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P04418

- END5_BPT4

UniProt

P04418 - END5_BPT4

Protein

Endonuclease V

Gene

denV

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
  1. Functioni

    This enzyme is a pyrimidine dimer DNA glycosylase. Excises pyrimidine dimers that are the major UV-lesion of a DNA duplex. It first hydrolyzes the glycosylic bond of the 5' pyrimidine of the dimer and then the intrapyrimidine phosphodiester bond.

    Catalytic activityi

    Endonucleolytic cleavage near pyrimidine dimers to products with 5'-phosphate.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei23 – 231Proton acceptor

    GO - Molecular functioni

    1. deoxyribonuclease (pyrimidine dimer) activity Source: UniProtKB-EC
    2. hydrolase activity, acting on glycosyl bonds Source: UniProtKB-KW

    GO - Biological processi

    1. DNA repair Source: UniProtKB-KW

    Keywords - Molecular functioni

    Endonuclease, Glycosidase, Hydrolase, Nuclease

    Keywords - Biological processi

    DNA damage, DNA repair

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Endonuclease V (EC:3.1.25.1)
    Gene namesi
    Name:denV
    OrganismiEnterobacteria phage T4 (Bacteriophage T4)
    Taxonomic identifieri10665 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4likevirus
    Virus hostiEscherichia coli [TaxID: 562]
    ProteomesiUP000009087: Genome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 138138Endonuclease VPRO_0000164934Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.

    Structurei

    Secondary structure

    1
    138
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 113
    Helixi14 – 2310
    Helixi26 – 3611
    Helixi41 – 433
    Turni54 – 574
    Helixi58 – 603
    Helixi64 – 8017
    Helixi98 – 1003
    Helixi108 – 12417
    Helixi126 – 1283
    Beta strandi131 – 1333

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ENIX-ray2.20A1-138[»]
    1ENJX-ray1.80A1-138[»]
    1ENKX-ray2.00A1-138[»]
    1VASX-ray2.75A2-138[»]
    2ENDX-ray1.45A1-138[»]
    2FCCX-ray2.30A/B2-138[»]
    ProteinModelPortaliP04418.
    SMRiP04418. Positions 2-138.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04418.

    Family & Domainsi

    Family and domain databases

    Gene3Di1.10.440.10. 1 hit.
    InterProiIPR004260. Pyr-dimer_DNA_glycosylase.
    IPR021143. Pyr-dimer_DNAGlyclase_EndonucV.
    IPR024796. T4_endonuc_V.
    [Graphical view]
    PfamiPF03013. Pyr_excise. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001000. PDG_ENDV. 1 hit.
    ProDomiPD021350. Pyr-dimer_DNA_glycosylase. 1 hit.
    [Graphical view] [Entries sharing at least one domain]

    Sequencei

    Sequence statusi: Complete.

    P04418-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTRINLTLVS ELADQHLMAE YRELPRVFGA VRKHVANGKR VRDFKISPTF    50
    ILGAGHVTFF YDKLEFLRKR QIELIAECLK RGFNIKDTTV QDISDIPQEF 100
    RGDYIPHEAS IAISQARLDE KIAQRPTWYK YYGKAIYA 138
    Length:138
    Mass (Da):16,079
    Last modified:August 13, 1987 - v1
    Checksum:i90B889C8E6686697
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X04567 Genomic DNA. Translation: CAA28215.1.
    AF158101 Genomic DNA. Translation: AAD42563.1.
    PIRiA93540. NEBPT4.
    RefSeqiNP_049733.1. NC_000866.4.

    Genome annotation databases

    GeneIDi1258606.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X04567 Genomic DNA. Translation: CAA28215.1 .
    AF158101 Genomic DNA. Translation: AAD42563.1 .
    PIRi A93540. NEBPT4.
    RefSeqi NP_049733.1. NC_000866.4.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1ENI X-ray 2.20 A 1-138 [» ]
    1ENJ X-ray 1.80 A 1-138 [» ]
    1ENK X-ray 2.00 A 1-138 [» ]
    1VAS X-ray 2.75 A 2-138 [» ]
    2END X-ray 1.45 A 1-138 [» ]
    2FCC X-ray 2.30 A/B 2-138 [» ]
    ProteinModelPortali P04418.
    SMRi P04418. Positions 2-138.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 1258606.

    Miscellaneous databases

    EvolutionaryTracei P04418.

    Family and domain databases

    Gene3Di 1.10.440.10. 1 hit.
    InterProi IPR004260. Pyr-dimer_DNA_glycosylase.
    IPR021143. Pyr-dimer_DNAGlyclase_EndonucV.
    IPR024796. T4_endonuc_V.
    [Graphical view ]
    Pfami PF03013. Pyr_excise. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001000. PDG_ENDV. 1 hit.
    ProDomi PD021350. Pyr-dimer_DNA_glycosylase. 1 hit.
    [Graphical view ] [Entries sharing at least one domain ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification, physical map location and sequence of the denV gene from bacteriophage T4."
      Valerie K., Henderson E.E., Deriel J.K.
      Nucleic Acids Res. 12:8085-8096(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4."
      Valerie K., Stevens J., Lynch M., Henderson E.E., de Riel J.K.
      Nucleic Acids Res. 14:8637-8654(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Physical mapping and complete nucleotide sequence of the denV gene of bacteriophage T4."
      Radany E.H., Naumovski L., Love J.D., Gutekunst K.A., Hall D.H., Friedberg E.C.
      J. Virol. 52:846-856(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "Site-directed deletion mutagenesis within the T4 endonuclease V gene: dispensable sequences within putative loop regions."
      Dodson M.L., Prince M.A., Anderson W.F., Lloyd R.S.
      Mutat. Res. 255:19-29(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS.
    6. "Participation of glutamic acid 23 of T4 endonuclease V in the beta-elimination reaction of an abasic site in a synthetic duplex DNA."
      Hori N., Doi T., Karaki Y., Kikuchi M., Ikehara M., Ohtsuka E.
      Nucleic Acids Res. 20:4761-4764(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS.
    7. "X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer."
      Morikawa K., Matsumoto O., Tsujimoto M., Katayanagi K., Ariyoshi M., Doi T., Ikehara M., Inaoka T., Ohtsuka E.
      Science 256:523-526(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

    Entry informationi

    Entry nameiEND5_BPT4
    AccessioniPrimary (citable) accession number: P04418
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: August 13, 1987
    Last modified: May 14, 2014
    This is version 97 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Phage T4 deficient in the enzymes are extremely sensitive to UV.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references

    External Data

    Dasty 3