ID   UBP4_YEAS1              Reviewed;         926 AA.
AC   B3LGK1;
DT   16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT   02-SEP-2008, sequence version 1.
DT   03-AUG-2022, entry version 59.
DE   RecName: Full=Ubiquitin carboxyl-terminal hydrolase 4;
DE            EC=3.4.19.12;
DE   AltName: Full=Deubiquitinating enzyme 4;
DE   AltName: Full=Ubiquitin thioesterase 4;
DE   AltName: Full=Ubiquitin-specific-processing protease 4;
DE   AltName: Full=Vacuole biogenesis protein SSV7;
GN   Name=DOA4; Synonyms=DOS1, MUT4, NPI2, SSV7, UBP4; ORFNames=SCRG_00446;
OS   Saccharomyces cerevisiae (strain RM11-1a) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=285006;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=RM11-1a;
RG   The Broad Institute Genome Sequencing Platform;
RA   Birren B.W., Lander E.S., Galagan J.E., Nusbaum C., Devon K., Cuomo C.,
RA   Jaffe D.B., Butler J., Alvarez P., Gnerre S., Grabherr M., Kleber M.,
RA   Mauceli E.W., Brockman W., MacCallum I.A., Rounsley S., Young S.K.,
RA   LaButti K., Pushparaj V., DeCaprio D., Crawford M., Koehrsen M., Engels R.,
RA   Montgomery P., Pearson M., Howarth C., Larson L., Luoma S., White J.,
RA   O'Leary S., Kodira C.D., Zeng Q., Yandava C., Alvarado L., Pratt S.,
RA   Kruglyak L.;
RT   "Annotation of the Saccharomyces cerevisiae RM11-1a genome.";
RL   Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Ubiquitin thioesterase that acts at the late
CC       endosome/prevacuolar compartment to recover ubiquitin from
CC       ubiquitinated membrane proteins en route to the vacuole. Removes also
CC       ubiquitin from soluble proteins targeted to proteasomes. Is essential
CC       to maintain a normal level of free ubiquitin. Involved in the ammonium-
CC       induced down-regulation of the GAP1 permease and the UME3 destruction
CC       in response to oxidative stress. Has a role in the RAD9 checkpoint
CC       response to TOP1 poisons. Required for promoting coordination of DNA
CC       replication and avoids DNA overreplication (By similarity).
CC       {ECO:0000250}.
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: RFU1 is an inhibitor of deubiquitination activity.
CC       {ECO:0000250}.
CC   -!- SUBUNIT: Interacts with BRO1, RFU1 and VPS32. Associates with the 26S
CC       proteasome (By similarity). {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Late endosome membrane
CC       {ECO:0000250}; Peripheral membrane protein {ECO:0000250}.
CC       Note=Recruited to the late endosome by BRO1. {ECO:0000250}.
CC   -!- DOMAIN: Residues 1-208 are essential for the localization to the late
CC       endosome and constitute a late endosome localization (LEL) domain.
CC       {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR   EMBL; CH408043; EDV08230.1; -; Genomic_DNA.
DR   AlphaFoldDB; B3LGK1; -.
DR   SMR; B3LGK1; -.
DR   TopDownProteomics; B3LGK1; -.
DR   EnsemblFungi; EDV08230; EDV08230; SCRG_00446.
DR   HOGENOM; CLU_005922_1_0_1; -.
DR   Proteomes; UP000008335; Unassembled WGS sequence.
DR   GO; GO:0031902; C:late endosome membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR   GO; GO:0016579; P:protein deubiquitination; IEA:InterPro.
DR   GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR   Gene3D; 3.40.250.10; -; 1.
DR   InterPro; IPR038765; Papain-like_cys_pep_sf.
DR   InterPro; IPR001394; Peptidase_C19_UCH.
DR   InterPro; IPR001763; Rhodanese-like_dom.
DR   InterPro; IPR036873; Rhodanese-like_dom_sf.
DR   InterPro; IPR018200; USP_CS.
DR   InterPro; IPR028889; USP_dom.
DR   Pfam; PF00581; Rhodanese; 1.
DR   Pfam; PF00443; UCH; 1.
DR   SMART; SM00450; RHOD; 1.
DR   SUPFAM; SSF52821; SSF52821; 1.
DR   SUPFAM; SSF54001; SSF54001; 1.
DR   PROSITE; PS50206; RHODANESE_3; 1.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS00973; USP_2; 1.
DR   PROSITE; PS50235; USP_3; 1.
PE   3: Inferred from homology;
KW   Cytoplasm; Endosome; Hydrolase; Membrane; Phosphoprotein; Protease;
KW   Thiol protease; Ubl conjugation pathway.
FT   CHAIN           1..926
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 4"
FT                   /id="PRO_0000376822"
FT   DOMAIN          205..328
FT                   /note="Rhodanese"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00173"
FT   DOMAIN          562..923
FT                   /note="USP"
FT   ACT_SITE        571
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        880
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   MOD_RES         443
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:P32571"
SQ   SEQUENCE   926 AA;  105188 MW;  BE75CFBAE9C1A9F6 CRC64;
     MEQNIISTIR DECIRHRSKY LTIAQLTAIA EAKINEFIIT GKAKDQDLSS LLDKCIDILS
     IYKKNSKDIK NIISCKNKGA MISSNSVMII QLNYVYYKVI HIIVTTNIPH LSEFAKIKLH
     KSTSDEGNGN NNNNEFQLMN IYNTLLETLL KDENIAKIKS FIKSSIKQTK LNHEQEECNL
     MRTGSYITSN QLNSLISSSA NSASSQMEIL LIDIRSRLEF NKSHIDTKNI ICLEPISFKM
     SYSDHDLEKK SLITSPNSEI KMFQSRNLFK FIILYTDANE YNVKQQSVLL DILVNHSFEK
     PISDDFTKIF ILESGFPGWL KSNYGRQVSS SFPSNNNIKD DSVYINGNTS GLSLQHLPKM
     SPSIRHSMDD SMKEMLVAPT PLNHLQQQQQ QQSDNDHVLK RSSSFKKLFS NYTSPNPKNS
     NSNLYSISSL SISSSPSPLP LHSPDPVKGN SLPINYPETP HLWKNSETDF MTNQREQLNH
     NSFAHVAPIN TKAITSPSRT ATPKLQRFPQ TISMNLNMNS NGHSSATSTI QPSCLSLSNN
     DSLDHTDVTP TSSHNYDLDF AVGLENLGNS CYMNCIIQCI LGTHELTQIF LDDSYAKHIN
     INSKLGSKGI LAKYFARLVH MMYKEQVDGS KKIPISPIKF KLACGSVNSL FKTASQQDCQ
     EFCQFLLDGL HEDLNQCGSN PPLKELSQEA EARREKLSLR IASSIEWERF LTTDFSVIVD
     LFQGQYASRL KCKVCSHTST TYQPFTVLSI PIPKKNSRNN ITIEDCFREF TKCENLEVDE
     QWLCPHCEKR QPSTKQLTIT RLPRNLIVHL KRFDNLLNKN NDFVIYPFLL DLTPFWANDF
     DGVFPPGVND DELPIRGQIP PFKYELYGVA CHFGTLYGGH YTAYVKKGLK KGWLYFDDTK
     YKPVKNKADA INSNAYVLFY HRVYGV