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    UFD4 putative ubiquitin-protein ligase UFD4 [ Saccharomyces cerevisiae S288C ]

    Gene ID: 853859, updated on 7-Jul-2024

    Summary

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    Gene symbol
    UFD4
    Gene description
    putative ubiquitin-protein ligase UFD4
    Primary source
    FungiDB:YKL010C
    Locus tag
    YKL010C
    See related
    SGD:S000001493; AllianceGenome:SGD:S000001493; VEuPathDB:YKL010C
    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 proteasome regulatory particle binding activity and ubiquitin protein ligase activity. Involved in cellular protein metabolic process; free ubiquitin chain polymerization; and negative regulation of telomerase activity. Located in mitochondrion and nucleus. Human ortholog(s) of this gene implicated in Clark-Baraitser syndrome. Orthologous to human TRIP12 (thyroid hormone receptor interactor 12). [provided by Alliance of Genome Resources, Apr 2022]
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    Genomic context

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    See UFD4 in Genome Data Viewer
    Location:
    chromosome: XI
    Exon count:
    1
    Sequence:
    Chromosome: XI; NC_001143.9 (421424..425875, complement)

    Chromosome XI - NC_001143.9Genomic Context describing neighboring genes Neighboring gene Prp40p Neighboring gene cruciform cutting endonuclease Neighboring gene Mrt4p Neighboring gene sphingosine N-acyltransferase LAC1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001143.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The armadillo repeats of the Ufd4 ubiquitin ligase recognize ubiquitin-fusion proteins. Ju D, et al. FEBS Lett, 2007 Jan 23. PMID 17204268
    2. Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Khmelinskii A, et al. Nat Biotechnol, 2012 Jun 24. PMID 22729030
    3. Rad25 protein is targeted for degradation by the Ubc4-Ufd4 pathway. Bao X, et al. J Biol Chem, 2015 Mar 27. PMID 25670855, Free PMC Article
    4. The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification. Tsuchiya H, et al. Biochem Biophys Res Commun, 2013 Jun 28. PMID 23726910
    5. Generation of free ubiquitin chains is up-regulated in stress and facilitated by the HECT domain ubiquitin ligases UFD4 and HUL5. Braten O, et al. Biochem J, 2012 Jun 15. PMID 22497224

    See all (75) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Proteasome-dependent protein quality control of the peroxisomal membrane protein Pxa1p.
      Title: Proteasome-dependent protein quality control of the peroxisomal membrane protein Pxa1p.
    2. Rad25 turnover requires the ubiquitin-conjugating enzyme Ubc4 and the ubiquitin ligase Ufd4.
      Title: Rad25 protein is targeted for degradation by the Ubc4-Ufd4 pathway.
    3. Data suggest that Ufd4 assembles the K29-linked ubiquitin chain(s) on Ub-P-betagal in vivo.
      Title: The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification.
    4. Study shows that the RING-type Ubr1 E3 and the HECT-type Ufd4 E3 interact, both physically and functionally.
      Title: The N-end rule pathway is mediated by a complex of the RING-type Ubr1 and HECT-type Ufd4 ubiquitin ligases.
    5. Armadillo repeats of Ufd4, the E3 component of the UFD (Ub fusion degradation) pathway, recognize the Ub degradation signal of the UFD substrates.
      Title: The armadillo repeats of the Ufd4 ubiquitin ligase recognize ubiquitin-fusion proteins.
    6. Ufd4, the E3 component of the UFD pathway, is involved in controlling the degradation of Rad4, and Ufd4 and Rad23 exhibit a synthetic inhibitory effect on Rad4 degradation
      Title: A synthetic defect in protein degradation caused by loss of Ufd4 and Rad23.
    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 proteasome regulatory particle binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin protein ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in free ubiquitin chain polymerization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein K29-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm HDA PubMed 
    located_in mitochondrion HDA PubMed 
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    putative ubiquitin-protein ligase UFD4
    NP_012915.3
    • Ubiquitin-protein ligase (E3); interacts with Rpt4p and Rpt6p, two subunits of the 19S particle of the 26S proteasome; involved in K29-linked ubiquitin-dependent protein catabolism, including ubiquitin fusion proteins; relative distribution to the nucleus increases upon DNA replication stress

    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_001143.9 Reference assembly

      Range
      421424..425875 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001179576.3 → NP_012915.3  TPA: putative ubiquitin-protein ligase UFD4 [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_012915.3

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D6VXS6, P33202
      UniProtKB/TrEMBL
      A0A8H4BY08, A6ZZV5, G2WI21, N1P2I8
      Conserved Domains (1) summary
      COG5021
      Location:581 → 1482
      HUL4; Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P33202.1

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