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P0CG63

- UBI4P_YEAST

UniProt

P0CG63 - UBI4P_YEAST

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Protein

Polyubiquitin

Gene

UBI4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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

  1. ATP-dependent protein binding Source: SGD
  2. protein tag Source: FlyBase

GO - Biological processi

  1. ascospore formation Source: SGD
  2. protein deubiquitination Source: SGD
  3. protein monoubiquitination Source: SGD
  4. protein polyubiquitination Source: SGD
  5. protein ubiquitination Source: FlyBase
Complete GO annotation...

Enzyme and pathway databases

BioCyciYEAST:G3O-32141-MONOMER.
ReactomeiREACT_270320. ISG15 antiviral mechanism.

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
ProteomesiUP000002311: Chromosome XII

Organism-specific databases

SGDiS000003962. UBI4.

Subcellular locationi

Cytoplasm By similarity. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi29 – 291K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication
Mutagenesisi48 – 481K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication
Mutagenesisi63 – 631K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_0000396306Add
BLAST
Chaini77 – 15276UbiquitinPRO_0000396307Add
BLAST
Chaini153 – 22876UbiquitinPRO_0000396308Add
BLAST
Chaini229 – 30476UbiquitinPRO_0000396309Add
BLAST
Chaini305 – 38076UbiquitinPRO_0000396310Add
BLAST
Propeptidei381 – 3811PRO_0000396311

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PRIDEiP0CG63.

2D gel databases

SWISS-2DPAGEP61864.

Expressioni

Gene expression databases

GenevestigatoriP61864.

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

Protein-protein interaction databases

BioGridi31215. 3499 interactions.
IntActiP0CG63. 151 interactions.
MINTiMINT-545233.

Structurei

Secondary structure

1
381
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76Combined sources
Beta strandi12 – 165Combined sources
Helixi23 – 3412Combined sources
Turni38 – 403Combined sources
Beta strandi41 – 455Combined sources
Beta strandi52 – 554Combined sources
Helixi56 – 594Combined sources
Beta strandi66 – 716Combined sources
Beta strandi88 – 947Combined sources
Beta strandi101 – 1066Combined sources
Beta strandi143 – 1497Combined sources
Beta strandi157 – 1626Combined sources
Helixi163 – 1697Combined sources
Helixi170 – 1723Combined sources
Helixi180 – 1823Combined sources
Beta strandi184 – 1907Combined sources
Beta strandi207 – 2137Combined sources
Beta strandi227 – 2326Combined sources
Beta strandi236 – 2383Combined sources
Beta strandi241 – 2433Combined sources
Helixi251 – 2566Combined sources
Helixi266 – 2683Combined sources
Beta strandi270 – 2723Combined sources
Beta strandi274 – 2774Combined sources
Helixi285 – 2873Combined sources
Beta strandi294 – 2985Combined sources
Beta strandi306 – 3105Combined sources
Turni312 – 3143Combined sources
Beta strandi316 – 3205Combined sources
Beta strandi323 – 3264Combined sources
Helixi327 – 33812Combined sources
Turni342 – 3443Combined sources
Beta strandi345 – 3495Combined sources
Beta strandi351 – 3533Combined sources
Beta strandi358 – 3603Combined sources
Helixi361 – 3633Combined sources
Beta strandi370 – 3756Combined sources
Helixi377 – 3793Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 1-379.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0CG63.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7676Ubiquitin-like 1PROSITE-ProRule annotationAdd
BLAST
Domaini77 – 15276Ubiquitin-like 2PROSITE-ProRule annotationAdd
BLAST
Domaini153 – 22876Ubiquitin-like 3PROSITE-ProRule annotationAdd
BLAST
Domaini229 – 30476Ubiquitin-like 4PROSITE-ProRule annotationAdd
BLAST
Domaini305 – 38076Ubiquitin-like 5PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ubiquitin family.Curated
Contains 5 ubiquitin-like domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00760000119340.
InParanoidiP0CG63.
KOiK08770.
OMAiEKNISAW.
OrthoDBiEOG7D5B06.

Family and domain databases

InterProiIPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti352 – 3521K → N in CAA25706. (PubMed:6095120)Curated

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 .
PIRi D29456. UQBY.
RefSeqi NP_013061.1. NM_001181859.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1OTR NMR - B 1-76 [» ]
1Q0W NMR - B 1-76 [» ]
1WR1 NMR - A 1-76 [» ]
1ZW7 NMR - A 1-76 [» ]
2G3Q NMR - B 1-76 [» ]
2JT4 NMR - B 1-76 [» ]
2JWZ NMR - A 1-76 [» ]
2KDI NMR - A 2-76 [» ]
2L00 NMR - B 1-76 [» ]
3CMM X-ray 2.70 B/D 1-76 [» ]
3L0W X-ray 2.80 B 1-76 [» ]
3L10 X-ray 2.80 B 1-76 [» ]
3OLM X-ray 2.50 D 1-76 [» ]
4HCN X-ray 2.60 B 1-76 [» ]
4NNJ X-ray 2.40 B/D/E 305-380 [» ]
4Q5E X-ray 1.87 B 305-380 [» ]
4Q5H X-ray 2.00 B 305-380 [» ]
ProteinModelPortali P0CG63.
SMRi P0CG63. Positions 1-379.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31215. 3499 interactions.
IntActi P0CG63. 151 interactions.
MINTi MINT-545233.

2D gel databases

SWISS-2DPAGE P61864.

Proteomic databases

PRIDEi P0CG63.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YLL039C ; YLL039C ; YLL039C .
GeneIDi 850620.
KEGGi sce:YLL039C.

Organism-specific databases

SGDi S000003962. UBI4.

Phylogenomic databases

GeneTreei ENSGT00760000119340.
InParanoidi P0CG63.
KOi K08770.
OMAi EKNISAW.
OrthoDBi EOG7D5B06.

Enzyme and pathway databases

BioCyci YEAST:G3O-32141-MONOMER.
Reactomei REACT_270320. ISG15 antiviral mechanism.

Miscellaneous databases

EvolutionaryTracei P0CG63.
NextBioi 966520.
PROi P0CG63.

Gene expression databases

Genevestigatori P61864.

Family and domain databases

InterProi IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view ]
Pfami PF00240. ubiquitin. 5 hits.
[Graphical view ]
PRINTSi PR00348. UBIQUITIN.
SMARTi SM00213. UBQ. 5 hits.
[Graphical view ]
SUPFAMi SSF54236. SSF54236. 5 hits.
PROSITEi PS00299. UBIQUITIN_1. 5 hits.
PS50053. UBIQUITIN_2. 5 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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. 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.

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 26, 2014
This is version 38 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

External Data

Dasty 3