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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...

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.