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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

Miscellaneous

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei2Nucleophile; via amide nitrogenCombined sources1 Publication1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei3Substrate binding2 Publications1
Sitei22Substrate binding1 Publication1
Active sitei23Proton acceptorCombined sources1 Publication1
Sitei26Transition state stabilizerCombined sources1
Sitei117Substrate binding1 Publication1
Sitei121Substrate binding1 Publication1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionEndonuclease, Glycosidase, Hydrolase, Lyase, Multifunctional enzyme, Nuclease
Biological processDNA damage, DNA repair

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
3.1.25.1 732

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEnterobacteria phage T4 (Bacteriophage T4)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10665 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4virus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiEscherichia coli [TaxID: 562]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000009087 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome
  • UP000001092 Componenti: Genome
  • UP000185270 Componenti: Genome
  • UP000185269 Componenti: Genome
  • UP000185271 Componenti: Genome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi3R → K: Complete loss of DNA glycosylase activity. 1 Publication1
Mutagenesisi11E → Q: 24% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi16H → A: 30% decrease in enzymatic activity. 1 Publication1
Mutagenesisi16H → C: 40% decrease in enzymatic activity. 1 Publication1
Mutagenesisi16H → D: 60% decrease in enzymatic activity. 1 Publication1
Mutagenesisi16H → E: 50% decrease in enzymatic activity. 1 Publication1
Mutagenesisi16H → K: 75% decrease in enzymatic activity. 1 Publication1
Mutagenesisi16H → Q: 60% decrease in enzymatic activity. 1 Publication1
Mutagenesisi16H → S: 70% decrease in enzymatic activity. 1 Publication1
Mutagenesisi21Y → F: No effect on DNA glycosylase activity. 1 Publication1
Mutagenesisi22R → Q: Almost complete loss of DNA glycosylase activity. 1 Publication1
Mutagenesisi23E → D: Complete loss of DNA glycosylase activity. No effect on AP lyase activity. 2 Publications1
Mutagenesisi23E → Q: Complete loss of DNA glycosylase activity. Complete loss of AP lyase activity. 2 Publications1
Mutagenesisi26R → Q: Almost complete loss of DNA glycosylase activity. 1 Publication1
Mutagenesisi32R → Q: 10% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi40R → Q: 20% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi42R → Q: 25% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi68R → Q: 35% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi86K → Q: No effect on DNA glycosylase activity. 1 Publication1
Mutagenesisi87D → E: No effect on DNA glycosylase activity. 1 Publication1
Mutagenesisi87D → N: 20% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi117R → Q: 60% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi119D → N: 5% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi120E → Q: 10% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi121K → Q: 90% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi125R → Q: 10% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi129Y → F: 65% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi132Y → W: 10% decrease in DNA glycosylase activity. 1 Publication1
Mutagenesisi134K → Q: 20% decrease in DNA glycosylase activity. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001649341 – 138Endonuclease VAdd BLAST138

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Monomer.

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1138
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P04418

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P04418

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

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EvolutionaryTracei
P04418

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Phylogenomic databases

KEGG Orthology (KO)

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KOi
K21522

Database of Orthologous Groups

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OrthoDBi
VOG09000111

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
1.10.440.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR004260 Pyr-dimer_DNA_glycosylase
IPR021143 Pyr-dimer_DNAGlyclase_EndonucV
IPR024796 T4_endonuc_V

Pfam protein domain database

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Pfami
View protein in Pfam
PF03013 Pyr_excise, 1 hit

PIRSF; a whole-protein classification database

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PIRSFi
PIRSF001000 PDG_ENDV, 1 hit

ProDom; a protein domain database

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ProDomi
View protein in ProDom or Entries sharing at least one domain
PD021350 Pyr-dimer_DNA_glycosylase, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i90B889C8E6686697
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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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

Protein sequence database of the Protein Information Resource

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PIRi
A93540 NEBPT4

NCBI Reference Sequences

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RefSeqi
NP_049733.1, NC_000866.4

Genome annotation databases

Database of genes from NCBI RefSeq genomes

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GeneIDi
1258606

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
vg:1258606

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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:

Protein Data Bank Europe

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PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB 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
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1258606
KEGGivg:1258606

Phylogenomic databases

KOiK21522
OrthoDBiVOG09000111

Enzyme and pathway databases

BRENDAi3.1.25.1 732

Miscellaneous databases

EvolutionaryTraceiP04418

Family and domain databases

Gene3Di1.10.440.10, 1 hit
InterProiView protein in InterPro
IPR004260 Pyr-dimer_DNA_glycosylase
IPR021143 Pyr-dimer_DNAGlyclase_EndonucV
IPR024796 T4_endonuc_V
PfamiView protein in Pfam
PF03013 Pyr_excise, 1 hit
PIRSFiPIRSF001000 PDG_ENDV, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD021350 Pyr-dimer_DNA_glycosylase, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiEND5_BPT4
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P04418
Secondary accession number(s): D9IEF4
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: December 5, 2018
This is version 117 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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