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    UFD1 polyubiquitin-binding protein UFD1 [ Saccharomyces cerevisiae S288C ]

    Gene ID: 852939, updated on 9-Dec-2024

    Summary

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    Official Symbol
    UFD1
    Official Full Name
    polyubiquitin-binding protein UFD1
    Primary source
    SGD:S000003280
    Locus tag
    YGR048W
    See related
    AllianceGenome:SGD:S000003280; FungiDB:YGR048W; VEuPathDB:YGR048W
    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 polyubiquitin modification-dependent protein binding activity and ubiquitin binding activity. Involved in several processes, including nonfunctional rRNA decay; positive regulation of protein localization to nucleus; and proteasomal protein catabolic process. Located in nucleus. Part of RQC complex; endoplasmic reticulum membrane; and replisome. Used to study cleft palate. Human ortholog(s) of this gene implicated in DiGeorge syndrome and schizophrenia. Orthologous to human UFD1 (ubiquitin recognition factor in ER associated degradation 1). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See UFD1 in Genome Data Viewer
    Location:
    chromosome: VII
    Exon count:
    1
    Sequence:
    Chromosome: VII; NC_001139.9 (589826..590911)

    Chromosome VII - NC_001139.9Genomic Context describing neighboring genes Neighboring gene putative phosphatidate cytidylyltransferase Neighboring gene transcription factor TFIIIC subunit TFC4 Neighboring gene Scm4p Neighboring gene uncharacterized protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_001139.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex. Lee HG, et al. Proc Natl Acad Sci U S A, 2023 Jan 3. PMID 36574706, Free PMC Article
    2. Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites. Park S, et al. Structure, 2005 Jul. PMID 16004872
    3. Analysis of a degron-containing reporter protein GFP-CL1 reveals a role for SUMO1 in cytosolic protein quality control. Wang W, et al. J Biol Chem, 2023 Feb. PMID 36587767, Free PMC Article
    4. HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Bays NW, et al. Mol Biol Cell, 2001 Dec. PMID 11739805, Free PMC Article
    5. The Cdc48 N-terminal domain has a molecular switch that mediates the Npl4-Ufd1-Cdc48 complex formation. Oppenheim T, et al. Structure, 2023 Jul 6. PMID 37311459

    See all (115) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Cdc48Ufd1/Npl4 segregase removes mislocalized centromeric histone H3 variant CENP-A from non-centromeric chromatin.
      Title: Cdc48Ufd1/Npl4 segregase removes mislocalized centromeric histone H3 variant CENP-A from non-centromeric chromatin.
    2. Study reports the crystal structures of yeast Npl4 in complex with Lys48-linked diubiquitin and with the Npl4-binding motif of Ufd1. The distal and proximal ubiquitin moieties of Lys48-linked diubiquitin primarily interact with the C-terminal helix and N-terminal loop of the Npl4 C-terminal domain (CTD), respectively.
      Title: Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.
    3. Ssz1 restores endoplasmic reticulum-associated protein degradation in cells expressing defective cdc48-ufd1-npl4 complex by upregulating cdc48.
      Title: Ssz1 restores endoplasmic reticulum-associated protein degradation in cells expressing defective cdc48-ufd1-npl4 complex by upregulating cdc48.
    4. One Ufd1-Npl4 heterodimer is shown to interact with one p97 hexamer to form the p97-Ufd1-Npl4 complex.
      Title: Structural insights into the p97-Ufd1-Npl4 complex.
    5. analysis of the AAA-ATPase fold in Ufd1
      Title: Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    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 polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA replication termination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ERAD pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ERAD pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cytoplasm protein quality control by the ubiquitin-proteasome system IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in mitochondria-associated ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nonfunctional rRNA decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein localization to nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to vacuole IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retrograde protein transport, ER to cytosol IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosome-associated ubiquitin-dependent protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Doa10p ubiquitin ligase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Hrd1p ubiquitin ligase ERAD-L complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of RQC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of VCP-NPL4-UFD1 AAA ATPase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of VCP-NPL4-UFD1 AAA ATPase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol HDA PubMed 
    located_in nucleus HDA PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of replisome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    polyubiquitin-binding protein UFD1
    NP_011562.1
    • Substrate-recruiting cofactor of the Cdc48p-Npl4p-Ufd1p segregase; polyubiquitin binding protein that assists in the dislocation of misfolded, ERAD substrates that are subsequently delivered to the proteasome for degradation; involved in regulated destruction of ER membrane proteins such as HMG-CoA reductase (Hmg1/2p) and cytoplasmic proteins (Fbp1p); involved in mobilizing membrane bound transcription factors by regulated Ub/proteasome-dependent processing (RUP)

    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_001139.9 Reference assembly

      Range
      589826..590911
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001181177.1 → NP_011562.1  TPA: polyubiquitin-binding protein UFD1 [Saccharomyces cerevisiae S288C]

      See identical proteins and their annotated locations for NP_011562.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      D6VUI5, P53044, Q45U36
      UniProtKB/TrEMBL
      A6ZV35, B3LIH3, B5VJ00, C7GXN3, C8Z8U3, G2WED7, N1P5Q9
      Conserved Domains (1) summary
      COG5140
      Location:16 → 361
      UFD1; Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P53044.1

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