Nickel-responsive regulator - Escherichia coli (strain K12)

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P0A6Z6 (NIKR_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 78. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Nickel-responsive regulator

Gene names

Name:	nikR
Synonyms:	yhhG
Ordered Locus Names:	b3481, JW3446

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	133 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Transcriptional repressor of the nikABCDE operon. Is active in the presence of excessive concentrations of intracellular nickel. HAMAP-Rule MF_00476
Cofactor	Binds 1 nickel ion per subunit.
Subunit structure	Homotetramer.
Sequence similarities	Belongs to the transcriptional regulatory CopG/NikR family.
Sequence caution	The sequence BAA04676.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding Metal-binding Nickel
Molecular function	Repressor
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	regulation of transcription, DNA-dependent Inferred from mutant phenotype Ref.1. Source: EcoCyc response to nickel cation Inferred from electronic annotation. Source: InterPro transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	protein-DNA complex Inferred from direct assay Ref.7. Source: EcoCyc
Molecular_function	DNA binding Inferred from direct assay Ref.7. Source: EcoCyc nickel cation binding Traceable author statement Ref.7. Source: EcoCyc sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
rplL	P0A7K2	1	EBI-562488,EBI-543702
tufA	P0CE47	1	EBI-562488,EBI-301077

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 133

133

Nickel-responsive regulator HAMAP-Rule MF_00476

PRO_0000139274

Sites

Metal binding

Nickel

Metal binding

Nickel

Metal binding

Nickel

Metal binding

Nickel

Experimental info

Mutagenesis

R → A: Loss of DNA-binding. Ref.7

Sequence conflict

131 – 132

KE → EGRLSLLLGPLVN in BAA04676. Ref.6

Secondary structure

133

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A6Z6 [UniParc].

Last modified June 7, 2005. Version 1.
Checksum: 9A9E9F838D3FFEF1
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FASTA

133

15,094

        10         20         30         40         50         60 
MQRVTITLDD DLLETLDSLS QRRGYNNRSE AIRDILRSAL AQEATQQHGT QGFAVLSYVY 

        70         80         90        100        110        120 
EHEKRDLASR IVSTQHHHHD LSVATLHVHI NHDDCLEIAV LKGDMGDVQH FADDVIAQRG 

       130 
VRHGHLQCLP KED

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

S47700.

RefSeq

NP_417938.1. NC_000913.2.
YP_491953.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Q5V	X-ray	2.30	A/B/C/D	1-133	[»]
1Q5Y	X-ray	1.40	A/B/C/D	49-133	[»]
2HZA	X-ray	2.10	A/B	1-133	[»]
2HZV	X-ray	3.10	A/B/C/D/E/F/G/H	1-133	[»]
3BKF	X-ray	1.90	A	48-133	[»]
3BKT	X-ray	1.50	A/B/C/D	48-133	[»]
3BKU	X-ray	2.10	A/B/C/D	48-133	[»]
3OD2	X-ray	2.60	A/B	1-133	[»]

ProteinModelPortal

P0A6Z6.

SMR

P0A6Z6. Positions 1-131.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48066N.

IntAct

P0A6Z6. 3 interactions.

STRING

511145.b3481.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76506; AAC76506; b3481.
BAE77812; BAE77812; BAE77812.

GeneID

12933515.
947995.

KEGG

ecj:Y75_p3697.
eco:b3481.

PATRIC

32122406. VBIEscCol129921_3580.

Organism-specific databases

EchoBASE

EB1481.

EcoGene

EG11519. nikR.

Phylogenomic databases

eggNOG

COG0864.

HOGENOM

HOG000102781.

K07722.

OMA

DAHNCLE.

ProtClustDB

PRK02967.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11519-MONOMER.
ECOL316407:JW3446-MONOMER.

Gene expression databases

Genevestigator

P0A6Z6.

Family and domain databases

Gene3D

1.10.1220.10. 1 hit.

HAMAP

MF_00476. NikR.

InterPro

IPR013321. 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]

Pfam

PF08753. NikR_C. 1 hit.
PF01402. RHH_1. 1 hit.
[Graphical view]

SUPFAM

SSF47598. Met_repress_like. 1 hit.

TIGRFAMs

TIGR02793. nikR. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0A6Z6.

Entry information

Entry name

NIKR_ECOLI

Accession

Primary (citable) accession number: P0A6Z6
Secondary accession number(s): P28910, Q2M7E4, Q47559

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	May 1, 2013
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents