Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P0CG63

- UBI4P_YEAST

UniProt

P0CG63 - UBI4P_YEAST

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
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 36 (01 Oct 2014)
      Sequence version 1 (10 Aug 2010)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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 binding Source: IntAct
    3. 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

    Enzyme and pathway databases

    BioCyciYEAST:G3O-32141-MONOMER.

    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-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi29 – 291K → R: Deficiency in ubiquitin-protein conjugate formation. 2 Publications
    Mutagenesisi48 – 481K → R: Deficiency in ubiquitin-protein conjugate formation. 2 Publications
    Mutagenesisi63 – 631K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 2 Publications

    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. 3473 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 – 76
    Beta strandi12 – 165
    Helixi23 – 3412
    Turni38 – 403
    Beta strandi41 – 455
    Beta strandi52 – 554
    Helixi56 – 594
    Beta strandi66 – 716
    Beta strandi88 – 947
    Beta strandi101 – 1066
    Beta strandi143 – 1497
    Beta strandi157 – 1626
    Helixi163 – 1697
    Helixi170 – 1723
    Helixi180 – 1823
    Beta strandi184 – 1907
    Beta strandi207 – 2137
    Beta strandi227 – 2326
    Beta strandi236 – 2383
    Beta strandi241 – 2433
    Helixi251 – 2566
    Helixi266 – 2683
    Beta strandi270 – 2723
    Beta strandi274 – 2774
    Helixi285 – 2873
    Beta strandi294 – 2985
    Beta strandi305 – 3117
    Turni312 – 3143
    Beta strandi316 – 3227
    Beta strandi323 – 3264
    Helixi327 – 33812
    Helixi342 – 3443
    Beta strandi346 – 3494
    Beta strandi351 – 3533
    Beta strandi358 – 3603
    Helixi361 – 3633
    Beta strandi370 – 3745
    Helixi377 – 3793

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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[»]
    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

    GeneTreeiENSGT00750000117776.
    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

    MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL    50
    EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVESSDTID 100
    NVKSKIQDKE GIPPDQQRLI FAGKQLEDGR TLSDYNIQKE STLHLVLRLR 150
    GGMQIFVKTL TGKTITLEVE SSDTIDNVKS KIQDKEGIPP DQQRLIFAGK 200
    QLEDGRTLSD YNIQKESTLH LVLRLRGGMQ IFVKTLTGKT ITLEVESSDT 250
    IDNVKSKIQD KEGIPPDQQR LIFAGKQLED GRTLSDYNIQ KESTLHLVLR 300
    LRGGMQIFVK TLTGKTITLE VESSDTIDNV KSKIQDKEGI PPDQQRLIFA 350
    GKQLEDGRTL SDYNIQKEST LHLVLRLRGG N 381
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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 [» ]
    ProteinModelPortali P0CG63.
    SMRi P0CG63. Positions 1-379.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31215. 3473 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 ENSGT00750000117776.
    KOi K08770.
    OMAi EKNISAW.
    OrthoDBi EOG7D5B06.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-32141-MONOMER.

    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

    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: October 1, 2014
    This is version 36 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