CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-022178
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Tyrosyl-DNA phosphodiesterase 1 
Protein Synonyms/Alias
 Tyr-DNA phosphodiesterase 1 
Gene Name
 TDP1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
114KVVIKKEKDISAPNDubiquitination[1]
139APACHRLKEEEDEYEubiquitination[2]
367GRFQGSQKDNWGHFRubiquitination[1]
417KWLCSEFKESMLTLGubiquitination[1]
432KESKTPGKSSVPLYLubiquitination[1]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983] 
Functional 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. 
Sequence Annotation
 REGION 400 403 Interaction with DNA.
 ACT_SITE 263 263 Nucleophile.
 ACT_SITE 493 493 Proton donor.
 BINDING 265 265 Substrate.
 BINDING 495 495 Substrate.
 MOD_RES 61 61 Phosphoserine.
 MOD_RES 147 147 Phosphothreonine.
 MOD_RES 148 148 Phosphoserine.  
Keyword
 3D-structure; Complete proteome; Cytoplasm; Disease mutation; DNA damage; DNA repair; Exonuclease; Hydrolase; Neurodegeneration; Nuclease; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 608 AA 
Protein Sequence
MSQEGDYGRW TISSSDESEE EKPKPDKPST SSLLCARQGA ANEPRYTCSE AQKAAHKRKI 60
SPVKFSNTDS VLPPKRQKSG SQEDLGWCLS SSDDELQPEM PQKQAEKVVI KKEKDISAPN 120
DGTAQRTENH GAPACHRLKE EEDEYETSGE GQDIWDMLDK GNPFQFYLTR VSGVKPKYNS 180
GALHIKDILS PLFGTLVSSA QFNYCFDVDW LVKQYPPEFR KKPILLVHGD KREAKAHLHA 240
QAKPYENISL CQAKLDIAFG THHTKMMLLL YEEGLRVVIH TSNLIHADWH QKTQGIWLSP 300
LYPRIADGTH KSGESPTHFK ADLISYLMAY NAPSLKEWID VIHKHDLSET NVYLIGSTPG 360
RFQGSQKDNW GHFRLKKLLK DHASSMPNAE SWPVVGQFSS VGSLGADESK WLCSEFKESM 420
LTLGKESKTP GKSSVPLYLI YPSVENVRTS LEGYPAGGSL PYSIQTAEKQ NWLHSYFHKW 480
SAETSGRSNA MPHIKTYMRP SPDFSKIAWF LVTSANLSKA AWGALEKNGT QLMIRSYELG 540
VLFLPSAFGL DSFKVKQKFF AGSQEPMATF PVPYDLPPEL YGSKDRPWIW NIPYVKAPDT 600
HGNMWVPS 608 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:UniProtKB.
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0017005; F:3'-tyrosyl-DNA phosphodiesterase activity; IDA:UniProtKB.
 GO:0003690; F:double-stranded DNA binding; IDA:UniProtKB.
 GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
 GO:0003697; F:single-stranded DNA binding; IDA:UniProtKB.
 GO:0008219; P:cell death; IEA:UniProtKB-KW.
 GO:0006302; P:double-strand break repair; IDA:UniProtKB.
 GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IEA:GOC.
 GO:0000012; P:single strand break repair; IDA:UniProtKB. 
Interpro
 IPR027415; TDP_C.
 IPR010347; Tyr-DNA_phospho. 
Pfam
 PF06087; Tyr-DNA_phospho 
SMART
  
PROSITE
  
PRINTS