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P50102

- UBP8_YEAST

UniProt

P50102 - UBP8_YEAST

Protein

Ubiquitin carboxyl-terminal hydrolase 8

Gene

UBP8

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 134 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    Functions as histone deubiquitinating component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Together with SGF11, is required for histone H2B deubiquitination.3 Publications

    Catalytic activityi

    Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei146 – 1461Nucleophile
    Active sitei427 – 4271Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri44 – 10562UBP-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. protein complex scaffold Source: SGD
    3. ubiquitin-specific protease activity Source: SGD
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. histone deubiquitination Source: SGD
    2. histone H3-K4 methylation Source: SGD
    3. histone H3-K79 methylation Source: SGD
    4. regulation of transcription, DNA-templated Source: UniProtKB-KW
    5. RNA splicing Source: SGD
    6. transcription, DNA-templated Source: UniProtKB-KW
    7. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Transcription, Transcription regulation, Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciYEAST:G3O-32904-MONOMER.

    Protein family/group databases

    MEROPSiC19.087.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 8 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 8
    Ubiquitin thioesterase 8
    Ubiquitin-specific-processing protease 8
    Gene namesi
    Name:UBP8
    Ordered Locus Names:YMR223W
    ORF Names:YM9959.05
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIII

    Organism-specific databases

    CYGDiYMR223w.
    SGDiS000004836. UBP8.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. DUBm complex Source: SGD
    2. SAGA complex Source: SGD
    3. SLIK (SAGA-like) complex Source: SGD

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi46 – 461C → A: Lowers histone H2B deubiquitination activity; when associated with A-49. 1 Publication
    Mutagenesisi49 – 491C → A: Lowers histone H2B deubiquitination activity; when associated with A-46. 1 Publication
    Mutagenesisi77 – 771H → A: Lowers histone H2B deubiquitination activity. 1 Publication
    Mutagenesisi146 – 1461C → S: Lowers histone H2B deubiquitination activity. 1 Publication
    Mutagenesisi419 – 4191H → A: Lowers histone H2B deubiquitination activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 471471Ubiquitin carboxyl-terminal hydrolase 8PRO_0000080593Add
    BLAST

    Proteomic databases

    MaxQBiP50102.
    PaxDbiP50102.
    PeptideAtlasiP50102.

    Expressioni

    Gene expression databases

    GenevestigatoriP50102.

    Interactioni

    Subunit structurei

    Component of the 1.8 MDa SAGA complex, which consists of at least of TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1. TAF5, TAF6, TAF9, TAF19, TAF12 and ADA1 seem to be present in 2 copies. SAGA is built of 5 distinct domains with specialized functions. Domain I (containing TRA1) probably represents the activator interaction surface. Domain II (containing TAF5 and TAF6, and probably TAF9 and TAF10), domain III (containing GCN5, TAF10, SPT7, TAF5 and ADA1, and probably ADA2, ADA3 and TAF12), and domain IV (containing HFI1/ADA1 and TAF6, and probably TAF9) are believed to play primarily an architectural role. Domain III also harbors the HAT activity. Domain V (containing SPT3 and SPT20, and probably SPT8) represents the TBP-interacting module, which may be associated transiently with SAGA. UBP8 interacts with SGF11. Component of the SLIK complex, which consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8, GCN5, ADA2, SPT3, TAF10 and TAF9.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    HFI1Q120609EBI-19863,EBI-8287

    Protein-protein interaction databases

    BioGridi35401. 284 interactions.
    DIPiDIP-1506N.
    IntActiP50102. 164 interactions.
    MINTiMINT-393758.
    STRINGi4932.YMR223W.

    Structurei

    Secondary structure

    1
    471
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 106
    Helixi14 – 3219
    Helixi36 – 438
    Turni47 – 493
    Beta strandi54 – 6411
    Beta strandi66 – 683
    Turni69 – 724
    Helixi73 – 819
    Beta strandi85 – 884
    Turni89 – 913
    Beta strandi94 – 963
    Turni97 – 1004
    Beta strandi101 – 1033
    Helixi107 – 1104
    Helixi112 – 1176
    Helixi118 – 1247
    Helixi130 – 1323
    Beta strandi142 – 1443
    Helixi146 – 15611
    Helixi159 – 1668
    Helixi169 – 1735
    Turni179 – 1813
    Helixi183 – 19513
    Helixi214 – 22613
    Helixi228 – 2303
    Beta strandi231 – 2344
    Helixi238 – 25619
    Helixi260 – 2678
    Helixi274 – 2785
    Beta strandi281 – 2888
    Turni290 – 2923
    Beta strandi297 – 3048
    Beta strandi306 – 3083
    Helixi316 – 3249
    Beta strandi327 – 3293
    Turni337 – 3404
    Beta strandi341 – 3433
    Beta strandi346 – 3549
    Beta strandi356 – 3627
    Beta strandi365 – 3673
    Beta strandi369 – 3713
    Beta strandi373 – 3753
    Beta strandi384 – 3874
    Helixi389 – 3913
    Beta strandi409 – 42214
    Beta strandi425 – 4339
    Turni435 – 4373
    Beta strandi439 – 4435
    Beta strandi446 – 4505
    Helixi452 – 4554
    Beta strandi460 – 47011

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3M99X-ray2.70A1-471[»]
    3MHHX-ray2.45A1-471[»]
    3MHSX-ray1.89A1-471[»]
    4FIPX-ray2.69A/E1-471[»]
    4FJCX-ray2.83A/E1-471[»]
    4FK5X-ray2.03A1-471[»]
    ProteinModelPortaliP50102.
    SMRiP50102. Positions 1-471.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP50102.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini137 – 468332USPAdd
    BLAST

    Domaini

    The UBP-type zinc finger domain is required for the interaction with the SAGA complex.

    Sequence similaritiesi

    Belongs to the peptidase C19 family. UBP8 subfamily.Curated
    Contains 1 UBP-type zinc finger.PROSITE-ProRule annotation
    Contains 1 USP domain.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri44 – 10562UBP-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5533.
    GeneTreeiENSGT00750000117288.
    HOGENOMiHOG000216626.
    KOiK11366.
    OMAiNCKSHES.
    OrthoDBiEOG7R2BSX.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view]
    PfamiPF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view]
    SMARTiSM00290. ZnF_UBP. 1 hit.
    [Graphical view]
    PROSITEiPS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P50102-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSICPHIQQV FQNEKSKDGV LKTCNAARYI LNHSVPKEKF LNTMKCGTCH    50
    EINSGATFMC LQCGFCGCWN HSHFLSHSKQ IGHIFGINSN NGLLFCFKCE 100
    DYIGNIDLIN DAILAKYWDD VCTKTMVPSM ERRDGLSGLI NMGSTCFMSS 150
    ILQCLIHNPY FIRHSMSQIH SNNCKVRSPD KCFSCALDKI VHELYGALNT 200
    KQASSSSTST NRQTGFIYLL TCAWKINQNL AGYSQQDAHE FWQFIINQIH 250
    QSYVLDLPNA KEVSRANNKQ CECIVHTVFE GSLESSIVCP GCQNNSKTTI 300
    DPFLDLSLDI KDKKKLYECL DSFHKKEQLK DFNYHCGECN STQDAIKQLG 350
    IHKLPSVLVL QLKRFEHLLN GSNRKLDDFI EFPTYLNMKN YCSTKEKDKH 400
    SENGKVPDII YELIGIVSHK GTVNEGHYIA FCKISGGQWF KFNDSMVSSI 450
    SQEEVLKEQA YLLFYTIRQV N 471
    Length:471
    Mass (Da):53,623
    Last modified:October 1, 1996 - v1
    Checksum:iBC632F12FBD0F73C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49939 Genomic DNA. Translation: CAA90194.1.
    BK006946 Genomic DNA. Translation: DAA10122.1.
    PIRiS57591.
    RefSeqiNP_013950.1. NM_001182730.1.

    Genome annotation databases

    EnsemblFungiiYMR223W; YMR223W; YMR223W.
    GeneIDi855263.
    KEGGisce:YMR223W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49939 Genomic DNA. Translation: CAA90194.1 .
    BK006946 Genomic DNA. Translation: DAA10122.1 .
    PIRi S57591.
    RefSeqi NP_013950.1. NM_001182730.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3M99 X-ray 2.70 A 1-471 [» ]
    3MHH X-ray 2.45 A 1-471 [» ]
    3MHS X-ray 1.89 A 1-471 [» ]
    4FIP X-ray 2.69 A/E 1-471 [» ]
    4FJC X-ray 2.83 A/E 1-471 [» ]
    4FK5 X-ray 2.03 A 1-471 [» ]
    ProteinModelPortali P50102.
    SMRi P50102. Positions 1-471.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35401. 284 interactions.
    DIPi DIP-1506N.
    IntActi P50102. 164 interactions.
    MINTi MINT-393758.
    STRINGi 4932.YMR223W.

    Protein family/group databases

    MEROPSi C19.087.

    Proteomic databases

    MaxQBi P50102.
    PaxDbi P50102.
    PeptideAtlasi P50102.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YMR223W ; YMR223W ; YMR223W .
    GeneIDi 855263.
    KEGGi sce:YMR223W.

    Organism-specific databases

    CYGDi YMR223w.
    SGDi S000004836. UBP8.

    Phylogenomic databases

    eggNOGi COG5533.
    GeneTreei ENSGT00750000117288.
    HOGENOMi HOG000216626.
    KOi K11366.
    OMAi NCKSHES.
    OrthoDBi EOG7R2BSX.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-32904-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P50102.
    NextBioi 978861.

    Gene expression databases

    Genevestigatori P50102.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view ]
    SMARTi SM00290. ZnF_UBP. 1 hit.
    [Graphical view ]
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "Expanded lysine acetylation specificity of Gcn5 in native complexes."
      Grant P.A., Eberharter A., John S., Cook R.G., Turner B.M., Workman J.L.
      J. Biol. Chem. 274:5895-5900(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN HISTONE ACETYLATION AT THE SAGA COMPLEX.
    4. "The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway."
      Pray-Grant M.G., Schieltz D., McMahon S.J., Wood J.M., Kennedy E.L., Cook R.G., Workman J.L., Yates J.R. III, Grant P.A.
      Mol. Cell. Biol. 22:8774-8786(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE SLIK COMPLEX.
    5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    6. "Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription."
      Daniel J.A., Torok M.S., Sun Z.W., Schieltz D., Allis C.D., Yates J.R. III, Grant P.A.
      J. Biol. Chem. 279:1867-1871(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN HISTONE DEUBIQUITINATION ACTIVITY OF THE SAGA COMPLEX, IDENTIFICATION IN THE SAGA COMPLEX, IDENTIFICATION IN THE SLIK COMPLEX.
    7. "H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex."
      Ingvarsdottir K., Krogan N.J., Emre N.C.T., Wyce A., Thompson N.J., Emili A., Hughes T.R., Greenblatt J.F., Berger S.L.
      Mol. Cell. Biol. 25:1162-1172(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN HISTONE DEUBIQUITINATION ACTIVITY OF THE SAGA COMPLEX, IDENTIFICATION IN THE SAGA COMPLEX, INTERACTION WITH SGF11, MUTAGENESIS OF CYS-46; CYS-49; HIS-77; CYS-146 AND HIS-419.
    8. "Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation."
      Pray-Grant M.G., Daniel J.A., Schieltz D., Yates J.R. III, Grant P.A.
      Nature 433:434-438(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION IN THE SLIK COMPLEX.

    Entry informationi

    Entry nameiUBP8_YEAST
    AccessioniPrimary (citable) accession number: P50102
    Secondary accession number(s): D6W048
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 134 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 1030 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

    External Data

    Dasty 3