ID   UBP13_XENTR             Reviewed;         846 AA.
AC   F6V6I0;
DT   13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT   13-JUN-2012, sequence version 2.
DT   03-AUG-2022, entry version 56.
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   Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC   Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX   NCBI_TaxID=8364;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=20431018; DOI=10.1126/science.1183670;
RA   Hellsten U., Harland R.M., Gilchrist M.J., Hendrix D., Jurka J.,
RA   Kapitonov V., Ovcharenko I., Putnam N.H., Shu S., Taher L., Blitz I.L.,
RA   Blumberg B., Dichmann D.S., Dubchak I., Amaya E., Detter J.C., Fletcher R.,
RA   Gerhard D.S., Goodstein D., Graves T., Grigoriev I.V., Grimwood J.,
RA   Kawashima T., Lindquist E., Lucas S.M., Mead P.E., Mitros T., Ogino H.,
RA   Ohta Y., Poliakov A.V., Pollet N., Robert J., Salamov A., Sater A.K.,
RA   Schmutz J., Terry A., Vize P.D., Warren W.C., Wells D., Wills A.,
RA   Wilson R.K., Zimmerman L.B., Zorn A.M., Grainger R., Grammer T.,
RA   Khokha M.K., Richardson P.M., Rokhsar D.S.;
RT   "The genome of the Western clawed frog Xenopus tropicalis.";
RL   Science 328:633-636(2010).
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}.
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DR   EMBL; AAMC01001929; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AAMC01001930; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AAMC01001931; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AAMC01001932; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AAMC01001933; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AAMC01001934; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   AlphaFoldDB; F6V6I0; -.
DR   SMR; F6V6I0; -.
DR   STRING; 8364.ENSXETP00000015787; -.
DR   PaxDb; F6V6I0; -.
DR   eggNOG; KOG0944; Eukaryota.
DR   HOGENOM; CLU_009884_1_0_1; -.
DR   InParanoid; F6V6I0; -.
DR   Proteomes; UP000008143; Genome assembly.
DR   Proteomes; UP000790000; Unplaced.
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: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; 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; 1.
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; 1.
DR   SMART; SM00290; ZnF_UBP; 1.
DR   SUPFAM; SSF54001; SSF54001; 1.
DR   PROSITE; PS50030; UBA; 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; Metal-binding; Protease; Reference proteome; Repeat;
KW   Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger.
FT   CHAIN           1..846
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 13"
FT                   /id="PRO_0000418014"
FT   DOMAIN          317..844
FT                   /note="USP"
FT   DOMAIN          633..676
FT                   /note="UBA 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT   DOMAIN          708..748
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   ACT_SITE        806
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"
SQ   SEQUENCE   846 AA;  95089 MW;  139B256C047BE39A CRC64;
     MAEDLGELLV PYMPTIRVPK SGDRVYKTEC AFSYDSPESD GGLYVCMSTF LGFGREHVER
     HYRKTGQSVY MHLKRHIRLK ATGASGGAFP KRINGRLFLD LENNTEMNTE DYEYEDEAKL
     VIFPDHFEIA LPNIEELPAL VTIACDAVLN SKSPYRKLDQ ESWEEELQVS KFANNLVQID
     NGVKIPPSGW KCSKCDLQEN LWLNLTDGSI MCGRWFCSGS GGNGHALEHH KQMGYPLAVR
     LGSITPDGAD VYSFDEEEAV IDPHLAKHLA HFGIDMLQMQ GSENGVLDNE VKPRVNEWEV
     IQETGLKLKP MFGSGYTGIK NLGNSSYLTT VMQVIFSIPE FQRAYVGNLT RIFDYAPLDP
     TQDFSTQMAK LGHGLLSGQF SKPPMKSELI EQVMKEEHKP QPKGINTRMF KALMSKGHTE
     FSSNRQQDAE EFFLHFINLV ERNSIGAENP SDVFRFLVEE RTQCCQSRKV RYTERVDYIM
     QLPVPMETAT NKEELIAYDL KRREAESAKR PPPELVRAKI PFSACLQAFT EPENVPDFWS
     SALQAKSAGV KTSRFASFPE YLVVQIKKFT FGLDWVPKKL DVSIDMPDLL DINHLRATGL
     KSGEEELPDI APPIIIPDDP NGRMAESLLS GSGSNVNSSF KGAQPLNLPF GKKEAKLLRY
     MERMVEKFGF KFSVRLSVEI DFAEPLIIPG CGTVTSTSSH GQNALLNQPP EEIVALICSM
     GFPRNHALQA LRATNNNLER ALDWMFSHPE SEEGADNVSG CVDTENNPNG IITDSEQEGP
     RIKDGNGRYE LFGIISHAGT STMSGHYVCH IKKEGRWVIY NDHKVSASER PPKELGYIYF
     YHRISC