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P38187

- UBP13_YEAST

UniProt

P38187 - UBP13_YEAST

Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

UBP13

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 116 (01 Oct 2014)
      Sequence version 3 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    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 sitei149 – 1491NucleophilePROSITE-ProRule annotation
    Active sitei619 – 6191Proton acceptorPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ubiquitin-specific protease activity Source: SGD

    GO - Biological processi

    1. free ubiquitin chain depolymerization Source: SGD
    2. 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-28963-MONOMER.

    Protein family/group databases

    MEROPSiC19.100.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 13 (EC:3.4.19.12)
    Alternative name(s):
    Deubiquitinating enzyme 13
    Ubiquitin thioesterase 13
    Ubiquitin-specific-processing protease 13
    Gene namesi
    Name:UBP13
    Ordered Locus Names:YBL067C
    ORF Names:YBL0621
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome II

    Organism-specific databases

    CYGDiYBL067c.
    SGDiS000000163. UBP13.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 747747Ubiquitin carboxyl-terminal hydrolase 13PRO_0000080598Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei198 – 1981Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP38187.
    PaxDbiP38187.

    Expressioni

    Gene expression databases

    GenevestigatoriP38187.

    Interactioni

    Protein-protein interaction databases

    BioGridi32633. 103 interactions.
    DIPiDIP-795N.
    IntActiP38187. 2 interactions.
    MINTiMINT-2783268.
    STRINGi4932.YBL067C.

    Structurei

    3D structure databases

    ProteinModelPortaliP38187.
    SMRiP38187. Positions 431-665.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini140 – 668529USPAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase C19 family.Curated
    Contains 1 USP domain.Curated

    Phylogenomic databases

    eggNOGiCOG5077.
    GeneTreeiENSGT00650000093027.
    HOGENOMiHOG000141813.
    KOiK11872.
    OMAiHESTARP.
    OrthoDBiEOG7TF7JV.

    Family and domain databases

    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [Graphical view]
    PfamiPF00443. UCH. 1 hit.
    [Graphical view]
    PROSITEiPS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P38187-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIRRWLTISK SGKKKKAVND TITEEVEKVD FKPVNHDIND ELCYSESSDN    50
    PSSSLFVSNL DTKETFLNED NNLQISSGLD YSSETCNQGS NYSQDGIFYI 100
    SNAKAINAYG GIITQGPEAP ILAMKVSDSM PYGDGSNKVF GYENFGNTCY 150
    CNSVLQCLYN LSSLRENILQ FPKKSRESDQ PRKKEMRGKK PRIFTEASFE 200
    KSIAGTNGHL PNPKPQSVDD GKPTPVNSVN SNTAGPSEKK SKFFKSFSAK 250
    HVQDNNKKEG SPAILTTGKP SSRPQDAPPL IVETPNEPGA PSRLSFENVT 300
    DRPPDVPRKI IVGRVLNYEN PSRGSSNSNN LDLKGESNSS LSTPLDKKDT 350
    RRSSSSSQIS PEHRKKSALI RGPVLNIDHS LNGSDKATLY SSLRDIFECI 400
    TENTYLTGVV SPSSFVDVLK RENVLFNTTM HQDAHEFFNF LLNELSEYIE 450
    RENKKIAASD INSDSEPSKS KNFISDLFQG TLTNQIKCLT CDNITSRDEP 500
    FLDFPIEVQG DEETDIQEIL KSYHQREMLN GSNKFYCDEC CGLQEAERLV 550
    GLKQLPDTLT LHLKRFKYSE KQNCNIKLFN NIHYPLTLNV CSSINSKVCQ 600
    KYELAGIVVH MGGGPQHGHY VSLCKHEKFG WLLFDDETVE AVKEETVLEF 650
    TGESPNMATA YVLFYKAMYS NAVEKNDREN MAKEQDDNID NLIKYDDWLR 700
    TCNSGQKKKE ELPIADDLDT AIDDSFVSNT PIKSSKKKSR MFSFRKS 747
    Length:747
    Mass (Da):83,856
    Last modified:July 27, 2011 - v3
    Checksum:i817DE2F89ED8EEA4
    GO

    Sequence cautioni

    The sequence CAA84887.1 differs from that shown. Reason: Frameshift at position 663.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti180 – 1801Q → H in CAA84887. (PubMed:7813418)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z35828 Genomic DNA. Translation: CAA84887.1. Frameshift.
    BK006936 Genomic DNA. Translation: DAA07054.2.
    PIRiS45803.
    RefSeqiNP_009486.3. NM_001178307.2.

    Genome annotation databases

    EnsemblFungiiYBL067C; YBL067C; YBL067C.
    GeneIDi852212.
    KEGGisce:YBL067C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z35828 Genomic DNA. Translation: CAA84887.1 . Frameshift.
    BK006936 Genomic DNA. Translation: DAA07054.2 .
    PIRi S45803.
    RefSeqi NP_009486.3. NM_001178307.2.

    3D structure databases

    ProteinModelPortali P38187.
    SMRi P38187. Positions 431-665.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32633. 103 interactions.
    DIPi DIP-795N.
    IntActi P38187. 2 interactions.
    MINTi MINT-2783268.
    STRINGi 4932.YBL067C.

    Protein family/group databases

    MEROPSi C19.100.

    Proteomic databases

    MaxQBi P38187.
    PaxDbi P38187.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YBL067C ; YBL067C ; YBL067C .
    GeneIDi 852212.
    KEGGi sce:YBL067C.

    Organism-specific databases

    CYGDi YBL067c.
    SGDi S000000163. UBP13.

    Phylogenomic databases

    eggNOGi COG5077.
    GeneTreei ENSGT00650000093027.
    HOGENOMi HOG000141813.
    KOi K11872.
    OMAi HESTARP.
    OrthoDBi EOG7TF7JV.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-28963-MONOMER.

    Miscellaneous databases

    NextBioi 970718.

    Gene expression databases

    Genevestigatori P38187.

    Family and domain databases

    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR028889. UCH/PAN2.
    [Graphical view ]
    Pfami PF00443. UCH. 1 hit.
    [Graphical view ]
    PROSITEi PS00972. USP_1. 1 hit.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Complete DNA sequence of yeast chromosome II."
      Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C.
      , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K.
      EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 180.
      Strain: ATCC 204508 / S288c.
    3. "Sequencing and comparison of yeast species to identify genes and regulatory elements."
      Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.
      Nature 423:241-254(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF FRAMESHIFT.
    4. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    5. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-198, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    6. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiUBP13_YEAST
    AccessioniPrimary (citable) accession number: P38187
    Secondary accession number(s): D6VPT4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 116 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 125 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    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 II
      Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

    External Data

    Dasty 3