UBP2_YEAST
ID UBP2_YEAST Reviewed; 1272 AA.
AC Q01476; D6W2I2; Q99357;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 192.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 2;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 2;
DE AltName: Full=Ubiquitin thioesterase 2;
DE AltName: Full=Ubiquitin-specific-processing protease 2;
GN Name=UBP2; OrderedLocusNames=YOR124C; ORFNames=O3281, YOR3281C;
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=1429680; DOI=10.1016/s0021-9258(18)50100-9;
RA Baker R.T., Tobias J.W., Varshavsky A.;
RT "Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2
RT and UBP3, and functional analysis of the UBP gene family.";
RL J. Biol. Chem. 267:23364-23375(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=8904341;
RX DOI=10.1002/(sici)1097-0061(19960315)12:3<281::aid-yea904>3.0.co;2-o;
RA Wiemann S., Rechmann S., Benes V., Voss H., Schwager C., Vlcek C.,
RA Stegemann J., Zimmermann J., Erfle H., Paces V., Ansorge W.;
RT "Sequencing and analysis of 51 kb on the right arm of chromosome XV from
RT Saccharomyces cerevisiae reveals 30 open reading frames.";
RL Yeast 12:281-288(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9200815;
RX DOI=10.1002/(sici)1097-0061(19970615)13:7<655::aid-yea120>3.0.co;2-i;
RA Voss H., Benes V., Andrade M.A., Valencia A., Rechmann S., Teodoru C.,
RA Schwager C., Paces V., Sander C., Ansorge W.;
RT "DNA sequencing and analysis of 130 kb from yeast chromosome XV.";
RL Yeast 13:655-672(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [5]
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 [6]
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 [7]
RP FUNCTION, AND INTERACTION WITH RSP5 AND RUP1.
RX PubMed=15933713; DOI=10.1038/sj.emboj.7600710;
RA Kee Y., Lyon N., Huibregtse J.M.;
RT "The Rsp5 ubiquitin ligase is coupled to and antagonized by the Ubp2
RT deubiquitinating enzyme.";
RL EMBO J. 24:2414-2424(2005).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-907, AND IDENTIFICATION BY
RP MASS 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 [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-907, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE 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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-907, AND IDENTIFICATION BY
RP 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).
RN [11]
RP FUNCTION IN DEUBIQUITINATION OF FZO1, AND INTERACTION WITH FZO1.
RX PubMed=23317502; DOI=10.1016/j.molcel.2012.12.003;
RA Anton F., Dittmar G., Langer T., Escobar-Henriques M.;
RT "Two deubiquitylases act on mitofusin and regulate mitochondrial fusion
RT along independent pathways.";
RL Mol. Cell 49:487-498(2013).
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. Removes ubiquitin chains that initiate
CC proteolysis of FZO1 and inhibit mitochondrial fusion.
CC {ECO:0000269|PubMed:15933713, ECO:0000269|PubMed:23317502}.
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 -!- SUBUNIT: Forms a ternary complex with RSP5 and RUP1. Interacts with
CC FZO1. {ECO:0000269|PubMed:15933713, ECO:0000269|PubMed:23317502}.
CC -!- INTERACTION:
CC Q01476; Q12242: RUP1; NbExp=3; IntAct=EBI-19826, EBI-38794;
CC -!- MISCELLANEOUS: Present with 2420 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; M94916; AAA35190.1; -; Genomic_DNA.
DR EMBL; X94335; CAA64043.1; -; Genomic_DNA.
DR EMBL; X90518; CAA62120.1; -; Genomic_DNA.
DR EMBL; Z75032; CAA99323.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10898.1; -; Genomic_DNA.
DR PIR; S60999; S60999.
DR RefSeq; NP_014767.3; NM_001183543.3.
DR AlphaFoldDB; Q01476; -.
DR BioGRID; 34519; 156.
DR DIP; DIP-2647N; -.
DR IntAct; Q01476; 11.
DR MINT; Q01476; -.
DR STRING; 4932.YOR124C; -.
DR MEROPS; C19.003; -.
DR iPTMnet; Q01476; -.
DR MaxQB; Q01476; -.
DR PaxDb; Q01476; -.
DR PRIDE; Q01476; -.
DR EnsemblFungi; YOR124C_mRNA; YOR124C; YOR124C.
DR GeneID; 854291; -.
DR KEGG; sce:YOR124C; -.
DR SGD; S000005650; UBP2.
DR VEuPathDB; FungiDB:YOR124C; -.
DR eggNOG; KOG1863; Eukaryota.
DR GeneTree; ENSGT00940000175922; -.
DR HOGENOM; CLU_003155_1_0_1; -.
DR InParanoid; Q01476; -.
DR OMA; CDIKVDV; -.
DR BioCyc; YEAST:G3O-33651-MON; -.
DR PRO; PR:Q01476; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q01476; protein.
DR GO; GO:0005737; C:cytoplasm; IC:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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:0016578; P:histone deubiquitination; IBA:GO_Central.
DR GO; GO:0010636; P:positive regulation of mitochondrial fusion; IMP:SGD.
DR GO; GO:0016579; P:protein deubiquitination; IDA:SGD.
DR GO; GO:0010992; P:ubiquitin recycling; IMP:SGD.
DR GO; GO:0043162; P:ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway; IMP:SGD.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR025305; UCH_repeat_domain.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR Pfam; PF13446; RPT; 3.
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..1272
FT /note="Ubiquitin carboxyl-terminal hydrolase 2"
FT /id="PRO_0000080586"
FT DOMAIN 736..1258
FT /note="USP"
FT REGION 884..918
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 890..905
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 745
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 1209
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT MOD_RES 907
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT CONFLICT 658..665
FT /note="Missing (in Ref. 1)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1272 AA; 146355 MW; 6D106539AE5C5F3F CRC64;
MPNEDNELQK AIENHHNQLL NQDKENADRN GSVIEDLPLY GTSINQQSTP GDVDDGKHLL
YPDIATNLPL KTSDRLLDDI LCDTIFLNST DPKVMQKGLQ SRGILKESML SYSTFRSSIR
PNCLGSLTDQ VVFQTKSEYD SISCPKYNKI HVFQAVIFNP SLAEQQISTF DDIVKIPIYH
LKVSVKVRQE LERLKKHVGV TQFHSLDHLH EYDRVDLSTF DSSDPNLLDY GIYVSDDTNK
LILIEIFKPE FNSPEEHESF TADAIKKRYN AMCVKNESLD KSETPSQVDC FYTLFKIFKG
PLTRKSKAEP TKTIDSGNLA LNTHLNPEWL TSKYGFQASS EIDEETNEIF TEYVPPDMVD
YVNDLETRKI RESFVRKCLQ LIFWGQLSTS LLAPNSPLKN TKSVKGMSSL QTSFSTLPWF
HLLGESRARI LLNSNEQTHS PLDAEPHFIN LSVSHYYTDR DIIRNYESLS SLDPENIGLY
FDALTYIANR KGAYQLIAYC GKQDIIGQEA LENALLMFKI NPKECNISEL NEATLLSIYK
YETSNKSQVT SNHLTNLKNA LRLLAKYTKS DKLKFYVDHE PYRALSQAYD TLSIDESVDE
DIIKTAYSVK INDSPGLKLD CDRALYTIAI SKRSLDLFNF LTEECPQFSN YYGPEKLDYQ
EALKLLQVNE NASDETILKI FKQKWFDENV YEPDQFLILR AALTKISIER NSTLITNFLL
TGTIDPNSLP PENWPTGINN IGNTCYLNSL LQYYFSIAPL RRYVLEYQKT VENFNDHLSN
SGHIRRIGGR EISRGEVERS IQFIYQLRNL FYAMVHTRER CVTPSKELAY LAFAPSNVEV
EFEVEGNKVV DQTGVLSDSK KETTDDAFTT KIKDTSLIDL EMEDGLNGDV GTDANRKKNE
SNDAEVSENE DTTGLTSPTR VAKISSDQLE NALEMGRQQD VTECIGNVLF QIESGSEPIR
YDEDNEQYDL VKQLFYGTTK QSIVPLSATN KVRTKVERFL SLLINIGDHP KDIYDAFDSY
FKDEYLTMEE YGDVIRTVAV TTFPTILQVQ IQRVYYDRER LMPFKSIEPL PFKEVIYMDR
YADTENPLLL AKKKETEEMK QKLKVMKNRQ RELLSRDDSG LTRKDAFLES IKLLESDTIK
KTPLKIEAAN DVIKTLRNNV QNIDNELMKL YNDINSLEEK ISHQFDDFKE YGYSLFSVFI
HRGEASYGHY WIYIKDRNRN GIWRKYNDET ISEVQEEEVF NFNEGNTATP YFLVYVKQGQ
EGDIEPLKRI LK
