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    TPA1 oxidative DNA demethylase [ Saccharomyces cerevisiae S288C ]

    Gene ID: 856775, updated on 9-Dec-2024

    Summary

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    Official Symbol
    TPA1
    Official Full Name
    oxidative DNA demethylase
    Primary source
    SGD:S000000851
    Locus tag
    YER049W
    See related
    AllianceGenome:SGD:S000000851; FungiDB:YER049W; VEuPathDB:YER049W
    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 ferrous iron binding activity; peptidyl-proline dioxygenase activity; and poly(A) binding activity. Involved in several processes, including nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; peptidyl-proline di-hydroxylation; and translational termination. Located in nucleus. Orthologous to human OGFOD1 (2-oxoglutarate and iron dependent oxygenase domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See TPA1 in Genome Data Viewer
    Location:
    chromosome: V
    Exon count:
    1
    Sequence:
    Chromosome: V; NC_001137.3 (251728..253662)

    Chromosome V - NC_001137.3Genomic Context describing neighboring genes Neighboring gene tRNA-Gln Neighboring gene Isd11p Neighboring gene mitochondrial 37S ribosomal protein RSM18 Neighboring gene [Histone H3]-lysine-36 demethylase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001137.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Structure of the ribosomal oxygenase OGFOD1 provides insights into the regio- and stereoselectivity of prolyl hydroxylases. Horita S, et al. Structure, 2015 Apr 7. PMID 25728928, Free PMC Article
    2. Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex. Kim HS, et al. Nucleic Acids Res, 2010 Apr. PMID 20040577, Free PMC Article
    3. Tpa1p is part of an mRNP complex that influences translation termination, mRNA deadenylation, and mRNA turnover in Saccharomyces cerevisiae. Keeling KM, et al. Mol Cell Biol, 2006 Jul. PMID 16809762, Free PMC Article
    4. Expansion of base excision repair compensates for a lack of DNA repair by oxidative dealkylation in budding yeast. Admiraal SJ, et al. J Biol Chem, 2019 Sep 13. PMID 31320474, Free PMC Article
    5. Structural and functional insights into Saccharomyces cerevisiae Tpa1, a putative prolylhydroxylase influencing translation termination and transcription. Henri J, et al. J Biol Chem, 2010 Oct 1. PMID 20630870, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tpa1 is a hitherto unidentified DNA repair protein in yeast and that it plays a crucial role in reverting alkylated DNA base lesions and cytotoxicity.
      Title: A role for Saccharomyces cerevisiae Tpa1 protein in direct alkylation repair.
    2. Tpa1 binds to poly(rA), suggesting its direct interaction with mRNA in the mRNP complex.
      Title: Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex.
    3. Tpa1p is a component of a messenger ribonucleoprotein complex bound to the 3' untranslated region of mRNAs that affects translation termination, deadenylation, and mRNA decay.
      Title: Tpa1p is part of an mRNP complex that influences translation termination, mRNA deadenylation, and mRNA turnover in Saccharomyces cerevisiae.
    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 2-oxoglutarate-dependent dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables L-ascorbic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ferrous iron binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidyl-proline dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables peptidyl-proline dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables peptidyl-proline dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(A) binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in peptidyl-proline di-hydroxylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of translational fidelity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of translational termination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in translational termination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus HDA PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    oxidative DNA demethylase
    NP_010969.1
    • Prolyl hydroxylase; catalyzes oxygen-dependent dihydroxylation of Rps23a/b, a 40S ribosomal decoding center subunit; influences translational termination and regulates translational accuracy; interacts with Sup45p (eRF1), Sup35p (eRF3) and Pab1p; disputed role as a oxidative dealkylase repairing DNA methyl-base lesions; poly(rA)-binding protein affecting poly(A) tail length and mRNA stability; Fe(II)/2-oxoglutarate-dependent dioxygenase family member similar to human prolyl 4-hydroxylase OGFOD1

    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_001137.3 Reference assembly

      Range
      251728..253662
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001178940.1 → NP_010969.1  TPA: oxidative DNA demethylase [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_010969.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D3DLV1, P40032
      UniProtKB/TrEMBL
      B5VHI2, C8Z753, N1PA39
      Conserved Domains (2) summary
      COG3751
      Location:9 → 262
      EGL9; Proline 4-hydroxylase (includes Rps23 Pro-64 3,4-dihydroxylase Tpa1), contains SM-20 domain [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones]
      pfam10637
      Location:333 → 638
      Ofd1_CTDD; Oxoglutarate and iron-dependent oxygenase degradation C-term
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P40032.1

    Gene LinkOut

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