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Protein

Polyubiquitin

Gene

UBI4

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

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

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
Complete GO annotation...

Enzyme and pathway databases

BioCyciYEAST:G3O-32141-MONOMER.
ReactomeiR-SCE-110312. Translesion synthesis by REV1.
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-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-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-69229. Ubiquitin-dependent degradation of Cyclin D1.
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-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

GO - Cellular componenti

  • cytoplasm Source: SGD
  • nucleus Source: UniProtKB-SubCell
Complete GO annotation...

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-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP0CG63.
PRIDEiP0CG63.
TopDownProteomicsiP0CG63.

2D gel databases

SWISS-2DPAGEP61864.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
DDI1P400873EBI-7000452,EBI-5717
DSK2P485103EBI-7000452,EBI-6174
GYP7P483652EBI-7000452,EBI-8018
RAD23P326284EBI-7000452,EBI-14668
TDH2P003582EBI-7000452,EBI-7212

GO - Molecular functioni

  • ATP-dependent protein binding Source: SGD

Protein-protein interaction databases

BioGridi31215. 328 interactors.
IntActiP0CG63. 151 interactors.
MINTiMINT-545233.

Structurei

Secondary structure

1381
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Beta strandi12 – 16Combined sources5
Helixi23 – 34Combined sources12
Turni38 – 40Combined sources3
Beta strandi41 – 45Combined sources5
Beta strandi52 – 55Combined sources4
Helixi56 – 59Combined sources4
Beta strandi66 – 71Combined sources6
Beta strandi88 – 94Combined sources7
Beta strandi101 – 106Combined sources6
Beta strandi143 – 149Combined sources7
Beta strandi157 – 162Combined sources6
Helixi163 – 169Combined sources7
Helixi170 – 172Combined sources3
Helixi180 – 182Combined sources3
Beta strandi184 – 190Combined sources7
Beta strandi207 – 213Combined sources7
Beta strandi227 – 232Combined sources6
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OTRNMR-B1-76[»]
1Q0WNMR-B1-76[»]
1WR1NMR-A1-76[»]
1ZW7NMR-A1-76[»]
2G3QNMR-B1-76[»]
2JT4NMR-B1-76[»]
2JWZNMR-A1-76[»]
2KDINMR-A2-76[»]
2L00NMR-B1-76[»]
3CMMX-ray2.70B/D1-76[»]
3L0WX-ray2.80B1-76[»]
3L10X-ray2.80B1-76[»]
3OLMX-ray2.50D1-76[»]
4HCNX-ray2.60B1-76[»]
4NNJX-ray2.40B/D/E305-380[»]
4Q5EX-ray1.87B305-380[»]
4Q5HX-ray2.00B305-380[»]
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
Contains 5 ubiquitin-like domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00810000125435.
InParanoidiP0CG63.
KOiK08770.
OMAiGKIQEKE.
OrthoDBiEOG092C5P9Y.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 5 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 5 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 5 hits.
PROSITEiPS00299. UBIQUITIN_1. 5 hits.
PS50053. UBIQUITIN_2. 5 hits.
[Graphical view]

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.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OTRNMR-B1-76[»]
1Q0WNMR-B1-76[»]
1WR1NMR-A1-76[»]
1ZW7NMR-A1-76[»]
2G3QNMR-B1-76[»]
2JT4NMR-B1-76[»]
2JWZNMR-A1-76[»]
2KDINMR-A2-76[»]
2L00NMR-B1-76[»]
3CMMX-ray2.70B/D1-76[»]
3L0WX-ray2.80B1-76[»]
3L10X-ray2.80B1-76[»]
3OLMX-ray2.50D1-76[»]
4HCNX-ray2.60B1-76[»]
4NNJX-ray2.40B/D/E305-380[»]
4Q5EX-ray1.87B305-380[»]
4Q5HX-ray2.00B305-380[»]
ProteinModelPortaliP0CG63.
SMRiP0CG63.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31215. 328 interactors.
IntActiP0CG63. 151 interactors.
MINTiMINT-545233.

2D gel databases

SWISS-2DPAGEP61864.

Proteomic databases

MaxQBiP0CG63.
PRIDEiP0CG63.
TopDownProteomicsiP0CG63.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLL039C; YLL039C; YLL039C.
GeneIDi850620.
KEGGisce:YLL039C.

Organism-specific databases

EuPathDBiFungiDB:YLL039C.
SGDiS000003962. UBI4.

Phylogenomic databases

GeneTreeiENSGT00810000125435.
InParanoidiP0CG63.
KOiK08770.
OMAiGKIQEKE.
OrthoDBiEOG092C5P9Y.

Enzyme and pathway databases

BioCyciYEAST:G3O-32141-MONOMER.
ReactomeiR-SCE-110312. Translesion synthesis by REV1.
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-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-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-69229. Ubiquitin-dependent degradation of Cyclin D1.
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-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

EvolutionaryTraceiP0CG63.
PROiP0CG63.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF00240. ubiquitin. 5 hits.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. UBQ. 5 hits.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 5 hits.
PROSITEiPS00299. UBIQUITIN_1. 5 hits.
PS50053. UBIQUITIN_2. 5 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiUBI4P_YEAST
AccessioniPrimary (citable) accession number: P0CG63
Secondary accession number(s): D6VXW7
, P04838, P61864, Q6LA96
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: November 30, 2016
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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.

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

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.