RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

nfo gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	nfo
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
OU-MICROARRAY:	b2159
PortEco:	nfo
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 -> 239	AAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLAAIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNI

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:

ECOCYC:

EG10651-MONOMER

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MINT:

MODBASE:

PANTHER:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PFAM:

PRIDE:

PRODB:

PROSITE:

PROSITE:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

nfo

Operon arrangement:

Transcription unit	Promoter
nfo	nfop

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 sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.496. P-value: 5.545e-5 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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