties have been studied.
      Title: The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.
    2. crystal structure of the H416I NikA mutant; results confirm the essential role of His416 in nickel transport by NikA
      Title: Histidine 416 of the periplasmic binding protein NikA is essential for nickel uptake in Escherichia coli.
    3. the NikA ribbon-helix-helix domain has a role in initiating bacterial conjugation
      Title: Structural basis of the role of the NikA ribbon-helix-helix domain in initiating bacterial conjugation.
    4. N-terminus verified by Edman degradation on mature peptide
      Title: Purification and characterization of the periplasmic nickel-binding protein NikA of Escherichia coli K12.
    5. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site
      Title: Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.
    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 heme binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables heme binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal cluster binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nickel cation binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nickel cation binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptide transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transition metal ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nickel cation import across plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in nickel cation transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nickel cation transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in peptide transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of ATP-binding cassette (ABC) transporter complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in outer membrane-bounded periplasmic space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in outer membrane-bounded periplasmic space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in outer membrane-bounded periplasmic space IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in outer membrane-bounded periplasmic space ISM
    Inferred from Sequence Model
    more info
    		 PubMed 
    located_in periplasmic space IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in periplasmic space IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    Ni(2(+)) ABC transporter periplasmic binding protein

    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
      3613667..3615241
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417933.1 Ni(2(+)) ABC transporter periplasmic binding protein [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417933.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A6N8NF58
      Conserved Domains (1) summary
      TIGR02294
      Location:21 → 520
      nickel_nikA; nickel ABC transporter, nickel/metallophore periplasmic binding protein
    Nucleotide Protein
    Heading Accession and Version

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