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Probable tyrosyl-DNA phosphodiesterase (Tyr-DNA phosphodiesterase) (EC 3.1.4.-) (Protein glaikit)

 TYDP1_DROME             Reviewed;         580 AA.
Q9VQM4; Q95SG3; Q9NFM9;
24-OCT-2003, integrated into UniProtKB/Swiss-Prot.
01-MAY-2000, sequence version 1.
23-MAY-2018, entry version 131.
RecName: Full=Probable tyrosyl-DNA phosphodiesterase;
Short=Tyr-DNA phosphodiesterase;
EC=3.1.4.- {ECO:0000250|UniProtKB:Q9NUW8};
AltName: Full=Protein glaikit;
Name=gkt; Synonyms=Tdp1; ORFNames=CG8825, CG8826;
Drosophila melanogaster (Fruit fly).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophila; Sophophora.
NCBI_TaxID=7227;
[1]
NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, AND DEVELOPMENTAL
STAGE.
PubMed=10940635; DOI=10.1016/S0925-4773(00)00381-6;
Dunlop J., Corominas M., Serras F.;
"The novel gene glaikit, is expressed during neurogenesis in the
Drosophila melanogaster embryo.";
Mech. Dev. 96:133-136(2000).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
PubMed=10731132; DOI=10.1126/science.287.5461.2185;
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I.,
Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P.,
de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M.,
Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P.,
Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W.,
Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K.,
Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J.,
Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C.,
Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A.,
Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z.,
Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X.,
Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D.,
Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A.,
Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L.,
Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M.,
Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G.,
Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H.,
Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
Spier E., Spradling A.C., Stapleton M., Strong R., Sun E.,
Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X.,
Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J.,
Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A.,
Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L.,
Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X.,
Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[3]
GENOME REANNOTATION.
STRAIN=Berkeley;
PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q.,
Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
Lewis S.E.;
"Annotation of the Drosophila melanogaster euchromatic genome: a
systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=Berkeley; TISSUE=Embryo, and Head;
PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M.,
George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H.,
Rubin G.M., Celniker S.E.;
"A Drosophila full-length cDNA resource.";
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
[5]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=15556867; DOI=10.1016/j.cub.2004.10.048;
Dunlop J., Morin X., Corominas M., Serras F., Tear G.;
"glaikit is essential for the formation of epithelial polarity and
neuronal development.";
Curr. Biol. 14:2039-2045(2004).
-!- FUNCTION: DNA repair enzyme that can remove a variety of covalent
adducts from DNA through hydrolysis of a 3'-phosphodiester bond,
giving rise to DNA with a free 3' phosphate. Catalyzes the
hydrolysis of dead-end complexes between DNA and the topoisomerase
I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on
protruding 3' ends on DNA double-strand breaks due to DNA damage
by radiation and free radicals. Acts on blunt-ended double-strand
DNA breaks and on single-stranded DNA. May have low 3'exonuclease
activity and may be able to remove a single nucleoside from the
3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no
exonuclease activity towards DNA or RNA with a 3'phosphate (By
similarity). Required for normal polarization of epidermal cells,
correct subcellular location of the Crb complex to the apical
lateral membrane, and for normal neuronal development during
embryonic development. {ECO:0000250|UniProtKB:Q9NUW8,
ECO:0000269|PubMed:15556867}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9NUW8}.
Cytoplasm {ECO:0000269|PubMed:15556867}.
-!- TISSUE SPECIFICITY: Expressed in the delaminating neuroblasts and
a few ganglion mother cells in stage 11-14 embryonic central
nervous system. Weak expression is seen in gonads at stage 16.
{ECO:0000269|PubMed:10940635}.
-!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically.
{ECO:0000269|PubMed:10940635}.
-!- SIMILARITY: Belongs to the tyrosyl-DNA phosphodiesterase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAL28358.1; Type=Erroneous initiation; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
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EMBL; AJ277122; CAB86488.1; -; mRNA.
EMBL; AE014134; AAF51141.1; -; Genomic_DNA.
EMBL; AY051884; AAK93308.1; -; mRNA.
EMBL; AY060810; AAL28358.1; ALT_INIT; mRNA.
RefSeq; NP_523465.2; NM_078741.4.
UniGene; Dm.3843; -.
ProteinModelPortal; Q9VQM4; -.
SMR; Q9VQM4; -.
BioGrid; 59746; 5.
STRING; 7227.FBpp0077263; -.
PaxDb; Q9VQM4; -.
PRIDE; Q9VQM4; -.
EnsemblMetazoa; FBtr0077574; FBpp0077263; FBgn0260817.
GeneID; 33530; -.
KEGG; dme:Dmel_CG8825; -.
CTD; 33530; -.
FlyBase; FBgn0260817; gkt.
eggNOG; KOG2031; Eukaryota.
eggNOG; ENOG410XQPZ; LUCA.
GeneTree; ENSGT00390000002211; -.
InParanoid; Q9VQM4; -.
KO; K10862; -.
OMA; NEPRYTC; -.
OrthoDB; EOG091G0DQF; -.
PhylomeDB; Q9VQM4; -.
Reactome; R-DME-5693571; Nonhomologous End-Joining (NHEJ).
GenomeRNAi; 33530; -.
PRO; PR:Q9VQM4; -.
Proteomes; UP000000803; Chromosome 2L.
Bgee; FBgn0260817; -.
Genevisible; Q9VQM4; DM.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; ISS:UniProtKB.
GO; GO:0017005; F:3'-tyrosyl-DNA phosphodiesterase activity; ISS:UniProtKB.
GO; GO:0003690; F:double-stranded DNA binding; IBA:GO_Central.
GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
GO; GO:0007417; P:central nervous system development; IMP:FlyBase.
GO; GO:0006281; P:DNA repair; ISS:UniProtKB.
GO; GO:0006302; P:double-strand break repair; IBA:GO_Central.
GO; GO:0045197; P:establishment or maintenance of epithelial cell apical/basal polarity; IMP:FlyBase.
GO; GO:0000012; P:single strand break repair; IBA:GO_Central.
Gene3D; 3.30.870.20; -; 1.
InterPro; IPR010347; Tdp1.
InterPro; IPR027415; TDP_C.
InterPro; IPR019406; Znf_C2H2_APLF-like.
PANTHER; PTHR12415; PTHR12415; 1.
Pfam; PF06087; Tyr-DNA_phospho; 1.
Pfam; PF10283; zf-CCHH; 1.
2: Evidence at transcript level;
Complete proteome; Cytoplasm; DNA damage; DNA repair; Exonuclease;
Hydrolase; Nuclease; Nucleus; Reference proteome; Repeat.
CHAIN 1 580 Probable tyrosyl-DNA phosphodiesterase.
/FTId=PRO_0000212489.
REGION 387 390 Interaction with DNA.
{ECO:0000250|UniProtKB:Q9NUW8}.
COMPBIAS 87 94 Poly-Ser.
ACT_SITE 248 248 Nucleophile.
{ECO:0000250|UniProtKB:Q9NUW8}.
ACT_SITE 479 479 Proton donor/acceptor.
{ECO:0000250|UniProtKB:Q9NUW8}.
BINDING 250 250 Substrate.
{ECO:0000250|UniProtKB:Q9NUW8}.
BINDING 481 481 Substrate.
{ECO:0000250|UniProtKB:Q9NUW8}.
SITE 504 504 Interaction with DNA.
{ECO:0000250|UniProtKB:Q9NUW8}.
CONFLICT 214 214 L -> V (in Ref. 1; CAB86488).
{ECO:0000305}.
CONFLICT 300 300 G -> R (in Ref. 1; CAB86488).
{ECO:0000305}.
CONFLICT 310 310 L -> R (in Ref. 1; CAB86488).
{ECO:0000305}.
CONFLICT 327 327 A -> P (in Ref. 1; CAB86488).
{ECO:0000305}.
CONFLICT 407 407 L -> P (in Ref. 1; CAB86488).
{ECO:0000305}.
CONFLICT 455 455 K -> N (in Ref. 1; CAB86488).
{ECO:0000305}.
SEQUENCE 580 AA; 64194 MW; 14EC03C1E993BE87 CRC64;
MKECPYGEKC YRKNPIHFGE FSHAHLDAIY AKGNESGDYE IPANYSSEMI HTQLKLLEKL
FPKQATNKEQ EAHSSSSKPA VTAPVASGSS SSGSLDTNPS GSSASGPAAS QDTSNLAKKQ
KLNAKNIRDY IPVVIEKGGM AKKLERAAPY NMFLTAITDS KPTHSEPLSI TLQEILDESL
GEIESTVQIN FMVDIGWLLG HYYFAGILDK PLLLLYGDES PELLSIGKFK QQVTAIRVKM
PTPFATSHTK MMFLGYSDGS MRVVISTANL YEDDWHNRTQ GLWISPKLPA LPVDADTGAG
ESLTGFKQDL MLYLVEYKIS QLQPWIARIR NSDFSAINVF FLGSVPGGHR EGSVRGHPWG
HARLASLLAK HAAPIDDRIP VVCQSSSIGS LGANVQAWIQ QDFVNSLKKD STPVGKLRQM
PPFKMIYPSY GNVAGSHDGM LGGGCLPYGK NTNDKQPWLK DYLQQWKSSD RFRSRAMPHI
KSYTRFNLED QSVYWFVLTS ANLSKAAWGC FNKNSNIQPC LRIANYEAGV LFLPRFVTGE
DTFPLGNNRD GVPAFPLPYD VPLTPYAPDD KPFLMDYLQG


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