UBP13_DANRE
ID UBP13_DANRE Reviewed; 860 AA.
AC F1QFS9; A5D8T1;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 70.
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; ORFNames=wu:fc61g08;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Deubiquitinase that mediates deubiquitination of target
CC proteins and is involved in various processes such as autophagy and
CC endoplasmic reticulum-associated degradation (ERAD).
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. {ECO:0000250}.
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL928701; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CU459215; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC141800; AAI41801.1; -; mRNA.
DR RefSeq; NP_001091856.1; NM_001098386.1.
DR AlphaFoldDB; F1QFS9; -.
DR SMR; F1QFS9; -.
DR BioGRID; 284243; 1.
DR STRING; 7955.ENSDARP00000065292; -.
DR MEROPS; C19.012; -.
DR PaxDb; F1QFS9; -.
DR Ensembl; ENSDART00000065293; ENSDARP00000065292; ENSDARG00000079198.
DR GeneID; 558011; -.
DR KEGG; dre:558011; -.
DR CTD; 8975; -.
DR ZFIN; ZDB-GENE-080724-7; usp13.
DR eggNOG; KOG0944; Eukaryota.
DR GeneTree; ENSGT00940000157401; -.
DR HOGENOM; CLU_009884_1_0_1; -.
DR InParanoid; F1QFS9; -.
DR OMA; TMDMENN; -.
DR OrthoDB; 556111at2759; -.
DR PhylomeDB; F1QFS9; -.
DR TreeFam; TF300576; -.
DR Reactome; R-DRE-5689880; Ub-specific processing proteases.
DR Reactome; R-DRE-8948751; Regulation of PTEN stability and activity.
DR PRO; PR:F1QFS9; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 6.
DR Bgee; ENSDARG00000079198; Expressed in cardiac ventricle and 19 other tissues.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0043130; F:ubiquitin binding; ISS:UniProtKB.
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:0016579; P:protein deubiquitination; IBA:GO_Central.
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; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS50271; ZF_UBP; 1.
PE 2: Evidence at transcript level;
KW Autophagy; Hydrolase; Metal-binding; Protease; Reference proteome; Repeat;
KW Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..860
FT /note="Ubiquitin carboxyl-terminal hydrolase 13"
FT /id="PRO_0000418013"
FT DOMAIN 318..857
FT /note="USP"
FT DOMAIN 635..676
FT /note="UBA 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 710..750
FT /note="UBA 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT ZN_FING 168..276
FT /note="UBP-type; degenerate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT REGION 611..636
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 755..795
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 620..636
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 764..790
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 327
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 819
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10093"
FT BINDING 192
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 195
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 212
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT BINDING 225
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00502"
FT CONFLICT 731
FT /note="Q -> R (in Ref. 2; AAI41801)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 860 AA; 97452 MW; 456C6827F7D0DCC1 CRC64;
MATDLGELLV PYMPTIRVPR TGDRVFKSEC AFSYDSPESE GGLYVCMNSF LGFGREHVER
HYRKTGQSVY MHLKRHVKEK ATGAAGGAIP RRRNGKVFLD LELNRDFNGD DYEYEDEAKL
VIFPDHYEIP LPNIEELPAL VTIACDAVLN APSPYKKQES DSWEEEIQVS RHARSLRQLD
NGVRIPPSGW KCAKCEMREN LWLNLTDGSV LCGKWFFDGS GGNGHALEHY RESNFPLAVK
LNTITPDGAD IYSFDEEEAV LDPHISEHLL HFGIDMLQMQ RTENGHHTDN HVQPRISDWE
VIQEAGLKLK PVYGSGYTGI KNLGNSCYLS TTMQVLFSIP EFQRAYAGNL QRIFDYSPLD
PTQDFNTQMA KLGHGLLSGQ YSKPPMKSEL IEQVMKEEHK QQQQRGISPK MFKALVSKGH
PEFSSNRQQD AHEFLLHLIN LVERNNSGSE NPSDVFRFIV EERTQCCQSQ KVRYTQRVDY
LMQLPVPLEA ASNREELIAY EGKRKEAEEN MRPLPEVVRA RVPFTACLQA FTEPENVPDF
WSSALQAKSA GVKTSRFATF PEYMIVQLKK FTFGVDWVPK KLDMSVDVPD FLDLNRLRAT
GLQAGEEELP DLTPPIVIPE DTRDSSTNNS LESPEIDESS VMQLAEMGFP LEACRKAVYY
TGNMGAEMAF NWIIAHMEEP DFAEPLAVPT YMESDLPSPS LPTTSALDNQ PPEESISILT
SMGFPRHHTI QALKASNNNL ERALDWIFTH PDCEDESEAM SDTADTEPND NSFSNANAHT
DSSLSPDQDL SSPRVRDGPG RYELFAFISH MGTSTMSGHY VCHIKKEGRW LIYNDHKVCL
SERPPKDLGY MYFYRRLSSC
