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E1BMF7

- UBP13_BOVIN

UniProt

E1BMF7 - UBP13_BOVIN

Protein

Ubiquitin carboxyl-terminal hydrolase 13

Gene

USP13

Organism
Bos taurus (Bovine)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 31 (01 Oct 2014)
      Sequence version 2 (16 Nov 2011)
      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 sitei345 – 3451NucleophilePROSITE-ProRule annotation
    Active sitei823 – 8231Proton acceptorPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri209 – 28173UBP-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
    OrganismiBos taurus (Bovine)
    Taxonomic identifieri9913 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
    ProteomesiUP000009136: Chromosome 1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 863863Ubiquitin carboxyl-terminal hydrolase 13PRO_0000418010Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei114 – 1141PhosphoserineBy similarity
    Modified residuei122 – 1221PhosphothreonineBy similarity

    Keywords - PTMi

    Phosphoprotein

    Interactioni

    Subunit structurei

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

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini336 – 861526USPAdd
    BLAST
    Domaini652 – 69342UBA 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini727 – 76741UBA 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 fingeri209 – 28173UBP-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.
    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.

    E1BMF7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQRRGALFGM PGGSGSRKMA AGDIGELLVP HMPTIRVPRS GDRVYKNECA    50
    FSYDSPNSEG GLYVCMNTFL AFGREHVERH FRKTGQSVYM HLKRHVREKV 100
    RGASGGALPK RRNSKMFLDL DTDDDLNSDD YEYEDEAKLV IFPDHYEIAL 150
    PNIEELPALV TIACDAVLSS KSPYRKQDPD TWENELPVSK YANNLTQLDN 200
    GVRIPPSGWK CARCDLRENL WLNLTDGSVL CGKWFFDSSG GNGHALEHYR 250
    DTGYPLAVKL GTITPDGADV YSFQEEEAVL DPHLAKHLAH FGIDMLHMHG 300
    TENGLQDNDI KPRVSEWEVI QETGTKLKPM YGPGYTGLKN LGNSCYLSSV 350
    MQAIFSIPEF QRAYVGNLPR IFDYSPLDPT QDFNTQMTKL GHGLLSGQYS 400
    KPPVKSELIE QVMKEEHKPQ QNGISPRMFK AFVSKSHPEF SSNRQQDAQE 450
    FFLHLVNLVE RNRIGSENPS DVFRFLVEER IQCCQTRKVR YTERVDYLMQ 500
    LPVAMEAATN KDELIAYELT RREAESNRRP LPELVRAKIP FSACLQAFSE 550
    PENVDDFWSS ALQAKSAGVK TSRFASFPEY LVVQIKKFTF GLDWVPKKFD 600
    VSVDMPDLLD INHLRARGLQ PGEEELPDIS PPIVIPDDSK DRLMTQLIDP 650
    SDIDESSVMQ LAEMGFPLEA CRKAVYFTGN MGAEVAFNWI VVHMEEPDFA 700
    EPLTMPGYGG AASAGASVFG ATGLDNQPPE ETVAIITSMG FHRNQAIQAL 750
    RATNSNLERA LDWIFSHPEF EEDSDFVIEM ENNANANIVS EAKPEGPRVK 800
    DGSGMYELFA FISHMGTSTM SGHYVCHIKK EGRWVIYNDH KVCASERPPK 850
    DLGYMYFYRR IPS 863
    Length:863
    Mass (Da):97,278
    Last modified:November 16, 2011 - v2
    Checksum:i04357616964550B5
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    DAAA02001954 Genomic DNA. No translation available.
    DAAA02001955 Genomic DNA. No translation available.
    DAAA02001956 Genomic DNA. No translation available.
    DAAA02001957 Genomic DNA. No translation available.
    DAAA02001958 Genomic DNA. No translation available.
    RefSeqiNP_001178195.1. NM_001191266.1.
    UniGeneiBt.74584.

    Genome annotation databases

    EnsembliENSBTAT00000061390; ENSBTAP00000053221; ENSBTAG00000005946.
    GeneIDi100141289.
    KEGGibta:100141289.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    DAAA02001954 Genomic DNA. No translation available.
    DAAA02001955 Genomic DNA. No translation available.
    DAAA02001956 Genomic DNA. No translation available.
    DAAA02001957 Genomic DNA. No translation available.
    DAAA02001958 Genomic DNA. No translation available.
    RefSeqi NP_001178195.1. NM_001191266.1.
    UniGenei Bt.74584.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSBTAT00000061390 ; ENSBTAP00000053221 ; ENSBTAG00000005946 .
    GeneIDi 100141289.
    KEGGi bta:100141289.

    Organism-specific databases

    CTDi 8975.

    Phylogenomic databases

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

    Miscellaneous databases

    NextBioi 20791338.

    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: Hereford.

    Entry informationi

    Entry nameiUBP13_BOVIN
    AccessioniPrimary (citable) accession number: E1BMF7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 13, 2012
    Last sequence update: November 16, 2011
    Last modified: October 1, 2014
    This is version 31 of the entry and version 2 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