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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

Miscellaneous

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

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.1 Publication

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

  • ubiquitin-ubiquitin ligase activity Source: SGD

GO - Biological processi

  • cellular response to ethanol Source: SGD
  • positive regulation of protein ubiquitination Source: SGD
  • protein polyubiquitination Source: GO_Central
  • protein ubiquitination Source: SGD
  • ubiquitin-dependent ERAD pathway Source: SGD
  • ubiquitin-dependent protein catabolic process Source: SGD

Keywordsi

Molecular functionTransferase
Biological processUbl 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:2.3.2.271 Publication)
Alternative name(s):
RING-type E3 ubiquitin transferase UFD2
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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001949971 – 961E4 ubiquitin-protein ligase UFD2Add BLAST961

Proteomic databases

MaxQBiP54860.
PRIDEiP54860.

PTM databases

iPTMnetiP54860.

Interactioni

Subunit structurei

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

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi31855. 204 interactors.
DIPiDIP-5925N.
IntActiP54860. 17 interactors.
MINTiMINT-680185.
STRINGi4932.YDL190C.

Structurei

Secondary structure

1961
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1 – 8Combined sources8
Beta strandi10 – 13Combined sources4
Beta strandi16 – 19Combined sources4
Helixi28 – 30Combined sources3
Helixi36 – 38Combined sources3
Helixi39 – 48Combined sources10
Helixi56 – 75Combined sources20
Helixi80 – 83Combined sources4
Helixi84 – 101Combined sources18
Beta strandi107 – 110Combined sources4
Helixi113 – 122Combined sources10
Helixi123 – 126Combined sources4
Helixi128 – 141Combined sources14
Helixi144 – 161Combined sources18
Beta strandi162 – 164Combined sources3
Helixi171 – 185Combined sources15
Helixi188 – 193Combined sources6
Helixi194 – 196Combined sources3
Helixi208 – 210Combined sources3
Helixi211 – 214Combined sources4
Helixi218 – 221Combined sources4
Helixi228 – 234Combined sources7
Turni235 – 237Combined sources3
Helixi243 – 274Combined sources32
Helixi276 – 291Combined sources16
Helixi294 – 297Combined sources4
Beta strandi298 – 300Combined sources3
Helixi303 – 305Combined sources3
Helixi309 – 323Combined sources15
Helixi324 – 327Combined sources4
Helixi334 – 336Combined sources3
Turni339 – 343Combined sources5
Beta strandi347 – 349Combined sources3
Beta strandi356 – 358Combined sources3
Helixi361 – 371Combined sources11
Helixi381 – 395Combined sources15
Helixi397 – 405Combined sources9
Helixi407 – 421Combined sources15
Helixi429 – 460Combined sources32
Helixi463 – 484Combined sources22
Beta strandi485 – 487Combined sources3
Turni490 – 492Combined sources3
Beta strandi507 – 509Combined sources3
Helixi512 – 517Combined sources6
Helixi523 – 525Combined sources3
Helixi529 – 541Combined sources13
Turni548 – 551Combined sources4
Helixi555 – 567Combined sources13
Helixi575 – 589Combined sources15
Helixi601 – 606Combined sources6
Helixi608 – 624Combined sources17
Helixi625 – 627Combined sources3
Beta strandi633 – 635Combined sources3
Helixi637 – 654Combined sources18
Helixi656 – 668Combined sources13
Helixi670 – 706Combined sources37
Helixi720 – 754Combined sources35
Helixi756 – 759Combined sources4
Helixi762 – 780Combined sources19
Helixi782 – 785Combined sources4
Helixi792 – 795Combined sources4
Helixi799 – 812Combined sources14
Turni813 – 815Combined sources3
Helixi817 – 825Combined sources9
Turni827 – 829Combined sources3
Helixi832 – 842Combined sources11
Beta strandi843 – 846Combined sources4
Helixi851 – 878Combined sources28
Helixi883 – 885Combined sources3
Turni888 – 890Combined sources3
Beta strandi895 – 899Combined sources5
Turni901 – 903Combined sources3
Beta strandi906 – 908Combined sources3
Helixi909 – 916Combined sources8
Turni923 – 925Combined sources3
Helixi931 – 933Combined sources3
Helixi938 – 952Combined sources15

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP54860.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini880 – 954U-boxAdd BLAST75

Domaini

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

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000009300.
HOGENOMiHOG000248797.
InParanoidiP54860.
KOiK10597.
OMAiAMWNHEL.
OrthoDBiEOG092C0O9I.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiView protein in InterPro
IPR019474. Ub_conjug_fac_E4_core.
IPR003613. Ubox_domain.
IPR013083. Znf_RING/FYVE/PHD.
PfamiView protein in Pfam
PF04564. U-box. 1 hit.
PF10408. Ufd2P_core. 1 hit.
SMARTiView protein in SMART
SM00504. Ubox. 1 hit.
PROSITEiView protein in PROSITE
PS51698. U_BOX. 1 hit.

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)DescriptionActionsGraphical viewLength
Sequence conflicti102L → S in CAA58257 (PubMed:8896272).Curated1
Sequence conflicti102L → S in CAA98767 (PubMed:9169867).Curated1
Sequence conflicti677V → D in CAA58257 (PubMed:8896272).Curated1
Sequence conflicti677V → D in CAA98767 (PubMed:9169867).Curated1

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.

Similar proteinsi

Entry informationi

Entry nameiUFD2_YEAST
AccessioniPrimary (citable) accession number: P54860
Secondary accession number(s): D6VRG3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: July 27, 2011
Last modified: November 22, 2017
This is version 147 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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