TYDP2_XENTR
ID TYDP2_XENTR Reviewed; 373 AA.
AC Q28FQ5;
DT 15-DEC-2009, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2009, sequence version 2.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=Tyrosyl-DNA phosphodiesterase 2;
DE Short=Tyr-DNA phosphodiesterase 2;
DE EC=3.1.4.- {ECO:0000250|UniProtKB:Q9JJX7};
DE AltName: Full=5'-tyrosyl-DNA phosphodiesterase;
DE Short=5'-Tyr-DNA phosphodiesterase;
DE AltName: Full=TRAF and TNF receptor-associated protein homolog;
GN Name=tdp2; Synonyms=ttrap; ORFNames=TGas102g02.1;
OS Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX NCBI_TaxID=8364;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Gastrula;
RG Sanger Xenopus tropicalis EST/cDNA project;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAI66146.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAJ81630.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CR761829; CAJ81630.1; ALT_INIT; mRNA.
DR EMBL; BC166146; AAI66146.1; ALT_INIT; mRNA.
DR RefSeq; NP_001016944.1; NM_001016944.2.
DR RefSeq; XP_012820215.1; XM_012964761.1.
DR AlphaFoldDB; Q28FQ5; -.
DR SMR; Q28FQ5; -.
DR PaxDb; Q28FQ5; -.
DR PRIDE; Q28FQ5; -.
DR GeneID; 549698; -.
DR KEGG; xtr:549698; -.
DR CTD; 51567; -.
DR Xenbase; XB-GENE-967013; tdp2.
DR eggNOG; KOG2756; Eukaryota.
DR HOGENOM; CLU_047318_0_0_1; -.
DR InParanoid; Q28FQ5; -.
DR OrthoDB; 1612152at2759; -.
DR Reactome; R-XTR-5693571; Nonhomologous End-Joining (NHEJ).
DR Proteomes; UP000008143; Chromosome 6.
DR Proteomes; UP000790000; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0016605; C:PML body; ISS:UniProtKB.
DR GO; GO:0070260; F:5'-tyrosyl-DNA phosphodiesterase activity; ISS:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; ISS:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; ISS:UniProtKB.
DR GO; GO:0004518; F:nuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0003697; F:single-stranded DNA binding; ISS:UniProtKB.
DR GO; GO:0006302; P:double-strand break repair; ISS:UniProtKB.
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 2: Evidence at transcript level;
KW DNA damage; DNA repair; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleus; Receptor; Reference proteome.
FT CHAIN 1..373
FT /note="Tyrosyl-DNA phosphodiesterase 2"
FT /id="PRO_0000390452"
FT REGION 131..135
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT REGION 237..242
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT REGION 275..277
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT ACT_SITE 273
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:O95551"
FT BINDING 133
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT BINDING 163
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 189
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 308
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 326
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 362
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
SQ SEQUENCE 373 AA; 41519 MW; 7E9CDB9892717604 CRC64;
MEKEDAGAVQ CGTGEGEAVV LNERSEQCSA FASIAGCDEA VAQCFLAEND WDMERAINSF
FEPGVESALQ NKAAADIADP LKQETMSGTA SDSCIDLTGD DLVVTKSEAT TSNSSTVKQE
DESHFSFLTW NIDGLDESNV AERARGVCSY LALYSPDVVF LQEVIPPYYE YLKKRAVSYT
IITGNEDEYF TAMMLKKSRV KLISQEIVPY PSTVMMRNLL VANVNISGNS ICLMTSHLES
TKDHSKERLK QLDIVLKKMM DAPPLATVIF GGDTNLRDQE VAKIGGMPNN ILDVWDFLGK
PEHCRYTWDT KVNKNLRAPY ICRLRFDRIF FRASQEGSQV IPQSLYLAGT EKLDCGRFPS
DHWGLLCDFA IIL
