ID   UBP1_YEAST              Reviewed;         809 AA.
AC   P25037; D6VRM8; Q07543;
DT   01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT   05-OCT-2010, sequence version 2.
DT   27-MAR-2024, entry version 186.
DE   RecName: Full=Ubiquitin carboxyl-terminal hydrolase 1;
DE            EC=3.4.19.12;
DE   AltName: Full=Deubiquitinating enzyme 1;
DE   AltName: Full=Ubiquitin thioesterase 1;
DE   AltName: Full=Ubiquitin-specific-processing protease 1;
GN   Name=UBP1; OrderedLocusNames=YDL122W; ORFNames=D2250;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=2050695; DOI=10.1016/s0021-9258(18)99059-9;
RA   Tobias J.W., Varshavsky A.;
RT   "Cloning and functional analysis of the ubiquitin-specific protease gene
RT   UBP1 of Saccharomyces cerevisiae.";
RL   J. Biol. Chem. 266:12021-12028(1991).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169867;
RA   Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA   Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA   Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA   Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA   Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA   Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA   Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA   Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA   Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA   Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA   Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA   Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA   Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA   Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA   Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA   Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA   Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA   Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA   Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA   Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA   Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA   Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA   Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA   Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA   Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA   Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA   Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA   Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA   Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA   Mewes H.-W., Zollner A., Zaccaria P.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL   Nature 387:75-78(1997).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [5]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-530; SER-531; SER-555;
RP   SER-618; SER-638; SER-670 AND SER-755, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=ADR376;
RX   PubMed=17330950; DOI=10.1021/pr060559j;
RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA   Elias J.E., Gygi S.P.;
RT   "Large-scale phosphorylation analysis of alpha-factor-arrested
RT   Saccharomyces cerevisiae.";
RL   J. Proteome Res. 6:1190-1197(2007).
RN   [6]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA   Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA   Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT   "Analysis of phosphorylation sites on proteins from Saccharomyces
RT   cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL   Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN   [7]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-530; SER-531; SER-618;
RP   SER-638 AND SER-755, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
RP   ANALYSIS].
RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT   "A multidimensional chromatography technology for in-depth phosphoproteome
RT   analysis.";
RL   Mol. Cell. Proteomics 7:1389-1396(2008).
RN   [8]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-530; SER-531; SER-555;
RP   SER-618; SER-638; THR-652; SER-653; SER-654 AND SER-755, AND IDENTIFICATION
RP   BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19779198; DOI=10.1126/science.1172867;
RA   Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT   "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT   into evolution.";
RL   Science 325:1682-1686(2009).
CC   -!- FUNCTION: Has an ATP-independent isopeptidase activity, cleaving at the
CC       C-terminus of the ubiquitin moiety in natural or engineered linear
CC       fusion proteins, irrespective of their size or the presence of an N-
CC       terminal extension to ubiquitin.
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   -!- MISCELLANEOUS: Present with 8970 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR   EMBL; M63484; AAA35189.1; -; Genomic_DNA.
DR   EMBL; Z74170; CAA98690.1; -; Genomic_DNA.
DR   EMBL; BK006938; DAA11738.1; -; Genomic_DNA.
DR   PIR; S67665; S67665.
DR   RefSeq; NP_010161.1; NM_001180181.1.
DR   AlphaFoldDB; P25037; -.
DR   BioGRID; 31941; 258.
DR   IntAct; P25037; 23.
DR   MINT; P25037; -.
DR   STRING; 4932.YDL122W; -.
DR   MEROPS; C19.002; -.
DR   iPTMnet; P25037; -.
DR   MaxQB; P25037; -.
DR   PaxDb; 4932-YDL122W; -.
DR   PeptideAtlas; P25037; -.
DR   EnsemblFungi; YDL122W_mRNA; YDL122W; YDL122W.
DR   GeneID; 851435; -.
DR   KEGG; sce:YDL122W; -.
DR   AGR; SGD:S000002280; -.
DR   SGD; S000002280; UBP1.
DR   VEuPathDB; FungiDB:YDL122W; -.
DR   eggNOG; KOG1867; Eukaryota.
DR   GeneTree; ENSGT00940000176220; -.
DR   HOGENOM; CLU_008279_6_1_1; -.
DR   InParanoid; P25037; -.
DR   OMA; VECNRCA; -.
DR   OrthoDB; 1749511at2759; -.
DR   BioCyc; YEAST:G3O-29521-MONOMER; -.
DR   Reactome; R-SCE-9664873; Pexophagy.
DR   BioGRID-ORCS; 851435; 2 hits in 10 CRISPR screens.
DR   PRO; PR:P25037; -.
DR   Proteomes; UP000002311; Chromosome IV.
DR   RNAct; P25037; Protein.
DR   GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0005783; C:endoplasmic reticulum; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:SGD.
DR   GO; GO:0016579; P:protein deubiquitination; IDA:SGD.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   CDD; cd02662; Peptidase_C19F; 1.
DR   Gene3D; 3.90.70.10; Cysteine proteinases; 1.
DR   InterPro; IPR038765; Papain-like_cys_pep_sf.
DR   InterPro; IPR001394; Peptidase_C19_UCH.
DR   InterPro; IPR018200; USP_CS.
DR   InterPro; IPR028889; USP_dom.
DR   PANTHER; PTHR24006; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1.
DR   PANTHER; PTHR24006:SF932; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 1; 1.
DR   Pfam; PF00443; UCH; 1.
DR   SUPFAM; SSF54001; Cysteine proteinases; 1.
DR   PROSITE; PS00972; USP_1; 1.
DR   PROSITE; PS00973; USP_2; 1.
DR   PROSITE; PS50235; USP_3; 1.
PE   1: Evidence at protein level;
KW   Hydrolase; Phosphoprotein; Protease; Reference proteome; Thiol protease;
KW   Ubl conjugation pathway.
FT   CHAIN           1..809
FT                   /note="Ubiquitin carboxyl-terminal hydrolase 1"
FT                   /id="PRO_0000080585"
FT   DOMAIN          101..738
FT                   /note="USP"
FT   REGION          143..195
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          569..596
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          750..809
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        143..165
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        166..181
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        761..778
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        786..809
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        110
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   ACT_SITE        697
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT                   ECO:0000255|PROSITE-ProRule:PRU10093"
FT   MOD_RES         530
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT   MOD_RES         531
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT   MOD_RES         555
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         618
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT   MOD_RES         638
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT   MOD_RES         652
FT                   /note="Phosphothreonine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         653
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         654
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         670
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950"
FT   MOD_RES         755
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:17330950,
FT                   ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT   CONFLICT        418
FT                   /note="L -> P (in Ref. 1; AAA35189)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   809 AA;  92769 MW;  07BA266FB43C2C04 CRC64;
     MDLFIESKIN SLLQFLFGSR QDFLRNFKTW SNNNNNLSIY LLIFGIVVFF YKKPDHLNYI
     VESVSEMTTN FRNNNSLSRW LPRSKFTHLD EEILKRGGFI AGLVNDGNTC FMNSVLQSLA
     SSRELMEFLD NNVIRTYEEI EQNEHNEEGN GQESAQDEAT HKKNTRKGGK VYGKHKKKLN
     RKSSSKEDEE KSQEPDITFS VALRDLLSAL NAKYYRDKPY FKTNSLLKAM SKSPRKNILL
     GYDQEDAQEF FQNILAELES NVKSLNTEKL DTTPVAKSEL PDDALVGQLN LGEVGTVYIP
     TEQIDPNSIL HDKSIQNFTP FKLMTPLDGI TAERIGCLQC GENGGIRYSV FSGLSLNLPN
     ENIGSTLKLS QLLSDWSKPE IIEGVECNRC ALTAAHSHLF GQLKEFEKKP EGSIPEKLIN
     AVKDRVHQIE EVLAKPVIDD EDYKKLHTAN MVRKCSKSKQ ILISRPPPLL SIHINRSVFD
     PRTYMIRKNN SKVLFKSRLN LAPWCCDINE INLDARLPMS KKEKAAQQDS SEDENIGGEY
     YTKLHERFEQ EFEDSEEEKE YDDAEGNYAS HYNHTKDISN YDPLNGEVDG VTSDDEDEYI
     EETDALGNTI KKRIIEHSDV ENENVKDNEE LQEIDNVSLD EPKINVEDQL ETSSDEEDVI
     PAPPINYARS FSTVPATPLT YSLRSVIVHY GTHNYGHYIA FRKYRGCWWR ISDETVYVVD
     EAEVLSTPGV FMLFYEYDFD EETGKMKDDL EAIQSNNEED DEKEQEQKGV QEPKESQEQG
     EGEEQEEGQE QMKFERTEDH RDISGKDVN
//