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P0A6C1

- END4_ECOLI

UniProt

P0A6C1 - END4_ECOLI

Protein

Endonuclease 4

Gene

nfo

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 92 (01 Oct 2014)
      Sequence version 1 (07 Jun 2005)
      Previous versions | rss
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    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

    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.

    Subcellular locationi

    GO - Cellular componenti

    1. intracellular Source: InterPro

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6C1.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the AP endonuclease 2 family.Curated

    Phylogenomic databases

    eggNOGiCOG0648.
    HOGENOMiHOG000224893.
    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

    MKYIGAHVSA AGGLANAAIR AAEIDATAFA LFTKNQRQWR AAPLTTQTID    50
    EFKAACEKYH YTSAQILPHD SYLINLGHPV TEALEKSRDA FIDEMQRCEQ 100
    LGLSLLNFHP GSHLMQISEE DCLARIAESI NIALDKTQGV TAVIENTAGQ 150
    GSNLGFKFEH LAAIIDGVED KSRVGVCIDT CHAFAAGYDL RTPAECEKTF 200
    ADFARTVGFK YLRGMHLNDA KSTFGSRVDR HHSLGEGNIG HDAFRWIMQD 250
    DRFDGIPLIL ETINPDIWAE EIAWLKAQQT EKAVA 285
    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.
    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.
    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

    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 1, 2014
    This is version 92 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