NIKR_ECOLI
ID NIKR_ECOLI Reviewed; 133 AA.
AC P0A6Z6; P28910; Q2M7E4; Q47559;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Nickel-responsive regulator;
GN Name=nikR; Synonyms=yhhG; OrderedLocusNames=b3481, JW3446;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-7, AND
RP CHARACTERIZATION.
RX PubMed=9882686; DOI=10.1128/jb.181.2.670-674.1999;
RA De Pina K., Desjardin V., Mandrand-Berthelot M.-A., Giordano G., Wu L.-F.;
RT "Isolation and characterization of the nikR gene encoding a nickel-
RT responsive regulator in Escherichia coli.";
RL J. Bacteriol. 181:670-674(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=8387990; DOI=10.1128/jb.175.10.2799-2808.1993;
RA Zhao S., Sandt C.H., Feulner G., Vlazny D.A., Gray J.A., Hill C.W.;
RT "Rhs elements of Escherichia coli K-12: complex composites of shared and
RT unique components that have different evolutionary histories.";
RL J. Bacteriol. 175:2799-2808(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8041620; DOI=10.1093/nar/22.13.2576;
RA Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.;
RT "Analysis of the Escherichia coli genome. V. DNA sequence of the region
RT from 76.0 to 81.5 minutes.";
RL Nucleic Acids Res. 22:2576-2586(1994).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 101-133.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=7764507; DOI=10.1271/bbb.58.117;
RA Talukder A.A., Yanai S., Yamada M.;
RT "Analysis of products of the Escherichia coli genomic genes and regulation
RT of their expressions: an applicable procedure for genomic analysis of other
RT microorganisms.";
RL Biosci. Biotechnol. Biochem. 58:117-120(1994).
RN [7]
RP CHARACTERIZATION, AND MUTAGENESIS OF ARG-3.
RC STRAIN=K12 / MC1061 / ATCC 53338 / DSM 7140;
RX PubMed=10595554; DOI=10.1110/ps.8.11.2494;
RA Chivers P.T., Sauer R.T.;
RT "NikR is a ribbon-helix-helix DNA-binding protein.";
RL Protein Sci. 8:2494-2500(1999).
RN [8]
RP CHARACTERIZATION.
RC STRAIN=K12 / MC1061 / ATCC 53338 / DSM 7140;
RX PubMed=10787413; DOI=10.1074/jbc.m002232200;
RA Chivers P.T., Sauer R.T.;
RT "Regulation of high affinity nickel uptake in bacteria. Ni2+-dependent
RT interaction of NikR with wild-type and mutant operator sites.";
RL J. Biol. Chem. 275:19735-19741(2000).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
RX PubMed=12970756; DOI=10.1038/nsb985;
RA Schreiter E.R., Sintchak M.D., Guo Y., Chivers P.T., Sauer R.T.,
RA Drennan C.L.;
RT "Crystal structure of the nickel-responsive transcription factor NikR.";
RL Nat. Struct. Biol. 10:794-799(2003).
CC -!- FUNCTION: Transcriptional repressor of the nikABCDE operon. Is active
CC in the presence of excessive concentrations of intracellular nickel.
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Note=Binds 1 nickel ion per subunit.;
CC -!- SUBUNIT: Homotetramer.
CC -!- INTERACTION:
CC P0A6Z6; P77650: hcaD; NbExp=2; IntAct=EBI-562488, EBI-1129389;
CC P0A6Z6; P0A7K2: rplL; NbExp=3; IntAct=EBI-562488, EBI-543702;
CC P0A6Z6; P0CE47: tufA; NbExp=3; IntAct=EBI-562488, EBI-301077;
CC -!- SIMILARITY: Belongs to the transcriptional regulatory CopG/NikR family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA04676.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; Y08952; CAA70150.1; -; Genomic_DNA.
DR EMBL; L02370; AAC61882.1; -; Genomic_DNA.
DR EMBL; U00039; AAB18456.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76506.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77812.1; -; Genomic_DNA.
DR EMBL; D21140; BAA04676.1; ALT_INIT; Genomic_DNA.
DR PIR; S47700; S47700.
DR RefSeq; NP_417938.1; NC_000913.3.
DR RefSeq; WP_001190062.1; NZ_STEB01000004.1.
DR PDB; 1Q5V; X-ray; 2.30 A; A/B/C/D=1-133.
DR PDB; 1Q5Y; X-ray; 1.40 A; A/B/C/D=49-133.
DR PDB; 2HZA; X-ray; 2.10 A; A/B=1-133.
DR PDB; 2HZV; X-ray; 3.10 A; A/B/C/D/E/F/G/H=1-133.
DR PDB; 3BKF; X-ray; 1.90 A; A=48-133.
DR PDB; 3BKT; X-ray; 1.50 A; A/B/C/D=48-133.
DR PDB; 3BKU; X-ray; 2.10 A; A/B/C/D=48-133.
DR PDB; 3OD2; X-ray; 2.60 A; A/B=1-133.
DR PDBsum; 1Q5V; -.
DR PDBsum; 1Q5Y; -.
DR PDBsum; 2HZA; -.
DR PDBsum; 2HZV; -.
DR PDBsum; 3BKF; -.
DR PDBsum; 3BKT; -.
DR PDBsum; 3BKU; -.
DR PDBsum; 3OD2; -.
DR AlphaFoldDB; P0A6Z6; -.
DR SMR; P0A6Z6; -.
DR BioGRID; 4262509; 16.
DR BioGRID; 852304; 12.
DR DIP; DIP-48066N; -.
DR IntAct; P0A6Z6; 15.
DR STRING; 511145.b3481; -.
DR jPOST; P0A6Z6; -.
DR PaxDb; P0A6Z6; -.
DR PRIDE; P0A6Z6; -.
DR EnsemblBacteria; AAC76506; AAC76506; b3481.
DR EnsemblBacteria; BAE77812; BAE77812; BAE77812.
DR GeneID; 67417111; -.
DR GeneID; 947995; -.
DR KEGG; ecj:JW3446; -.
DR KEGG; eco:b3481; -.
DR PATRIC; fig|1411691.4.peg.3244; -.
DR EchoBASE; EB1481; -.
DR eggNOG; COG0864; Bacteria.
DR HOGENOM; CLU_113319_1_4_6; -.
DR InParanoid; P0A6Z6; -.
DR OMA; AHNCLET; -.
DR PhylomeDB; P0A6Z6; -.
DR BioCyc; EcoCyc:EG11519-MON; -.
DR EvolutionaryTrace; P0A6Z6; -.
DR PRO; PR:P0A6Z6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR CollecTF; EXPREG_00000790; -.
DR GO; GO:0032993; C:protein-DNA complex; IMP:CollecTF.
DR GO; GO:0005667; C:transcription regulator complex; IDA:EcoCyc.
DR GO; GO:0001046; F:core promoter sequence-specific DNA binding; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0001217; F:DNA-binding transcription repressor activity; IMP:CollecTF.
DR GO; GO:0016151; F:nickel cation binding; IDA:EcoCyc.
DR GO; GO:0043565; F:sequence-specific DNA binding; IMP:CollecTF.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IMP:CollecTF.
DR GO; GO:2000143; P:negative regulation of DNA-templated transcription, initiation; IMP:EcoCyc.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0010045; P:response to nickel cation; IEA:InterPro.
DR Gene3D; 1.10.1220.10; -; 1.
DR Gene3D; 3.30.70.1150; -; 1.
DR HAMAP; MF_00476; NikR; 1.
DR InterPro; IPR027271; Acetolactate_synth/TF_NikR_C.
DR InterPro; IPR045865; ACT-like_dom_sf.
DR InterPro; IPR013321; Arc_rbn_hlx_hlx.
DR InterPro; IPR002145; CopG.
DR InterPro; IPR022988; Ni_resp_reg_NikR.
DR InterPro; IPR014160; Nickel_NikR_proteobac.
DR InterPro; IPR010985; Ribbon_hlx_hlx.
DR InterPro; IPR014864; TF_NikR_Ni-bd_C.
DR Pfam; PF08753; NikR_C; 1.
DR Pfam; PF01402; RHH_1; 1.
DR SUPFAM; SSF47598; SSF47598; 1.
DR SUPFAM; SSF55021; SSF55021; 1.
DR TIGRFAMs; TIGR02793; nikR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA-binding; Metal-binding;
KW Nickel; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..133
FT /note="Nickel-responsive regulator"
FT /id="PRO_0000139274"
FT BINDING 76
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 87
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 89
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 95
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT MUTAGEN 3
FT /note="R->A: Loss of DNA-binding."
FT /evidence="ECO:0000269|PubMed:10595554"
FT CONFLICT 131..132
FT /note="KE -> EGRLSLLLGPLVN (in Ref. 6; BAA04676)"
FT /evidence="ECO:0000305"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:2HZA"
FT HELIX 10..22
FT /evidence="ECO:0007829|PDB:2HZA"
FT HELIX 28..45
FT /evidence="ECO:0007829|PDB:2HZA"
FT STRAND 46..49
FT /evidence="ECO:0007829|PDB:2HZV"
FT STRAND 51..61
FT /evidence="ECO:0007829|PDB:1Q5Y"
FT HELIX 65..77
FT /evidence="ECO:0007829|PDB:1Q5Y"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:1Q5Y"
FT STRAND 82..89
FT /evidence="ECO:0007829|PDB:1Q5Y"
FT STRAND 91..104
FT /evidence="ECO:0007829|PDB:1Q5Y"
FT HELIX 105..116
FT /evidence="ECO:0007829|PDB:1Q5Y"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:1Q5V"
FT STRAND 122..130
FT /evidence="ECO:0007829|PDB:1Q5Y"
SQ SEQUENCE 133 AA; 15094 MW; 9A9E9F838D3FFEF1 CRC64;
MQRVTITLDD DLLETLDSLS QRRGYNNRSE AIRDILRSAL AQEATQQHGT QGFAVLSYVY
EHEKRDLASR IVSTQHHHHD LSVATLHVHI NHDDCLEIAV LKGDMGDVQH FADDVIAQRG
VRHGHLQCLP KED
