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    USB1 phosphoric diester hydrolase [ Saccharomyces cerevisiae S288C ]

    Gene ID: 850823, updated on 9-Dec-2024

    Summary

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    Official Symbol
    USB1
    Official Full Name
    phosphoric diester hydrolase
    Primary source
    SGD:S000004122
    Locus tag
    YLR132C
    See related
    AllianceGenome:SGD:S000004122; FungiDB:YLR132C; VEuPathDB:YLR132C
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Saccharomyces cerevisiae S288C (strain: S288C)
    Lineage
    Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
    Summary
    Predicted to enable poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends. Involved in U6 snRNA 3'-end processing. Located in mitochondrion and nucleus. Human ortholog(s) of this gene implicated in poikiloderma with neutropenia. Orthologous to human USB1 (U6 snRNA biogenesis phosphodiesterase 1). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See USB1 in Genome Data Viewer
    Location:
    chromosome: XII
    Exon count:
    1
    Sequence:
    Chromosome: XII; NC_001144.5 (407283..408155, complement)

    Chromosome XII - NC_001144.5Genomic Context describing neighboring genes Neighboring gene low-affinity Zn(2+) transporter ZRT2 Neighboring gene DNA-binding transcription factor ACE2 Neighboring gene bifunctional choline kinase/ethanolamine kinase CKI1 Neighboring gene indolepyruvate decarboxylase 5

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001144.5

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1. Nomura Y, et al. Nucleic Acids Res, 2020 Feb 20. PMID 31832688, Free PMC Article
    2. An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae. Glatigny A, et al. BMC Syst Biol, 2011 Oct 25. PMID 22027258, Free PMC Article
    3. C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification. Mroczek S, et al. Genes Dev, 2012 Sep 1. PMID 22899009, Free PMC Article
    4. Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA. Shchepachev V, et al. Cell Rep, 2012 Oct 25. PMID 23022480
    5. Defining essential elements and genetic interactions of the yeast Lsm2-8 ring and demonstration that essentiality of Lsm2-8 is bypassed via overexpression of U6 snRNA or the U6 snRNP subunit Prp24. Roth AJ, et al. RNA, 2018 Jun. PMID 29615482, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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'-5'-RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables lyase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in U6 snRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in U6 snRNA 3'-end processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in U6 snRNA 3'-end processing IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in U6 snRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm HDA PubMed 
    located_in mitochondrion HDA PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus HDA 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
    phosphoric diester hydrolase
    NP_013233.1
    • Putative poly(U)-specific 3'-to-5' RNA exonuclease; involved in 3'-end processing of U6 snRNA removing uridines and generating a terminal 2',3' cyclic phosphate; essential protein that localizes to the nucleus and mitochondria; overexpression suppresses the respiratory defects of oxa1 and mtf2 mutants; homolog of S.pombe gene, mpn1 and human gene, hUSB1; mutations in hUSB1 are associated with a rare genodermatosis, poikiloderma with neutropenia (OMIM 604173)

    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_001144.5 Reference assembly

      Range
      407283..408155 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001182019.1 → NP_013233.1  TPA: phosphoric diester hydrolase [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_013233.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D6VYC7, Q12208
      UniProtKB/TrEMBL
      B3LT93, C7GQC4, C8ZDA1, N1NZB3
      Conserved Domains (1) summary
      pfam09749
      Location:45 → 278
      HVSL; Uncharacterized conserved protein
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q12208.1

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