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Protein

Endonuclease V

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

Functioni

Participates in the repair of UV-damaged DNA by excising pyrimidine dimers that are the major UV-lesions (PubMed:6254991). DNA glycosylase activity hydrolyzes the glycosylic bond of the 5' pyrimidine of the dimer (PubMed:6254991). This leaves apurinic/apyrimidic (AP) sites in the DNA. These AP sites are removed by the AP lyase activity which cleaves the intrapyrimidine phosphodiester bond (PubMed:6254991). Catalysis proceeds via a protonated imine covalent intermediate between the alpha-amino group of the N-terminal threonine residue and the C1' of the deoxyribose sugar of the 5' pyrimidine at the dimer site (PubMed:8347626) (PubMed:16916523).3 Publications

Catalytic activityi

Cleaves the N-glycosidic bond between the 5'-pyrimidine residue in cyclobutadipyrimidine (in DNA) and the corresponding deoxy-D-ribose residue.2 Publications
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei2 – 21Nucleophile; via amide nitrogenCombined sources1 Publication
Sitei3 – 31Substrate binding2 Publications
Sitei22 – 221Substrate binding1 Publication
Active sitei23 – 231Proton acceptorCombined sources1 Publication
Sitei26 – 261Transition state stabilizerCombined sources
Sitei117 – 1171Substrate binding1 Publication
Sitei121 – 1211Substrate binding1 Publication

GO - Molecular functioni

  • deoxyribodipyrimidine endonucleosidase activity Source: UniProtKB-EC
  • DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB
  • pyrimidine dimer DNA N-glycosylase activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Glycosidase, Hydrolase, Lyase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Enzyme and pathway databases

BRENDAi3.1.25.1. 732.

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease V1 Publication (EC:3.2.2.172 Publications)
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase (EC:4.2.99.182 Publications)
Short name:
AP lyase
T4 pyrimidine dimer glycosylase1 Publication
Short name:
T4-Pdg1 Publication
OrganismiEnterobacteria phage T4 (Bacteriophage T4)
Taxonomic identifieri10665 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4likevirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000009087 Componenti: Genome
  • UP000001092 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi3 – 31R → K: Complete loss of DNA glycosylase activity. 1 Publication
Mutagenesisi11 – 111E → Q: 24% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi16 – 161H → A: 30% decrease in enzymatic activity. 1 Publication
Mutagenesisi16 – 161H → C: 40% decrease in enzymatic activity. 1 Publication
Mutagenesisi16 – 161H → D: 60% decrease in enzymatic activity. 1 Publication
Mutagenesisi16 – 161H → E: 50% decrease in enzymatic activity. 1 Publication
Mutagenesisi16 – 161H → K: 75% decrease in enzymatic activity. 1 Publication
Mutagenesisi16 – 161H → Q: 60% decrease in enzymatic activity. 1 Publication
Mutagenesisi16 – 161H → S: 70% decrease in enzymatic activity. 1 Publication
Mutagenesisi21 – 211Y → F: No effect on DNA glycosylase activity. 1 Publication
Mutagenesisi22 – 221R → Q: Almost complete loss of DNA glycosylase activity. 1 Publication
Mutagenesisi23 – 231E → D: Complete loss of DNA glycosylase activity. No effect on AP lyase activity. 2 Publications
Mutagenesisi23 – 231E → Q: Complete loss of DNA glycosylase activity. Complete loss of AP lyase activity. 2 Publications
Mutagenesisi26 – 261R → Q: Almost complete loss of DNA glycosylase activity. 1 Publication
Mutagenesisi32 – 321R → Q: 10% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi40 – 401R → Q: 20% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi42 – 421R → Q: 25% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi68 – 681R → Q: 35% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi86 – 861K → Q: No effect on DNA glycosylase activity. 1 Publication
Mutagenesisi87 – 871D → E: No effect on DNA glycosylase activity. 1 Publication
Mutagenesisi87 – 871D → N: 20% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi117 – 1171R → Q: 60% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi119 – 1191D → N: 5% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi120 – 1201E → Q: 10% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi121 – 1211K → Q: 90% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi125 – 1251R → Q: 10% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi129 – 1291Y → F: 65% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi132 – 1321Y → W: 10% decrease in DNA glycosylase activity. 1 Publication
Mutagenesisi134 – 1341K → Q: 20% decrease in DNA glycosylase activity. 1 Publication

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 – 113Combined sources
Helixi14 – 2310Combined sources
Helixi26 – 3611Combined sources
Helixi41 – 433Combined sources
Turni54 – 574Combined sources
Helixi58 – 603Combined sources
Helixi64 – 8017Combined sources
Helixi98 – 1003Combined sources
Helixi108 – 12417Combined sources
Helixi126 – 1283Combined sources
Beta strandi131 – 1333Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MTRINLTLVS ELADQHLMAE YRELPRVFGA VRKHVANGKR VRDFKISPTF
60 70 80 90 100
ILGAGHVTFF YDKLEFLRKR QIELIAECLK RGFNIKDTTV QDISDIPQEF
110 120 130
RGDYIPHEAS IAISQARLDE KIAQRPTWYK YYGKAIYA
Length:138
Mass (Da):16,079
Last modified:August 13, 1987 - v1
Checksum:i90B889C8E6686697
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04567 Genomic DNA. Translation: CAA28215.1.
AF158101 Genomic DNA. Translation: AAD42563.1.
HM137666 Genomic DNA. Translation: ADJ39840.1.
KJ477684 Genomic DNA. Translation: AHY83587.1.
KJ477685 Genomic DNA. Translation: AHY83780.1.
KJ477686 Genomic DNA. Translation: AHY83971.1.
PIRiA93540. NEBPT4.
RefSeqiNP_049733.1. NC_000866.4.

Genome annotation databases

GeneIDi1258606.
KEGGivg:1258606.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04567 Genomic DNA. Translation: CAA28215.1.
AF158101 Genomic DNA. Translation: AAD42563.1.
HM137666 Genomic DNA. Translation: ADJ39840.1.
KJ477684 Genomic DNA. Translation: AHY83587.1.
KJ477685 Genomic DNA. Translation: AHY83780.1.
KJ477686 Genomic DNA. Translation: AHY83971.1.
PIRiA93540. NEBPT4.
RefSeqiNP_049733.1. NC_000866.4.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1258606.
KEGGivg:1258606.

Enzyme and pathway databases

BRENDAi3.1.25.1. 732.

Miscellaneous databases

EvolutionaryTraceiP04418.

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]
ProtoNetiSearch...

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. "Genomes of the T4-related bacteriophages as windows on microbial genome evolution."
    Petrov V.M., Ratnayaka S., Nolan J.M., Miller E.S., Karam J.D.
    Virol. J. 7:292-292(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9."
    Bryson A.L., Hwang Y., Sherrill-Mix S., Wu G.D., Lewis J.D., Black L., Clark T.A., Bushman F.D.
    MBio 6:E00648-E00648(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 147Imported, GT7Imported and WildImported.
  7. "Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V."
    Doi T., Recktenwald A., Karaki Y., Kikuchi M., Morikawa K., Ikehara M., Inaoka T., Hori N., Ohtsuka E.
    Proc. Natl. Acad. Sci. U.S.A. 89:9420-9424(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-11; HIS-16; TYR-21; ARG-22; GLU-23; ARG-26; ARG-40; ARG-42; ARG-68; LYS-86; ASP-87; ARG-117; ASP-119; GLU-120; LYS-121; ARG-125; TYR-129; TYR-132 AND LYS-134.
  8. "Evidence for an imino intermediate in the T4 endonuclease V reaction."
    Dodson M.L., Schrock R.D. III, Lloyd R.S.
    Biochemistry 32:8284-8290(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION.
  9. "Role of His-16 in turnover of T4 pyrimidine dimer glycosylase."
    Meador M.G., Rajagopalan L., Lloyd R.S., Dodson M.L.
    J. Biol. Chem. 279:3348-3353(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF HIS-16.
  10. "Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus UV-specific endonucleases."
    Gordon L.K., Haseltine W.A.
    J. Biol. Chem. 255:12047-12050(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION.
  11. "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 OF GLU-23.
  12. "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).
  13. "Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition."
    Vassylyev D.G., Kashiwagi T., Mikami Y., Ariyoshi M., Iwai S., Ohtsuka E., Morikawa K.
    Cell 83:773-782(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF 2-138 IN COMPLEX WITH DNA, ACTIVE SITE.
  14. "Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 A and X-ray analysis of the three active site mutants."
    Morikawa K., Ariyoshi M., Vassylyev D.G., Matsumoto O., Katayanagi K., Ohtsuka E.
    J. Mol. Biol. 249:360-375(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS).
  15. "Structure of T4 pyrimidine dimer glycosylase in a reduced imine covalent complex with abasic site-containing DNA."
    Golan G., Zharkov D.O., Grollman A.P., Dodson M.L., McCullough A.K., Lloyd R.S., Shoham G.
    J. Mol. Biol. 362:241-258(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 2-138 IN COMPLEX WITH ABASIC SITE-CONTAINING DNA, FUNCTION.

Entry informationi

Entry nameiEND5_BPT4
AccessioniPrimary (citable) accession number: P04418
Secondary accession number(s): D9IEF4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: June 8, 2016
This is version 107 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, Multifunctional enzyme, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.