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Protein

Ubiquitin fusion degradation protein 1

Gene

UFD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

  • polyubiquitin binding Source: SGD
  • ubiquitin binding Source: SGD

GO - Biological processi

  • cytoplasm-associated proteasomal ubiquitin-dependent protein catabolic process Source: SGD
  • ER-associated misfolded protein catabolic process Source: SGD
  • ER-associated ubiquitin-dependent protein catabolic process Source: SGD
  • nonfunctional rRNA decay Source: SGD
  • positive regulation of protein localization to nucleus Source: SGD
  • proteasome-mediated ubiquitin-dependent protein catabolic process Source: SGD
  • retrograde protein transport, ER to cytosol Source: SGD
  • ribosome-associated ubiquitin-dependent protein catabolic process Source: SGD
Complete GO annotation...

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-30766-MONOMER.
ReactomeiREACT_326247. Translesion Synthesis by POLH.

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 Componenti: Chromosome VII

Organism-specific databases

CYGDiYGR048w.
EuPathDBiFungiDB:YGR048W.
SGDiS000003280. UFD1.

Subcellular locationi

GO - Cellular componenti

  • Doa10p ubiquitin ligase complex Source: SGD
  • Hrd1p ubiquitin ligase ERAD-L complex Source: SGD
  • nucleus Source: SGD
  • RQC complex Source: SGD
  • VCP-NPL4-UFD1 AAA ATPase complex Source: SGD
Complete GO annotation...

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.

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
NPL4P3375511EBI-19997,EBI-12193
UBX2Q042285EBI-19997,EBI-27730

Protein-protein interaction databases

BioGridi33295. 78 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 – 2911Combined sources
Helixi30 – 323Combined sources
Turni35 – 373Combined sources
Helixi40 – 445Combined sources
Beta strandi45 – 506Combined sources
Helixi52 – 609Combined sources
Beta strandi69 – 724Combined sources
Turni74 – 763Combined sources
Beta strandi79 – 879Combined sources
Beta strandi93 – 964Combined sources
Helixi98 – 1047Combined sources
Beta strandi111 – 1188Combined sources
Beta strandi123 – 1286Combined sources
Helixi131 – 1355Combined sources
Helixi140 – 15011Combined sources
Beta strandi154 – 16411Combined sources
Beta strandi167 – 17711Combined sources
Beta strandi188 – 1903Combined sources
Beta strandi192 – 1965Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP53044.
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

        10         20         30         40         50
MFSGFSSFGG GNGFVNMPQT FEEFFRCYPI AMMNDRIRKD DANFGGKIFL
60 70 80 90 100
PPSALSKLSM LNIRYPMLFK LTANETGRVT HGGVLEFIAE EGRVYLPQWM
110 120 130 140 150
METLGIQPGS LLQISSTDVP LGQFVKLEPQ SVDFLDISDP KAVLENVLRN
160 170 180 190 200
FSTLTVDDVI EISYNGKTFK IKILEVKPES SSKSICVIET DLVTDFAPPV
210 220 230 240 250
GYVEPDYKAL KAQQDKEKKN SFGKGQVLDP SVLGQGSMST RIDYAGIANS
260 270 280 290 300
SRNKLSKFVG QGQNISGKAP KAEPKQDIKD MKITFDGEPA KLDLPEGQLF
310 320 330 340 350
FGFPMVLPKE DEESAAGSKS SEQNFQGQGI SLRKSNKRKT KSDHDSSKSK
360
APKSPEVIEI D
Length:361
Mass (Da):39,810
Last modified:October 1, 1996 - v1
Checksum:i198E0CD48B863B98
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

BioGridi33295. 78 interactions.
DIPiDIP-1476N.
IntActiP53044. 16 interactions.
MINTiMINT-393265.
STRINGi4932.YGR048W.

Proteomic databases

MaxQBiP53044.
PaxDbiP53044.
PeptideAtlasiP53044.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CYGDiYGR048w.
EuPathDBiFungiDB:YGR048W.
SGDiS000003280. UFD1.

Phylogenomic databases

eggNOGiCOG5140.
GeneTreeiENSGT00390000002408.
HOGENOMiHOG000212737.
InParanoidiP53044.
KOiK14016.
OMAiINTDIAQ.
OrthoDBiEOG7N0CF5.

Enzyme and pathway databases

BioCyciYEAST:G3O-30766-MONOMER.
ReactomeiREACT_326247. Translesion Synthesis by POLH.

Miscellaneous databases

EvolutionaryTraceiP53044.
NextBioi972678.
PROiP53044.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  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: June 24, 2015
This is version 127 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.