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Protein

Nickel-responsive regulator

Gene

nikR

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptional repressor of the nikABCDE operon. Is active in the presence of excessive concentrations of intracellular nickel.

Cofactori

Ni2+Note: Binds 1 nickel ion per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi76 – 761Nickel
Metal bindingi87 – 871Nickel
Metal bindingi89 – 891Nickel
Metal bindingi95 – 951Nickel

GO - Molecular functioni

  • DNA binding Source: EcoCyc
  • nickel cation binding Source: EcoCyc
  • transcription factor activity, sequence-specific DNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  • regulation of transcription, DNA-templated Source: EcoCyc
  • response to nickel cation Source: InterPro
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Nickel

Enzyme and pathway databases

BioCyciEcoCyc:EG11519-MONOMER.
ECOL316407:JW3446-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Nickel-responsive regulator
Gene namesi
Name:nikR
Synonyms:yhhG
Ordered Locus Names:b3481, JW3446
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11519. nikR.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi3 – 31R → A: Loss of DNA-binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 133133Nickel-responsive regulatorPRO_0000139274Add
BLAST

Proteomic databases

PaxDbiP0A6Z6.

Expressioni

Gene expression databases

CollecTFiEXPREG_00000790.

Interactioni

Subunit structurei

Homotetramer.

Binary interactionsi

WithEntry#Exp.IntActNotes
hcaDP776502EBI-562488,EBI-1129389

Protein-protein interaction databases

BioGridi4262509. 11 interactions.
DIPiDIP-48066N.
IntActiP0A6Z6. 15 interactions.
STRINGi511145.b3481.

Structurei

Secondary structure

1
133
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87Combined sources
Helixi10 – 2213Combined sources
Helixi28 – 4518Combined sources
Beta strandi46 – 494Combined sources
Beta strandi51 – 6111Combined sources
Helixi65 – 7713Combined sources
Helixi79 – 813Combined sources
Beta strandi82 – 898Combined sources
Beta strandi91 – 10414Combined sources
Helixi105 – 11612Combined sources
Beta strandi118 – 1203Combined sources
Beta strandi122 – 1309Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q5VX-ray2.30A/B/C/D1-133[»]
1Q5YX-ray1.40A/B/C/D49-133[»]
2HZAX-ray2.10A/B1-133[»]
2HZVX-ray3.10A/B/C/D/E/F/G/H1-133[»]
3BKFX-ray1.90A48-133[»]
3BKTX-ray1.50A/B/C/D48-133[»]
3BKUX-ray2.10A/B/C/D48-133[»]
3OD2X-ray2.60A/B1-133[»]
ProteinModelPortaliP0A6Z6.
SMRiP0A6Z6. Positions 1-131.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A6Z6.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105MRR. Bacteria.
COG0864. LUCA.
HOGENOMiHOG000102781.
InParanoidiP0A6Z6.
KOiK07722.
OMAiAHNCLET.
OrthoDBiEOG65QWK8.
PhylomeDBiP0A6Z6.

Family and domain databases

Gene3Di1.10.1220.10. 1 hit.
HAMAPiMF_00476. NikR.
InterProiIPR013321. Arc_rbn_hlx_hlx.
IPR002145. CopG.
IPR022988. Ni_resp_reg_NikR.
IPR014160. Nickel_NikR_proteobac.
IPR010985. Ribbon_hlx_hlx.
IPR014864. TF_NikR_Ni-bd_C.
[Graphical view]
PfamiPF08753. NikR_C. 1 hit.
PF01402. RHH_1. 1 hit.
[Graphical view]
SUPFAMiSSF47598. SSF47598. 1 hit.
TIGRFAMsiTIGR02793. nikR. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A6Z6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQRVTITLDD DLLETLDSLS QRRGYNNRSE AIRDILRSAL AQEATQQHGT
60 70 80 90 100
QGFAVLSYVY EHEKRDLASR IVSTQHHHHD LSVATLHVHI NHDDCLEIAV
110 120 130
LKGDMGDVQH FADDVIAQRG VRHGHLQCLP KED
Length:133
Mass (Da):15,094
Last modified:June 7, 2005 - v1
Checksum:i9A9E9F838D3FFEF1
GO

Sequence cautioni

The sequence BAA04676.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti131 – 1322KE → EGRLSLLLGPLVN in BAA04676 (PubMed:7764507).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08952 Genomic DNA. Translation: CAA70150.1.
L02370 Genomic DNA. Translation: AAC61882.1.
U00039 Genomic DNA. Translation: AAB18456.1.
U00096 Genomic DNA. Translation: AAC76506.1.
AP009048 Genomic DNA. Translation: BAE77812.1.
D21140 Genomic DNA. Translation: BAA04676.1. Different initiation.
PIRiS47700.
RefSeqiNP_417938.1. NC_000913.3.
WP_001190062.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76506; AAC76506; b3481.
BAE77812; BAE77812; BAE77812.
GeneIDi947995.
KEGGiecj:JW3446.
eco:b3481.
PATRICi32122406. VBIEscCol129921_3580.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08952 Genomic DNA. Translation: CAA70150.1.
L02370 Genomic DNA. Translation: AAC61882.1.
U00039 Genomic DNA. Translation: AAB18456.1.
U00096 Genomic DNA. Translation: AAC76506.1.
AP009048 Genomic DNA. Translation: BAE77812.1.
D21140 Genomic DNA. Translation: BAA04676.1. Different initiation.
PIRiS47700.
RefSeqiNP_417938.1. NC_000913.3.
WP_001190062.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1Q5VX-ray2.30A/B/C/D1-133[»]
1Q5YX-ray1.40A/B/C/D49-133[»]
2HZAX-ray2.10A/B1-133[»]
2HZVX-ray3.10A/B/C/D/E/F/G/H1-133[»]
3BKFX-ray1.90A48-133[»]
3BKTX-ray1.50A/B/C/D48-133[»]
3BKUX-ray2.10A/B/C/D48-133[»]
3OD2X-ray2.60A/B1-133[»]
ProteinModelPortaliP0A6Z6.
SMRiP0A6Z6. Positions 1-131.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262509. 11 interactions.
DIPiDIP-48066N.
IntActiP0A6Z6. 15 interactions.
STRINGi511145.b3481.

Proteomic databases

PaxDbiP0A6Z6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76506; AAC76506; b3481.
BAE77812; BAE77812; BAE77812.
GeneIDi947995.
KEGGiecj:JW3446.
eco:b3481.
PATRICi32122406. VBIEscCol129921_3580.

Organism-specific databases

EchoBASEiEB1481.
EcoGeneiEG11519. nikR.

Phylogenomic databases

eggNOGiENOG4105MRR. Bacteria.
COG0864. LUCA.
HOGENOMiHOG000102781.
InParanoidiP0A6Z6.
KOiK07722.
OMAiAHNCLET.
OrthoDBiEOG65QWK8.
PhylomeDBiP0A6Z6.

Enzyme and pathway databases

BioCyciEcoCyc:EG11519-MONOMER.
ECOL316407:JW3446-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A6Z6.
PROiP0A6Z6.

Gene expression databases

CollecTFiEXPREG_00000790.

Family and domain databases

Gene3Di1.10.1220.10. 1 hit.
HAMAPiMF_00476. NikR.
InterProiIPR013321. Arc_rbn_hlx_hlx.
IPR002145. CopG.
IPR022988. Ni_resp_reg_NikR.
IPR014160. Nickel_NikR_proteobac.
IPR010985. Ribbon_hlx_hlx.
IPR014864. TF_NikR_Ni-bd_C.
[Graphical view]
PfamiPF08753. NikR_C. 1 hit.
PF01402. RHH_1. 1 hit.
[Graphical view]
SUPFAMiSSF47598. SSF47598. 1 hit.
TIGRFAMsiTIGR02793. nikR. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli."
    De Pina K., Desjardin V., Mandrand-Berthelot M.-A., Giordano G., Wu L.-F.
    J. Bacteriol. 181:670-674(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-7, CHARACTERIZATION.
  2. "Rhs elements of Escherichia coli K-12: complex composites of shared and unique components that have different evolutionary histories."
    Zhao S., Sandt C.H., Feulner G., Vlazny D.A., Gray J.A., Hill C.W.
    J. Bacteriol. 175:2799-2808(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. "Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes."
    Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.
    Nucleic Acids Res. 22:2576-2586(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Analysis of products of the Escherichia coli genomic genes and regulation of their expressions: an applicable procedure for genomic analysis of other microorganisms."
    Talukder A.A., Yanai S., Yamada M.
    Biosci. Biotechnol. Biochem. 58:117-120(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 101-133.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  7. "NikR is a ribbon-helix-helix DNA-binding protein."
    Chivers P.T., Sauer R.T.
    Protein Sci. 8:2494-2500(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, MUTAGENESIS OF ARG-3.
    Strain: K12 / MC1061 / ATCC 53338 / DSM 7140.
  8. "Regulation of high affinity nickel uptake in bacteria. Ni2+-dependent interaction of NikR with wild-type and mutant operator sites."
    Chivers P.T., Sauer R.T.
    J. Biol. Chem. 275:19735-19741(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
    Strain: K12 / MC1061 / ATCC 53338 / DSM 7140.
  9. "Crystal structure of the nickel-responsive transcription factor NikR."
    Schreiter E.R., Sintchak M.D., Guo Y., Chivers P.T., Sauer R.T., Drennan C.L.
    Nat. Struct. Biol. 10:794-799(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).

Entry informationi

Entry nameiNIKR_ECOLI
AccessioniPrimary (citable) accession number: P0A6Z6
Secondary accession number(s): P28910, Q2M7E4, Q47559
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: January 20, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.