RegulonDB RegulonDB 11.1: Gene Form
   

nikR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rhsB nikE nikR yhhH nikD rhsBp8 rhsBp8 TSS_4088 TSS_4088 rhsBp10 rhsBp10 rhsBp12 rhsBp12 rhsBp3 rhsBp3 rhsBp9 rhsBp9 rhsBp11 rhsBp11 nikRp nikRp

Gene      
Name: nikR    Texpresso search in the literature
Synonym(s): ECK3465, EG11519, b3481, yhhG
Genome position(nucleotides): 3618588 --> 3618989
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 57.21
Reference(s): [1] De Pina K., et al., 1999
External database links:  
ASAP:
 ABE-0011366
ECHOBASE:
 EB1481
ECOLIHUB:
 nikR
OU-MICROARRAY:
 b3481
STRING:
 511145.b3481
COLOMBOS: nikR


Product      
Name: DNA-binding transcriptional repressor NikR
Synonym(s): NikR, YhhG
Sequence: Get amino acid sequence Fasta Format
Regulator Family: CopG
Cellular location: cytosol
Molecular weight: 15.094
Isoelectric point: 6.211
Motif(s):
 
Type Positions Sequence Comment
3 -> 3 R UniProt: Loss of DNA-binding..
54 -> 127 AVLSYVYEHEKRDLASRIVSTQHHHHDLSVATLHVHINHDDCLEIAVLKGDMGDVQHFADDVIAQRGVRHGHLQ
131 -> 132 KE UniProt: In Ref. 6; BAA04676..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005667 - transcription regulator complex
GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0003700 - DNA-binding transcription factor activity
GO:0016151 - nickel cation binding
GO:0043565 - sequence-specific DNA binding
GO:0042802 - identical protein binding
GO:0000976 - transcription cis-regulatory region binding
GO:0001046 - core promoter sequence-specific DNA binding
GO:0001217 - DNA-binding transcription repressor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0010045 - response to nickel cation
GO:2000143 - negative regulation of DNA-templated transcription, initiation
Reference(s): [2] Chivers PT., et al., 2000
External database links:  
ALPHAFOLD:
 P0A6Z6
DIP:
 DIP-48066N
ECOCYC:
 EG11519-MONOMER
ECOLIWIKI:
 b3481
INTERPRO:
 IPR010985
INTERPRO:
 IPR002145
INTERPRO:
 IPR013321
INTERPRO:
 IPR027271
INTERPRO:
 IPR022988
INTERPRO:
 IPR014864
INTERPRO:
 IPR014160
MODBASE:
 P0A6Z6
PDB:
 3OD2
PDB:
 3BKU
PDB:
 3BKT
PDB:
 3BKF
PDB:
 2HZV
PDB:
 2HZA
PDB:
 1Q5V
PDB:
 1Q5Y
PFAM:
 PF08753
PFAM:
 PF01402
PRIDE:
 P0A6Z6
PRODB:
 PRO_000023389
REFSEQ:
 NP_417938
SMR:
 P0A6Z6
UNIPROT:
 P0A6Z6


Operon      
Name: nikABCDER         
Operon arrangement:
Transcription unit        Promoter
nikABCDER
nikABCDER
nikR


Transcriptional Regulation      
Display Regulation             
Activated by: FNR
Repressed by: NarL, NikR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter rhsBp11 3619003 forward nd [COMP-AINF] [3]
  promoter rhsBp9 3619044 forward nd [COMP-AINF] [3]
  promoter rhsBp3 3619074 forward nd [COMP-AINF] [3]
  promoter rhsBp12 3619097 forward nd [COMP-AINF] [3]
  promoter rhsBp10 3619113 forward nd [COMP-AINF] [3]
  promoter TSS_4088 3619164 reverse nd [RS-EPT-CBR] [4]
  promoter rhsBp8 3619178 forward nd [COMP-AINF] [3]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] De Pina K., Desjardin V., Mandrand-Berthelot MA., Giordano G., Wu LF., 1999, Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli., J Bacteriol 181(2):670-4

 [2] Chivers PT., Sauer RT., 2000, Regulation of high affinity nickel uptake in bacteria. Ni2+-Dependent interaction of NikR with wild-type and mutant operator sites., J Biol Chem 275(26):19735-41

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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