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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: -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

Miscellaneous

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

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
  • double-stranded DNA binding Source: GO_Central
  • exonuclease activity Source: UniProtKB-KW
  • single-stranded DNA binding Source: GO_Central

GO - Biological processi

  • DNA repair Source: SGD
  • double-strand break repair Source: GO_Central
  • single strand break repair Source: GO_Central

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease
Biological processDNA 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

SGDiS000000427 TDP1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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
PaxDbiP38319
PRIDEiP38319

PTM databases

CarbonylDBiP38319

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei467Interaction with DNABy similarity1

Protein-protein interaction databases

BioGridi32920, 109 interactors
DIPiDIP-4945N
IntActiP38319, 16 interactors
MINTiP38319
STRINGi4932.YBR223C

Structurei

Secondary structure

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

3D structure databases

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
OMAiAHSKFYM
OrthoDBiEOG092C27GH

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

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

Similar proteinsi

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

PTM databases

CarbonylDBiP38319

Proteomic databases

MaxQBiP38319
PaxDbiP38319
PRIDEiP38319

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBR223C; YBR223C; YBR223C
GeneIDi852525
KEGGisce:YBR223C

Organism-specific databases

SGDiS000000427 TDP1

Phylogenomic databases

GeneTreeiENSGT00390000002211
HOGENOMiHOG000142329
InParanoidiP38319
KOiK10862
OMAiAHSKFYM
OrthoDBiEOG092C27GH

Enzyme and pathway databases

BioCyciYEAST:G3O-29158-MONOMER

Miscellaneous databases

EvolutionaryTraceiP38319
PROiPR:P38319

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
ProtoNetiSearch...

Entry informationi

Entry nameiTYDP1_YEAST
AccessioniPrimary (citable) accession number: P38319
Secondary accession number(s): D6VQM0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: November 7, 2018
This is version 143 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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
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Main funding by: National Institutes of Health

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