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P0A6C1

- END4_ECOLI

UniProt

P0A6C1 - END4_ECOLI

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Protein

Endonuclease 4

Gene

nfo

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.

Cofactori

Binds 3 zinc ions. Can also bind manganese.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi69 – 691Zinc 1
Metal bindingi109 – 1091Zinc 1
Metal bindingi145 – 1451Zinc 1
Metal bindingi145 – 1451Zinc 2
Metal bindingi179 – 1791Zinc 2
Metal bindingi182 – 1821Zinc 3
Metal bindingi216 – 2161Zinc 2
Metal bindingi229 – 2291Zinc 3
Metal bindingi231 – 2311Zinc 3
Metal bindingi261 – 2611Zinc 2

GO - Molecular functioni

  1. deoxyribonuclease IV (phage-T4-induced) activity Source: UniProtKB-HAMAP
  2. DNA-(apurinic or apyrimidinic site) lyase activity Source: RefGenome
  3. DNA binding Source: InterPro
  4. endonuclease activity Source: EcoCyc
  5. phosphoric diester hydrolase activity Source: RefGenome
  6. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. base-excision repair Source: RefGenome
  2. DNA catabolic process, endonucleolytic Source: GOC
  3. non-recombinational repair Source: EcoCyc
  4. nucleic acid phosphodiester bond hydrolysis Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Manganese, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10651-MONOMER.
ECOL316407:JW2146-MONOMER.
MetaCyc:EG10651-MONOMER.
BRENDAi3.1.21.2. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease 4 (EC:3.1.21.2)
Alternative name(s):
Endodeoxyribonuclease IV
Endonuclease IV
Gene namesi
Name:nfo
Ordered Locus Names:b2159, JW2146
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10651. nfo.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 285285Endonuclease 4PRO_0000190838Add
BLAST

Proteomic databases

PaxDbiP0A6C1.
PRIDEiP0A6C1.

Expressioni

Inductioni

Endonuclease IV is induced by agents which generate superoxide radical anions.

Gene expression databases

GenevestigatoriP0A6C1.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

DIPiDIP-47966N.
IntActiP0A6C1. 10 interactions.
MINTiMINT-1242700.
STRINGi511145.b2159.

Structurei

Secondary structure

1
285
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 75
Helixi14 – 2310
Beta strandi27 – 304
Beta strandi32 – 343
Helixi46 – 5813
Helixi63 – 653
Beta strandi66 – 694
Helixi81 – 10020
Beta strandi105 – 1084
Turni114 – 1163
Helixi119 – 13618
Beta strandi141 – 1455
Helixi158 – 16710
Helixi171 – 1733
Beta strandi174 – 1796
Helixi180 – 1867
Helixi193 – 20614
Helixi209 – 2113
Beta strandi212 – 2176
Beta strandi219 – 2224
Turni234 – 2363
Beta strandi237 – 2393
Helixi242 – 2487
Helixi251 – 2533
Beta strandi256 – 2605
Helixi265 – 2673
Helixi268 – 27811

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QTWX-ray1.02A1-285[»]
1QUMX-ray1.55A1-285[»]
2NQ9X-ray1.45A1-285[»]
2NQHX-ray1.10A1-285[»]
2NQJX-ray2.45A/B1-285[»]
4K1GX-ray1.90A/B1-285[»]
ProteinModelPortaliP0A6C1.
SMRiP0A6C1. Positions 1-285.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A6C1.

Family & Domainsi

Sequence similaritiesi

Belongs to the AP endonuclease 2 family.Curated

Phylogenomic databases

eggNOGiCOG0648.
HOGENOMiHOG000224893.
InParanoidiP0A6C1.
KOiK01151.
OMAiIAWLKSE.
OrthoDBiEOG6Z0QCM.
PhylomeDBiP0A6C1.

Family and domain databases

Gene3Di3.20.20.150. 1 hit.
HAMAPiMF_00152. Nfo.
InterProiIPR001719. AP_endonuc_2.
IPR018246. AP_endonuc_F2_Zn_BS.
IPR013022. Xyl_isomerase-like_TIM-brl.
[Graphical view]
PANTHERiPTHR21445. PTHR21445. 1 hit.
PfamiPF01261. AP_endonuc_2. 1 hit.
[Graphical view]
SMARTiSM00518. AP2Ec. 1 hit.
[Graphical view]
SUPFAMiSSF51658. SSF51658. 1 hit.
TIGRFAMsiTIGR00587. nfo. 1 hit.
PROSITEiPS00729. AP_NUCLEASE_F2_1. 1 hit.
PS00730. AP_NUCLEASE_F2_2. 1 hit.
PS00731. AP_NUCLEASE_F2_3. 1 hit.
PS51432. AP_NUCLEASE_F2_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A6C1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKYIGAHVSA AGGLANAAIR AAEIDATAFA LFTKNQRQWR AAPLTTQTID
60 70 80 90 100
EFKAACEKYH YTSAQILPHD SYLINLGHPV TEALEKSRDA FIDEMQRCEQ
110 120 130 140 150
LGLSLLNFHP GSHLMQISEE DCLARIAESI NIALDKTQGV TAVIENTAGQ
160 170 180 190 200
GSNLGFKFEH LAAIIDGVED KSRVGVCIDT CHAFAAGYDL RTPAECEKTF
210 220 230 240 250
ADFARTVGFK YLRGMHLNDA KSTFGSRVDR HHSLGEGNIG HDAFRWIMQD
260 270 280
DRFDGIPLIL ETINPDIWAE EIAWLKAQQT EKAVA
Length:285
Mass (Da):31,480
Last modified:June 7, 2005 - v1
Checksum:iEAAE5861E54C47FD
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti10 – 101A → R in AAA24216. (PubMed:2460435)Curated
Sequence conflicti273 – 2731A → T in AAA60529. 1 PublicationCurated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M22591 Genomic DNA. Translation: AAA24216.1.
U00007 Genomic DNA. Translation: AAA60529.1.
U00096 Genomic DNA. Translation: AAC75220.1.
AP009048 Genomic DNA. Translation: BAE76636.1.
PIRiF64984. NDEC4.
RefSeqiNP_416664.1. NC_000913.3.
YP_490398.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75220; AAC75220; b2159.
BAE76636; BAE76636; BAE76636.
GeneIDi12932805.
946669.
KEGGiecj:Y75_p2121.
eco:b2159.
PATRICi32119667. VBIEscCol129921_2244.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M22591 Genomic DNA. Translation: AAA24216.1 .
U00007 Genomic DNA. Translation: AAA60529.1 .
U00096 Genomic DNA. Translation: AAC75220.1 .
AP009048 Genomic DNA. Translation: BAE76636.1 .
PIRi F64984. NDEC4.
RefSeqi NP_416664.1. NC_000913.3.
YP_490398.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1QTW X-ray 1.02 A 1-285 [» ]
1QUM X-ray 1.55 A 1-285 [» ]
2NQ9 X-ray 1.45 A 1-285 [» ]
2NQH X-ray 1.10 A 1-285 [» ]
2NQJ X-ray 2.45 A/B 1-285 [» ]
4K1G X-ray 1.90 A/B 1-285 [» ]
ProteinModelPortali P0A6C1.
SMRi P0A6C1. Positions 1-285.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-47966N.
IntActi P0A6C1. 10 interactions.
MINTi MINT-1242700.
STRINGi 511145.b2159.

Chemistry

ChEMBLi CHEMBL1293285.

Proteomic databases

PaxDbi P0A6C1.
PRIDEi P0A6C1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75220 ; AAC75220 ; b2159 .
BAE76636 ; BAE76636 ; BAE76636 .
GeneIDi 12932805.
946669.
KEGGi ecj:Y75_p2121.
eco:b2159.
PATRICi 32119667. VBIEscCol129921_2244.

Organism-specific databases

EchoBASEi EB0645.
EcoGenei EG10651. nfo.

Phylogenomic databases

eggNOGi COG0648.
HOGENOMi HOG000224893.
InParanoidi P0A6C1.
KOi K01151.
OMAi IAWLKSE.
OrthoDBi EOG6Z0QCM.
PhylomeDBi P0A6C1.

Enzyme and pathway databases

BioCyci EcoCyc:EG10651-MONOMER.
ECOL316407:JW2146-MONOMER.
MetaCyc:EG10651-MONOMER.
BRENDAi 3.1.21.2. 2026.

Miscellaneous databases

EvolutionaryTracei P0A6C1.
PROi P0A6C1.

Gene expression databases

Genevestigatori P0A6C1.

Family and domain databases

Gene3Di 3.20.20.150. 1 hit.
HAMAPi MF_00152. Nfo.
InterProi IPR001719. AP_endonuc_2.
IPR018246. AP_endonuc_F2_Zn_BS.
IPR013022. Xyl_isomerase-like_TIM-brl.
[Graphical view ]
PANTHERi PTHR21445. PTHR21445. 1 hit.
Pfami PF01261. AP_endonuc_2. 1 hit.
[Graphical view ]
SMARTi SM00518. AP2Ec. 1 hit.
[Graphical view ]
SUPFAMi SSF51658. SSF51658. 1 hit.
TIGRFAMsi TIGR00587. nfo. 1 hit.
PROSITEi PS00729. AP_NUCLEASE_F2_1. 1 hit.
PS00730. AP_NUCLEASE_F2_2. 1 hit.
PS00731. AP_NUCLEASE_F2_3. 1 hit.
PS51432. AP_NUCLEASE_F2_4. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the nfo gene of Escherichia coli K-12."
    Saporito S.M., Cunningham R.P.
    J. Bacteriol. 170:5141-5145(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Automated multiplex sequencing of the E.coli genome."
    Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
    Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / BHB2600.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Metalloenzymes in DNA repair. Escherichia coli endonuclease IV and Saccharomyces cerevisiae Apn1."
    Levin J.D., Shapiro R., Demple B.
    J. Biol. Chem. 266:22893-22898(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: METAL-BINDING STUDIES.
  6. "Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis."
    Hosfield D.J., Guan Y., Haas B.J., Cunningham R.P., Tainer J.A.
    Cell 98:397-408(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.02 ANGSTROMS).

Entry informationi

Entry nameiEND4_ECOLI
AccessioniPrimary (citable) accession number: P0A6C1
Secondary accession number(s): P12638, P78086, Q2MAS0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: October 29, 2014
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3