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P0CG63 (UBI4P_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 31. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Polyubiquitin

Cleaved into the following chain:

  1. Ubiquitin
Gene names
Name:UBI4
Synonyms:SCD2
Ordered Locus Names:YLL039C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length381 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subcellular location

Cytoplasm By similarity. Nucleus 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.

Sequence similarities

Belongs to the ubiquitin family.

Contains 5 ubiquitin-like domains.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 7676Ubiquitin
PRO_0000396306
Chain77 – 15276Ubiquitin
PRO_0000396307
Chain153 – 22876Ubiquitin
PRO_0000396308
Chain229 – 30476Ubiquitin
PRO_0000396309
Chain305 – 38076Ubiquitin
PRO_0000396310
Propeptide3811
PRO_0000396311

Regions

Domain1 – 7676Ubiquitin-like 1
Domain77 – 15276Ubiquitin-like 2
Domain153 – 22876Ubiquitin-like 3
Domain229 – 30476Ubiquitin-like 4
Domain305 – 38076Ubiquitin-like 5

Amino acid modifications

Cross-link6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7 Ref.8
Cross-link27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7
Cross-link48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7 Ref.8
Cross-link63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.7 Ref.8
Cross-link76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Experimental info

Mutagenesis291K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.5 Ref.6
Mutagenesis481K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.5 Ref.6
Mutagenesis631K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. Ref.5 Ref.6
Sequence conflict3521K → N in CAA25706. Ref.4

Secondary structure

.................................................................... 381
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0CG63 [UniParc].

Last modified August 10, 2010. Version 1.
Checksum: 68C6235F9909A2AE

FASTA38142,826
        10         20         30         40         50         60 
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 

        70         80         90        100        110        120 
IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID NVKSKIQDKE GIPPDQQRLI 

       130        140        150        160        170        180 
FAGKQLEDGR TLSDYNIQKE STLHLVLRLR GGMQIFVKTL TGKTITLEVE SSDTIDNVKS 

       190        200        210        220        230        240 
KIQDKEGIPP DQQRLIFAGK QLEDGRTLSD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT 

       250        260        270        280        290        300 
ITLEVESSDT IDNVKSKIQD KEGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR 

       310        320        330        340        350        360 
LRGGMQIFVK TLTGKTITLE VESSDTIDNV KSKIQDKEGI PPDQQRLIFA GKQLEDGRTL 

       370        380 
SDYNIQKEST LHLVLRLRGG N 

« Hide

References

« Hide 'large scale' references
[1]"The yeast ubiquitin genes: a family of natural gene fusions."
Oezkaynak E., Finley D., Solomon M.J., Varshavsky A.
EMBO J. 6:1429-1439(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. expand/collapse author list , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"The yeast ubiquitin gene: head-to-tail repeats encoding a polyubiquitin precursor protein."
Oezkaynak E., Finley D., Varshavsky A.
Nature 312:663-666(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 191-381.
[5]"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: MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63.
[6]"A ubiquitin mutant with specific defects in DNA repair and multiubiquitination."
Spence J., Sadis S., Haas A.L., Finley D.
Mol. Cell. Biol. 15:1265-1273(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LYSINE RESIDUES.
[7]"A proteomics approach to understanding protein ubiquitination."
Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P.
Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63.
Strain: SUB592.
[8]"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-48 AND LYS-63.
[9]"Structural basis for the specificity of ubiquitin C-terminal hydrolases."
Johnston S.C., Riddle S.M., Cohen R.E., Hill C.P.
EMBO J. 18:3877-3887(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH YUH1.
[10]"A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain."
Shih S.C., Prag G., Francis S.A., Sutanto M.A., Hurley J.H., Hicke L.
EMBO J. 22:1273-1281(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH VPS9.
[11]"Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail."
Hamilton K.S., Ellison M.J., Barber K.R., Williams R.S., Huzil J.T., McKenna S., Ptak C., Glover M., Shaw G.S.
Structure 9:897-904(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR IN COMPLEX WITH UBC1.
[12]"Solution structure of a CUE-ubiquitin complex reveals a conserved mode of ubiquitin binding."
Kang R.S., Daniels C.M., Francis S.A., Shih S.C., Salerno W.J., Hicke L., Radhakrishnan I.
Cell 113:621-630(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF COMPLEX WITH CUE2 N-TERMINAL DOMAIN.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRUQBY. D29456.
RefSeqNP_013061.1. NM_001181859.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP0CG63.
SMRP0CG63. Positions 1-379.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31215. 3255 interactions.
IntActP0CG63. 151 interactions.
MINTMINT-545233.

2D gel databases

SWISS-2DPAGEP61864.

Proteomic databases

PRIDEP0CG63.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYLL039C; YLL039C; YLL039C.
GeneID850620.
KEGGsce:YLL039C.

Organism-specific databases

SGDS000003962. UBI4.

Phylogenomic databases

GeneTreeENSGT00750000117776.
KOK08770.
OMAIQKESTH.
OrthoDBEOG7D5B06.

Enzyme and pathway databases

BioCycYEAST:G3O-32141-MONOMER.

Gene expression databases

GenevestigatorP61864.

Family and domain databases

InterProIPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamPF00240. ubiquitin. 5 hits.
[Graphical view]
PRINTSPR00348. UBIQUITIN.
SMARTSM00213. UBQ. 5 hits.
[Graphical view]
PROSITEPS00299. UBIQUITIN_1. 5 hits.
PS50053. UBIQUITIN_2. 5 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0CG63.
NextBio966520.
PROP0CG63.

Entry information

Entry nameUBI4P_YEAST
AccessionPrimary (citable) accession number: P0CG63
Secondary accession number(s): D6VXW7 expand/collapse secondary AC list , P04838, P61864, Q6LA96
Entry history
Integrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: April 16, 2014
This is version 31 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XII

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

Yeast

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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references