ID   OTU1_DANRE              Reviewed;         301 AA.
AC   Q567B1;
DT   03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT   10-MAY-2005, sequence version 1.
DT   03-AUG-2022, entry version 101.
DE   RecName: Full=Ubiquitin thioesterase OTU1;
DE            EC=3.4.19.12 {ECO:0000250|UniProtKB:Q5VVQ6};
GN   Name=yod1; ORFNames=zgc:112182;
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 MRNA].
RC   TISSUE=Embryo;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Hydrolase that can remove conjugated ubiquitin from proteins
CC       and participates in endoplasmic reticulum-associated degradation (ERAD)
CC       for misfolded lumenal proteins. May act by triming the ubiquitin chain
CC       on the associated substrate to facilitate their threading through the
CC       VCP/p97 pore. Ubiquitin moieties on substrates may present a steric
CC       impediment to the threading process when the substrate is transferred
CC       to the VCP pore and threaded through VCP's axial channel. Mediates
CC       deubiquitination of 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked
CC       polyubiquitin chains. Also able to hydrolyze 'Lys-11'-linked ubiquitin
CC       chains. Cleaves both polyubiquitin and di-ubiquitin.
CC       {ECO:0000250|UniProtKB:Q5VVQ6}.
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; Evidence={ECO:0000250|UniProtKB:Q5VVQ6};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q5VVQ6}.
CC       Note=Recruited to damaged lysosomes decorated with K48-linked ubiquitin
CC       chains. {ECO:0000250|UniProtKB:Q5VVQ6}.
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DR   EMBL; BC093247; AAH93247.1; -; mRNA.
DR   RefSeq; NP_001017716.1; NM_001017716.2.
DR   AlphaFoldDB; Q567B1; -.
DR   SMR; Q567B1; -.
DR   STRING; 7955.ENSDARP00000003565; -.
DR   MEROPS; C85.007; -.
DR   PaxDb; Q567B1; -.
DR   PRIDE; Q567B1; -.
DR   Ensembl; ENSDART00000023388; ENSDARP00000003565; ENSDARG00000008542.
DR   Ensembl; ENSDART00000177280; ENSDARP00000143479; ENSDARG00000008542.
DR   GeneID; 550411; -.
DR   KEGG; dre:550411; -.
DR   CTD; 55432; -.
DR   ZFIN; ZDB-GENE-050417-217; yod1.
DR   eggNOG; KOG3288; Eukaryota.
DR   GeneTree; ENSGT00390000009989; -.
DR   HOGENOM; CLU_049327_1_0_1; -.
DR   InParanoid; Q567B1; -.
DR   OMA; NEEYCDW; -.
DR   OrthoDB; 1327072at2759; -.
DR   PhylomeDB; Q567B1; -.
DR   TreeFam; TF323700; -.
DR   Reactome; R-DRE-5689896; Ovarian tumor domain proteases.
DR   PRO; PR:Q567B1; -.
DR   Proteomes; UP000000437; Genome assembly.
DR   Proteomes; UP000814640; Chromosome 11.
DR   Bgee; ENSDARG00000008542; Expressed in testis and 24 other tissues.
DR   ExpressionAtlas; Q567B1; baseline.
DR   GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; ISS:UniProtKB.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0030968; P:endoplasmic reticulum unfolded protein response; ISS:UniProtKB.
DR   GO; GO:0016236; P:macroautophagy; ISS:UniProtKB.
DR   GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR   GO; GO:0035871; P:protein K11-linked deubiquitination; ISS:UniProtKB.
DR   GO; GO:1990167; P:protein K27-linked deubiquitination; ISS:UniProtKB.
DR   GO; GO:0035523; P:protein K29-linked deubiquitination; ISS:UniProtKB.
DR   GO; GO:1990168; P:protein K33-linked deubiquitination; ISS:UniProtKB.
DR   GO; GO:0071108; P:protein K48-linked deubiquitination; ISS:UniProtKB.
DR   GO; GO:0070536; P:protein K63-linked deubiquitination; ISS:UniProtKB.
DR   GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; ISS:UniProtKB.
DR   InterPro; IPR039138; OTU1_2_3.
DR   InterPro; IPR003323; OTU_dom.
DR   InterPro; IPR038765; Papain-like_cys_pep_sf.
DR   InterPro; IPR000626; Ubiquitin-like_dom.
DR   InterPro; IPR029071; Ubiquitin-like_domsf.
DR   PANTHER; PTHR13312; PTHR13312; 1.
DR   Pfam; PF02338; OTU; 1.
DR   Pfam; PF14560; Ubiquitin_2; 1.
DR   SUPFAM; SSF54001; SSF54001; 1.
DR   SUPFAM; SSF54236; SSF54236; 1.
DR   PROSITE; PS50802; OTU; 1.
DR   PROSITE; PS50053; UBIQUITIN_2; 1.
DR   PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
PE   2: Evidence at transcript level;
KW   Cytoplasm; Hydrolase; Metal-binding; Protease; Reference proteome;
KW   Thiol protease; Ubl conjugation pathway; Unfolded protein response; Zinc;
KW   Zinc-finger.
FT   CHAIN           1..301
FT                   /note="Ubiquitin thioesterase OTU1"
FT                   /id="PRO_0000282360"
FT   DOMAIN          102..227
FT                   /note="OTU"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00139"
FT   ZN_FING         271..295
FT                   /note="C2H2-type"
FT   REGION          5..83
FT                   /note="UBX-like"
FT   REGION          107..113
FT                   /note="Cys-loop"
FT                   /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
FT   REGION          166..176
FT                   /note="Variable-loop"
FT                   /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
FT   REGION          216..220
FT                   /note="His-loop"
FT                   /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
FT   REGION          244..249
FT                   /note="S2 site"
FT                   /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
FT   ACT_SITE        110
FT                   /evidence="ECO:0000250|UniProtKB:Q96FW1"
FT   ACT_SITE        113
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
FT   ACT_SITE        220
FT                   /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
FT   ACT_SITE        295
FT                   /evidence="ECO:0000250|UniProtKB:Q96FW1"
FT   BINDING         219
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250|UniProtKB:Q5VVQ6"
SQ   SEQUENCE   301 AA;  33486 MW;  70D85A2694B56198 CRC64;
     MLRLRCKAKN GTHLMQGLTH QSCVQELKDK IEELTGIPCD VQKIMVGYPP SSLDLRNGEA
     HLKDYPIKSG DTLIVEEEKN KPKPPVQPTV TKGPSFEVTP VVERRVVPAD NSCLFTSVNY
     VMEGGVYDPA CASEMRGLIA QIVASDPTAY SEAVLGKTNE EYCTWIRRDD TWGGAIEVSI
     LSKFYQCEIC VVDTQTVRVD RFGEDAGYTK RVLLIYDGIH YDPLQKVLPG SDVPAQTVFS
     TVDDVILAQA LELADEARRK RQFTDVNRFA LRCMVCQTGL VGQKEAREHA KETGHTNFGE
     V