RegulonDB RegulonDB 10.9: Gene Form
   

nfo gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yeiI yeiH nfo SoxS SoxS Rob MarA terminator yeiIp2 yeiIp2 nfop nfop

Gene      
Name: nfo    Texpresso search in the literature
Synonym(s): ECK2152, EG10651, b2159
Genome position(nucleotides): 2250840 --> 2251697 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.45
External database links:  
ASAP:
ABE-0007146
CGSC:
14161
ECHOBASE:
EB0645
ECOLIHUB:
nfo
OU-MICROARRAY:
b2159
STRING:
511145.b2159
COLOMBOS: nfo


Shine dalgarno      
Sequence: cgggtttaacAGGAGTcctcgcATG


Product      
Name: endonuclease IV
Synonym(s): Nfo
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 31.479
Isoelectric point: 5.525
Motif(s):
 
Type Positions Sequence
145 -> 145 E
149 -> 149 G
10 -> 10 A
273 -> 273 A
21 -> 277 AAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHDAFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKA

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
  5 - cell processes --> 5.6 - protection --> 5.6.1 - radiation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0016787 - hydrolase activity
GO:0008296 - 3'-5'-exodeoxyribonuclease activity
GO:0046872 - metal ion binding
GO:0008081 - phosphoric diester hydrolase activity
GO:0016791 - phosphatase activity
GO:0008270 - zinc ion binding
GO:0003906 - DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0008833 - deoxyribonuclease IV (phage-T4-induced) activity
biological_process GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0006284 - base-excision repair
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
Note(s): Note(s): ...[more].
Reference(s): [1] Greenberg MM., et al., 2004
[2] Hang B., et al., 1996
[3] Kanchan S., et al., 2019
[4] Mazouzi A., et al., 2013
[5] Takeshita M., et al., 1987
[6] Takeuchi M., et al., 1994
[7] Yang X., et al., 1999
External database links:  
DIP:
DIP-47966N
ECOCYC:
EG10651-MONOMER
ECOLIWIKI:
b2159
INTERPRO:
IPR036237
INTERPRO:
IPR018246
INTERPRO:
IPR013022
INTERPRO:
IPR001719
MODBASE:
P0A6C1
PANTHER:
PTHR21445
PDB:
1QTW
PDB:
2NQ9
PDB:
2NQJ
PDB:
4K1G
PDB:
2NQH
PDB:
1QUM
PFAM:
PF01261
PRIDE:
P0A6C1
PRODB:
PRO_000023374
PROSITE:
PS00729
PROSITE:
PS51432
PROSITE:
PS00730
PROSITE:
PS00731
REFSEQ:
NP_416664
SMART:
SM00518
SMR:
P0A6C1
UNIPROT:
P0A6C1


Operon      
Name: nfo         
Operon arrangement:
Transcription unit        Promoter
nfo


Transcriptional Regulation      
Display Regulation             
Activated by: MarA, Rob, SoxS
Growth Conditions:

[1] 

C: Escherichia coli| LB medium| glucose 2 mg/mL| 37.0 C| OD600 of 0.3
E: Escherichia coli| LB medium| glucose 2 mg/mL; paraquat 0.5 mM| 37.0 C| OD600 of 0.3

[2] 

C: Escherichia coli| LB medium| 37.0 C| OD600 of 0.3
E: Escherichia coli| LB medium| paraquat 0.5 mM| 37.0 C| OD600 of 0.3



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 yeiIp2 2251653 forward Similarity to the consensus
Read more >
[ICWHO] [8]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Greenberg MM., Weledji YN., Kim J., Bales BC., 2004, Repair of oxidized abasic sites by exonuclease III, endonuclease IV, and endonuclease III., Biochemistry 43(25):8178-83

 [2] Hang B., Chenna A., Fraenkel-Conrat H., Singer B., 1996, An unusual mechanism for the major human apurinic/apyrimidinic (AP) endonuclease involving 5' cleavage of DNA containing a benzene-derived exocyclic adduct in the absence of an AP site., Proc Natl Acad Sci U S A 93(24):13737-41

 [3] Kanchan S., Sharma P., Chowdhury S., 2019, Evolution of endonuclease IV protein family: an in silico analysis., 3 Biotech 9(5):168

 [4] Mazouzi A., Vigouroux A., Aikeshev B., Brooks PJ., Saparbaev MK., Morera S., Ishchenko AA., 2013, Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases., Proc Natl Acad Sci U S A 110(33):E3071-80

 [5] Takeshita M., Chang CN., Johnson F., Will S., Grollman AP., 1987, Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases., J Biol Chem 262(21):10171-9

 [6] Takeuchi M., Lillis R., Demple B., Takeshita M., 1994, Interactions of Escherichia coli endonuclease IV and exonuclease III with abasic sites in DNA., J Biol Chem 269(34):21907-14

 [7] Yang X., Tellier P., Masson JY., Vu T., Ramotar D., 1999, Characterization of amino acid substitutions that severely alter the DNA repair functions of Escherichia coli endonuclease IV., Biochemistry 38(12):3615-23

 [8] 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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