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Aliases for TDP1 Gene

Aliases for TDP1 Gene

  • Tyrosyl-DNA Phosphodiesterase 1 2 3
  • Tyr-DNA Phosphodiesterase 1 4
  • EC 3.1.4.- 4
  • EC 3.1.4 64

External Ids for TDP1 Gene

Summaries for TDP1 Gene

Entrez Gene Summary for TDP1 Gene

  • 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 topoisomerase I 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. [provided by RefSeq, Jul 2008]

GeneCards Summary for TDP1 Gene

TDP1 (Tyrosyl-DNA Phosphodiesterase 1) is a Protein Coding gene. Diseases associated with TDP1 include spinocerebellar ataxia, autosomal recessive with axonal neuropathy and axonal neuropathy. Among its related pathways are Homologous Recombination Repair and DNA Repair. GO annotations related to this gene include double-stranded DNA binding and exonuclease activity.

UniProtKB/Swiss-Prot for TDP1 Gene

  • 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 3exonuclease activity and can remove a single nucleoside from the 3end of DNA and RNA molecules with 3hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3phosphate.

Gene Wiki entry for TDP1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TDP1 Gene

Genomics for TDP1 Gene

Genomic Location for TDP1 Gene

Start:
89,954,939 bp from pter
End:
90,044,768 bp from pter
Size:
89,830 bases
Orientation:
Plus strand

Genomic View for TDP1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for TDP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TDP1 Gene

Regulatory Elements for TDP1 Gene

Proteins for TDP1 Gene

  • Protein details for TDP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUW8-TYDP1_HUMAN
    Recommended name:
    Tyrosyl-DNA phosphodiesterase 1
    Protein Accession:
    Q9NUW8
    Secondary Accessions:
    • Q2HXX4
    • Q86TV8
    • Q96BK7
    • Q9NZM7
    • Q9NZM8

    Protein attributes for TDP1 Gene

    Size:
    608 amino acids
    Molecular mass:
    68420 Da
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for TDP1 Gene

    Alternative splice isoforms for TDP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TDP1 Gene

Proteomics data for TDP1 Gene at MOPED

Selected DME Specific Peptides for TDP1 Gene

Post-translational modifications for TDP1 Gene

  • Phosphorylated on serine and/or threonine residues, but not on tyrosine residues.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains for TDP1 Gene

Protein Domains for TDP1 Gene

InterPro:
Blocks:
ProtoNet:

UniProtKB/Swiss-Prot:

TYDP1_HUMAN
Family:
  • Belongs to the tyrosyl-DNA phosphodiesterase family.:
    • Q9NUW8
genes like me logo Genes that share domains with TDP1: view

No data available for Gene Families for TDP1 Gene

Function for TDP1 Gene

Molecular function for TDP1 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties: Kinetic parameters: KM=0.08 uM for 14-mer single-stranded oligo with a 3- phosphotyrosine {ECO:0000269 PubMed:22822062}; Note=kcat is 7 sec(-1) with single-stranded 5-tyrosyl DNA as substrate.;
UniProtKB/Swiss-Prot 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. Has low 3exonuclease activity and can remove a single nucleoside from the 3end of DNA and RNA molecules with 3hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3phosphate.

Enzyme Numbers (IUBMB) for TDP1 Gene

Gene Ontology (GO) - Molecular Function for TDP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003690 double-stranded DNA binding IDA 15811850
GO:0003697 single-stranded DNA binding IDA 15811850
GO:0004527 exonuclease activity IEA --
GO:0005515 protein binding IPI 15744309
GO:0008081 phosphoric diester hydrolase activity --
genes like me logo Genes that share ontologies with TDP1: view

Phenotypes for TDP1 Gene

genes like me logo Genes that share phenotypes with TDP1: view

miRNA for TDP1 Gene

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for TDP1 Gene

Localization for TDP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TDP1 Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TDP1 Gene COMPARTMENTS Subcellular localization image for TDP1 gene
Compartment Confidence
nucleus 5
cytosol 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for TDP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IDA 17948061
genes like me logo Genes that share ontologies with TDP1: view

Pathways for TDP1 Gene

genes like me logo Genes that share pathways with TDP1: view

Gene Ontology (GO) - Biological Process for TDP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000012 single strand break repair IMP 17600775
GO:0006281 DNA repair IDA 17948061
GO:0006302 double-strand break repair IDA 12023295
GO:0008219 cell death --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with TDP1: view

Compounds for TDP1 Gene

(7) Novoseek inferred chemical compound relationships for TDP1 Gene

Compound -log(P) Hits PubMed IDs
tdp-1 99.4 185
phosphonate 83.8 9
camptothecin 80 10
phosphodiester 76.7 9
vanadate 57.3 8
genes like me logo Genes that share compounds with TDP1: view

Transcripts for TDP1 Gene

Unigene Clusters for TDP1 Gene

Tyrosyl-DNA phosphodiesterase 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TDP1 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^
SP1: - - - - - - - -
SP2: - - -
SP3: - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - - -
SP6: -
SP7: - - - - -
SP8: - - -
SP9: -
SP10:

ExUns: 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b
SP1: -
SP2: - -
SP3: - -
SP4: - -
SP5: - -
SP6: -
SP7:
SP8:
SP9:
SP10:

Relevant External Links for TDP1 Gene

GeneLoc Exon Structure for
TDP1
ECgene alternative splicing isoforms for
TDP1

Expression for TDP1 Gene

mRNA expression in normal human tissues for TDP1 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for TDP1 Gene

SOURCE GeneReport for Unigene cluster for TDP1 Gene Hs.209945

mRNA Expression by UniProt/SwissProt for TDP1 Gene

Q9NUW8-TYDP1_HUMAN
Tissue specificity: Ubiquitously expressed. Similar expression throughout the central nervous system (whole brain, amygdala, caudate nucleus, cerebellum, cerebral cortex, frontal lobe, hippocampus, medulla oblongata, occipital lobe, putamen, substantia nigra, temporal lobe, thalamus, nucleus accumbens and spinal cord) and increased expression in testis and thymus.
genes like me logo Genes that share expressions with TDP1: view

Orthologs for TDP1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TDP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TDP1 36
  • 99.34 (n)
  • 99.01 (a)
TDP1 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TDP1 36
  • 84.07 (n)
  • 83.03 (a)
TDP1 37
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TDP1 36
  • 87.55 (n)
  • 87.01 (a)
TDP1 37
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tdp1 36
  • 81.25 (n)
  • 81.58 (a)
Tdp1 16
Tdp1 37
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TDP1 37
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TDP1 37
  • 75 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tdp1 36
  • 82.24 (n)
  • 82.24 (a)
chicken
(Gallus gallus)
Aves TDP1 36
  • 68.94 (n)
  • 70.22 (a)
TDP1 37
  • 68 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TDP1 37
  • 64 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.16878 36
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.15945 36
tdp1 36
  • 66.44 (n)
  • 67.87 (a)
zebrafish
(Danio rerio)
Actinopterygii tdp1 36
  • 61.71 (n)
  • 60.17 (a)
tdp1 37
  • 56 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010577 36
  • 47.97 (n)
  • 39.08 (a)
fruit fly
(Drosophila melanogaster)
Insecta gkt 36
  • 48.05 (n)
  • 39.61 (a)
gkt 37
  • 31 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F52C12.1 36
  • 46.93 (n)
  • 38.57 (a)
F52C12.1 37
  • 35 (a)
OneToOne
F52C12.1 38
  • 34 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TDP1 39
thale cress
(Arabidopsis thaliana)
eudicotyledons TDP1 36
  • 48.85 (n)
  • 39.87 (a)
rice
(Oryza sativa)
Liliopsida Os.9987 36
Os07g0530100 36
  • 47.96 (n)
  • 39.96 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1071 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 52 (a)
OneToOne
Species with no ortholog for TDP1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TDP1 Gene

ENSEMBL:
Gene Tree for TDP1 (if available)
TreeFam:
Gene Tree for TDP1 (if available)

Paralogs for TDP1 Gene

No data available for Paralogs for TDP1 Gene

Variants for TDP1 Gene

Sequence variations from dbSNP and Humsavar for TDP1 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs9488 -- 90,043,220(+) GATGT(C/T)CACTT utr-variant-3-prime
rs728286 -- 90,032,980(+) AAATA(A/C/G)CTCCA intron-variant
rs746752 -- 89,992,365(+) ATTCT(A/T)TGCTG intron-variant
rs1072511 -- 89,978,200(-) GGGCT(G/T)GTGGC intron-variant
rs1286927 -- 90,015,612(+) agtgt(A/G)ccagc intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TDP1 Gene

Variant ID Type Subtype PubMed ID
nsv832853 CNV Gain 17160897
nsv832854 CNV Gain 17160897
nsv521779 CNV Loss 19592680
nsv1392 CNV Loss 18451855

Relevant External Links for TDP1 Gene

HapMap Linkage Disequilibrium report
TDP1
Human Gene Mutation Database (HGMD)
TDP1

Disorders for TDP1 Gene

(1) OMIM Diseases for TDP1 Gene (607198)

UniProtKB/Swiss-Prot

TYDP1_HUMAN
  • Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy (SCAN1) [MIM:607250]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence. {ECO:0000269 PubMed:12244316}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for TDP1 Gene

(6) Novoseek inferred disease relationships for TDP1 Gene

Disease -log(P) Hits PubMed IDs
scan1 98.9 19
spinocerebellar ataxias 87.3 12
spinocerebellar degenerations 78.3 4
neurodegenerative diseases 43.4 4
cancer 2.73 2

Relevant External Links for TDP1

GeneTests
TDP1
GeneReviews
TDP1
Genetic Association Database (GAD)
TDP1
Human Genome Epidemiology (HuGE) Navigator
TDP1
genes like me logo Genes that share disorders with TDP1: view

Publications for TDP1 Gene

  1. The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1. (PMID: 11839309) Davies D.R. … Hol W.G.J. (Structure 2002) 2 3 4 23
  2. Insights into substrate binding and catalytic mechanism of human tyrosyl-DNA phosphodiesterase (Tdp1) from vanadate and tungstate- inhibited structures. (PMID: 12470949) Davies D.R. … Hol W.G.J. (J. Mol. Biol. 2002) 3 4 23
  3. Crystal structure of a transition state mimic for TDP1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide. (PMID: 12618186) Davies D.R. … Hol W.G.J. (Chem. Biol. 2003) 3 4 23
  4. Explorations of peptide and oligonucleotide binding sites of tyrosyl- DNA phosphodiesterase using vanadate complexes. (PMID: 14761185) Davies D.R. … Hol W.G.J. (J. Med. Chem. 2004) 3 4 23
  5. Analysis of human tyrosyl-DNA phosphodiesterase I catalytic residues. (PMID: 15111055) Raymond A.C. … Burgin A.B. Jr. (J. Mol. Biol. 2004) 3 4 23

Products for TDP1 Gene

Sources for TDP1 Gene

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