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    TDP1 tyrosyl-DNA phosphodiesterase 1 [ Saccharomyces cerevisiae S288C ]

    Gene ID: 852525, updated on 9-Dec-2024

    Summary

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    Official Symbol
    TDP1
    Official Full Name
    tyrosyl-DNA phosphodiesterase 1
    Primary source
    SGD:S000000427
    Locus tag
    YBR223C
    See related
    AllianceGenome:SGD:S000000427; FungiDB:YBR223C; VEuPathDB:YBR223C
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Saccharomyces cerevisiae S288C (strain: S288C)
    Lineage
    Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
    Summary
    Enables 3'-tyrosyl-DNA phosphodiesterase activity and 5'-tyrosyl-DNA phosphodiesterase activity. Involved in DNA repair. Located in mitochondrion and nucleus. Used to study spinocerebellar ataxia with axonal neuropathy 1. Human ortholog(s) of this gene implicated in spinocerebellar ataxia with axonal neuropathy 1. Orthologous to human TDP1 (tyrosyl-DNA phosphodiesterase 1). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See TDP1 in Genome Data Viewer
    Location:
    chromosome: II
    Exon count:
    1
    Sequence:
    Chromosome: II; NC_001134.8 (668663..670297, complement)

    Chromosome II - NC_001134.8Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene Pcs60p Neighboring gene uncharacterized protein Neighboring gene Mcx1p

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001134.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The role of TDP1 from budding yeast in the repair of DNA damage. Liu C, et al. DNA Repair (Amst), 2004 Jun 3. PMID 15135727
    2. Processing of nucleopeptides mimicking the topoisomerase I-DNA covalent complex by tyrosyl-DNA phosphodiesterase. Debéthune L, et al. Nucleic Acids Res, 2002 Mar 1. PMID 11861912, Free PMC Article
    3. Tyrosyl-DNA phosphodiesterase I catalytic mutants reveal an alternative nucleophile that can catalyze substrate cleavage. Comeaux EQ, et al. J Biol Chem, 2015 Mar 6. PMID 25609251, Free PMC Article
    4. Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. Gajewski S, et al. J Mol Biol, 2012 Jan 27. PMID 22155078, Free PMC Article
    5. N-terminal domain of tyrosyl-DNA phosphodiesterase I regulates topoisomerase I-induced toxicity in cells. Brettrager EJ, et al. Sci Rep, 2023 Jan 25. PMID 36697463, Free PMC Article

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MUS81 cleaves TOP1-derived lesions and other DNA-protein cross-links.
      Title: MUS81 cleaves TOP1-derived lesions and other DNA-protein cross-links.
    2. N-terminal domain of tyrosyl-DNA phosphodiesterase I regulates topoisomerase I-induced toxicity in cells.
      Title: N-terminal domain of tyrosyl-DNA phosphodiesterase I regulates topoisomerase I-induced toxicity in cells.
    3. We show that two genes, TDP1, a tyrosyl-DNA-phosphdiesterase, and TAF12, an RNA polymerase II TATA-box binding factor, cause CIN when overexpressed in human cells. Using SDL screens in yeast, we identified a set of genes that when deleted specifically kill cells with high levels of Tdp1
      Title: Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer.
    4. Data show that mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison.
      Title: Mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by SGD

    Function Evidence Code Pubs
    enables 3'-tyrosyl-DNA phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 3'-tyrosyl-DNA phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5'-tyrosyl-DNA phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoric diester hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    tyrosyl-DNA phosphodiesterase 1
    NP_009782.3
    • Tyrosyl-DNA phosphodiesterase I; hydrolyzes 3' and 5'-phosphotyrosyl bonds; involved in the repair of DNA lesions created by topo I and topo II, including DNA-protein cross-links; mutations in the human homolog, TDP1, result in the neurodegenerative disease, spinocerebellar ataxia with axonal neuropathy (SCAN1); yeast cells and human rhabdomyosarcoma lines that overexpress TDP1 both exhibit elevated dosage chromosomal instability (dCIN)

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_001134.8 Reference assembly

      Range
      668663..670297 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001178571.3 → NP_009782.3  TPA: tyrosyl-DNA phosphodiesterase 1 [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_009782.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D6VQM0, P38319
      UniProtKB/TrEMBL
      G2W9M7
      Conserved Domains (1) summary
      pfam06087
      Location:83 → 525
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P38319.1

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