TYDP2_CAEEL
ID TYDP2_CAEEL Reviewed; 362 AA.
AC Q9XWG3;
DT 15-DEC-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=5'-tyrosyl-DNA phosphodiesterase;
DE Short=5'-Tyr-DNA phosphodiesterase;
DE EC=3.1.4.-;
GN ORFNames=Y63D3A.4;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [2] {ECO:0007744|PDB:4F1I, ECO:0007744|PDB:4FVA, ECO:0007744|PDB:4GEW}
RP X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS) OF 107-362 IN COMPLEX WITH
RP MAGNESIUM, AND COFACTOR.
RX PubMed=23104058; DOI=10.1038/nsmb.2423;
RA Shi K., Kurahashi K., Gao R., Tsutakawa S.E., Tainer J.A., Pommier Y.,
RA Aihara H.;
RT "Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.";
RL Nat. Struct. Mol. Biol. 19:1372-1377(2012).
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:0000269|PubMed:23104058};
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:0000269|PubMed:23104058};
CC -!- INTERACTION:
CC Q9XWG3; Q9XWG3: Y63D3A.4; NbExp=3; IntAct=EBI-331496, EBI-331496;
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; AL032652; CAA21707.1; -; Genomic_DNA.
DR PIR; T27272; T27272.
DR RefSeq; NP_493461.1; NM_061060.3.
DR PDB; 4F1I; X-ray; 2.50 A; A=21-362.
DR PDB; 4FVA; X-ray; 2.07 A; A/B/C/D=107-362.
DR PDB; 4GEW; X-ray; 2.35 A; A=1-362.
DR PDBsum; 4F1I; -.
DR PDBsum; 4FVA; -.
DR PDBsum; 4GEW; -.
DR AlphaFoldDB; Q9XWG3; -.
DR SMR; Q9XWG3; -.
DR BioGRID; 38665; 26.
DR DIP; DIP-25336N; -.
DR IntAct; Q9XWG3; 12.
DR STRING; 6239.Y63D3A.4; -.
DR EPD; Q9XWG3; -.
DR PaxDb; Q9XWG3; -.
DR PeptideAtlas; Q9XWG3; -.
DR EnsemblMetazoa; Y63D3A.4.1; Y63D3A.4.1; WBGene00013405.
DR GeneID; 173276; -.
DR KEGG; cel:CELE_Y63D3A.4; -.
DR UCSC; Y63D3A.4; c. elegans.
DR CTD; 173276; -.
DR WormBase; Y63D3A.4; CE20335; WBGene00013405; -.
DR eggNOG; KOG2756; Eukaryota.
DR GeneTree; ENSGT00390000014242; -.
DR HOGENOM; CLU_047318_0_0_1; -.
DR InParanoid; Q9XWG3; -.
DR OMA; AENDWDM; -.
DR OrthoDB; 1612152at2759; -.
DR PhylomeDB; Q9XWG3; -.
DR PRO; PR:Q9XWG3; -.
DR Proteomes; UP000001940; Chromosome I.
DR Bgee; WBGene00013405; Expressed in germ line (C elegans) and 4 other tissues.
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:0042802; F:identical protein binding; IPI:IntAct.
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 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; Hydrolase; Magnesium; Metal-binding;
KW Nuclease; Nucleus; Reference proteome.
FT CHAIN 1..362
FT /note="5'-tyrosyl-DNA phosphodiesterase"
FT /id="PRO_0000390454"
FT REGION 1..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 126..130
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT REGION 232..237
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 COMPBIAS 7..43
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 271
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:O95551"
FT BINDING 128
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23104058,
FT ECO:0007744|PDB:4FVA"
FT BINDING 158
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23104058,
FT ECO:0007744|PDB:4FVA"
FT SITE 185
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 303
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 321
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT SITE 353
FT /note="Interaction with 5' end of substrate DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT HELIX 45..56
FT /evidence="ECO:0007829|PDB:4GEW"
FT HELIX 60..66
FT /evidence="ECO:0007829|PDB:4GEW"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:4GEW"
FT HELIX 74..83
FT /evidence="ECO:0007829|PDB:4GEW"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:4GEW"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:4GEW"
FT TURN 114..117
FT /evidence="ECO:0007829|PDB:4GEW"
FT STRAND 119..126
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 135..149
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 152..159
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 165..168
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 169..172
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 174..180
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 183..192
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 196..204
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 213..221
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 224..232
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 237..239
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 240..260
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 265..271
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 276..278
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 289..292
FT /evidence="ECO:0007829|PDB:4FVA"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 302..304
FT /evidence="ECO:0007829|PDB:4FVA"
FT TURN 305..307
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 322..329
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 332..338
FT /evidence="ECO:0007829|PDB:4FVA"
FT TURN 344..346
FT /evidence="ECO:0007829|PDB:4FVA"
FT STRAND 355..361
FT /evidence="ECO:0007829|PDB:4FVA"
SQ SEQUENCE 362 AA; 40893 MW; 7895C47504866E52 CRC64;
MSNSDDEIQE IEAKRQKMSQ EDSEVEIEIL DEPEQGKLKN SSMSDEQKLH EFAIITATDE
AFAQSILQDV DWDLKKALDV FYGSEAFAEA RSAAVMGASS SMASSGAAVM TAEDLKGFEV
SVMSWNIDGL DGRSLLTRMK AVAHIVKNVN PDILFLQEVV DRDLAPIDKL QSLYKIYYSN
KGCQYYTAIL VSKMFDVEKH DVIHFQNSGM YRTLQILEGS IGGLKVFLLN THLESTREHR
PQRCAQFGFC MDKVREIIAQ NPGALVFFGG DLNLRDEEVS RVPDGVKDAW EAAGSDNKTK
FTWDTFKNDN KQGFHGAKMR FDRLYWSGPL DKVKFTLEGR QRIRSCLCFP SDHWAINATF
FA
