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Protein

E4 ubiquitin-protein ligase UFD2

Gene

UFD2

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

E4 ubiquitin chain-elongation enzyme specifically involved in polyubiquitin chain assembly. Binds to CDC48 and elongates mono- and diubiquitinated ERAD substrates presented by the UFD1-NPL4-CDC48/p97 (UNC) AAA ATPase complex to a chain length of 4 to 6 ubiquitin moieties. Delivers these polyubiquitinated substrates to RAD23 and DSK2, which target them to the proteasome. Has E3 ubiquitin-protein ligase activity, accepting ubiquitin from its cognate E2 ubiquitin-conjugating enzyme UBC4. Enhances ubiquitination at 'Lys-48', but not at 'Lys-29' of the Ub moiety. Promotes ubiquitin chain elongation at 'Lys-48' on the DOA10 substrate PEX29. Also involved in the proteolytic processing of the ER-bound transcription factor SPT23.5 Publications

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.1 Publication
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

GO - Molecular functioni

  • ligase activity Source: UniProtKB-KW
  • ubiquitin-ubiquitin ligase activity Source: SGD

GO - Biological processi

  • cellular response to ethanol Source: SGD
  • ER-associated ubiquitin-dependent protein catabolic process Source: SGD
  • protein ubiquitination Source: SGD
  • ubiquitin-dependent protein catabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-29575-MONOMER.
BRENDAi2.3.2.B12. 984.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E4 ubiquitin-protein ligase UFD2 (EC:6.3.2.-1 Publication)
Alternative name(s):
Ubiquitin conjugation factor E4
Ubiquitin fusion degradation protein 2
Short name:
UB fusion protein 2
Gene namesi
Name:UFD2
Ordered Locus Names:YDL190C
ORF Names:D1255
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDL190C.
SGDiS000002349. UFD2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 961961E4 ubiquitin-protein ligase UFD2PRO_0000194997Add
BLAST

Proteomic databases

MaxQBiP54860.

PTM databases

iPTMnetiP54860.

Interactioni

Subunit structurei

Interacts with CDC48. Interacts with the ubiquitin-like domain of RAD23 and DSK2. Interacts with PEX29.6 Publications

Protein-protein interaction databases

BioGridi31855. 97 interactions.
DIPiDIP-5925N.
IntActiP54860. 8 interactions.
MINTiMINT-680185.

Structurei

Secondary structure

961
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi1 – 88Combined sources
Beta strandi10 – 134Combined sources
Beta strandi16 – 194Combined sources
Helixi28 – 303Combined sources
Helixi36 – 383Combined sources
Helixi39 – 4810Combined sources
Helixi56 – 7520Combined sources
Helixi80 – 834Combined sources
Helixi84 – 10118Combined sources
Beta strandi107 – 1104Combined sources
Helixi113 – 12210Combined sources
Helixi123 – 1264Combined sources
Helixi128 – 14114Combined sources
Helixi144 – 16118Combined sources
Beta strandi162 – 1643Combined sources
Helixi171 – 18515Combined sources
Helixi188 – 1936Combined sources
Helixi194 – 1963Combined sources
Helixi208 – 2103Combined sources
Helixi211 – 2144Combined sources
Helixi218 – 2214Combined sources
Helixi228 – 2347Combined sources
Turni235 – 2373Combined sources
Helixi243 – 27432Combined sources
Helixi276 – 29116Combined sources
Helixi294 – 2974Combined sources
Beta strandi298 – 3003Combined sources
Helixi303 – 3053Combined sources
Helixi309 – 32315Combined sources
Helixi324 – 3274Combined sources
Helixi334 – 3363Combined sources
Turni339 – 3435Combined sources
Beta strandi347 – 3493Combined sources
Beta strandi356 – 3583Combined sources
Helixi361 – 37111Combined sources
Helixi381 – 39515Combined sources
Helixi397 – 4059Combined sources
Helixi407 – 42115Combined sources
Helixi429 – 46032Combined sources
Helixi463 – 48422Combined sources
Beta strandi485 – 4873Combined sources
Turni490 – 4923Combined sources
Beta strandi507 – 5093Combined sources
Helixi512 – 5176Combined sources
Helixi523 – 5253Combined sources
Helixi529 – 54113Combined sources
Turni548 – 5514Combined sources
Helixi555 – 56713Combined sources
Helixi575 – 58915Combined sources
Helixi601 – 6066Combined sources
Helixi608 – 62417Combined sources
Helixi625 – 6273Combined sources
Beta strandi633 – 6353Combined sources
Helixi637 – 65418Combined sources
Helixi656 – 66813Combined sources
Helixi670 – 70637Combined sources
Helixi720 – 75435Combined sources
Helixi756 – 7594Combined sources
Helixi762 – 78019Combined sources
Helixi782 – 7854Combined sources
Helixi792 – 7954Combined sources
Helixi799 – 81214Combined sources
Turni813 – 8153Combined sources
Helixi817 – 8259Combined sources
Turni827 – 8293Combined sources
Helixi832 – 84211Combined sources
Beta strandi843 – 8464Combined sources
Helixi851 – 87828Combined sources
Helixi883 – 8853Combined sources
Turni888 – 8903Combined sources
Beta strandi895 – 8995Combined sources
Turni901 – 9033Combined sources
Beta strandi906 – 9083Combined sources
Helixi909 – 9168Combined sources
Turni923 – 9253Combined sources
Helixi931 – 9333Combined sources
Helixi938 – 95215Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2QIZX-ray2.56A1-961[»]
2QJ0X-ray2.65A1-961[»]
3M62X-ray2.40A1-961[»]
3M63X-ray2.40A1-961[»]
ProteinModelPortaliP54860.
SMRiP54860. Positions 1-955.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP54860.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini880 – 95475U-boxAdd
BLAST

Domaini

The U-box domain is required for the ubiquitin protein ligase activity.1 Publication

Sequence similaritiesi

Contains 1 U-box domain.Curated

Phylogenomic databases

GeneTreeiENSGT00390000009300.
HOGENOMiHOG000248797.
InParanoidiP54860.
KOiK10597.
OMAiDKLCYEA.
OrthoDBiEOG092C0O9I.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR019474. Ub_conjug_fac_E4_core.
IPR003613. Ubox_domain.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF04564. U-box. 1 hit.
PF10408. Ufd2P_core. 1 hit.
[Graphical view]
SMARTiSM00504. Ubox. 1 hit.
[Graphical view]
PROSITEiPS51698. U_BOX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P54860-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAIEDILQI TTDPSDTRGY SLLKSEEVPQ GSTLGVDFID TLLLYQLTEN
60 70 80 90 100
EKLDKPFEYL NDCFRRNQQQ KRITKNKPNA ESLHSTFQEI DRLVIGYGVV
110 120 130 140 150
ALQIENFCMN GAFINYITGI VSNVNSYTDF LSQIIQRAIL EGTALDLLNA
160 170 180 190 200
VFPTLLEYCN KHVSHFDLNE SVIYNNVLTI FELFVTFKPI AEIFTKIDGF
210 220 230 240 250
FADYSCKPQD FERKTILGPI LSLSPIEAAV AIRNYGDNLL RSKQQTAMIH
260 270 280 290 300
ESLQAEHKVV IDRLFFIVDK LVRGSLNSRT DMISYFAHIA NKNHLRRADH
310 320 330 340 350
PPFKELSSNG FMSNITLLLV RFSQPFLDIS YKKIDKIDAN YFNNPSLFID
360 370 380 390 400
LSGETRLNSD FKEADAFYDK NRKTADSKPN FISDCFFLTL TYLHYGLGGT
410 420 430 440 450
LSFEEKMGSE IKALKEEIEK VKKIAANHDV FARFITAQLS KMEKALKTTE
460 470 480 490 500
SLRFALQGFF AHRSLQLEVF DFICGASTFL IRVVDPEHEF PFKQIKLPLI
510 520 530 540 550
PDQIGVENVD NADFLRAHAP VPFKYYPEFV VEGPVNYSLY ISKYQTSPIF
560 570 580 590 600
RNPRLGSFVE FTTMVLRCPE LVSNPHLKGK LVQLLSVGAM PLTDNSPGFM
610 620 630 640 650
MDIFEHDELV NKNLLYALLD FYVIVEKTGS SSQFYDKFNS RYSISIILEE
660 670 680 690 700
LYYKIPSYKN QLIWQSQNNA DFFVRFVARM LNDLTFLLDE GLSNLAEVHN
710 720 730 740 750
IQNELDNRAR GAPPTREEED KELQTRLASA SRQAKSSCGL ADKSMKLFEI
760 770 780 790 800
YSKDIPAAFV TPEIVYRLAS MLNYNLESLV GPKCGELKVK DPQSYSFNPK
810 820 830 840 850
DLLKALTTVY INLSEQSEFI SAVAKDERSF NRNLFVRAVD ILGRKTGLAS
860 870 880 890 900
PEFIEKLLNF ANKAEEQRKA DEEEDLEYGD VPDEFLDPLM YTIMKDPVIL
910 920 930 940 950
PASKMNIDRS TIKAHLLSDS TDPFNRMPLK LEDVTPNEEL RQKILCFKKQ
960
KKEEAKHKAS E
Length:961
Mass (Da):109,916
Last modified:July 27, 2011 - v3
Checksum:i877ACB59AC29634A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti102 – 1021L → S in CAA58257 (PubMed:8896272).Curated
Sequence conflicti102 – 1021L → S in CAA98767 (PubMed:9169867).Curated
Sequence conflicti677 – 6771V → D in CAA58257 (PubMed:8896272).Curated
Sequence conflicti677 – 6771V → D in CAA98767 (PubMed:9169867).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U22154 Genomic DNA. Translation: AAC49024.1.
X83276 Genomic DNA. Translation: CAA58257.1.
Z74238 Genomic DNA. Translation: CAA98767.1.
BK006938 Genomic DNA. Translation: DAA11673.2.
PIRiS58787.
RefSeqiNP_010091.2. NM_001180250.2.

Genome annotation databases

EnsemblFungiiYDL190C; YDL190C; YDL190C.
GeneIDi851337.
KEGGisce:YDL190C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U22154 Genomic DNA. Translation: AAC49024.1.
X83276 Genomic DNA. Translation: CAA58257.1.
Z74238 Genomic DNA. Translation: CAA98767.1.
BK006938 Genomic DNA. Translation: DAA11673.2.
PIRiS58787.
RefSeqiNP_010091.2. NM_001180250.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2QIZX-ray2.56A1-961[»]
2QJ0X-ray2.65A1-961[»]
3M62X-ray2.40A1-961[»]
3M63X-ray2.40A1-961[»]
ProteinModelPortaliP54860.
SMRiP54860. Positions 1-955.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31855. 97 interactions.
DIPiDIP-5925N.
IntActiP54860. 8 interactions.
MINTiMINT-680185.

PTM databases

iPTMnetiP54860.

Proteomic databases

MaxQBiP54860.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDL190C; YDL190C; YDL190C.
GeneIDi851337.
KEGGisce:YDL190C.

Organism-specific databases

EuPathDBiFungiDB:YDL190C.
SGDiS000002349. UFD2.

Phylogenomic databases

GeneTreeiENSGT00390000009300.
HOGENOMiHOG000248797.
InParanoidiP54860.
KOiK10597.
OMAiDKLCYEA.
OrthoDBiEOG092C0O9I.

Enzyme and pathway databases

UniPathwayiUPA00143.
BioCyciYEAST:G3O-29575-MONOMER.
BRENDAi2.3.2.B12. 984.

Miscellaneous databases

EvolutionaryTraceiP54860.
PROiP54860.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR019474. Ub_conjug_fac_E4_core.
IPR003613. Ubox_domain.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF04564. U-box. 1 hit.
PF10408. Ufd2P_core. 1 hit.
[Graphical view]
SMARTiSM00504. Ubox. 1 hit.
[Graphical view]
PROSITEiPS51698. U_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUFD2_YEAST
AccessioniPrimary (citable) accession number: P54860
Secondary accession number(s): D6VRG3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: July 27, 2011
Last modified: September 7, 2016
This is version 135 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2600 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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 one 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.