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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.
OMAiITIVYNH.
PhylomeDBiP0A6Z6.

Family and domain databases

Gene3Di1.10.1220.10. 1 hit.
HAMAPiMF_00476. NikR. 1 hit.
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 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.
OMAiITIVYNH.
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. 1 hit.
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...

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: September 7, 2016
This is version 100 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.