UBP4_YEAS7
ID UBP4_YEAS7 Reviewed; 926 AA.
AC A6ZY34;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 1.
DT 03-AUG-2022, entry version 67.
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=SCY_0972;
OS Saccharomyces cerevisiae (strain YJM789) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=307796;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YJM789;
RX PubMed=17652520; DOI=10.1073/pnas.0701291104;
RA Wei W., McCusker J.H., Hyman R.W., Jones T., Ning Y., Cao Z., Gu Z.,
RA Bruno D., Miranda M., Nguyen M., Wilhelmy J., Komp C., Tamse R., Wang X.,
RA Jia P., Luedi P., Oefner P.J., David L., Dietrich F.S., Li Y., Davis R.W.,
RA Steinmetz L.M.;
RT "Genome sequencing and comparative analysis of Saccharomyces cerevisiae
RT strain YJM789.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:12825-12830(2007).
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; AAFW02000145; EDN60414.1; -; Genomic_DNA.
DR AlphaFoldDB; A6ZY34; -.
DR SMR; A6ZY34; -.
DR EnsemblFungi; EDN60414; EDN60414; SCY_0972.
DR HOGENOM; CLU_005922_1_0_1; -.
DR Proteomes; UP000007060; 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_0000376823"
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; 105092 MW; F1B6D2ACE736DD00 CRC64;
MEQNIISTIR DECIRHRSKY LTIAQLTAIA EAKINEFIIT GKAKDQDLSS LLDKCIDILS
IYKKNSKDIK NIISCKNKGA MISSNSVMII QLNYVYYKVI HIIVTTNIPH LSEFAKIKLH
KSTSDEGNGN NNNNEFQLMN IYNTLLETLL KDENIAKIKS FIKSSIKQTK LNHEQEECNL
MRTGSYITSN QLNSLISSSA NSTSSQMEIL LIDIRSRLEF NKSHIDTKNI ICLEPISFKM
SYSDHDLEKK SLITSPNSEI KMFQSRNLFK FIILYTDANE YNVKQQSVLL DILVNHSFEK
PISDDFTKIF ILESGFPGWL KSNYGSQVSS SSPSNNNIKD DSVYINGNTS GLSLQHLPKM
SPSIRHSMDD SMKEMLVAPT PLNHLQQQQQ QQSDNDHVLK RSSSFKKLFS NYTSPNPKNS
NSNLYSISSL SISSSPSPLP LHSPDPVKGN SLPINYPETP HLWKNSETDF MTNQREQLNH
NSFAHIAPIN TKAITSPSRT ATPKLQRFPQ TISMNLNMNS NGHSSATSTI QPSCLSLSNN
DSLDHTDVTP TSSHNYDLDF AVGLENLGNS CYMNCIIQCI LGTHELTQIF LDDSYAKHIN
INSKLGSKGI LAKYFARLVH MMYKEQVDGS KKISISPIKF KLACGSVNSL FKTASQQDCQ
EFCQFLLDGL HEDLNQCGSN PPLKELSQEA EARREKLSLR IASSIEWERF LTTDFSVIVD
LFQGQYASRL KCKVCSHTST TYQPFTVLSI PIPKKNSRNN ITIEDCFREF TKCENLEVDE
QWLCPHCKKR QPSTKQLTIT RLPRNLIVHL KRFDNLLNKN NDFVIYPFLL DLTPFWANDF
DGVFPPGVND DELPIRGQIP PFKYELYGVA CHFGTLYGGH YTAYVKKGLK KGWLYFDDTK
YKPVKNKADA INSNAYVLFY HRVYGV
