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UniProtKB - P38319 (TYDP1_YEAST)

Entry version 157 (02 Jun 2021)
Sequence version 1 (01 Oct 1994)
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Protein

Tyrosyl-DNA phosphodiesterase 1

Gene

TDP1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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

DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Cleaves also 5' phosphotyrosyl adducts resulting from dead-end complexes between DNA and the active site tyrosine of topoisomerase II. Contributes to DNA repair after radiation damage. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. May have low 3'exonuclease activity and may be able to remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate (By similarity).

By similarity2 Publications

Miscellaneous

Present with 2130 molecules/cell in log phase SD medium.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 sitei182Nucleophile1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei184SubstrateBy similarity1
Active sitei432Proton donor/acceptor1 Publication1
Binding sitei434SubstrateBy similarity1

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 functionExonuclease, Hydrolase, Nuclease
Biological processDNA damage, DNA repair

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		3.1.4.1, 984

<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%5Fand%5Ftaxonomy%5Fsection">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:
Tyrosyl-DNA phosphodiesterase 1 (EC:3.1.4.-1 Publication)
Short name:
Tyr-DNA phosphodiesterase 1
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:TDP1
Ordered Locus Names:YBR223C
ORF Names:YBR1520
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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: Chromosome II

Organism-specific databases

Saccharomyces Genome Database

More...SGDi		S000000427, TDP1

Eukaryotic Pathogen, Vector and Host Database Resources

More...VEuPathDBi		FungiDB:YBR223C

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Nucleus

<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%5Fand%5Fbiotech%5Fsection">'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>Mutagenesisi182H → A: Loss of activity. 1 Publication1
Mutagenesisi432H → N: Strongly reduced release of the covalent intermediate with DNA that is formed during the enzyme reaction, leading to the accumulation of toxic adducts. No effect on bleomycin sensitivity. 1 Publication1
Mutagenesisi432H → R: Interferes with the hydrolysis of the covalent intermediate with DNA that is formed during the enzyme reaction. No effect on bleomycin sensitivity. 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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002124901 – 544Tyrosyl-DNA phosphodiesterase 1Add BLAST544

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		P38319

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P38319

PRoteomics IDEntifications database

More...PRIDEi		P38319

PTM databases

CarbonylDB database of protein carbonylation sites

More...CarbonylDBi		P38319

<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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<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>Sitei467Interaction with DNABy similarity1

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		32920, 110 interactors

Database of interacting proteins

More...DIPi		DIP-4945N

Protein interaction database and analysis system

More...IntActi		P38319, 16 interactors

Molecular INTeraction database

More...MINTi		P38319

STRING: functional protein association networks

More...STRINGi		4932.YBR223C

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...RNActi		P38319, protein

<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

1544
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...SMRi		P38319

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P38319

<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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni312 – 316Interaction with DNABy similarity5

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the tyrosyl-DNA phosphodiesterase family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG2031, Eukaryota

Ensembl GeneTree

More...GeneTreei		ENSGT00390000002211

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_010413_2_1_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P38319

Identification of Orthologs from Complete Genome Data

More...OMAi		AHSKFYM

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.870.20, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR010347, Tdp1
IPR027415, TDP_C

The PANTHER Classification System

More...PANTHERi		PTHR12415, PTHR12415, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF06087, Tyr-DNA_phospho, 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%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P38319-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSRETNFNGT KRKRSDVAEK VAQRWKSVRY SAEMENMAPV NSNNDSDDCV 
        60         70         80         90        100
IVSESKIIDL TNQEQDLSER IETNDTAKGA VFKLMKSDFY EREDFMGEVE 
       110        120        130        140        150
DMITLKDIFG TETLKRSILF SFQYELDFLL RQFHQNVENI TIVGQKGTIM 
       160        170        180        190        200
PIEARAMDAT LAVILKKVKL IEITMPPFAS HHTKLIINFY DNGECKIFLP 
       210        220        230        240        250
SNNFTSMETN LPQQVCWCSP LLKIGKEGLP VPFKRSLIEY LNSYHLKDID 
       260        270        280        290        300
ELITKSVEEV NFAPLSELEF VYSTPSKFQS SGLLSFYNKL EKLSAGTSAS 
       310        320        330        340        350
DTAKHYLCQT SSIGTSLSRA RDENLWTHLM IPLFTGIMSP PAKDTAGRKK 
       360        370        380        390        400
AEILPTNSLI NEYSQRKIKP YIIFPTEQEF VTSPLKWSSS GWFHFQYLQK 
       410        420        430        440        450
KSYYEMLRNK FKVFYKQDPA MVTRRRGTTP AHSKFYMHCA TNSAGPCDAS 
       460        470        480        490        500
QVFKELEWCL YTSANLSQTA WGTVSRKPRN YEAGVLYHSR RLANTRKVTC 
       510        520        530        540 
RTFTRDRRGC AGNPTHVAVP FTLPVIPYDL AEDECFCLAR HEND
Length:544
Mass (Da):62,333
Last modified:October 1, 1994 - 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:iE84C6685312DEC3F
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
Z36092 Genomic DNA Translation: CAA85186.1
BK006936 Genomic DNA Translation: DAA07340.1

Protein sequence database of the Protein Information Resource

More...PIRi		S46099

NCBI Reference Sequences

More...RefSeqi		NP_009782.3, NM_001178571.3

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		YBR223C_mRNA; YBR223C; YBR223C

Database of genes from NCBI RefSeq genomes

More...GeneIDi		852525

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		sce:YBR223C

<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
Z36092 Genomic DNA Translation: CAA85186.1
BK006936 Genomic DNA Translation: DAA07340.1
PIRiS46099
RefSeqiNP_009782.3, NM_001178571.3

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Q32X-ray2.03A/B/C/D1-544[»]
3SQ3X-ray2.50A/B/C/D79-539[»]
3SQ5X-ray2.30A/B/C/D79-539[»]
3SQ7X-ray2.00A/B/C/D79-539[»]
3SQ8X-ray2.10A/B/C/D79-539[»]
SMRiP38319
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi32920, 110 interactors
DIPiDIP-4945N
IntActiP38319, 16 interactors
MINTiP38319
STRINGi4932.YBR223C

PTM databases

CarbonylDBiP38319

Proteomic databases

MaxQBiP38319
PaxDbiP38319
PRIDEiP38319

Genome annotation databases

EnsemblFungiiYBR223C_mRNA; YBR223C; YBR223C
GeneIDi852525
KEGGisce:YBR223C

Organism-specific databases

SGDiS000000427, TDP1
VEuPathDBiFungiDB:YBR223C

Phylogenomic databases

eggNOGiKOG2031, Eukaryota
GeneTreeiENSGT00390000002211
HOGENOMiCLU_010413_2_1_1
InParanoidiP38319
OMAiAHSKFYM

Enzyme and pathway databases

BRENDAi3.1.4.1, 984

Miscellaneous databases

EvolutionaryTraceiP38319

Protein Ontology

More...PROi		PR:P38319
RNActiP38319, protein

Family and domain databases

Gene3Di3.30.870.20, 1 hit
InterProiView protein in InterPro
IPR010347, Tdp1
IPR027415, TDP_C
PANTHERiPTHR12415, PTHR12415, 1 hit
PfamiView protein in Pfam
PF06087, Tyr-DNA_phospho, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		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 nameiTYDP1_YEAST
<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: P38319
Secondary accession number(s): D6VQM0
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: June 2, 2021
This is version 157 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 programFungal 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, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
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