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P04418

- END5_BPT4

UniProt

P04418 - END5_BPT4

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Protein

Endonuclease V

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

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
Complete GO annotation...

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.

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

« Hide 'large scale' publications
  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

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