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P43593

- UBP6_YEAST

UniProt

P43593 - UBP6_YEAST

Protein

Ubiquitin carboxyl-terminal hydrolase 6

Gene

UBP6

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 137 (01 Oct 2014)
      Sequence version 1 (01 Nov 1995)
      Previous versions | rss
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    Functioni

    Predominant proteasome-associated deubiquitinase which releases ubiquitin from the proteasome targeted ubiquitinated proteins. Ensures the regeneration of ubiquitin at the proteasome. Has proteasome-inhibitory activity and delays the degradation of ubiquitinated proteins to provide a time window allowing gradual deubiquitination of the substrate. Stabilizes the association of HUL5 with proteasomes and works in opposition to polyubiquitin elongation activity of HUL5.6 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).

    Enzyme regulationi

    Activated by it's association with the proteasome.1 Publication

    pH dependencei

    Optimum pH is 8.5-9.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei118 – 1181NucleophilePROSITE-ProRule annotation
    Active sitei447 – 4471Proton acceptorPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ubiquitin-specific protease activity Source: SGD

    GO - Biological processi

    1. negative regulation of proteasomal protein catabolic process Source: SGD
    2. protein deubiquitination Source: SGD
    3. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Ubl conjugation pathway

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30463-MONOMER.

    Protein family/group databases

    MEROPSiC19.079.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 6 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 6
    Ubiquitin thioesterase 6
    Ubiquitin-specific-processing protease 6
    Gene namesi
    Name:UBP6
    Ordered Locus Names:YFR010W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome VI

    Organism-specific databases

    CYGDiYFR010w.
    SGDiS000001906. UBP6.

    Subcellular locationi

    GO - Cellular componenti

    1. proteasome complex Source: SGD
    2. proteasome regulatory particle Source: SGD

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 499499Ubiquitin carboxyl-terminal hydrolase 6PRO_0000080591Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei389 – 3891Phosphothreonine3 Publications
    Modified residuei470 – 4701Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP43593.
    PaxDbiP43593.
    PeptideAtlasiP43593.

    Expressioni

    Gene expression databases

    GenevestigatoriP43593.

    Interactioni

    Subunit structurei

    Associates with the regulatory particle (RP) of the proteasome.

    Protein-protein interaction databases

    BioGridi31160. 361 interactions.
    DIPiDIP-6731N.
    IntActiP43593. 25 interactions.
    MINTiMINT-619095.
    STRINGi4932.YFR010W.

    Structurei

    Secondary structure

    1
    499
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi118 – 12912
    Helixi131 – 1388
    Helixi142 – 1443
    Helixi154 – 17219
    Helixi182 – 19110
    Helixi193 – 1964
    Helixi210 – 22516
    Helixi227 – 2304
    Turni231 – 2333
    Beta strandi235 – 2439
    Beta strandi246 – 2538
    Beta strandi257 – 2593
    Beta strandi261 – 2633
    Helixi272 – 2809
    Beta strandi297 – 3059
    Beta strandi307 – 3148
    Beta strandi317 – 3204
    Turni321 – 3244
    Beta strandi325 – 3284
    Beta strandi337 – 3404
    Helixi342 – 3443
    Helixi347 – 36923
    Helixi390 – 41324
    Beta strandi426 – 44217
    Beta strandi445 – 4539
    Beta strandi461 – 4655
    Beta strandi468 – 4725
    Helixi474 – 4785
    Helixi479 – 4813
    Beta strandi488 – 4969

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1VJVX-ray1.74A97-499[»]
    ProteinModelPortaliP43593.
    SMRiP43593. Positions 103-499.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP43593.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini6 – 8075Ubiquitin-likeAdd
    BLAST
    Domaini109 – 497389USPAdd
    BLAST

    Domaini

    The N-terminal ubiquitin-like domain is required for proteasome association and UBP6 activation at the proteasome.2 Publications

    Sequence similaritiesi

    Contains 1 ubiquitin-like domain.Curated
    Contains 1 USP domain.Curated

    Phylogenomic databases

    eggNOGiNOG286607.
    GeneTreeiENSGT00390000009615.
    HOGENOMiHOG000202292.
    KOiK11843.
    OMAiELCTTEL.
    OrthoDBiEOG789CMF.

    Family and domain databases

    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR000626. Ubiquitin-like.
    IPR029071. Ubiquitin-rel_dom.
    IPR028889. UCH/PAN2.
    [Graphical view]
    PfamiPF00443. UCH. 1 hit.
    [Graphical view]
    SMARTiSM00213. UBQ. 1 hit.
    [Graphical view]
    SUPFAMiSSF54236. SSF54236. 1 hit.
    PROSITEiPS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P43593-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSGETFEFNI RHSGKVYPIT LSTDATSADL KSKAEELTQV PSARQKYMVK    50
    GGLSGEESIK IYPLIKPGST VMLLGTPDAN LISKPAKKNN FIEDLAPEQQ 100
    VQQFAQLPVG FKNMGNTCYL NATLQALYRV NDLRDMILNY NPSQGVSNSG 150
    AQDEEIHKQI VIEMKRCFEN LQNKSFKSVL PIVLLNTLRK CYPQFAERDS 200
    QGGFYKQQDA EELFTQLFHS MSIVFGDKFS EDFRIQFKTT IKDTANDNDI 250
    TVKENESDSK LQCHISGTTN FMRNGLLEGL NEKIEKRSDL TGANSIYSVE 300
    KKISRLPKFL TVQYVRFFWK RSTNKKSKIL RKVVFPFQLD VADMLTPEYA 350
    AEKVKVRDEL RKVEKEKNEK EREIKRRKFD PSSSENVMTP REQYETQVAL 400
    NESEKDQWLE EYKKHFPPNL EKGENPSCVY NLIGVITHQG ANSESGHYQA 450
    FIRDELDENK WYKFNDDKVS VVEKEKIESL AGGGESDSAL ILMYKGFGL 499
    Length:499
    Mass (Da):57,111
    Last modified:November 1, 1995 - v1
    Checksum:iDAE54D1F8AC9960C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D50617 Genomic DNA. Translation: BAA09249.1.
    BK006940 Genomic DNA. Translation: DAA12450.1.
    PIRiS56265.
    RefSeqiNP_116665.1. NM_001179975.1.

    Genome annotation databases

    EnsemblFungiiYFR010W; YFR010W; YFR010W.
    GeneIDi850562.
    KEGGisce:YFR010W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D50617 Genomic DNA. Translation: BAA09249.1 .
    BK006940 Genomic DNA. Translation: DAA12450.1 .
    PIRi S56265.
    RefSeqi NP_116665.1. NM_001179975.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1VJV X-ray 1.74 A 97-499 [» ]
    ProteinModelPortali P43593.
    SMRi P43593. Positions 103-499.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31160. 361 interactions.
    DIPi DIP-6731N.
    IntActi P43593. 25 interactions.
    MINTi MINT-619095.
    STRINGi 4932.YFR010W.

    Protein family/group databases

    MEROPSi C19.079.

    Proteomic databases

    MaxQBi P43593.
    PaxDbi P43593.
    PeptideAtlasi P43593.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YFR010W ; YFR010W ; YFR010W .
    GeneIDi 850562.
    KEGGi sce:YFR010W.

    Organism-specific databases

    CYGDi YFR010w.
    SGDi S000001906. UBP6.

    Phylogenomic databases

    eggNOGi NOG286607.
    GeneTreei ENSGT00390000009615.
    HOGENOMi HOG000202292.
    KOi K11843.
    OMAi ELCTTEL.
    OrthoDBi EOG789CMF.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30463-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P43593.
    NextBioi 966361.
    PROi P43593.

    Gene expression databases

    Genevestigatori P43593.

    Family and domain databases

    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR000626. Ubiquitin-like.
    IPR029071. Ubiquitin-rel_dom.
    IPR028889. UCH/PAN2.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    [Graphical view ]
    SMARTi SM00213. UBQ. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54236. SSF54236. 1 hit.
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 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. "Purification and characterization of UBP6, a new ubiquitin-specific protease in Saccharomyces cerevisiae."
      Park K.C., Woo S.K., Yoo Y.J., Wyndham A.M., Baker R.T., Chung C.H.
      Arch. Biochem. Biophys. 347:78-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    4. "Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes."
      Layfield R., Franklin K., Landon M., Walker G., Wang P., Ramage R., Brown A., Love S., Urquhart K., Muir T., Baker R., Mayer R.J.
      Anal. Biochem. 274:40-49(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. "The Ubp6 family of deubiquitinating enzymes contains a ubiquitin-like domain: SUb."
      Wyndham A.M., Baker R.T., Chelvanayagam G.
      Protein Sci. 8:1268-1275(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: DOMAIN.
    6. "Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes."
      Verma R., Chen S., Feldman R., Schieltz D., Yates J., Dohmen J., Deshaies R.J.
      Mol. Biol. Cell 11:3425-3439(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: ASSOCIATION WITH THE 26S PROTEASOME, IDENTIFICATION BY MASS SPECTROMETRY.
    7. "Multiple associated proteins regulate proteasome structure and function."
      Leggett D.S., Hanna J., Borodovsky A., Crosas B., Schmidt M., Baker R.T., Walz T., Ploegh H., Finley D.
      Mol. Cell 10:495-507(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, ASSOCIATION WITH THE 26S PROTEASOME, FUNCTION, ENZYME REGULATION, DOMAIN.
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "Complementary roles for Rpn11 and Ubp6 in deubiquitination and proteolysis by the proteasome."
      Guterman A., Glickman M.H.
      J. Biol. Chem. 279:1729-1738(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    10. "Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation."
      Hanna J., Hathaway N.A., Tone Y., Crosas B., Elsasser S., Kirkpatrick D.S., Leggett D.S., Gygi S.P., King R.W., Finley D.
      Cell 127:99-111(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    11. "Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities."
      Crosas B., Hanna J., Kirkpatrick D.S., Zhang D.P., Tone Y., Hathaway N.A., Buecker C., Leggett D.S., Schmidt M., King R.W., Gygi S.P., Finley D.
      Cell 127:1401-1413(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    12. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-389, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    13. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-389 AND SER-470, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-389, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "Crystal structure of ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from saccharomyces cerevisiae at 1.74 a resolution."
      Joint center for structural genomics (JCSG)
      Submitted (JUL-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) OF 97-499.

    Entry informationi

    Entry nameiUBP6_YEAST
    AccessioniPrimary (citable) accession number: P43593
    Secondary accession number(s): D6VTP0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: October 1, 2014
    This is version 137 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 6770 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 VI
      Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names

    External Data

    Dasty 3