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TYDP2_BOVIN
ID   TYDP2_BOVIN             Reviewed;         364 AA.
AC   A7YWI9;
DT   15-DEC-2009, integrated into UniProtKB/Swiss-Prot.
DT   23-OCT-2007, sequence version 1.
DT   03-AUG-2022, entry version 83.
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;
GN   Name=TDP2; Synonyms=TTRAP;
OS   Bos taurus (Bovine).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC   Bovinae; Bos.
OX   NCBI_TaxID=9913;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=Hereford; TISSUE=Basal ganglia;
RG   NIH - Mammalian Gene Collection (MGC) project;
RL   Submitted (MAR-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. The 5'-tyrosyl DNA phosphodiesterase activity can
CC       enable the repair of TOP2-induced DNA double-strand breaks/DSBs without
CC       the need for nuclease activity, creating a 'clean' DSB with 5'-
CC       phosphate termini that are ready for ligation. Thereby, protects the
CC       transcription of many genes involved in neurological development and
CC       maintenance from the abortive activity of TOP2. Hydrolyzes 5'-
CC       phosphoglycolates on protruding 5' ends on DSBs due to DNA damage by
CC       radiation and free radicals. Has preference for single-stranded DNA or
CC       duplex DNA with a 4 base pair overhang as substrate. Has also 3'-
CC       tyrosyl DNA phosphodiesterase activity, but less efficiently and much
CC       slower than TDP1. Constitutes the major if not only 5'-tyrosyl-DNA
CC       phosphodiesterase in cells. Also acts as an adapter by participating in
CC       the specific activation of MAP3K7/TAK1 in response to TGF-beta:
CC       associates with components of the TGF-beta receptor-TRAF6-TAK1
CC       signaling module and promotes their ubiquitination dependent complex
CC       formation. Involved in non-canonical TGF-beta induced signaling routes.
CC       May also act as a negative regulator of ETS1 and may inhibit NF-kappa-B
CC       activation. Acts as a regulator of ribosome biogenesis following
CC       stress. {ECO:0000250|UniProtKB:O95551}.
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   -!- SUBUNIT: Interacts with TRAF2, TRAF3, TRAF5, TRAF6, TNFRSF8/CD30,
CC       TNFRSF5/CD40, TNFRSF1B/TNF-R75, ETS1, ETS2, FLI1, SMAD3 and
CC       ACVR1B/ALK4. {ECO:0000250|UniProtKB:O95551}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O95551}. Nucleus,
CC       PML body {ECO:0000250|UniProtKB:O95551}. Nucleus, nucleolus
CC       {ECO:0000250|UniProtKB:O95551}. Cytoplasm
CC       {ECO:0000250|UniProtKB:O95551}. Note=Localizes to nucleolar cavities
CC       following stress; localization to nucleolus is dependent on PML
CC       protein. {ECO:0000250|UniProtKB:O95551}.
CC   -!- PTM: Ubiquitinated by TRAF6. {ECO:0000250|UniProtKB:O95551}.
CC   -!- SIMILARITY: Belongs to the CCR4/nocturin family. {ECO:0000305}.
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DR   EMBL; BC134603; AAI34604.1; -; mRNA.
DR   RefSeq; NP_001098811.1; NM_001105341.1.
DR   AlphaFoldDB; A7YWI9; -.
DR   SMR; A7YWI9; -.
DR   STRING; 9913.ENSBTAP00000000472; -.
DR   PaxDb; A7YWI9; -.
DR   PRIDE; A7YWI9; -.
DR   Ensembl; ENSBTAT00000000472; ENSBTAP00000000472; ENSBTAG00000000365.
DR   GeneID; 507579; -.
DR   KEGG; bta:507579; -.
DR   CTD; 51567; -.
DR   VEuPathDB; HostDB:ENSBTAG00000000365; -.
DR   VGNC; VGNC:35714; TDP2.
DR   eggNOG; KOG2756; Eukaryota.
DR   GeneTree; ENSGT00390000014242; -.
DR   HOGENOM; CLU_047318_0_0_1; -.
DR   InParanoid; A7YWI9; -.
DR   OMA; AENDWDM; -.
DR   OrthoDB; 1612152at2759; -.
DR   TreeFam; TF314813; -.
DR   Reactome; R-BTA-5693571; Nonhomologous End-Joining (NHEJ).
DR   Proteomes; UP000009136; Chromosome 23.
DR   Bgee; ENSBTAG00000000365; Expressed in duodenum and 104 other tissues.
DR   GO; GO:0016235; C:aggresome; IEA:Ensembl.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
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:0036317; F:tyrosyl-RNA phosphodiesterase activity; IEA:Ensembl.
DR   GO; GO:0006302; P:double-strand break repair; ISS:UniProtKB.
DR   GO; GO:0048666; P:neuron development; 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   Acetylation; Cytoplasm; DNA damage; DNA repair; Hydrolase; Isopeptide bond;
KW   Magnesium; Metal-binding; Nuclease; Nucleus; Phosphoprotein;
KW   Reference proteome; Ubl conjugation.
FT   CHAIN           1..364
FT                   /note="Tyrosyl-DNA phosphodiesterase 2"
FT                   /id="PRO_0000390449"
FT   REGION          1..21
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          68..108
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          122..126
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   REGION          228..233
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   REGION          266..268
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   COMPBIAS        86..108
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        264
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:O95551"
FT   BINDING         124
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   BINDING         154
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   SITE            180
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   SITE            299
FT                   /note="Interaction with 5' end of substrate DNA"
FT                   /evidence="ECO:0000250|UniProtKB:Q9JJX7"
FT   SITE            317
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   MOD_RES         1
FT                   /note="N-acetylmethionine"
FT                   /evidence="ECO:0000250|UniProtKB:O95551"
FT   MOD_RES         88
FT                   /note="Phosphothreonine; by ACVR1B"
FT                   /evidence="ECO:0000250|UniProtKB:O95551"
FT   MOD_RES         92
FT                   /note="Phosphothreonine; by ACVR1B"
FT                   /evidence="ECO:0000250|UniProtKB:O95551"
FT   MOD_RES         95
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:O95551"
FT   CROSSLNK        23
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:O95551"
SQ   SEQUENCE   364 AA;  40826 MW;  1BEF10BA57C1199A CRC64;
     MERNSGPEAG PEAELEEGEP EVKKRKLMCV EFASVASCDA AVAQCYLAEN DWEMERALNS
     YFEPAVEESA SESRPESLSE PGSCVDLTKE ETNDSISSKT STSEDKSVQQ EDGSVFSFIT
     WNIDGLDMNN LLERARGVCS YLTLYSPDVI FLQEVIPPYY AYLKKKASSY KIITGREEGY
     FTAIMLKKSR VKFKSQEIIP FPNTQMMRNL LCVHVSVSGN ELCLMTSHLE STRGHAKERM
     NQFKMVLEKM QEAPGSATVI FAGDTNLRDQ EVTKCGGLPN NILDVWEFLG KPKHCQYTWD
     TQMNSNLGIA ANCKLRFDRI FFRAAAEGGH IIPQSLDLLG LEKLDCGRFP SDHWGLLCTL
     DVIL
 
 
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