UniProtKB - P38319 (TYDP1_YEAST)
Protein
Tyrosyl-DNA phosphodiesterase 1
Gene
TDP1
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 182 | Nucleophile1 Publication | 1 | |
Binding sitei | 184 | SubstrateBy similarity | 1 | |
Active sitei | 432 | Proton donor/acceptor1 Publication | 1 | |
Binding sitei | 434 | SubstrateBy similarity | 1 |
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 function | Exonuclease, Hydrolase, Nuclease |
Biological process | DNA damage, DNA repair |
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 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000000427, TDP1 |
VEuPathDBi | FungiDB:YBR223C |
Subcellular locationi
Nucleus
- Nucleus 1 Publication
Mitochondrion
- mitochondrion Source: SGD
Nucleus
- nucleus Source: SGD
Keywords - Cellular componenti
NucleusPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 182 | H → A: Loss of activity. 1 Publication | 1 | |
Mutagenesisi | 432 | H → 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 | 1 | |
Mutagenesisi | 432 | H → 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 | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000212490 | 1 – 544 | Tyrosyl-DNA phosphodiesterase 1Add BLAST | 544 |
Proteomic databases
MaxQBi | P38319 |
PaxDbi | P38319 |
PRIDEi | P38319 |
PTM databases
CarbonylDBi | P38319 |
Interactioni
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 467 | Interaction with DNABy similarity | 1 |
Protein-protein interaction databases
BioGRIDi | 32920, 110 interactors |
DIPi | DIP-4945N |
IntActi | P38319, 16 interactors |
MINTi | P38319 |
STRINGi | 4932.YBR223C |
Miscellaneous databases
RNActi | P38319, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P38319 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P38319 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 312 – 316 | Interaction with DNABy similarity | 5 |
Sequence similaritiesi
Belongs to the tyrosyl-DNA phosphodiesterase family.Curated
Keywords - Domaini
RepeatPhylogenomic databases
eggNOGi | KOG2031, Eukaryota |
GeneTreei | ENSGT00390000002211 |
HOGENOMi | CLU_010413_2_1_1 |
InParanoidi | P38319 |
OMAi | AHSKFYM |
Family and domain databases
Gene3Di | 3.30.870.20, 1 hit |
InterProi | View protein in InterPro IPR010347, Tdp1 IPR027415, TDP_C |
PANTHERi | PTHR12415, PTHR12415, 1 hit |
Pfami | View protein in Pfam PF06087, Tyr-DNA_phospho, 1 hit |
i Sequence
Sequence statusi: Complete.
P38319-1 [UniParc]FASTAAdd to basket
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
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | Z36092 Genomic DNA Translation: CAA85186.1 BK006936 Genomic DNA Translation: DAA07340.1 |
PIRi | S46099 |
RefSeqi | NP_009782.3, NM_001178571.3 |
Genome annotation databases
EnsemblFungii | YBR223C_mRNA; YBR223C; YBR223C |
GeneIDi | 852525 |
KEGGi | sce: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 |
PIRi | S46099 |
RefSeqi | NP_009782.3, NM_001178571.3 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1Q32 | X-ray | 2.03 | A/B/C/D | 1-544 | [»] | |
3SQ3 | X-ray | 2.50 | A/B/C/D | 79-539 | [»] | |
3SQ5 | X-ray | 2.30 | A/B/C/D | 79-539 | [»] | |
3SQ7 | X-ray | 2.00 | A/B/C/D | 79-539 | [»] | |
3SQ8 | X-ray | 2.10 | A/B/C/D | 79-539 | [»] | |
SMRi | P38319 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 32920, 110 interactors |
DIPi | DIP-4945N |
IntActi | P38319, 16 interactors |
MINTi | P38319 |
STRINGi | 4932.YBR223C |
PTM databases
CarbonylDBi | P38319 |
Proteomic databases
MaxQBi | P38319 |
PaxDbi | P38319 |
PRIDEi | P38319 |
Genome annotation databases
EnsemblFungii | YBR223C_mRNA; YBR223C; YBR223C |
GeneIDi | 852525 |
KEGGi | sce:YBR223C |
Organism-specific databases
SGDi | S000000427, TDP1 |
VEuPathDBi | FungiDB:YBR223C |
Phylogenomic databases
eggNOGi | KOG2031, Eukaryota |
GeneTreei | ENSGT00390000002211 |
HOGENOMi | CLU_010413_2_1_1 |
InParanoidi | P38319 |
OMAi | AHSKFYM |
Miscellaneous databases
EvolutionaryTracei | P38319 |
PROi | PR:P38319 |
RNActi | P38319, protein |
Family and domain databases
Gene3Di | 3.30.870.20, 1 hit |
InterProi | View protein in InterPro IPR010347, Tdp1 IPR027415, TDP_C |
PANTHERi | PTHR12415, PTHR12415, 1 hit |
Pfami | View protein in Pfam PF06087, Tyr-DNA_phospho, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | TYDP1_YEAST | |
Accessioni | P38319Primary (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: | April 7, 2021 | |
This is version 156 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome II
Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families