ID   UBP4_VANPO              Reviewed;         882 AA.
AC   A7TGY3;
DT   16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT   02-OCT-2007, sequence version 1.
DT   27-MAR-2024, entry version 84.
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;
GN   Name=DOA4; Synonyms=UBP4; ORFNames=Kpol_1032p28;
OS   Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294 / BCRC 21397 / CBS
OS   2163 / NBRC 10782 / NRRL Y-8283 / UCD 57-17) (Kluyveromyces polysporus).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Vanderwaltozyma.
OX   NCBI_TaxID=436907;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 22028 / DSM 70294 / BCRC 21397 / CBS 2163 / NBRC 10782 /
RC   NRRL Y-8283 / UCD 57-17;
RX   PubMed=17494770; DOI=10.1073/pnas.0608218104;
RA   Scannell D.R., Frank A.C., Conant G.C., Byrne K.P., Woolfit M., Wolfe K.H.;
RT   "Independent sorting-out of thousands of duplicated gene pairs in two yeast
RT   species descended from a whole-genome duplication.";
RL   Proc. Natl. Acad. Sci. U.S.A. 104:8397-8402(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. Required for promoting
CC       coordination of DNA replication and avoids DNA overreplication (By
CC       similarity). {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   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Late endosome membrane
CC       {ECO:0000250}; Peripheral membrane protein {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR   EMBL; DS480389; EDO18435.1; -; Genomic_DNA.
DR   RefSeq; XP_001646293.1; XM_001646243.1.
DR   AlphaFoldDB; A7TGY3; -.
DR   SMR; A7TGY3; -.
DR   STRING; 436907.A7TGY3; -.
DR   MEROPS; C19.005; -.
DR   GeneID; 5546722; -.
DR   KEGG; vpo:Kpol_1032p28; -.
DR   eggNOG; KOG1868; Eukaryota.
DR   HOGENOM; CLU_005922_1_0_1; -.
DR   InParanoid; A7TGY3; -.
DR   OMA; SIEWERY; -.
DR   OrthoDB; 227085at2759; -.
DR   PhylomeDB; A7TGY3; -.
DR   Proteomes; UP000000267; 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:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   CDD; cd02674; Peptidase_C19R; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 1.
DR   Gene3D; 3.40.250.10; Rhodanese-like domain; 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   PANTHER; PTHR21646; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR21646:SF95; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4-RELATED; 1.
DR   Pfam; PF00581; Rhodanese; 1.
DR   Pfam; PF00443; UCH; 1.
DR   SMART; SM00450; RHOD; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   SUPFAM; SSF52821; Rhodanese/Cell cycle control phosphatase; 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; Protease; Reference proteome;
KW   Thiol protease; Ubl conjugation pathway.
FT   CHAIN           1..882
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 4"
FT                   /id="PRO_0000376821"
FT   DOMAIN          182..308
FT                   /note="Rhodanese"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00173"
FT   DOMAIN          519..879
FT                   /note="USP"
FT   REGION          382..411
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        528
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        836
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
SQ   SEQUENCE   882 AA;  100061 MW;  2C55FD7734FDE34A CRC64;
     MVEVDSRKQL LYDPIVRLSG IADKFVMQDA TSSNMKVSLQ ECIDTLANYQ DECKKLKRNE
     PTLSPSERYS IYESAYIYYK IIHIMVLTRI PSLPQFSSAK SSDATNEDKE LMQIYNMLVK
     TLLSDEKIAQ IKSYLRANYP DKNSKGKESI VNKQLLNNEV FMLPLSGSPI SAVQLNHLIQ
     MYDSSLLLID VRPRAEFDSK HIKAKSVICV EPVSFKNSFT DLEVEKKSLI TSPQKEIALF
     QARDKYNYIV IYTQQSEKTQ FYMHQQLVLL DILMNKSFAK PLNEKNIKVF TLDKGFSGWV
     SKKGACETTT QNGDAIYISG NTSSLNLQNL PQLSPNIGSS MDKSMRDMMS TSADFEGRTY
     QLPQQQQPVF ARTPSFKNLF NKAKSSSTSS VTSSSPAPSQ LVRPQTSSMP PLEQNFTQYP
     ETPKLLTQIN TNTMPLSQIS PISSRAMSPM TKNMLTQSPQ LPMKISRTTI GNGAMLDLKP
     HPDSKPPGQP VPALPQLPHH MTGTYQNLNQ PKLDLDFTVG LENMGNSCYM NCIIQCLLST
     HELSQIFLNN SYEKHINLNS KLGSKGVLAK YFARLVHTMY REGSFKRPLE KNKPIQPIQF
     KMACGSINSL FKDNTQQDSQ EFCQFLLDGL HEDLNQCGAN PPLKELSEDA EKMREKLSMR
     IASSIEWERF LTTDFSVIVD LFQGQYASQL KCKVCGCTST TYQTFSVLSV PVPHVSSCHI
     LDCFNEFTKV EKLGTDELWS CPTCKKKQPS TKKLTITRLP RNLIIHLKRF DNMMNKNNVF
     VKYPFLLDLT PYWANDFDGR LPPGVTDELP TRGQVPPFRY KLNAVASHVG SLYGGHYTAY
     VNKGINRGWH YFDDTSYRPI KNETECITPN AYVLFYHRVY GV
//