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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-Experimental evidence at protein leveli

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei182Nucleophile1 Publication1
Binding sitei184SubstrateBy similarity1
Active sitei432Proton donor/acceptor1 Publication1
Binding sitei434SubstrateBy similarity1

GO - Molecular functioni

  • 3'-tyrosyl-DNA phosphodiesterase activity Source: SGD
  • 5'-tyrosyl-DNA phosphodiesterase activity Source: SGD
  • exonuclease activity Source: UniProtKB-KW

GO - Biological processi

  • DNA repair Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Enzyme and pathway databases

BioCyciYEAST:G3O-29158-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Tyrosyl-DNA phosphodiesterase 1 (EC:3.1.4.-1 Publication)
Short name:
Tyr-DNA phosphodiesterase 1
Gene namesi
Name:TDP1
Ordered Locus Names:YBR223C
ORF Names:YBR1520
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBR223C.
SGDiS000000427. TDP1.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002124901 – 544Tyrosyl-DNA phosphodiesterase 1Add BLAST544

Proteomic databases

MaxQBiP38319.
PRIDEiP38319.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei467Interaction with DNABy similarity1

Protein-protein interaction databases

BioGridi32920. 53 interactors.
DIPiDIP-4945N.
IntActiP38319. 2 interactors.
MINTiMINT-495737.

Structurei

Secondary structure

1544
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi81 – 85Combined sources5
Turni88 – 90Combined sources3
Helixi105 – 109Combined sources5
Beta strandi114 – 120Combined sources7
Helixi126 – 130Combined sources5
Beta strandi139 – 145Combined sources7
Beta strandi148 – 150Combined sources3
Helixi154 – 156Combined sources3
Helixi159 – 165Combined sources7
Beta strandi168 – 173Combined sources6
Beta strandi185 – 190Combined sources6
Beta strandi193 – 202Combined sources10
Helixi206 – 210Combined sources5
Beta strandi211 – 213Combined sources3
Beta strandi215 – 218Combined sources4
Beta strandi222 – 224Combined sources3
Helixi232 – 242Combined sources11
Helixi247 – 252Combined sources6
Helixi254 – 258Combined sources5
Helixi263 – 265Combined sources3
Beta strandi269 – 273Combined sources5
Beta strandi277 – 279Combined sources3
Helixi282 – 293Combined sources12
Turni294 – 296Combined sources3
Beta strandi301 – 309Combined sources9
Beta strandi311 – 313Combined sources3
Beta strandi319 – 321Combined sources3
Helixi325 – 328Combined sources4
Helixi330 – 334Combined sources5
Beta strandi336 – 338Combined sources3
Helixi356 – 366Combined sources11
Beta strandi368 – 373Combined sources6
Helixi378 – 380Combined sources3
Helixi386 – 392Combined sources7
Helixi398 – 400Combined sources3
Helixi401 – 409Combined sources9
Beta strandi414 – 416Combined sources3
Turni419 – 421Combined sources3
Turni424 – 428Combined sources5
Beta strandi434 – 441Combined sources8
Beta strandi454 – 463Combined sources10
Helixi468 – 471Combined sources4
Beta strandi474 – 476Combined sources3
Beta strandi479 – 488Combined sources10
Helixi489 – 491Combined sources3
Beta strandi492 – 495Combined sources4
Beta strandi498 – 502Combined sources5
Helixi503 – 505Combined sources3
Beta strandi516 – 521Combined sources6
Beta strandi523 – 527Combined sources5
Turni530 – 532Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
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[»]
ProteinModelPortaliP38319.
SMRiP38319.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38319.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni312 – 316Interaction with DNABy similarity5

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00390000002211.
HOGENOMiHOG000142329.
InParanoidiP38319.
KOiK10862.
OMAiWCLFTSA.
OrthoDBiEOG092C27GH.

Family and domain databases

Gene3Di3.30.870.20. 1 hit.
InterProiIPR010347. Tdp1.
IPR027415. TDP_C.
[Graphical view]
PANTHERiPTHR12415. PTHR12415. 1 hit.
PfamiPF06087. Tyr-DNA_phospho. 1 hit.
[Graphical view]

Sequencei

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
Checksum:iE84C6685312DEC3F
GO

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.

Genome annotation databases

EnsemblFungiiYBR223C; YBR223C; YBR223C.
GeneIDi852525.
KEGGisce:YBR223C.

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:
PDBei
RCSB PDBi
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[»]
ProteinModelPortaliP38319.
SMRiP38319.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32920. 53 interactors.
DIPiDIP-4945N.
IntActiP38319. 2 interactors.
MINTiMINT-495737.

Proteomic databases

MaxQBiP38319.
PRIDEiP38319.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBR223C; YBR223C; YBR223C.
GeneIDi852525.
KEGGisce:YBR223C.

Organism-specific databases

EuPathDBiFungiDB:YBR223C.
SGDiS000000427. TDP1.

Phylogenomic databases

GeneTreeiENSGT00390000002211.
HOGENOMiHOG000142329.
InParanoidiP38319.
KOiK10862.
OMAiWCLFTSA.
OrthoDBiEOG092C27GH.

Enzyme and pathway databases

BioCyciYEAST:G3O-29158-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP38319.
PROiP38319.

Family and domain databases

Gene3Di3.30.870.20. 1 hit.
InterProiIPR010347. Tdp1.
IPR027415. TDP_C.
[Graphical view]
PANTHERiPTHR12415. PTHR12415. 1 hit.
PfamiPF06087. Tyr-DNA_phospho. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTYDP1_YEAST
AccessioniPrimary (citable) accession number: P38319
Secondary accession number(s): D6VQM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: November 2, 2016
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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.