ID   TYDP2_XENLA             Reviewed;         371 AA.
AC   A5D8M0;
DT   15-DEC-2009, integrated into UniProtKB/Swiss-Prot.
DT   12-JUN-2007, sequence version 1.
DT   03-AUG-2022, entry version 42.
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;
OS   Xenopus laevis (African clawed frog).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC   Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX   NCBI_TaxID=8355;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Testis;
RG   NIH - Xenopus Gene Collection (XGC) project;
RL   Submitted (MAY-2007) 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}.
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DR   EMBL; BC141728; AAI41729.1; -; mRNA.
DR   RefSeq; NP_001092156.1; NM_001098686.1.
DR   AlphaFoldDB; A5D8M0; -.
DR   SMR; A5D8M0; -.
DR   DNASU; 100049743; -.
DR   GeneID; 100049743; -.
DR   KEGG; xla:100049743; -.
DR   CTD; 100049743; -.
DR   Xenbase; XB-GENE-967018; tdp2.S.
DR   OrthoDB; 1612152at2759; -.
DR   Proteomes; UP000186698; Chromosome 6S.
DR   Bgee; 100049743; Expressed in egg cell and 19 other tissues.
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; Reference proteome.
FT   CHAIN           1..371
FT                   /note="Tyrosyl-DNA phosphodiesterase 2"
FT                   /id="PRO_0000390451"
FT   REGION          129..133
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   REGION          235..240
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   REGION          273..275
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   ACT_SITE        271
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:O95551"
FT   BINDING         131
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   BINDING         161
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   SITE            187
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   SITE            306
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   SITE            324
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   SITE            360
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
SQ   SEQUENCE   371 AA;  41446 MW;  A13665618C465EEC CRC64;
     MEVEEAGAVQ TGTGEAVVAN ERTKQCSAFA SITGCDEAVA QCFLAENDWD MERAINSYFE
     PGVESTLQNK PAADLADPLK QEMHAVTSDA CIDLTSDDLV ATKSEAVTSN SSTVKQQEDE
     SHFTFLTWNI DGLDESNVAE RARAVCSCLA LYTPDVVFLQ EVIPPYCEYL KKRAVSYKII
     TGNEDEYFTA MMLKKSRVKL ISQEIVPYPS TLMMRNLLVA NVNISGNSIC LMTSHLESTK
     DHSKERLKQL DTVLKKMMDA PPSATVIFGG DTNLRDQEVA KIGGLPNTIL DVWEFLGKPE
     HCRYTWDTKL NNNLRACYTS RLRFDRILYR ASMEGSQVIP QFLNLVGTEK LDCGRFPSDH
     WGLLCDFDII L