UBP13_BOVIN
ID UBP13_BOVIN Reviewed; 863 AA.
AC E1BMF7;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 2.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 13;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 13;
DE AltName: Full=Ubiquitin thioesterase 13;
DE AltName: Full=Ubiquitin-specific-processing protease 13;
GN Name=USP13;
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Hereford;
RX PubMed=19393038; DOI=10.1186/gb-2009-10-4-r42;
RA Zimin A.V., Delcher A.L., Florea L., Kelley D.R., Schatz M.C., Puiu D.,
RA Hanrahan F., Pertea G., Van Tassell C.P., Sonstegard T.S., Marcais G.,
RA Roberts M., Subramanian P., Yorke J.A., Salzberg S.L.;
RT "A whole-genome assembly of the domestic cow, Bos taurus.";
RL Genome Biol. 10:R42.01-R42.10(2009).
CC -!- FUNCTION: Deubiquitinase that mediates deubiquitination of target
CC proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various
CC processes such as autophagy and endoplasmic reticulum-associated
CC degradation (ERAD). Component of a regulatory loop that controls
CC autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a
CC key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-
CC containing complexes. Also deubiquitinates USP10, an essential
CC regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing
CC complexes regulate USP13 stability, suggesting the existence of a
CC regulatory system by which PIK3C3/VPS34-containing complexes regulate
CC p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1
CC and mediates deubiquitination of SKP2, thereby regulating endoplasmic
CC reticulum-associated degradation (ERAD). Also regulates ERAD through
CC the deubiquitination of UBL4A a component of the BAG6/BAT3 complex.
CC Mediates stabilization of SIAH2 independently of deubiquitinase
CC activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2
CC autoubiquitination. Has a weak deubiquitinase activity in vitro and
CC preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In
CC contrast to USP5, it is not able to mediate unanchored polyubiquitin
CC disassembly. Able to cleave ISG15 in vitro; however, additional
CC experiments are required to confirm such data.
CC {ECO:0000250|UniProtKB:Q92995}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide
CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-
CC residue protein attached to proteins as an intracellular targeting
CC signal).; EC=3.4.19.12;
CC -!- ACTIVITY REGULATION: Specifically inhibited by spautin-1 (specific and
CC potent autophagy inhibitor-1), a derivative of MBCQ that binds to USP13
CC and inhibits deubiquitinase activity. Regulated by PIK3C3/VPS34-
CC containing complexes. The weak deubiquitinase activity in vitro
CC suggests the existence of some mechanism that activates the enzyme (By
CC similarity). {ECO:0000250}.
CC -!- SUBUNIT: Interacts with UFD1. Interacts (via UBA domains) with SIAH2
CC (when ubiquitinated). Interacts with BAG6; the interaction is direct
CC and may mediate UBL4A deubiquitination. Interacts (via UBA 2 domain)
CC with AMFR; the interaction is direct. Interacts with UBL4A; may be
CC indirect via BAG6. {ECO:0000250|UniProtKB:Q92995}.
CC -!- DOMAIN: The UBP-type zinc finger has lost its ability to bind ubiquitin
CC and USP13 is not activated by unanchored ubiquitin. {ECO:0000250}.
CC -!- DOMAIN: The UBA domains mediate binding to ubiquitin. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; DAAA02001954; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02001955; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02001956; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02001957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02001958; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001178195.1; NM_001191266.1.
DR AlphaFoldDB; E1BMF7; -.
DR BMRB; E1BMF7; -.
DR SMR; E1BMF7; -.
DR STRING; 9913.ENSBTAP00000053221; -.
DR MEROPS; C19.012; -.
DR PaxDb; E1BMF7; -.
DR PRIDE; E1BMF7; -.
DR Ensembl; ENSBTAT00000061390; ENSBTAP00000053221; ENSBTAG00000005946.
DR GeneID; 100141289; -.
DR KEGG; bta:100141289; -.
DR CTD; 8975; -.
DR VEuPathDB; HostDB:ENSBTAG00000005946; -.
DR VGNC; VGNC:52841; USP13.
DR eggNOG; KOG0944; Eukaryota.
DR GeneTree; ENSGT00940000157401; -.
DR HOGENOM; CLU_009884_1_0_1; -.
DR InParanoid; E1BMF7; -.
DR OMA; TMDMENN; -.
DR OrthoDB; 556111at2759; -.
DR TreeFam; TF300576; -.
DR Reactome; R-BTA-5689880; Ub-specific processing proteases.
DR Proteomes; UP000009136; Chromosome 1.
DR Bgee; ENSBTAG00000005946; Expressed in gluteal muscle and 94 other tissues.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:1904288; F:BAT3 complex binding; IEA:Ensembl.
DR GO; GO:0051087; F:chaperone binding; IEA:Ensembl.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISS:UniProtKB.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; ISS:UniProtKB.
DR GO; GO:1990380; F:Lys48-specific deubiquitinase activity; IEA:Ensembl.
DR GO; GO:0070628; F:proteasome binding; IEA:Ensembl.
DR GO; GO:0043130; F:ubiquitin binding; ISS:UniProtKB.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; IEA:Ensembl.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006914; P:autophagy; IEA:UniProtKB-KW.
DR GO; GO:0008283; P:cell population proliferation; ISS:UniProtKB.
DR GO; GO:1904378; P:maintenance of unfolded protein involved in ERAD pathway; IEA:Ensembl.
DR GO; GO:1904294; P:positive regulation of ERAD pathway; IEA:Ensembl.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0035523; P:protein K29-linked deubiquitination; IEA:Ensembl.
DR GO; GO:0044313; P:protein K6-linked deubiquitination; IEA:Ensembl.
DR GO; GO:0070536; P:protein K63-linked deubiquitination; ISS:UniProtKB.
DR GO; GO:0050821; P:protein stabilization; ISS:UniProtKB.
DR GO; GO:0010506; P:regulation of autophagy; ISS:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR016652; Ubiquitinyl_hydrolase.
DR InterPro; IPR041432; UBP13_Znf-UBP_var.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR InterPro; IPR001607; Znf_UBP.
DR Pfam; PF00627; UBA; 2.
DR Pfam; PF00443; UCH; 1.
DR Pfam; PF02148; zf-UBP; 1.
DR Pfam; PF17807; zf-UBP_var; 1.
DR PIRSF; PIRSF016308; UBP; 1.
DR SMART; SM00165; UBA; 2.
DR SMART; SM00290; ZnF_UBP; 1.
DR SUPFAM; SSF46934; SSF46934; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50030; UBA; 2.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS50271; ZF_UBP; 1.
PE 3: Inferred from homology;
KW Autophagy; Hydrolase; Isopeptide bond; Metal-binding; Phosphoprotein;
KW Protease; Reference proteome; Repeat; Thiol protease; Ubl conjugation;
KW Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..863
FT /note="Ubiquitin carboxyl-terminal hydrolase 13"
FT /id="PRO_0000418010"
FT DOMAIN 336..861
FT /note="USP"
FT DOMAIN 652..693
FT /note="UBA 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 727..767
FT /note="UBA 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT ZN_FING 187..295
FT /note="UBP-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT ACT_SITE 345
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 823
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT BINDING 211
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 214
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 231
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 244
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT MOD_RES 114
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q92995"
FT MOD_RES 122
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q92995"
FT CROSSLNK 311
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q92995"
FT CROSSLNK 405
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:Q92995"
SQ SEQUENCE 863 AA; 97278 MW; 04357616964550B5 CRC64;
MQRRGALFGM PGGSGSRKMA AGDIGELLVP HMPTIRVPRS GDRVYKNECA FSYDSPNSEG
GLYVCMNTFL AFGREHVERH FRKTGQSVYM HLKRHVREKV RGASGGALPK RRNSKMFLDL
DTDDDLNSDD YEYEDEAKLV IFPDHYEIAL PNIEELPALV TIACDAVLSS KSPYRKQDPD
TWENELPVSK YANNLTQLDN GVRIPPSGWK CARCDLRENL WLNLTDGSVL CGKWFFDSSG
GNGHALEHYR DTGYPLAVKL GTITPDGADV YSFQEEEAVL DPHLAKHLAH FGIDMLHMHG
TENGLQDNDI KPRVSEWEVI QETGTKLKPM YGPGYTGLKN LGNSCYLSSV MQAIFSIPEF
QRAYVGNLPR IFDYSPLDPT QDFNTQMTKL GHGLLSGQYS KPPVKSELIE QVMKEEHKPQ
QNGISPRMFK AFVSKSHPEF SSNRQQDAQE FFLHLVNLVE RNRIGSENPS DVFRFLVEER
IQCCQTRKVR YTERVDYLMQ LPVAMEAATN KDELIAYELT RREAESNRRP LPELVRAKIP
FSACLQAFSE PENVDDFWSS ALQAKSAGVK TSRFASFPEY LVVQIKKFTF GLDWVPKKFD
VSVDMPDLLD INHLRARGLQ PGEEELPDIS PPIVIPDDSK DRLMTQLIDP SDIDESSVMQ
LAEMGFPLEA CRKAVYFTGN MGAEVAFNWI VVHMEEPDFA EPLTMPGYGG AASAGASVFG
ATGLDNQPPE ETVAIITSMG FHRNQAIQAL RATNSNLERA LDWIFSHPEF EEDSDFVIEM
ENNANANIVS EAKPEGPRVK DGSGMYELFA FISHMGTSTM SGHYVCHIKK EGRWVIYNDH
KVCASERPPK DLGYMYFYRR IPS
