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P35127

- UBL1_YEAST

UniProt

P35127 - UBL1_YEAST

Protein

Ubiquitin carboxyl-terminal hydrolase YUH1

Gene

YUH1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 125 (01 Oct 2014)
      Sequence version 1 (01 Feb 1994)
      Previous versions | rss
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    Functioni

    Deubiquitinating enzyme (DUB) that controls levels of cellular ubiquitin through processing of ubiquitin precursors and ubiquitinated proteins. Thiol protease that recognizes and hydrolyzes a peptide bond at the C-terminal glycine of either ubiquitin or RUB1. Preferentially cleaves ubiquitin from peptides and small adducts.4 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).1 Publication

    pH dependencei

    Optimum pH is 8.5. Inactive at a pH below 6.5.1 Publication

    Temperature dependencei

    Optimum temperature is 27 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei84 – 841Transition state stabilizer
    Active sitei90 – 901NucleophilePROSITE-ProRule annotation
    Active sitei166 – 1661Proton donorPROSITE-ProRule annotation
    Sitei181 – 1811Important for enzyme activityBy similarity

    GO - Molecular functioni

    1. ubiquitin-specific protease activity Source: SGD

    GO - Biological processi

    1. ubiquitin-dependent protein catabolic process Source: InterPro
    2. ubiquitin homeostasis Source: SGD

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Ubl conjugation pathway

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31727-MONOMER.
    BRENDAi3.4.19.12. 984.

    Protein family/group databases

    MEROPSiC12.002.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase YUH1 (EC:3.4.19.12)
    Short name:
    UCH
    Alternative name(s):
    Ubiquitin thioesterase
    Gene namesi
    Name:YUH1
    Ordered Locus Names:YJR099W
    ORF Names:J1941
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome X

    Organism-specific databases

    CYGDiYJR099w.
    SGDiS000003860. YUH1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: SGD

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 236236Ubiquitin carboxyl-terminal hydrolase YUH1PRO_0000211073Add
    BLAST

    Proteomic databases

    MaxQBiP35127.
    PaxDbiP35127.

    Expressioni

    Gene expression databases

    GenevestigatoriP35127.

    Interactioni

    Protein-protein interaction databases

    BioGridi33854. 33 interactions.
    DIPiDIP-5052N.
    IntActiP35127. 1 interaction.
    MINTiMINT-488470.
    STRINGi4932.YJR099W.

    Structurei

    Secondary structure

    1
    236
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi15 – 2511
    Beta strandi31 – 366
    Helixi44 – 463
    Beta strandi54 – 607
    Helixi90 – 10011
    Helixi103 – 1053
    Helixi111 – 12212
    Beta strandi126 – 1294
    Helixi132 – 14312
    Helixi146 – 1505
    Beta strandi152 – 1543
    Beta strandi164 – 1729
    Beta strandi174 – 1807
    Beta strandi189 – 1935
    Helixi201 – 2033
    Helixi205 – 22117
    Beta strandi227 – 2337

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1CMXX-ray2.25A/C1-235[»]
    ProteinModelPortaliP35127.
    SMRiP35127. Positions 6-234.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP35127.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni10 – 156Interaction with ubiquitin
    Regioni149 – 1579Interaction with ubiquitin
    Regioni219 – 22810Interaction with ubiquitin

    Sequence similaritiesi

    Belongs to the peptidase C12 family.Curated

    Phylogenomic databases

    eggNOGiNOG327708.
    GeneTreeiENSGT00510000046640.
    HOGENOMiHOG000182400.
    KOiK05609.
    OMAiYMENANE.
    OrthoDBiEOG7PGF2F.

    Family and domain databases

    Gene3Di3.40.532.10. 1 hit.
    InterProiIPR001578. Peptidase_C12_UCH.
    [Graphical view]
    PANTHERiPTHR10589. PTHR10589. 1 hit.
    PfamiPF01088. Peptidase_C12. 1 hit.
    [Graphical view]
    PRINTSiPR00707. UBCTHYDRLASE.
    PROSITEiPS00140. UCH_1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P35127-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSGENRAVVP IESNPEVFTN FAHKLGLKNE WAYFDIYSLT EPELLAFLPR    50
    PVKAIVLLFP INEDRKSSTS QQITSSYDVI WFKQSVKNAC GLYAILHSLS 100
    NNQSLLEPGS DLDNFLKSQS DTSSSKNRFD DVTTDQFVLN VIKENVQTFS 150
    TGQSEAPEAT ADTNLHYITY VEENGGIFEL DGRNLSGPLY LGKSDPTATD 200
    LIEQELVRVR VASYMENANE EDVLNFAMLG LGPNWE 236
    Length:236
    Mass (Da):26,385
    Last modified:February 1, 1994 - v1
    Checksum:iD239FEE25798B395
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49599 Genomic DNA. Translation: CAA89629.1.
    BK006943 Genomic DNA. Translation: DAA08884.1.
    PIRiS51332.
    RefSeqiNP_012633.1. NM_001181757.1.

    Genome annotation databases

    EnsemblFungiiYJR099W; YJR099W; YJR099W.
    GeneIDi853562.
    KEGGisce:YJR099W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z49599 Genomic DNA. Translation: CAA89629.1 .
    BK006943 Genomic DNA. Translation: DAA08884.1 .
    PIRi S51332.
    RefSeqi NP_012633.1. NM_001181757.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1CMX X-ray 2.25 A/C 1-235 [» ]
    ProteinModelPortali P35127.
    SMRi P35127. Positions 6-234.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 33854. 33 interactions.
    DIPi DIP-5052N.
    IntActi P35127. 1 interaction.
    MINTi MINT-488470.
    STRINGi 4932.YJR099W.

    Protein family/group databases

    MEROPSi C12.002.

    Proteomic databases

    MaxQBi P35127.
    PaxDbi P35127.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YJR099W ; YJR099W ; YJR099W .
    GeneIDi 853562.
    KEGGi sce:YJR099W.

    Organism-specific databases

    CYGDi YJR099w.
    SGDi S000003860. YUH1.

    Phylogenomic databases

    eggNOGi NOG327708.
    GeneTreei ENSGT00510000046640.
    HOGENOMi HOG000182400.
    KOi K05609.
    OMAi YMENANE.
    OrthoDBi EOG7PGF2F.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-31727-MONOMER.
    BRENDAi 3.4.19.12. 984.

    Miscellaneous databases

    EvolutionaryTracei P35127.
    NextBioi 974317.
    PROi P35127.

    Gene expression databases

    Genevestigatori P35127.

    Family and domain databases

    Gene3Di 3.40.532.10. 1 hit.
    InterProi IPR001578. Peptidase_C12_UCH.
    [Graphical view ]
    PANTHERi PTHR10589. PTHR10589. 1 hit.
    Pfami PF01088. Peptidase_C12. 1 hit.
    [Graphical view ]
    PRINTSi PR00707. UBCTHYDRLASE.
    PROSITEi PS00140. UCH_1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and expression of a yeast ubiquitin-protein cleaving activity in Escherichia coli."
      Miller H.I., Henzel W.J., Ridgway J.B., Kuang W.-J., Chisholm V., Liu C.-C.
      Biotechnology (N.Y.) 7:698-704(1989)
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
      Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
      , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
      EMBO J. 15:2031-2049(1996) [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. "Purification of a ubiquitin protein peptidase from yeast with efficient in vitro assays."
      Liu C.C., Miller H.I., Kohr W.J., Silber J.I.
      J. Biol. Chem. 264:20331-20338(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. "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: CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
    6. "Rub1p processing by Yuh1p is required for wild-type levels of Rub1p conjugation to Cdc53p."
      Linghu B., Callis J., Goebl M.G.
      Eukaryot. Cell 1:491-494(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN RUB1 PROCESSING.
    7. "Characterization of ubiquitin C-terminal hydrolase 1 (YUH1) from Saccharomyces cerevisiae expressed in recombinant Escherichia coli."
      Yu H.A., Kim S.G., Kim E.J., Lee W.J., Kim D.O., Park K., Park Y.C., Seo J.H.
      Protein Expr. Purif. 56:20-26(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    8. "Mutant ubiquitin (UBB(+1)) associated with neurodegenerative disorders is hydrolyzed by ubiquitin C-terminal hydrolase L3 (UCH-L3)."
      Dennissen F.J., Kholod N., Hermes D.J., Kemmerling N., Steinbusch H.W., Dantuma N.P., van Leeuwen F.W.
      FEBS Lett. 585:2568-2574(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN UBB(+1) HYDROLYSIS.
    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 UBIQUITIN, ACTIVE SITE.

    Entry informationi

    Entry nameiUBL1_YEAST
    AccessioniPrimary (citable) accession number: P35127
    Secondary accession number(s): D6VWR8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1994
    Last sequence update: February 1, 1994
    Last modified: October 1, 2014
    This is version 125 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Can hydrolyze human UBB(+1), a mutated form of ubiquitin which is not effectively degraded by the proteasome and is associated with neurogenerative disorders. It can do so despite of the fact that the C-terminal 'Gly-76' of ubiquitin has been substituted for a tyrosine in UBB(+1).

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

    External Data

    Dasty 3