Ubiquitin fusion degradation protein 1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P53044 (UFD1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 108. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	361 AA.
Sequence status	Complete.
Protein existence	Evidence 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.16
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 process	Ubl conjugation pathway
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ER-associated misfolded protein catabolic process Inferred from mutant phenotype Ref.9 PubMed 11813000. Source: SGD cytoplasm-associated proteasomal ubiquitin-dependent protein catabolic process Inferred from mutant phenotype PubMed 18812321. Source: SGD positive regulation of protein localization to nucleus Inferred from mutant phenotype Ref.8 Ref.7. Source: SGD retrograde protein transport, ER to cytosol Inferred from mutant phenotype Ref.9 PubMed 11813000. Source: SGD
Cellular_component	Cdc48p-Npl4p-Ufd1p AAA ATPase complex Inferred from direct assay Ref.8 Ref.7. Source: SGD nucleus Inferred from direct assay Ref.7. Source: SGD
Molecular_function	polyubiquitin binding Inferred from direct assay Ref.16. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NPL4	P33755	8	EBI-19997,EBI-12193
UBX2	Q04228	5	EBI-19997,EBI-27730

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 361

361

Ubiquitin fusion degradation protein 1

PRO_0000194989

Regions

Region

27 – 28

Monoubiquitin-binding

Region

30 – 32

Monoubiquitin-binding

Region

99 – 101

Monoubiquitin-binding

Sites

Site

Monoubiquitin-binding

Site

Monoubiquitin-binding

Site

109

Monoubiquitin-binding

Amino acid modifications

Modified residue

251

Phosphoserine Ref.15

Modified residue

321

Phosphoserine Ref.15

Modified residue

354

Phosphoserine Ref.12 Ref.13 Ref.14 Ref.15

Experimental info

Mutagenesis

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

Secondary structure

361

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P53044 [UniParc].

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

FASTA

361

39,810

        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' referencesShow '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. Kleine K. Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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. 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]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, MASS SPECTROMETRY. Strain: YAL6B.
[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, MASS SPECTROMETRY. Strain: ADR376.
[14]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-354, MASS SPECTROMETRY.
[15]	"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-251; SER-321 AND SER-354, MASS SPECTROMETRY.
[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.
+	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.

PIR

S59814.

RefSeq

NP_011562.1. NM_001181177.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZC1	NMR	-	A	1-208	[»]

ProteinModelPortal

P53044.

SMR

P53044. Positions 15-208.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1476N.

IntAct

P53044. 15 interactions.

MINT

MINT-393265.

STRING

4932.YGR048W.

Proteomic databases

PaxDb

P53044.

PeptideAtlas

P53044.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YGR048W; YGR048W; YGR048W.

GeneID

852939.

KEGG

sce:YGR048W.

Organism-specific databases

CYGD

YGR048w.

SGD

S000003280. UFD1.

Phylogenomic databases

eggNOG

COG5140.

GeneTree

ENSGT00390000002408.

HOGENOM

HOG000212737.

K14016.

OMA

RCYPIAM.

OrthoDB

EOG4BP4N3.

Enzyme and pathway databases

BioCyc

YEAST:G3O-30766-MONOMER.

Gene expression databases

Genevestigator

P53044.

GermOnline

YGR048W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR004854. UFD1.
[Graphical view]

PANTHER

PTHR12555. PTHR12555. 1 hit.

Pfam

PF03152. UFD1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P53044.

NextBio

972678.

Entry information

Entry name

UFD1_YEAST

Accession

Primary (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:	May 29, 2013
This is version 108 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome VII

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents