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Q5BKP2

- UBP13_MOUSE

UniProt

Q5BKP2 - UBP13_MOUSE

Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

Usp13

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 85 (01 Oct 2014)
      Sequence version 1 (12 Apr 2005)
      Previous versions | rss
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    Functioni

    Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data By similarity.By similarity

    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

    Specifically inhibited by spautin-1 (specific and potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13 and inhibits deubiquitinase activity. Regulated by PIK3C3/VPS34-containing complexes. The weak deubiquitinase activity in vitro suggests the existence of some mechanism that activates the enzyme By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei343 – 3431NucleophilePROSITE-ProRule annotation
    Active sitei818 – 8181Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri207 – 27973UBP-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. cysteine-type endopeptidase activity Source: UniProtKB
    2. omega peptidase activity Source: InterPro
    3. ubiquitin binding Source: UniProtKB
    4. ubiquitin-specific protease activity Source: UniProtKB
    5. ubiquitin thiolesterase activity Source: UniProtKB
    6. zinc ion binding Source: InterPro

    GO - Biological processi

    1. autophagy Source: UniProtKB-KW
    2. cell proliferation Source: UniProtKB
    3. protein K63-linked deubiquitination Source: UniProtKB
    4. protein stabilization Source: UniProtKB
    5. regulation of autophagy Source: UniProtKB
    6. regulation of transcription, DNA-templated Source: UniProtKB
    7. ubiquitin-dependent protein catabolic process Source: InterPro

    Keywords - Molecular functioni

    Hydrolase, Protease, Thiol protease

    Keywords - Biological processi

    Autophagy, Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Protein family/group databases

    MEROPSiC19.012.

    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:Usp13
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 3

    Organism-specific databases

    MGIiMGI:1919857. Usp13.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 858858Ubiquitin carboxyl-terminal hydrolase 13PRO_0000418011Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei112 – 1121PhosphoserineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ5BKP2.
    PRIDEiQ5BKP2.

    PTM databases

    PhosphoSiteiQ5BKP2.

    Expressioni

    Gene expression databases

    ArrayExpressiQ5BKP2.
    BgeeiQ5BKP2.
    GenevestigatoriQ5BKP2.

    Interactioni

    Subunit structurei

    Interacts with UFD1. Interacts (via UBA domains) with SIAH2 (when ubiquitinated) By similarity.By similarity

    Protein-protein interaction databases

    STRINGi10090.ENSMUSP00000072155.

    Structurei

    3D structure databases

    ProteinModelPortaliQ5BKP2.
    SMRiQ5BKP2. Positions 24-858.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini334 – 856523USPAdd
    BLAST
    Domaini650 – 69142UBA 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini722 – 76241UBA 2PROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The UBP-type zinc finger has lost its ability to bind ubiquitin and USP13 is not activated by unanchored ubiquitin.By similarity
    The UBA domains mediate binding to ubiquitin.By similarity

    Sequence similaritiesi

    Belongs to the peptidase C19 family.Curated
    Contains 2 UBA domains.PROSITE-ProRule annotation
    Contains 1 UBP-type zinc finger.PROSITE-ProRule annotation
    Contains 1 USP domain.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri207 – 27973UBP-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5207.
    GeneTreeiENSGT00390000000874.
    HOGENOMiHOG000162311.
    HOVERGENiHBG002833.
    InParanoidiQ5BKP2.
    KOiK11836.
    OMAiPRMFKAF.
    OrthoDBiEOG7CNZF3.
    PhylomeDBiQ5BKP2.
    TreeFamiTF300576.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR009060. UBA-like.
    IPR015940. UBA/transl_elong_EF1B_N_euk.
    IPR000449. UBA/Ts_N.
    IPR016652. Ubiquitinyl_hydrolase.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view]
    PfamiPF00627. UBA. 2 hits.
    PF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view]
    PIRSFiPIRSF016308. UBP. 1 hit.
    SMARTiSM00165. UBA. 2 hits.
    SM00290. ZnF_UBP. 1 hit.
    [Graphical view]
    SUPFAMiSSF46934. SSF46934. 1 hit.
    PROSITEiPS50030. UBA. 2 hits.
    PS00972. 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.

    Q5BKP2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQRRGALFSV PGGGGKMAAG DLGELLVPHM PTIRVPRSGD RVYKNECAFS    50
    YDSPNSEGGL YVCMNTFLAF GREHVERHFR KTGQSVYMHL KRHMREKVRG 100
    ASGGALPKRR NSKIFLDLDM DDDLNSDDYE YEDEAKLVIF PDHYEIALPN 150
    IEELPALVTI ACDAVLSSKS PYRKQDPDTW ENEVPVSKYA NNLVQLDNGV 200
    RIPPSGWKCA RCDLRENLWL NLTDGSVLCG KWFFDSSGGN GHALEHYRDM 250
    GYPLAVKLGT ITPDGADVYS FQEEGPVSDP HLAKHLAHFG IDMLHTQGTE 300
    NGLRDNDIKP RVSEWEVIQE SGTKLKPMYG PGYTGLKNLG NSCYLSSVMQ 350
    AIFSIPEFQR AYVGNLPRIF DYSPLDPTQD FNTQMTKLGH GLLSGQYSKP 400
    PVKSELIEQV MKEEHKPQQN GISPRMFKAF VSKSHPEFSS NRQQDAQEFF 450
    LHLVNLVERN RIGSENPSDV FRFLVEERIQ CCQTRKVRYT ERVDYLMQLP 500
    VAMEAATNKD ELITYELMRR EAEANRRPLP ELVRAKIPFS ACLQAFAEPD 550
    NVDDFWSSAL QAKSAGVKTS RFASFPEYLV VQIKKFTFGL DWVPRKFDVS 600
    IDMPDLLDIS HLRARGLQPG EEELPDISPP IVIPDDSKDR LMNQLIDPSD 650
    IDESSVMQLA EMGFPLEACR KAVYFTGNTG AEVAFNWIIV HMEEPDFAEP 700
    LAIPGYGGAG ASVFGATGLD NQPPEEIVAI ITSMGFQRNQ AVQALQATNH 750
    NLERALDWIF SHPEFEEDSD FVIEMENNAN ANIVSEAKPE GPRVKDGSGM 800
    YELFAFISHM GTSTMSGHYV CHIKKEGRWV IYNDHKVCAS ERPPKDLGYM 850
    YFYRRIPS 858
    Length:858
    Mass (Da):96,723
    Last modified:April 12, 2005 - v1
    Checksum:i04989BACB784192C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC111140 Genomic DNA. No translation available.
    CH466530 Genomic DNA. Translation: EDL35015.1.
    BC090999 mRNA. Translation: AAH90999.1.
    CCDSiCCDS17301.1.
    RefSeqiNP_001013042.1. NM_001013024.2.
    UniGeneiMm.316153.

    Genome annotation databases

    EnsembliENSMUST00000072312; ENSMUSP00000072155; ENSMUSG00000056900.
    GeneIDi72607.
    KEGGimmu:72607.
    UCSCiuc008owr.1. mouse.
    uc008ows.1. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AC111140 Genomic DNA. No translation available.
    CH466530 Genomic DNA. Translation: EDL35015.1 .
    BC090999 mRNA. Translation: AAH90999.1 .
    CCDSi CCDS17301.1.
    RefSeqi NP_001013042.1. NM_001013024.2.
    UniGenei Mm.316153.

    3D structure databases

    ProteinModelPortali Q5BKP2.
    SMRi Q5BKP2. Positions 24-858.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10090.ENSMUSP00000072155.

    Protein family/group databases

    MEROPSi C19.012.

    PTM databases

    PhosphoSitei Q5BKP2.

    Proteomic databases

    PaxDbi Q5BKP2.
    PRIDEi Q5BKP2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000072312 ; ENSMUSP00000072155 ; ENSMUSG00000056900 .
    GeneIDi 72607.
    KEGGi mmu:72607.
    UCSCi uc008owr.1. mouse.
    uc008ows.1. mouse.

    Organism-specific databases

    CTDi 8975.
    MGIi MGI:1919857. Usp13.

    Phylogenomic databases

    eggNOGi COG5207.
    GeneTreei ENSGT00390000000874.
    HOGENOMi HOG000162311.
    HOVERGENi HBG002833.
    InParanoidi Q5BKP2.
    KOi K11836.
    OMAi PRMFKAF.
    OrthoDBi EOG7CNZF3.
    PhylomeDBi Q5BKP2.
    TreeFami TF300576.

    Miscellaneous databases

    NextBioi 336585.
    PROi Q5BKP2.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q5BKP2.
    Bgeei Q5BKP2.
    Genevestigatori Q5BKP2.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR018200. Pept_C19ubi-hydrolase_C_CS.
    IPR001394. Peptidase_C19_UCH.
    IPR009060. UBA-like.
    IPR015940. UBA/transl_elong_EF1B_N_euk.
    IPR000449. UBA/Ts_N.
    IPR016652. Ubiquitinyl_hydrolase.
    IPR028889. UCH/PAN2.
    IPR013083. Znf_RING/FYVE/PHD.
    IPR001607. Znf_UBP.
    [Graphical view ]
    Pfami PF00627. UBA. 2 hits.
    PF00443. UCH. 1 hit.
    PF02148. zf-UBP. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF016308. UBP. 1 hit.
    SMARTi SM00165. UBA. 2 hits.
    SM00290. ZnF_UBP. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46934. SSF46934. 1 hit.
    PROSITEi PS50030. UBA. 2 hits.
    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: C57BL/6J.
    2. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
      Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Heart.

    Entry informationi

    Entry nameiUBP13_MOUSE
    AccessioniPrimary (citable) accession number: Q5BKP2
    Secondary accession number(s): D3YYG7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 13, 2012
    Last sequence update: April 12, 2005
    Last modified: October 1, 2014
    This is version 85 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3