RegulonDB RegulonDB 11.1: Gene Form
   

nfi gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hemE nfi yjaG Fis Fis Fis Fis TSS_4827 TSS_4827 TSS_4826 (cluster) TSS_4826 (cluster) TSS_4825 TSS_4825 TSS_4824 (cluster) TSS_4824 (cluster) TSS_4823 (cluster) TSS_4823 (cluster) yjaGp4 yjaGp4 TSS_4822 TSS_4822 TSS_4821 (cluster) TSS_4821 (cluster)

Gene      
Name: nfi    Texpresso search in the literature
Synonym(s): ECK3990, EG11915, b3998, yjaF
Genome position(nucleotides): 4198790 --> 4199461
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 58.78


Product      
Name: endonuclease V
Synonym(s): EndoV, Nfi, YjaF, deoxyinosine 3'-endonuclease
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 24.673
Isoelectric point: 8.463
Motif(s):
 
Type Positions Sequence Comment
12 -> 206 ELASSVIREDRLDKDPPDLIAGADVGFEQGGEVTRAAMVLLKYPSLELVEYKVARIATTMPYIPGFLSFREYPALLAAWEMLSQKPDLVFVDGHGISHPRRLGVASHFGLLVDVPTIGVAKKRLCGKFEPLSSEPGALAPLMDKGEQLAWVWRSKARCNPLFIATGHRVSVDSALAWVQRCMKGYRLPEPTRWAD
35 -> 35 D UniProt: Lack of activity on RNA..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.2 - DNA
  2 - information transfer --> 2.1 - DNA related --> 2.1.5 - DNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0003727 - single-stranded RNA binding
GO:0016891 - endoribonuclease activity, producing 5'-phosphomonoesters
GO:0000287 - magnesium ion binding
GO:0043737 - deoxyribonuclease V activity
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic
Note(s): Note(s): ...[more].
Reference(s): [1] Budke B., et al., 2006
[2] Burgis NE., et al., 2003
[3] Guo G., et al., 1997
[4] Knutson SD., et al., 2020
[5] Majorek KA., et al., 2009
[6] Wu J., et al., 2019
[7] Zhang Z., et al., 2015
External database links:  
ALPHAFOLD:
 P68739
DIP:
 DIP-47986N
ECOCYC:
 EG11915-MONOMER
ECOLIWIKI:
 b3998
INTERPRO:
 IPR007581
PANTHER:
 PTHR28511
PDB:
 4XPU
PFAM:
 PF04493
PRIDE:
 P68739
PRODB:
 PRO_000023372
REFSEQ:
 NP_418426
SMR:
 P68739
UNIPROT:
 P68739


Operon      
Name: nudC-hemE-nfi         
Operon arrangement:
Transcription unit        Promoter
nudC-hemE-nfi


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_4821 (cluster) 4198655 forward nd [RS-EPT-CBR] [8]
  promoter TSS_4822 4198700 forward nd [RS-EPT-CBR] [8]
  promoter yjaGp4 4199373 forward nd [COMP-AINF] [9]
  promoter TSS_4823 (cluster) 4199461 forward nd [RS-EPT-CBR] [8]
  promoter TSS_4824 (cluster) 4199480 forward nd [RS-EPT-CBR] [8]
  promoter TSS_4825 4199483 forward nd [RS-EPT-CBR] [8]
  promoter TSS_4826 (cluster) 4199489 forward nd [RS-EPT-CBR] [8]
  promoter TSS_4827 4199519 forward nd [RS-EPT-CBR] [8]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Budke B., Kuzminov A., 2006, Hypoxanthine incorporation is nonmutagenic in Escherichia coli., J Bacteriol 188(18):6553-60

 [2] Burgis NE., Brucker JJ., Cunningham RP., 2003, Repair system for noncanonical purines in Escherichia coli., J Bacteriol 185(10):3101-10

 [3] Guo G., Ding Y., Weiss B., 1997, nfi, the gene for endonuclease V in Escherichia coli K-12., J Bacteriol 179(2):310-6

 [4] Knutson SD., Arthur RA., Johnston HR., Heemstra JM., 2020, Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V., J Am Chem Soc

 [5] Majorek KA., Bujnicki JM., 2009, Modeling of Escherichia coli Endonuclease V structure in complex with DNA., J Mol Model 15(2):173-82

 [6] Wu J., Samara NL., Kuraoka I., Yang W., 2019, Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase., Mol Cell 76(1):44-56.e3

 [7] Zhang Z., Jia Q., Zhou C., Xie W., 2015, Crystal structure of E. coli endonuclease V, an essential enzyme for deamination repair., Sci Rep 5:12754

 [8] 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.

 [9] 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

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