TYDP1_HUMAN - PTM Information in dbPTM

Basic Information of Protein

• UniProt ID: TYDP1_HUMAN
• UniProt AC: Q9NUW8
• Protein Name: Tyrosyl-DNA phosphodiesterase 1
• Gene Name: TDP1
• Organism: Homo sapiens (Human).
• Sequence Length: 608
• Subcellular Localization: Nucleus . Cytoplasm .
• Protein Description: 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. Has low 3'exonuclease activity and can 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..
• Protein Sequence: MSQEGDYGRWTISSSDESEEEKPKPDKPSTSSLLCARQGAANEPRYTCSEAQKAAHKRKISPVKFSNTDSVLPPKRQKSGSQEDLGWCLSSSDDELQPEMPQKQAEKVVIKKEKDISAPNDGTAQRTENHGAPACHRLKEEEDEYETSGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS

Overview of Protein Modification Sites with Functional and Structural Information

Experimental Post-Translational Modification Sites

* ASA = Accessible Surface Area

Locations	Modification	Substrate Peptides & Secondary Structure	ASA (%)	Reference
2	Phosphorylation	------MSQEGDYGR ------CCCCCCCCC	36.62	30177828
11	Phosphorylation	EGDYGRWTISSSDES CCCCCCEEECCCCCC	15.04	21406692
13	Phosphorylation	DYGRWTISSSDESEE CCCCEEECCCCCCCC	19.20	17081983
14	Phosphorylation	YGRWTISSSDESEEE CCCEEECCCCCCCCC	37.65	25159151
15	Phosphorylation	GRWTISSSDESEEEK CCEEECCCCCCCCCC	38.31	19276368
18	Phosphorylation	TISSSDESEEEKPKP EECCCCCCCCCCCCC	56.13	30108239
22	Sumoylation	SDESEEEKPKPDKPS CCCCCCCCCCCCCCC	62.72	-
22	Sumoylation	SDESEEEKPKPDKPS CCCCCCCCCCCCCCC	62.72	-
29	Phosphorylation	KPKPDKPSTSSLLCA CCCCCCCCHHHHHHH	46.81	27080861
30	Phosphorylation	PKPDKPSTSSLLCAR CCCCCCCHHHHHHHH	30.75	30108239
31	Phosphorylation	KPDKPSTSSLLCARQ CCCCCCHHHHHHHHC	24.27	27080861
32	Phosphorylation	PDKPSTSSLLCARQG CCCCCHHHHHHHHCC	26.00	27080861
53	Ubiquitination	YTCSEAQKAAHKRKI CCHHHHHHHHHHCCC	55.37	-
61	Phosphorylation	AAHKRKISPVKFSNT HHHHCCCCCCCCCCC	27.03	30278072
66	Phosphorylation	KISPVKFSNTDSVLP CCCCCCCCCCCCCCC	32.86	29214152
68	Phosphorylation	SPVKFSNTDSVLPPK CCCCCCCCCCCCCCC	28.58	30108239
70	Phosphorylation	VKFSNTDSVLPPKRQ CCCCCCCCCCCCCCC	24.42	29214152
79	Phosphorylation	LPPKRQKSGSQEDLG CCCCCCCCCCHHHHH	35.03	20873877
81	Phosphorylation	PKRQKSGSQEDLGWC CCCCCCCCHHHHHHH	37.17	23663014
90	Phosphorylation	EDLGWCLSSSDDELQ HHHHHHHCCCCCCCC	25.35	23663014
91	Phosphorylation	DLGWCLSSSDDELQP HHHHHHCCCCCCCCC	25.49	23663014
92	Phosphorylation	LGWCLSSSDDELQPE HHHHHCCCCCCCCCC	45.78	28102081
107	Acetylation	MPQKQAEKVVIKKEK CCHHHHHEEEEEECC	44.83	25953088
112	Sumoylation	AEKVVIKKEKDISAP HHEEEEEECCCCCCC	59.89	-
114	Acetylation	KVVIKKEKDISAPND EEEEEECCCCCCCCC	70.06	25953088
114	Ubiquitination	KVVIKKEKDISAPND EEEEEECCCCCCCCC	70.06	-
139	Sumoylation	APACHRLKEEEDEYE CCCCCCCCCHHCCCC	64.14	-
139	Ubiquitination	APACHRLKEEEDEYE CCCCCCCCCHHCCCC	64.14	21906983
139	Sumoylation	APACHRLKEEEDEYE CCCCCCCCCHHCCCC	64.14	-
145	Phosphorylation	LKEEEDEYETSGEGQ CCCHHCCCCCCCCCC	36.51	28796482
147	Phosphorylation	EEEDEYETSGEGQDI CHHCCCCCCCCCCCH	40.92	22617229
148	Phosphorylation	EEDEYETSGEGQDIW HHCCCCCCCCCCCHH	23.94	22617229
169	Phosphorylation	NPFQFYLTRVSGVKP CCCEEEEEEECCCCC	20.04	28555341
169	O-linked_Glycosylation	NPFQFYLTRVSGVKP CCCEEEEEEECCCCC	20.04	30379171
172	O-linked_Glycosylation	QFYLTRVSGVKPKYN EEEEEEECCCCCCCC	34.28	30379171
175	Acetylation	LTRVSGVKPKYNSGA EEEECCCCCCCCCCC	39.04	25953088
177	Acetylation	RVSGVKPKYNSGALH EECCCCCCCCCCCCC	51.88	25953088
222	Ubiquitination	YPPEFRKKPILLVHG CCHHHHCCCEEEEEC	32.79	-
231	Ubiquitination	ILLVHGDKREAKAHL EEEEECCHHHHHHHH	57.65	-
243	Ubiquitination	AHLHAQAKPYENISL HHHHCCCCCCCCCCC	35.73	-
311	Ubiquitination	RIADGTHKSGESPTH EECCCCCCCCCCCCC	61.05	-
334	Phosphorylation	LMAYNAPSLKEWIDV HHHHCCCCHHHHHHH	50.06	-
365	Phosphorylation	TPGRFQGSQKDNWGH CCCCCCCCCCCCCHH	24.23	17478428
367	Ubiquitination	GRFQGSQKDNWGHFR CCCCCCCCCCCHHHH	55.51	-
417	Acetylation	KWLCSEFKESMLTLG HHHHHHHHHHHHHCC	44.84	25953088
417	Ubiquitination	KWLCSEFKESMLTLG HHHHHHHHHHHHHCC	44.84	-
427	Phosphorylation	MLTLGKESKTPGKSS HHHCCCCCCCCCCCC	45.36	21712546
429	Phosphorylation	TLGKESKTPGKSSVP HCCCCCCCCCCCCCC	46.70	21712546
432	Ubiquitination	KESKTPGKSSVPLYL CCCCCCCCCCCCEEE	40.54	-
434	Phosphorylation	SKTPGKSSVPLYLIY CCCCCCCCCCEEEEC	31.10	21712546
459	Phosphorylation	EGYPAGGSLPYSIQT CCCCCCCCCCCCCHH	25.83	19690332
466	Phosphorylation	SLPYSIQTAEKQNWL CCCCCCHHHHHCCCH	34.80	19690332
469	Ubiquitination	YSIQTAEKQNWLHSY CCCHHHHHCCCHHHH	46.60	-
518	Phosphorylation	LVTSANLSKAAWGAL HHHHCCCCHHHHHHH	21.76	18452278
563	Phosphorylation	KQKFFAGSQEPMATF ECCCCCCCCCCCEEC	28.13	28464451
569	Phosphorylation	GSQEPMATFPVPYDL CCCCCCEECCCCCCC	23.40	22199227
581	Phosphorylation	YDLPPELYGSKDRPW CCCCHHHCCCCCCCE	20.07	22199227

Upstream regulatory proteins (kinases for phosphorylation sites, E3 ubiquitin ligases of ubiquitination sites, ...)

Modified Location	Modified Residue	Modification	Type of Upstream Proteins	Gene Name of Upstream Proteins	UniProt AC of Upstream Proteins	Sources
81	S	Phosphorylation	Kinase	ATM	Q13315	PSP
81	S	Phosphorylation	Kinase	PRKDC	P78527	GPS
365	S	Phosphorylation	Kinase	ATM	Q13315	PSP
563	S	Phosphorylation	Kinase	ATM	Q13315	PSP

Functions of PTM Sites

Oops, there are no descriptions of PTM sites of TYDP1_HUMAN !!

Disease-associated PTM Sites based on SAP

* Distance = the distance between SAP position and PTM sites.

Oops, there are no SNP-PTM records of TYDP1_HUMAN !!

Protein-Protein Interaction

Interacting Protein	Gene Name	Interaction Type	PPI Reference
VAMP2_HUMAN	VAMP2	physical	22939629
NU153_HUMAN	NUP153	physical	26186194
TERA_HUMAN	VCP	physical	26344197

Drug and Disease Associations

• Kegg Disease
• There are no disease associations of PTM sites.
• OMIM Disease
• 607250: Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy (SCAN1)
• Kegg Drug
• There are no disease associations of PTM sites.
• DrugBank
• There are no disease associations of PTM sites.

Related Literatures of Post-Translational Modification

Phosphorylation

"Quantitative phosphoproteomic analysis of T cell receptor signalingreveals system-wide modulation of protein-protein interactions.";
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,Rodionov V., Han D.K.;
Sci. Signal. 2:RA46-RA46(2009).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-147 AND SER-148, ANDMASS SPECTROMETRY.
PubMed: 19690332

"A quantitative atlas of mitotic phosphorylation.";
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,Elledge S.J., Gygi S.P.;
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-61, AND MASSSPECTROMETRY.
PubMed: 18669648

"Global, in vivo, and site-specific phosphorylation dynamics insignaling networks.";
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P.,Mann M.;
Cell 127:635-648(2006).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-11; SER-13; SER-14 ANDSER-15, AND MASS SPECTROMETRY.
PubMed: 17081983