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F1QFS9

- UBP13_DANRE

UniProt

F1QFS9 - UBP13_DANRE

Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

usp13

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 27 (01 Oct 2014)
      Sequence version 1 (03 May 2011)
      Previous versions | rss
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    Functioni

    Deubiquitinase that mediates deubiquitination of target proteins and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD).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.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei327 – 3271NucleophilePROSITE-ProRule annotation
    Active sitei819 – 8191Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri190 – 26273UBP-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

    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
    ORF Names:wu:fc61g08
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Chromosome 6

    Organism-specific databases

    ZFINiZDB-GENE-080724-7. usp13.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 860860Ubiquitin carboxyl-terminal hydrolase 13PRO_0000418013Add
    BLAST

    Expressioni

    Gene expression databases

    BgeeiF1QFS9.

    Interactioni

    Protein-protein interaction databases

    STRINGi7955.ENSDARP00000095070.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini318 – 857540USPAdd
    BLAST
    Domaini635 – 67642UBA 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini710 – 75041UBA 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 fingeri190 – 26273UBP-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    GeneTreeiENSGT00390000000874.
    KOiK11836.
    OMAiPRMFKAF.
    OrthoDBiEOG7CNZF3.
    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.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    F1QFS9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MATDLGELLV PYMPTIRVPR TGDRVFKSEC AFSYDSPESE GGLYVCMNSF    50
    LGFGREHVER HYRKTGQSVY MHLKRHVKEK ATGAAGGAIP RRRNGKVFLD 100
    LELNRDFNGD DYEYEDEAKL VIFPDHYEIP LPNIEELPAL VTIACDAVLN 150
    APSPYKKQES DSWEEEIQVS RHARSLRQLD NGVRIPPSGW KCAKCEMREN 200
    LWLNLTDGSV LCGKWFFDGS GGNGHALEHY RESNFPLAVK LNTITPDGAD 250
    IYSFDEEEAV LDPHISEHLL HFGIDMLQMQ RTENGHHTDN HVQPRISDWE 300
    VIQEAGLKLK PVYGSGYTGI KNLGNSCYLS TTMQVLFSIP EFQRAYAGNL 350
    QRIFDYSPLD PTQDFNTQMA KLGHGLLSGQ YSKPPMKSEL IEQVMKEEHK 400
    QQQQRGISPK MFKALVSKGH PEFSSNRQQD AHEFLLHLIN LVERNNSGSE 450
    NPSDVFRFIV EERTQCCQSQ KVRYTQRVDY LMQLPVPLEA ASNREELIAY 500
    EGKRKEAEEN MRPLPEVVRA RVPFTACLQA FTEPENVPDF WSSALQAKSA 550
    GVKTSRFATF PEYMIVQLKK FTFGVDWVPK KLDMSVDVPD FLDLNRLRAT 600
    GLQAGEEELP DLTPPIVIPE DTRDSSTNNS LESPEIDESS VMQLAEMGFP 650
    LEACRKAVYY TGNMGAEMAF NWIIAHMEEP DFAEPLAVPT YMESDLPSPS 700
    LPTTSALDNQ PPEESISILT SMGFPRHHTI QALKASNNNL ERALDWIFTH 750
    PDCEDESEAM SDTADTEPND NSFSNANAHT DSSLSPDQDL SSPRVRDGPG 800
    RYELFAFISH MGTSTMSGHY VCHIKKEGRW LIYNDHKVCL SERPPKDLGY 850
    MYFYRRLSSC 860
    Length:860
    Mass (Da):97,452
    Last modified:May 3, 2011 - v1
    Checksum:i456C6827F7D0DCC1
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti731 – 7311Q → R in AAI41801. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL928701 Genomic DNA. No translation available.
    CU459215 Genomic DNA. No translation available.
    BC141800 mRNA. Translation: AAI41801.1.
    RefSeqiNP_001091856.1. NM_001098386.1.
    UniGeneiDr.115281.

    Genome annotation databases

    EnsembliENSDART00000065293; ENSDARP00000065292; ENSDARG00000079198.
    GeneIDi558011.
    KEGGidre:558011.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL928701 Genomic DNA. No translation available.
    CU459215 Genomic DNA. No translation available.
    BC141800 mRNA. Translation: AAI41801.1 .
    RefSeqi NP_001091856.1. NM_001098386.1.
    UniGenei Dr.115281.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 7955.ENSDARP00000095070.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSDART00000065293 ; ENSDARP00000065292 ; ENSDARG00000079198 .
    GeneIDi 558011.
    KEGGi dre:558011.

    Organism-specific databases

    CTDi 8975.
    ZFINi ZDB-GENE-080724-7. usp13.

    Phylogenomic databases

    GeneTreei ENSGT00390000000874.
    KOi K11836.
    OMAi PRMFKAF.
    OrthoDBi EOG7CNZF3.
    TreeFami TF300576.

    Miscellaneous databases

    NextBioi 20882266.

    Gene expression databases

    Bgeei F1QFS9.

    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.
    PS00973. USP_2. 1 hit.
    PS50235. USP_3. 1 hit.
    PS50271. ZF_UBP. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The zebrafish reference genome sequence and its relationship to the human genome."
      Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
      , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
      Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Tuebingen.
    2. NIH - Zebrafish Gene Collection (ZGC) project
      Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Embryo.

    Entry informationi

    Entry nameiUBP13_DANRE
    AccessioniPrimary (citable) accession number: F1QFS9
    Secondary accession number(s): A5D8T1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 13, 2012
    Last sequence update: May 3, 2011
    Last modified: October 1, 2014
    This is version 27 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. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3