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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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei182 – 1821Nucleophile1 Publication
Binding sitei184 – 1841SubstrateBy similarity
Active sitei432 – 4321Proton donor/acceptor1 Publication
Binding sitei434 – 4341SubstrateBy similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi182 – 1821H → A: Loss of activity. 1 Publication
Mutagenesisi432 – 4321H → 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 Publication
Mutagenesisi432 – 4321H → R: Interferes with the hydrolysis of the covalent intermediate with DNA that is formed during the enzyme reaction. No effect on bleomycin sensitivity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 544544Tyrosyl-DNA phosphodiesterase 1PRO_0000212490Add
BLAST

Proteomic databases

MaxQBiP38319.

Interactioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei467 – 4671Interaction with DNABy similarity

Protein-protein interaction databases

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

Structurei

Secondary structure

1
544
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi81 – 855Combined sources
Turni88 – 903Combined sources
Helixi105 – 1095Combined sources
Beta strandi114 – 1207Combined sources
Helixi126 – 1305Combined sources
Beta strandi139 – 1457Combined sources
Beta strandi148 – 1503Combined sources
Helixi154 – 1563Combined sources
Helixi159 – 1657Combined sources
Beta strandi168 – 1736Combined sources
Beta strandi185 – 1906Combined sources
Beta strandi193 – 20210Combined sources
Helixi206 – 2105Combined sources
Beta strandi211 – 2133Combined sources
Beta strandi215 – 2184Combined sources
Beta strandi222 – 2243Combined sources
Helixi232 – 24211Combined sources
Helixi247 – 2526Combined sources
Helixi254 – 2585Combined sources
Helixi263 – 2653Combined sources
Beta strandi269 – 2735Combined sources
Beta strandi277 – 2793Combined sources
Helixi282 – 29312Combined sources
Turni294 – 2963Combined sources
Beta strandi301 – 3099Combined sources
Beta strandi311 – 3133Combined sources
Beta strandi319 – 3213Combined sources
Helixi325 – 3284Combined sources
Helixi330 – 3345Combined sources
Beta strandi336 – 3383Combined sources
Helixi356 – 36611Combined sources
Beta strandi368 – 3736Combined sources
Helixi378 – 3803Combined sources
Helixi386 – 3927Combined sources
Helixi398 – 4003Combined sources
Helixi401 – 4099Combined sources
Beta strandi414 – 4163Combined sources
Turni419 – 4213Combined sources
Turni424 – 4285Combined sources
Beta strandi434 – 4418Combined sources
Beta strandi454 – 46310Combined sources
Helixi468 – 4714Combined sources
Beta strandi474 – 4763Combined sources
Beta strandi479 – 48810Combined sources
Helixi489 – 4913Combined sources
Beta strandi492 – 4954Combined sources
Beta strandi498 – 5025Combined sources
Helixi503 – 5053Combined sources
Beta strandi516 – 5216Combined sources
Beta strandi523 – 5275Combined sources
Turni530 – 5323Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 79-539.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38319.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni312 – 3165Interaction with DNABy similarity

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00390000002211.
HOGENOMiHOG000142329.
InParanoidiP38319.
KOiK10862.
OMAiVYLFSFQ.
OrthoDBiEOG75B8F2.

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
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. Positions 79-539.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

MaxQBiP38319.

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.
OMAiVYLFSFQ.
OrthoDBiEOG75B8F2.

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...

Publicationsi

« Hide 'large scale' publications
  1. "Complete DNA sequence of yeast chromosome II."
    Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
    , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
    EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Yeast gene for a Tyr-DNA phosphodiesterase that repairs topoisomerase I complexes."
    Pouliot J.J., Yao K.C., Robertson C.A., Nash H.A.
    Science 286:552-555(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "Genome-wide nuclear morphology screen identifies novel genes involved in nuclear architecture and gene-silencing in Saccharomyces cerevisiae."
    Teixeira M.T., Dujon B., Fabre E.
    J. Mol. Biol. 321:551-561(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "Tyrosyl-DNA phosphodiesterase (Tdp1) participates in the repair of Top2-mediated DNA damage."
    Nitiss K.C., Malik M., He X., White S.W., Nitiss J.L.
    Proc. Natl. Acad. Sci. U.S.A. 103:8953-8958(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF HIS-182, ACTIVE SITE.
  7. "Mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison."
    He X., van Waardenburg R.C.A.M., Babaoglu K., Price A.C., Nitiss K.C., Nitiss J.L., Bjornsti M.-A., White S.W.
    J. Mol. Biol. 372:1070-1081(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), MUTAGENESIS OF HIS-432, ACTIVE SITE.

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: July 6, 2016
This is version 123 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.