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NfeR DNA-binding transcriptional repressor

Synonyms: NfeR, NfeR-Fe2+, NfeR-Ni2+
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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
NfeR Functional   Apo nd nd nd
NfeR-Fe2+ Non-Functional Allosteric Holo nd nd nd
NfeR-Ni2+ Non-Functional Allosteric Holo [EXP-IDA], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IPI] W [1]
Evolutionary Family: PadR
TFBs length: 20
TFBs symmetry: inverted-repeat
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

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
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  NfeR repressor nfeRp nd -7.0 -33.0 nfeR
  NfeR repressor yqjHp Sigma70 18.0 -30.0 nfeF

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