RegulonDB RegulonDB 10.9: Gene Form
   

ytfE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cycA ytfF ytfE NarP NarL NarP NarL NsrR GcvB ytfEp ytfEp TSS_5069 TSS_5069 TSS_5068 TSS_5068

Gene      
Name: ytfE    Texpresso search in the literature
Synonym(s): ECK4205, G7866, b4209, dnrN
Genome position(nucleotides): 4431321 <-- 4431983 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.09
External database links:  
ASAP:
ABE-0013766
ECHOBASE:
EB2398
ECOLIHUB:
ytfE
OU-MICROARRAY:
b4209
STRING:
511145.b4209
COLOMBOS: ytfE


Product      
Name: iron-sulfur cluster repair protein YtfE
Synonym(s): DnrN, RIC, YtfE, protein involved in repair of stress-damaged iron-sulfur clusters
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 24.883
Isoelectric point: 5.041
Motif(s):
 
Type Positions Sequence
77 -> 216 DHIIVRYHDRHREQLPELILQATKVERVHADKPSVPKGLTKYLTMLHEELSSHMMKEEQILFPMIKQGMGSQAMGPISVMESEHDEAGELLEVIKHTTNNVTPPPEACTTWKAMYNGINELIDDLMDHISLENNVLFPRA
5 -> 58 DQPLGELALSIPRASALFRKYDMDYCCGGKQTLARAAARKELDVEVIEAELAKL

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0046872 - metal ion binding
GO:0005506 - iron ion binding
biological_process GO:0006950 - response to stress
GO:0006979 - response to oxidative stress
GO:0030091 - protein repair
GO:0051409 - response to nitrosative stress
GO:0018283 - iron incorporation into metallo-sulfur cluster
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IMP] Inferred from mutant phenotype
Reference(s): [1] Justino MC., et al., 2006
[2] Justino MC., et al., 2007
[3] Justino MC., et al., 2005
[4] Rodionov DA., et al., 2005
[5] Todorovic S., et al., 2008
External database links:  
DIP:
DIP-35833N
ECOCYC:
G7866-MONOMER
ECOLIWIKI:
b4209
INTERPRO:
IPR023742
INTERPRO:
IPR012312
INTERPRO:
IPR019903
PANTHER:
PTHR36438
PDB:
5FNY
PDB:
5FNP
PDB:
5FNN
PFAM:
PF01814
PFAM:
PF04405
PRIDE:
P69506
REFSEQ:
NP_418630
SMR:
P69506
UNIPROT:
P69506


Operon      
Name: ytfE         
Operon arrangement:
Transcription unit        Promoter
ytfE


Transcriptional Regulation      
Display Regulation             
Activated by: NarL, NarP
Repressed by: NsrR, FNR


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 TSS_5068 4430493 forward nd [RS-EPT-CBR] [6]
  promoter TSS_5069 4431082 forward nd [RS-EPT-CBR] [6]


Evidence    

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



Reference(s)    

 [1] Justino MC., Almeida CC., Goncalves VL., Teixeira M., Saraiva LM., 2006, Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters., FEMS Microbiol Lett 257(2):278-84

 [2] Justino MC., Almeida CC., Teixeira M., Saraiva LM., 2007, Escherichia coli di-iron YtfE protein is necessary for the repair of stress damaged iron-sulfur clusters., J Biol Chem 282(14):10352-9

 [3] Justino MC., Vicente JB., Teixeira M., Saraiva LM., 2005, New genes implicated in the protection of anaerobically grown Escherichia coli against nitric oxide., J Biol Chem 280(4):2636-43

 [4] Rodionov DA., Dubchak IL., Arkin AP., Alm EJ., Gelfand MS., 2005, Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks., PLoS Comput Biol 1(5):e55

 [5] Todorovic S., Justino MC., Wellenreuther G., Hildebrandt P., Murgida DH., Meyer-Klaucke W., Saraiva LM., 2008, Iron-sulfur repair YtfE protein from Escherichia coli: structural characterization of the di-iron center., J Biol Inorg Chem 13(5):765-70

 [6] 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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