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NfeR DNA-binding transcriptional repressor

Synonyms: YqjI-nickel, NfeR
Summary:
YqjI is a local transcription regulator that represses expression of the divergent operon, yqjH-yqjI, related to its autorepression and the synthesis of an NADPH-dependent ferric reductase [1] This regulator forms a complex with DNA in the absence of nickel, binding to a 20-bp-long sequence with an imperfect palindromic sequence. YqjI is inactivated under conditions of elevated nickel levels, and the presence of this divalent metal prevents its binding to the target gene. Thus, this regulator maintains the iron homeostasis during high levels of nickel [1] However, in vitro studies have shown that YqjI can be affected by other divalent metals. The YqjI regulator is structurally related to the PadR family, which is characterized by a winged helix-turn-helix (WHTH) motif. The amino-terminal region of this protein is similar to the C-terminal SlyD protein and to the N-terminal RcnA protein [1] Comparison with the crystal structure of the AphA protein from Vibrio cholerae suggests that the amino terminal of YqjI contains the WHTH motif and that in the C-terminal domain is located the ligand-binding domain for oligomerization [1] YqjI has been observed to be a possible hexamer [1] The characterization of the nickel binding site(s) within YqjI were determined by X-ray absorption spectroscopy.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
NfeR Functional   [GEA], [IDA], [IPI] [1]
YqjI-nickel Non-Functional   [GEA], [IDA], [IPI] [1]
Evolutionary Family: PadR
Connectivity class: Local Regulator
Gene name: nfeR
  Genome position: 3216779-3217402
  Length: 624 bp / 207 aa
Operon name: nfeR
TU(s) encoding the TF:
Transcription unit        Promoter
yqjI
yqjIp


Regulon       
Regulated gene(s) nfeF, nfeR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Fe aquisition (1)
Transcription related (1)
transcriptional level (1)
Regulated operon(s) nfeF, nfeR
First gene in the operon(s) nfeF, nfeR
Simple and complex regulons FNR,NfeR
Fur,NfeR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[NfeR,-](2)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  NfeR repressor yqjHp Sigma70 18.0 -30.5 nfeF
ttgcgagtttTATTTAGATATATCTGATTAccatcacgaa
3216512 3216531 [BPP], [GEA], [HIBSCS], [SM] [1], [2]
  NfeR repressor yqjIp nd -7.0 -32.5 nfeR
aagaacgctcATATCAGATATAAATTAGATATATCTAATTAAgcaaaaggag
3216731 3216762 [BPP], [GEA], [HIBSCS], [SM] [1], [2]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [GEA] Gene expression analysis

 [IDA] Inferred from direct assay

 [IPI] Inferred from physical interaction

 [BPP] Binding of purified proteins

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation



Reference(s)    

 [1] Wang S., Wu Y., Outten FW., 2011, Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli., J Bacteriol 193(2):563-74

 [2] Wang S., Blahut M., Wu Y., Philipkosky KE., Outten FW., 2014, Communication between binding sites is required for YqjI regulation of target promoters within the yqjH-yqjI intergenic region., J Bacteriol 196(17):3199-207

 [3] Tan C, Terakawa T, Takada S, 2016, Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics., J Am Chem Soc, 2016 Jul 13



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