From Wikipedia, the free encyclopedia
Protein-coding gene in the species Homo sapiens
TDP1 Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1JY1 , 1MU7 , 1MU9 , 1NOP , 1QZQ , 1RFF , 1RFI , 1RG1 , 1RG2 , 1RGT , 1RGU , 1RH0
Identifiers Aliases TDP1 External IDs OMIM : 607198 ; MGI : 1920036 ; HomoloGene : 5424 ; GeneCards : TDP1 ; OMA :TDP1 - orthologs Wikidata
Tyrosyl-DNA phosphodiesterase 1 is an enzyme that in humans is encoded by the TDP1 gene .[ 5] [ 6] [ 7]
The protein encoded by this gene is involved in repairing stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of the phosphodiester bond between the tyrosine residue of Type I topoisomerase and the 3-prime phosphate of DNA . This protein may also remove glycolate from single-stranded DNA containing 3-prime phosphoglycolate, suggesting a role in repair of free-radical mediated DNA double-strand breaks.
This gene is a member of the phospholipase D family and contains two PLD phosphodiesterase domains. Mutations in this gene are associated with the disease spinocerebellar ataxia with axonal neuropathy (SCAN1). While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same isoform .[ 7]
^ a b c GRCh38: Ensembl release 89: ENSG00000042088 – Ensembl , May 2017^ a b c GRCm38: Ensembl release 89: ENSMUSG00000021177 – Ensembl , May 2017^ "Human PubMed Reference:" . National Center for Biotechnology Information, U.S. National Library of Medicine .^ "Mouse PubMed Reference:" . National Center for Biotechnology Information, U.S. National Library of Medicine .^ Davies DR, Interthal H, Champoux JJ, Hol WG (Feb 2002). "The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1" . Structure . 10 (2): 237–48. doi :10.1016/S0969-2126(02)00707-4 PMID 11839309 . ^ Takashima H, Boerkoel CF, John J, Saifi GM, Salih MA, Armstrong D, Mao Y, Quiocho FA, Roa BB, Nakagawa M, Stockton DW, Lupski JR (Sep 2002). "Mutation of TDP1, encoding a topoisomerase I-dependent DNA damage repair enzyme, in spinocerebellar ataxia with axonal neuropathy". Nat Genet . 32 (2): 267–72. doi :10.1038/ng987 . PMID 12244316 . S2CID 22725759 . ^ a b "Entrez Gene: TDP1 tyrosyl-DNA phosphodiesterase 1" .
El-Khamisy SF, Caldecott KW (2007). "TDP1-dependent DNA single-strand break repair and neurodegeneration" . Mutagenesis . 21 (4): 219–24. doi :10.1093/mutage/gel024 PMID 16775218 . Bonaldo MF, Lennon G, Soares MB (1997). "Normalization and subtraction: two approaches to facilitate gene discovery" . Genome Res . 6 (9): 791–806. doi :10.1101/gr.6.9.791 PMID 8889548 . Pouliot JJ, Yao KC, Robertson CA, Nash HA (1999). "Yeast gene for a Tyr-DNA phosphodiesterase that repairs topoisomerase I complexes" . Science . 286 (5439): 552–5. doi :10.1126/science.286.5439.552 . PMID 10521354 . Interthal H, Pouliot JJ, Champoux JJ (2001). "The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the phospholipase D superfamily" . Proc. Natl. Acad. Sci. U.S.A . 98 (21): 12009–14. Bibcode :2001PNAS...9812009I . doi :10.1073/pnas.211429198 PMC 59758 PMID 11572945 . Inamdar KV, Pouliot JJ, Zhou T, et al. (2002). "Conversion of phosphoglycolate to phosphate termini on 3' overhangs of DNA double strand breaks by the human tyrosyl-DNA phosphodiesterase hTdp1" . J. Biol. Chem . 277 (30): 27162–8. doi :10.1074/jbc.M204688200 PMID 12023295 . Davies DR, Interthal H, Champoux JJ, Hol WG (2003). "Insights into substrate binding and catalytic mechanism of human tyrosyl-DNA phosphodiesterase (Tdp1) from vanadate and tungstate-inhibited structures". J. Mol. Biol . 324 (5): 917–32. doi :10.1016/S0022-2836(02)01154-3 . PMID 12470949 . Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences" . Proc. Natl. Acad. Sci. U.S.A . 99 (26): 16899–903. Bibcode :2002PNAS...9916899M . doi :10.1073/pnas.242603899 PMC 139241 PMID 12477932 . Heilig R, Eckenberg R, Petit JL, et al. (2003). "The DNA sequence and analysis of human chromosome 14" . Nature . 421 (6923): 601–7. Bibcode :2003Natur.421..601H . doi :10.1038/nature01348 PMID 12508121 . Davies DR, Interthal H, Champoux JJ, Hol WG (2003). "Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide" . Chem. Biol . 10 (2): 139–47. doi :10.1016/S1074-5521(03)00021-8 PMID 12618186 . Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs" . Nat. Genet . 36 (1): 40–5. doi :10.1038/ng1285 PMID 14702039 . Davies DR, Interthal H, Champoux JJ, Hol WG (2004). "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes". J. Med. Chem . 47 (4): 829–37. doi :10.1021/jm030487x . PMID 14761185 . Raymond AC, Rideout MC, Staker B, et al. (2004). "Analysis of human tyrosyl-DNA phosphodiesterase I catalytic residues". J. Mol. Biol . 338 (5): 895–906. doi :10.1016/j.jmb.2004.03.013 . PMID 15111055 . Yang M, Kirley TL (2004). "Site-directed mutagenesis of human soluble calcium-activated nucleotidase 1 (hSCAN-1): identification of residues essential for enzyme activity and the Ca(2+)-induced conformational change". Biochemistry . 43 (28): 9185–94. doi :10.1021/bi049565o . PMID 15248776 . Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)" . Genome Res . 14 (10B): 2121–7. doi :10.1101/gr.2596504 . PMC 528928 PMID 15489334 . Barthelmes HU, Habermeyer M, Christensen MO, et al. (2005). "TDP1 overexpression in human cells counteracts DNA damage mediated by topoisomerases I and II" . J. Biol. Chem . 279 (53): 55618–25. doi :10.1074/jbc.M405042200 PMID 15494395 . Zhou T, Lee JW, Tatavarthi H, et al. (2005). "Deficiency in 3'-phosphoglycolate processing in human cells with a hereditary mutation in tyrosyl-DNA phosphodiesterase (TDP1)" . Nucleic Acids Res . 33 (1): 289–97. doi :10.1093/nar/gki170 . PMC 546157 PMID 15647511 . El-Khamisy SF, Saifi GM, Weinfeld M, et al. (2005). "Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1". Nature . 434 (7029): 108–13. Bibcode :2005Natur.434..108E . doi :10.1038/nature03314 . PMID 15744309 . S2CID 4423748 . Raymond AC, Staker BL, Burgin AB (2005). "Substrate specificity of tyrosyl-DNA phosphodiesterase I (Tdp1)" . J. Biol. Chem . 280 (23): 22029–35. doi :10.1074/jbc.M502148200 PMID 15811850 .
PDB gallery
1jy1 : CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1)
1mu7 : Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Tungstate Complex
1mu9 : Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex
1nop : Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
1qzq : human Tyrosyl DNA phosphodiesterase
1rff : Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.
1rfi : Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC
1rg1 : Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT
1rg2 : Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA
1rgt : Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC
1rgu : The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG
1rh0 : Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT
