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P53044 (UFD1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ubiquitin fusion degradation protein 1

Short name=UB fusion protein 1
Alternative name(s):
Polymerase-interacting protein 3
Gene names
Name:UFD1
Synonyms:PIP3
Ordered Locus Names:YGR048W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length361 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7 Ref.9 Ref.10 Ref.15

Subunit structure

Component of the heterotrimeric Ufd1-Npl4-Cdc48/p97 (UNC) complex. Interacts with NPL4. Ref.7 Ref.8

Miscellaneous

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

Sequence similarities

Belongs to the UFD1 family.

Ontologies

Keywords
   Biological processUbl conjugation pathway
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processER-associated misfolded protein catabolic process

Inferred from mutant phenotype Ref.9PubMed 11813000. Source: SGD

ER-associated ubiquitin-dependent protein catabolic process

Inferred from mutant phenotype PubMed 11739805. Source: SGD

cytoplasm-associated proteasomal ubiquitin-dependent protein catabolic process

Inferred from mutant phenotype PubMed 18812321. Source: SGD

nonfunctional rRNA decay

Inferred from mutant phenotype PubMed 22505030. Source: SGD

positive regulation of protein localization to nucleus

Inferred from mutant phenotype Ref.8Ref.7. Source: SGD

proteasome-mediated ubiquitin-dependent protein catabolic process

Inferred from mutant phenotype PubMed 20206597. Source: SGD

retrograde protein transport, ER to cytosol

Inferred from mutant phenotype Ref.9PubMed 11813000. Source: SGD

ribosome-associated ubiquitin-dependent protein catabolic process

Inferred from mutant phenotype PubMed 23358411. Source: SGD

   Cellular_componentCdc48p-Npl4p-Ufd1p AAA ATPase complex

Inferred from direct assay Ref.8Ref.7. Source: SGD

Doa10p ubiquitin ligase complex

Inferred from direct assay PubMed 16873065PubMed 16873066. Source: SGD

Hrd1p ubiquitin ligase ERAD-L complex

Inferred from direct assay PubMed 16873065PubMed 16873066. Source: SGD

RQC complex

Inferred from direct assay PubMed 23178123. Source: SGD

nucleus

Inferred from direct assay Ref.7. Source: SGD

   Molecular_functionpolyubiquitin binding

Inferred from direct assay Ref.15. Source: SGD

protein binding

Inferred from physical interaction PubMed 10688190PubMed 11283351PubMed 11805826PubMed 16179952PubMed 16429126PubMed 16873066PubMed 18407841PubMed 18467557. Source: IntAct

ubiquitin binding

Inferred from direct assay Ref.15. Source: SGD

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 361361Ubiquitin fusion degradation protein 1
PRO_0000194989

Regions

Region27 – 282Monoubiquitin-binding
Region30 – 323Monoubiquitin-binding
Region99 – 1013Monoubiquitin-binding

Sites

Site371Monoubiquitin-binding
Site391Monoubiquitin-binding
Site1091Monoubiquitin-binding

Amino acid modifications

Modified residue3541Phosphoserine Ref.12 Ref.13 Ref.14

Experimental info

Mutagenesis941V → D in UFD1-1; grows more slowly. Ref.1

Secondary structure

..................................... 361
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P53044 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 198E0CD48B863B98

FASTA36139,810
        10         20         30         40         50         60 
MFSGFSSFGG GNGFVNMPQT FEEFFRCYPI AMMNDRIRKD DANFGGKIFL PPSALSKLSM 

        70         80         90        100        110        120 
LNIRYPMLFK LTANETGRVT HGGVLEFIAE EGRVYLPQWM METLGIQPGS LLQISSTDVP 

       130        140        150        160        170        180 
LGQFVKLEPQ SVDFLDISDP KAVLENVLRN FSTLTVDDVI EISYNGKTFK IKILEVKPES 

       190        200        210        220        230        240 
SSKSICVIET DLVTDFAPPV GYVEPDYKAL KAQQDKEKKN SFGKGQVLDP SVLGQGSMST 

       250        260        270        280        290        300 
RIDYAGIANS SRNKLSKFVG QGQNISGKAP KAEPKQDIKD MKITFDGEPA KLDLPEGQLF 

       310        320        330        340        350        360 
FGFPMVLPKE DEESAAGSKS SEQNFQGQGI SLRKSNKRKT KSDHDSSKSK APKSPEVIEI 


D 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[6]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[12]"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.
[13]"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].
[14]"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].
[15]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS59814.
RefSeqNP_011562.1. NM_001181177.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZC1NMR-A1-208[»]
ProteinModelPortalP53044.
SMRP53044. Positions 15-208.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33295. 79 interactions.
DIPDIP-1476N.
IntActP53044. 16 interactions.
MINTMINT-393265.
STRING4932.YGR048W.

Proteomic databases

MaxQBP53044.
PaxDbP53044.
PeptideAtlasP53044.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYGR048W; YGR048W; YGR048W.
GeneID852939.
KEGGsce:YGR048W.

Organism-specific databases

CYGDYGR048w.
SGDS000003280. UFD1.

Phylogenomic databases

eggNOGCOG5140.
GeneTreeENSGT00390000002408.
HOGENOMHOG000212737.
KOK14016.
OMAINTDIAQ.
OrthoDBEOG7N0CF5.

Enzyme and pathway databases

BioCycYEAST:G3O-30766-MONOMER.

Gene expression databases

GenevestigatorP53044.

Family and domain databases

InterProIPR004854. UFD1.
[Graphical view]
PANTHERPTHR12555. PTHR12555. 1 hit.
PfamPF03152. UFD1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP53044.
NextBio972678.
PROP53044.

Entry information

Entry nameUFD1_YEAST
AccessionPrimary (citable) accession number: P53044
Secondary accession number(s): D6VUI5, Q45U36
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: June 11, 2014
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VII

Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references