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P53044

- UFD1_YEAST

UniProt

P53044 - UFD1_YEAST

Protein

Ubiquitin fusion degradation protein 1

Gene

UFD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway. Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1. Has an additional role in the turnover of OLE1 where it targets ubiquitinated OLE1 and other proteins to the ERAD.4 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei37 – 371Monoubiquitin-binding
    Sitei39 – 391Monoubiquitin-binding
    Sitei109 – 1091Monoubiquitin-binding

    GO - Molecular functioni

    1. polyubiquitin binding Source: SGD
    2. protein binding Source: IntAct
    3. ubiquitin binding Source: SGD

    GO - Biological processi

    1. cytoplasm-associated proteasomal ubiquitin-dependent protein catabolic process Source: SGD
    2. ER-associated misfolded protein catabolic process Source: SGD
    3. ER-associated ubiquitin-dependent protein catabolic process Source: SGD
    4. nonfunctional rRNA decay Source: SGD
    5. positive regulation of protein localization to nucleus Source: SGD
    6. proteasome-mediated ubiquitin-dependent protein catabolic process Source: SGD
    7. retrograde protein transport, ER to cytosol Source: SGD
    8. ribosome-associated ubiquitin-dependent protein catabolic process Source: SGD

    Keywords - Biological processi

    Ubl conjugation pathway

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30766-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin fusion degradation protein 1
    Short name:
    UB fusion protein 1
    Alternative name(s):
    Polymerase-interacting protein 3
    Gene namesi
    Name:UFD1
    Synonyms:PIP3
    Ordered Locus Names:YGR048W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGR048w.
    SGDiS000003280. UFD1.

    Subcellular locationi

    GO - Cellular componenti

    1. Cdc48p-Npl4p-Ufd1p AAA ATPase complex Source: SGD
    2. Doa10p ubiquitin ligase complex Source: SGD
    3. Hrd1p ubiquitin ligase ERAD-L complex Source: SGD
    4. nucleus Source: SGD
    5. RQC complex Source: SGD

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi94 – 941V → D in UFD1-1; grows more slowly. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 361361Ubiquitin fusion degradation protein 1PRO_0000194989Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei354 – 3541Phosphoserine3 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP53044.
    PaxDbiP53044.
    PeptideAtlasiP53044.

    Expressioni

    Gene expression databases

    GenevestigatoriP53044.

    Interactioni

    Subunit structurei

    Component of the HRD1 complex which contains HRD1, HRD3, USA1, DER1, YOS9, CDC48, NPL4, UFD1 AND UBX2/SEL1. The complex is composed of the core membrane complex, consisting of the E3 ligase HRD1 and its cofactors HRD3, DER1 and USA1, the substrate recruiting factor YOS9, and the heterotrimeric UFD1-NPL4-CDC48/p97 (UNC) ATPase complex recruited by UBX2/SEL1. Interacts with NPL4, CDC48 AND UBX2.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    DER1P383073EBI-19997,EBI-5761
    NPL4P337558EBI-19997,EBI-12193
    UBX2Q042285EBI-19997,EBI-27730

    Protein-protein interaction databases

    BioGridi33295. 79 interactions.
    DIPiDIP-1476N.
    IntActiP53044. 16 interactions.
    MINTiMINT-393265.
    STRINGi4932.YGR048W.

    Structurei

    Secondary structure

    1
    361
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi19 – 2911
    Helixi30 – 323
    Turni35 – 373
    Helixi40 – 445
    Beta strandi45 – 506
    Helixi52 – 609
    Beta strandi69 – 724
    Turni74 – 763
    Beta strandi79 – 879
    Beta strandi93 – 964
    Helixi98 – 1047
    Beta strandi111 – 1188
    Beta strandi123 – 1286
    Helixi131 – 1355
    Helixi140 – 15011
    Beta strandi154 – 16411
    Beta strandi167 – 17711
    Beta strandi188 – 1903
    Beta strandi192 – 1965

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ZC1NMR-A1-208[»]
    ProteinModelPortaliP53044.
    SMRiP53044. Positions 15-208.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP53044.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni27 – 282Monoubiquitin-binding
    Regioni30 – 323Monoubiquitin-binding
    Regioni99 – 1013Monoubiquitin-binding

    Sequence similaritiesi

    Belongs to the UFD1 family.Curated

    Phylogenomic databases

    eggNOGiCOG5140.
    GeneTreeiENSGT00390000002408.
    HOGENOMiHOG000212737.
    KOiK14016.
    OMAiINTDIAQ.
    OrthoDBiEOG7N0CF5.

    Family and domain databases

    InterProiIPR004854. UFD1.
    [Graphical view]
    PANTHERiPTHR12555. PTHR12555. 1 hit.
    PfamiPF03152. UFD1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P53044-1 [UniParc]FASTAAdd to Basket

    « Hide

    MFSGFSSFGG GNGFVNMPQT FEEFFRCYPI AMMNDRIRKD DANFGGKIFL    50
    PPSALSKLSM LNIRYPMLFK LTANETGRVT HGGVLEFIAE EGRVYLPQWM 100
    METLGIQPGS LLQISSTDVP LGQFVKLEPQ SVDFLDISDP KAVLENVLRN 150
    FSTLTVDDVI EISYNGKTFK IKILEVKPES SSKSICVIET DLVTDFAPPV 200
    GYVEPDYKAL KAQQDKEKKN SFGKGQVLDP SVLGQGSMST RIDYAGIANS 250
    SRNKLSKFVG QGQNISGKAP KAEPKQDIKD MKITFDGEPA KLDLPEGQLF 300
    FGFPMVLPKE DEESAAGSKS SEQNFQGQGI SLRKSNKRKT KSDHDSSKSK 350
    APKSPEVIEI D 361
    Length:361
    Mass (Da):39,810
    Last modified:October 1, 1996 - v1
    Checksum:i198E0CD48B863B98
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U22153 Genomic DNA. Translation: AAC49023.1.
    U17264 Genomic DNA. Translation: AAB46627.1.
    DQ115391 Genomic DNA. Translation: AAZ22463.1.
    Z72833 Genomic DNA. Translation: CAA97047.1.
    AY692806 Genomic DNA. Translation: AAT92825.1.
    BK006941 Genomic DNA. Translation: DAA08146.1.
    PIRiS59814.
    RefSeqiNP_011562.1. NM_001181177.1.

    Genome annotation databases

    EnsemblFungiiYGR048W; YGR048W; YGR048W.
    GeneIDi852939.
    KEGGisce:YGR048W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U22153 Genomic DNA. Translation: AAC49023.1 .
    U17264 Genomic DNA. Translation: AAB46627.1 .
    DQ115391 Genomic DNA. Translation: AAZ22463.1 .
    Z72833 Genomic DNA. Translation: CAA97047.1 .
    AY692806 Genomic DNA. Translation: AAT92825.1 .
    BK006941 Genomic DNA. Translation: DAA08146.1 .
    PIRi S59814.
    RefSeqi NP_011562.1. NM_001181177.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1ZC1 NMR - A 1-208 [» ]
    ProteinModelPortali P53044.
    SMRi P53044. Positions 15-208.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33295. 79 interactions.
    DIPi DIP-1476N.
    IntActi P53044. 16 interactions.
    MINTi MINT-393265.
    STRINGi 4932.YGR048W.

    Proteomic databases

    MaxQBi P53044.
    PaxDbi P53044.
    PeptideAtlasi P53044.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YGR048W ; YGR048W ; YGR048W .
    GeneIDi 852939.
    KEGGi sce:YGR048W.

    Organism-specific databases

    CYGDi YGR048w.
    SGDi S000003280. UFD1.

    Phylogenomic databases

    eggNOGi COG5140.
    GeneTreei ENSGT00390000002408.
    HOGENOMi HOG000212737.
    KOi K14016.
    OMAi INTDIAQ.
    OrthoDBi EOG7N0CF5.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30766-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P53044.
    NextBioi 972678.
    PROi P53044.

    Gene expression databases

    Genevestigatori P53044.

    Family and domain databases

    InterProi IPR004854. UFD1.
    [Graphical view ]
    PANTHERi PTHR12555. PTHR12555. 1 hit.
    Pfami PF03152. UFD1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A proteolytic pathway that recognizes ubiquitin as a degradation signal."
      Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A.
      J. Biol. Chem. 270:17442-17456(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF VAL-94.
      Strain: ATCC 204508 / S288c.
    2. "The Uba2 and Ufd1 proteins of Saccharomyces cerevisiae interact with poly(A) polymerase and affect the polyadenylation activity of cell extracts."
      del Olmo M., Mizrahi N., Gross S., Moore C.L.
      Mol. Gen. Genet. 255:209-218(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 200060 / W303.
    3. "Quantitative trait loci mapped to single-nucleotide resolution in yeast."
      Deutschbauer A.M., Davis R.W.
      Nat. Genet. 37:1333-1340(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: SK1.
    4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    6. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    7. "Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone."
      Rape M., Hoppe T., Gorr I., Kalocay M., Richly H., Jentsch S.
      Cell 107:667-677(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH NPL4, SUBCELLULAR LOCATION.
    8. "The conserved npl4 protein complex mediates proteasome-dependent membrane-bound transcription factor activation."
      Hitchcock A.L., Krebber H., Frietze S., Lin A., Latterich M., Silver P.A.
      Mol. Biol. Cell 12:3226-3241(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH NPL4.
    9. "The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol."
      Ye Y., Meyer H.H., Rapoport T.A.
      Nature 414:652-656(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "Role of the ubiquitin-selective CDC48(UFD1/NPL4) chaperone (segregase) in ERAD of OLE1 and other substrates."
      Braun S., Matuschewski K., Rape M., Thoms S., Jentsch S.
      EMBO J. 21:615-621(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    12. "Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins."
      Carvalho P., Goder V., Rapoport T.A.
      Cell 126:361-373(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE HRD1 COMPLEX, INTERACTION WITH UBX2 AND CDC48.
    13. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    14. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites."
      Park S., Isaacson R., Kim H.T., Silver P.A., Wagner G.
      Structure 13:995-1005(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 1-208, FUNCTION, UBIQUITINATION.

    Entry informationi

    Entry nameiUFD1_YEAST
    AccessioniPrimary (citable) accession number: P53044
    Secondary accession number(s): D6VUI5, Q45U36
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 120 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 3530 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

    External Data

    Dasty 3