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Protein

Polyubiquitin

Gene

UBI4

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

Functioni

Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).By similarity

Miscellaneous

Ubiquitin is encoded by 4 different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins L40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein S37. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.

GO - Molecular functioni

  • ATP-dependent protein binding Source: SGD
  • protein tag Source: FlyBase

GO - Biological processi

  • ascospore formation Source: SGD
  • protein deubiquitination Source: SGD
  • protein monoubiquitination Source: SGD
  • protein polyubiquitination Source: SGD
  • protein ubiquitination Source: FlyBase

Enzyme and pathway databases

BioCyciYEAST:G3O-32141-MONOMER
ReactomeiR-SCE-110312 Translesion synthesis by REV1
R-SCE-110314 Recognition of DNA damage by PCNA-containing replication complex
R-SCE-110320 Translesion Synthesis by POLH
R-SCE-1169408 ISG15 antiviral mechanism
R-SCE-174113 SCF-beta-TrCP mediated degradation of Emi1
R-SCE-187577 SCF(Skp2)-mediated degradation of p27/p21
R-SCE-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-SCE-382556 ABC-family proteins mediated transport
R-SCE-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA
R-SCE-5655862 Translesion synthesis by POLK
R-SCE-5656121 Translesion synthesis by POLI
R-SCE-5656169 Termination of translesion DNA synthesis
R-SCE-5675221 Negative regulation of MAPK pathway
R-SCE-5687128 MAPK6/MAPK4 signaling
R-SCE-5689603 UCH proteinases
R-SCE-5689880 Ub-specific processing proteases
R-SCE-5689901 Metalloprotease DUBs
R-SCE-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-SCE-5696394 DNA Damage Recognition in GG-NER
R-SCE-5696395 Formation of Incision Complex in GG-NER
R-SCE-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-SCE-5696400 Dual Incision in GG-NER
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-68949 Orc1 removal from chromatin
R-SCE-69017 CDK-mediated phosphorylation and removal of Cdc6
R-SCE-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-SCE-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-SCE-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-SCE-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-SCE-9033241 Peroxisomal protein import
R-SCE-917937 Iron uptake and transport
R-SCE-936440 Negative regulators of DDX58/IFIH1 signaling
R-SCE-983168 Antigen processing: Ubiquitination & Proteasome degradation

Names & Taxonomyi

Protein namesi
Recommended name:
Polyubiquitin
Cleaved into the following chain:
Gene namesi
Name:UBI4
Synonyms:SCD2
Ordered Locus Names:YLL039C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLL039C
SGDiS000003962 UBI4

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi29K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi48K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi63K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003963061 – 76UbiquitinAdd BLAST76
ChainiPRO_000039630777 – 152UbiquitinAdd BLAST76
ChainiPRO_0000396308153 – 228UbiquitinAdd BLAST76
ChainiPRO_0000396309229 – 304UbiquitinAdd BLAST76
ChainiPRO_0000396310305 – 380UbiquitinAdd BLAST76
PropeptideiPRO_00003963113811

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Keywords - PTMi

Isopeptide bond

Proteomic databases

MaxQBiP0CG63
PaxDbiP0CG63
PRIDEiP0CG63
TopDownProteomicsiP0CG63

2D gel databases

SWISS-2DPAGEiP61864

Interactioni

Binary interactionsi

Show more details

GO - Molecular functioni

  • ATP-dependent protein binding Source: SGD

Protein-protein interaction databases

BioGridi31215, 523 interactors
IntActiP0CG63, 180 interactors
MINTiP0CG63
STRINGi4932.YLL039C

Structurei

Secondary structure

1381
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi231 – 234Combined sources4
Beta strandi236 – 238Combined sources3
Beta strandi241 – 243Combined sources3
Helixi251 – 256Combined sources6
Helixi266 – 268Combined sources3
Beta strandi270 – 272Combined sources3
Beta strandi274 – 277Combined sources4
Helixi285 – 287Combined sources3
Beta strandi294 – 298Combined sources5
Beta strandi306 – 310Combined sources5
Turni312 – 314Combined sources3
Beta strandi316 – 320Combined sources5
Beta strandi323 – 326Combined sources4
Helixi327 – 338Combined sources12
Turni342 – 344Combined sources3
Beta strandi345 – 349Combined sources5
Beta strandi351 – 353Combined sources3
Beta strandi358 – 360Combined sources3
Helixi361 – 363Combined sources3
Beta strandi370 – 375Combined sources6
Helixi377 – 379Combined sources3

3D structure databases

ProteinModelPortaliP0CG63
SMRiP0CG63
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0CG63

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 76Ubiquitin-like 1PROSITE-ProRule annotationAdd BLAST76
Domaini77 – 152Ubiquitin-like 2PROSITE-ProRule annotationAdd BLAST76
Domaini153 – 228Ubiquitin-like 3PROSITE-ProRule annotationAdd BLAST76
Domaini229 – 304Ubiquitin-like 4PROSITE-ProRule annotationAdd BLAST76
Domaini305 – 380Ubiquitin-like 5PROSITE-ProRule annotationAdd BLAST76

Sequence similaritiesi

Belongs to the ubiquitin family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00810000125435
InParanoidiP0CG63
KOiK08770
OMAiVHENTRR
OrthoDBiEOG092C5P9Y

Family and domain databases

InterProiView protein in InterPro
IPR019956 Ubiquitin
IPR029071 Ubiquitin-like_domsf
IPR019954 Ubiquitin_CS
IPR000626 Ubiquitin_dom
PfamiView protein in Pfam
PF00240 ubiquitin, 5 hits
PRINTSiPR00348 UBIQUITIN
SMARTiView protein in SMART
SM00213 UBQ, 5 hits
SUPFAMiSSF54236 SSF54236, 5 hits
PROSITEiView protein in PROSITE
PS00299 UBIQUITIN_1, 5 hits
PS50053 UBIQUITIN_2, 5 hits

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0CG63-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID
110 120 130 140 150
NVKSKIQDKE GIPPDQQRLI FAGKQLEDGR TLSDYNIQKE STLHLVLRLR
160 170 180 190 200
GGMQIFVKTL TGKTITLEVE SSDTIDNVKS KIQDKEGIPP DQQRLIFAGK
210 220 230 240 250
QLEDGRTLSD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT
260 270 280 290 300
IDNVKSKIQD KEGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR
310 320 330 340 350
LRGGMQIFVK TLTGKTITLE VESSDTIDNV KSKIQDKEGI PPDQQRLIFA
360 370 380
GKQLEDGRTL SDYNIQKEST LHLVLRLRGG N
Length:381
Mass (Da):42,826
Last modified:August 10, 2010 - v1
Checksum:i68C6235F9909A2AE
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti352K → N in CAA25706 (PubMed:6095120).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X05731 Genomic DNA Translation: CAA29198.1
Z73144 Genomic DNA Translation: CAA97489.1
X01473 Genomic DNA Translation: CAA25704.1
X01474 Genomic DNA Translation: CAA25706.1
BK006945 Genomic DNA Translation: DAA09283.1
PIRiD29456 UQBY
RefSeqiNP_013061.1, NM_001181859.1

Genome annotation databases

EnsemblFungiiYLL039C; YLL039C; YLL039C
GeneIDi850620
KEGGisce:YLL039C

Similar proteinsi

Entry informationi

Entry nameiUBI4P_YEAST
AccessioniPrimary (citable) accession number: P0CG63
Secondary accession number(s): D6VXW7
, P04838, P61864, Q6LA96
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: July 18, 2018
This is version 76 of the entry and version 1 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. 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 XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

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