UBP1_YEAST
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 03-AUG-2022, entry version 178.
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; 202.
DR IntAct; P25037; 23.
DR MINT; P25037; -.
DR STRING; 4932.YDL122W; -.
DR MEROPS; C19.002; -.
DR iPTMnet; P25037; -.
DR MaxQB; P25037; -.
DR PaxDb; P25037; -.
DR PRIDE; P25037; -.
DR EnsemblFungi; YDL122W_mRNA; YDL122W; YDL122W.
DR GeneID; 851435; -.
DR KEGG; sce:YDL122W; -.
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 BioCyc; YEAST:G3O-29521-MON; -.
DR Reactome; R-SCE-110314; Recognition of DNA damage by PCNA-containing replication complex.
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:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:1905524; P:negative regulation of protein autoubiquitination; IDA:SGD.
DR GO; GO:0016579; P:protein deubiquitination; IDA:SGD.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
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 Pfam; PF00443; UCH; 1.
DR SUPFAM; SSF54001; SSF54001; 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
