TYDP2_CAEBR
ID TYDP2_CAEBR Reviewed; 337 AA.
AC A8XU68;
DT 15-DEC-2009, integrated into UniProtKB/Swiss-Prot.
DT 16-DEC-2008, sequence version 2.
DT 03-AUG-2022, entry version 59.
DE RecName: Full=5'-tyrosyl-DNA phosphodiesterase;
DE Short=5'-Tyr-DNA phosphodiesterase;
DE EC=3.1.4.- {ECO:0000250|UniProtKB:Q9JJX7};
GN ORFNames=CBG18823;
OS Caenorhabditis briggsae.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6238;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AF16;
RX PubMed=14624247; DOI=10.1371/journal.pbio.0000045;
RA Stein L.D., Bao Z., Blasiar D., Blumenthal T., Brent M.R., Chen N.,
RA Chinwalla A., Clarke L., Clee C., Coghlan A., Coulson A., D'Eustachio P.,
RA Fitch D.H.A., Fulton L.A., Fulton R.E., Griffiths-Jones S., Harris T.W.,
RA Hillier L.W., Kamath R., Kuwabara P.E., Mardis E.R., Marra M.A.,
RA Miner T.L., Minx P., Mullikin J.C., Plumb R.W., Rogers J., Schein J.E.,
RA Sohrmann M., Spieth J., Stajich J.E., Wei C., Willey D., Wilson R.K.,
RA Durbin R.M., Waterston R.H.;
RT "The genome sequence of Caenorhabditis briggsae: a platform for comparative
RT genomics.";
RL PLoS Biol. 1:166-192(2003).
CC -!- FUNCTION: DNA repair enzyme that can remove a variety of covalent
CC adducts from DNA through hydrolysis of a 5'-phosphodiester bond, giving
CC rise to DNA with a free 5' phosphate. Catalyzes the hydrolysis of dead-
CC end complexes between DNA and the topoisomerase 2 (top2) active site
CC tyrosine residue. Hydrolyzes 5'-phosphoglycolates on protruding 5' ends
CC on DNA double-strand breaks (DSBs) due to DNA damage by radiation and
CC free radicals. {ECO:0000250|UniProtKB:Q9JJX7}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:Q9JJX7};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q9JJX7};
CC Note=Binds 1 magnesium or manganese ion per subunit.
CC {ECO:0000250|UniProtKB:Q9JJX7};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O95551}. Nucleus,
CC PML body {ECO:0000250|UniProtKB:O95551}.
CC -!- SIMILARITY: Belongs to the CCR4/nocturin family. TTRAP/TDP2 subfamily.
CC {ECO:0000305}.
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DR EMBL; HE601380; CAP36193.2; -; Genomic_DNA.
DR AlphaFoldDB; A8XU68; -.
DR SMR; A8XU68; -.
DR STRING; 6238.CBG18823; -.
DR WormBase; CBG18823; CBP35925; WBGene00038163; -.
DR eggNOG; KOG2756; Eukaryota.
DR HOGENOM; CLU_047318_0_0_1; -.
DR InParanoid; A8XU68; -.
DR OMA; AENDWDM; -.
DR OrthoDB; 1612152at2759; -.
DR Proteomes; UP000008549; Chromosome I.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0016605; C:PML body; IBA:GO_Central.
DR GO; GO:0070260; F:5'-tyrosyl-DNA phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004518; F:nuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0006302; P:double-strand break repair; IBA:GO_Central.
DR Gene3D; 3.60.10.10; -; 1.
DR InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR InterPro; IPR009060; UBA-like_sf.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR SUPFAM; SSF46934; SSF46934; 1.
DR SUPFAM; SSF56219; SSF56219; 1.
PE 3: Inferred from homology;
KW DNA damage; DNA repair; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleus; Reference proteome.
FT CHAIN 1..337
FT /note="5'-tyrosyl-DNA phosphodiesterase"
FT /id="PRO_0000390453"
FT REGION 100..104
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT REGION 206..211
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT REGION 247..249
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT ACT_SITE 245
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:O95551"
FT BINDING 102
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT BINDING 132
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 159
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 277
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 295
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 327
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
SQ SEQUENCE 337 AA; 38304 MW; 4A2DFEE63A42FE7C CRC64;
MSSSDNDEPK VVEISDDEME CEGVVEVNNE QSDEAKMREF AEITATDEIM AQSILQDVGW
DLKRALDVFF GSDAFKETRN EAVMGPSSSA GFELSLMSWN IDGLDGRSLA TRMKAVATIV
KKVNPDILFL QEVVDRDLEP IDKLQSLYKI YYSNKGCQYY TAILVSKMFE VEKHDVVHFQ
NSGMYRTLQI VEGSIGGMKV FLVNTHLESM RDHRAQRMAQ FSFCMDRCAE IIANNPGCFL
FFGGDLNLRD EEISSIPDGV LDAWVSAGCD TKTKWTWDTY KNDNKQGFNG AKMRFDRIYW
HGPFNQVHFS LEGRQRIRSC LCFPSDHWAI NATFSAV
