UBP3_YEAST
ID UBP3_YEAST Reviewed; 912 AA.
AC Q01477; D3DM58;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1993, sequence version 1.
DT 03-AUG-2022, entry version 189.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 3;
DE EC=3.4.19.12 {ECO:0000269|PubMed:12778054, ECO:0000269|PubMed:17632125};
DE AltName: Full=Deubiquitinating enzyme 3;
DE AltName: Full=Ubiquitin thioesterase 3;
DE AltName: Full=Ubiquitin-specific-processing protease 3;
GN Name=UBP3; OrderedLocusNames=YER151C;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(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 FUNCTION.
RX PubMed=8752220; DOI=10.1016/s0092-8674(00)80139-7;
RA Moazed D., Johnson D.;
RT "A deubiquitinating enzyme interacts with SIR4 and regulates silencing in
RT S. cerevisiae.";
RL Cell 86:667-677(1996).
RN [5]
RP FUNCTION, SUBUNIT, AND CATALYTIC ACTIVITY.
RX PubMed=12778054; DOI=10.1038/ncb1003;
RA Cohen M., Stutz F., Belgareh N., Haguenauer-Tsapis R., Dargemont C.;
RT "Ubp3 requires a cofactor, Bre5, to specifically de-ubiquitinate the COPII
RT protein, Sec23.";
RL Nat. Cell Biol. 5:661-667(2003).
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 IDENTIFICATION BY 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 [8]
RP FUNCTION, IDENTIFICATION IN A COMPLEX WITH DOA1; BRE5 AND CDC48, AND
RP INTERACTION WITH DOA1 AND CDC48.
RX PubMed=20508643; DOI=10.1038/embor.2010.74;
RA Ossareh-Nazari B., Bonizec M., Cohen M., Dokudovskaya S., Delalande F.,
RA Schaeffer C., Van Dorsselaer A., Dargemont C.;
RT "Cdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required
RT for ribophagy.";
RL EMBO Rep. 11:548-554(2010).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) OF 190-233 IN COMPLEX WITH BRE5,
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=17632125; DOI=10.1016/j.jmb.2007.06.052;
RA Li K., Ossareh-Nazari B., Liu X., Dargemont C., Marmorstein R.;
RT "Molecular basis for bre5 cofactor recognition by the ubp3 deubiquitylating
RT enzyme.";
RL J. Mol. Biol. 372:194-204(2007).
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 (PubMed:12778054, PubMed:17632125).
CC Plays a role in regulation of silencing by interacting with SIR4
CC (PubMed:8752220). Also, in conjunction with BRE5, cleaves ubiquitin,
CC leading to the subsequent mono-ubiquitination of SEC23
CC (PubMed:12778054). Required for ribophagy, a process which relocalizes
CC ribosomal particles into the vacuole for degradation in response to
CC starvation (PubMed:20508643). {ECO:0000269|PubMed:12778054,
CC ECO:0000269|PubMed:17632125, ECO:0000269|PubMed:20508643,
CC ECO:0000269|PubMed:8752220}.
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; Evidence={ECO:0000269|PubMed:12778054,
CC ECO:0000269|PubMed:17632125};
CC -!- SUBUNIT: Heterotetramer with BRE5; contains two molecules of BRE5 and
CC two molecules of UBP3 (PubMed:12778054, PubMed:17632125). Forms a
CC complex composed of CDC48, DOA1, deubiquitinase UBP3 and probably BRE5.
CC Within the complex interacts directly with DOA1 and CDC48 in a BRE5-
CC independent manner (PubMed:20508643). {ECO:0000269|PubMed:12778054,
CC ECO:0000269|PubMed:17632125, ECO:0000269|PubMed:20508643}.
CC -!- INTERACTION:
CC Q01477; P53741: BRE5; NbExp=11; IntAct=EBI-19834, EBI-28528;
CC Q01477; P25694: CDC48; NbExp=4; IntAct=EBI-19834, EBI-4308;
CC Q01477; P36037: DOA1; NbExp=4; IntAct=EBI-19834, EBI-6017;
CC Q01477; P32485: HOG1; NbExp=3; IntAct=EBI-19834, EBI-8437;
CC -!- MISCELLANEOUS: Present with 2210 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; M94917; AAA35191.1; -; Genomic_DNA.
DR EMBL; U18917; AAB64678.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07812.1; -; Genomic_DNA.
DR PIR; B44450; B44450.
DR RefSeq; NP_011078.3; NM_001179041.3.
DR PDB; 2QIY; X-ray; 1.69 A; C/D=190-233.
DR PDBsum; 2QIY; -.
DR AlphaFoldDB; Q01477; -.
DR SMR; Q01477; -.
DR BioGRID; 36901; 1184.
DR ComplexPortal; CPX-1412; UBP3-BRE5 ubiquitin hydrolase complex.
DR DIP; DIP-4255N; -.
DR IntAct; Q01477; 404.
DR MINT; Q01477; -.
DR STRING; 4932.YER151C; -.
DR MEROPS; C19.004; -.
DR iPTMnet; Q01477; -.
DR MaxQB; Q01477; -.
DR PaxDb; Q01477; -.
DR PRIDE; Q01477; -.
DR EnsemblFungi; YER151C_mRNA; YER151C; YER151C.
DR GeneID; 856895; -.
DR KEGG; sce:YER151C; -.
DR SGD; S000000953; UBP3.
DR VEuPathDB; FungiDB:YER151C; -.
DR eggNOG; KOG1871; Eukaryota.
DR GeneTree; ENSGT00940000170514; -.
DR HOGENOM; CLU_015192_0_0_1; -.
DR InParanoid; Q01477; -.
DR OMA; LDPFQTI; -.
DR BioCyc; YEAST:G3O-30312-MON; -.
DR EvolutionaryTrace; Q01477; -.
DR PRO; PR:Q01477; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; Q01477; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IDA:ComplexPortal.
DR GO; GO:0005739; C:mitochondrion; IDA:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:1990861; C:Ubp3-Bre5 deubiquitination complex; IPI:SGD.
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:0003729; F:mRNA binding; IDA:SGD.
DR GO; GO:1901525; P:negative regulation of mitophagy; IMP:ComplexPortal.
DR GO; GO:0016579; P:protein deubiquitination; IDA:SGD.
DR GO; GO:0045053; P:protein retention in Golgi apparatus; IMP:SGD.
DR GO; GO:0060628; P:regulation of ER to Golgi vesicle-mediated transport; IMP:SGD.
DR GO; GO:0047484; P:regulation of response to osmotic stress; IMP:SGD.
DR GO; GO:2000156; P:regulation of retrograde vesicle-mediated transport, Golgi to ER; IC:ComplexPortal.
DR GO; GO:0034517; P:ribophagy; IMP:SGD.
DR GO; GO:0034063; P:stress granule assembly; IDA:ComplexPortal.
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 3D-structure; Hydrolase; Protease; Reference proteome; Thiol protease;
KW Ubl conjugation pathway.
FT CHAIN 1..912
FT /note="Ubiquitin carboxyl-terminal hydrolase 3"
FT /id="PRO_0000080588"
FT DOMAIN 460..911
FT /note="USP"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 68..176
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 241..384
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 396..417
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..16
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 244..309
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 333..348
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 355..384
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 469
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 861
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT STRAND 208..212
FT /evidence="ECO:0007829|PDB:2QIY"
FT HELIX 214..228
FT /evidence="ECO:0007829|PDB:2QIY"
SQ SEQUENCE 912 AA; 101917 MW; 337FD05527C5542D CRC64;
MNMQDANKEE SYSMYPKTSS PPPPTPTNMQ IPIYQAPLQM YGYTQAPYLY PTQIPAYSFN
MVNQNQPIYH QSGSPHHLPP QNNINGGSTT NNNNINKKKW HSNGITNNNG SSGNQGANSS
GSGMSYNKSH TYHHNYSNNH IPMMASPNSG SNAGMKKQTN SSNGNGSSAT SPSYSSYNSS
SQYDLYKFDV TKLKNLKENS SNLIQLPLFI NTTEAEFAAA SVQRYELNMK ALNLNSESLE
NSSVEKSSAH HHTKSHSIPK HNEEVKTETH GEEEDAHDKK PHASKDAHEL KKKTEVKKED
AKQDRNEKVI QEPQATVLPV VDKKEPEESV EENTSKTSSP SPSPPAAKSW SAIASDAIKS
RQASNKTVSG SMVTKTPISG TTAGVSSTNM AAATIGKSSS PLLSKQPQKK DKKYVPPSTK
GIEPLGSIAL RMCFDPDFIS YVLRNKDVEN KIPVHSIIPR GIINRANICF MSSVLQVLLY
CKPFIDVINV LSTRNTNSRV GTSSCKLLDA CLTMYKQFDK ETYEKKFLEN ADDAEKTTES
DAKKSSKSKS FQHCATADAV KPDEFYKTLS TIPKFKDLQW GHQEDAEEFL THLLDQLHEE
LISAIDGLTD NEIQNMLQSI NDEQLKVFFI RNLSRYGKAE FIKNASPRLK ELIEKYGVIN
DDSTEENGWH EVSGSSKRGK KTKTAAKRTV EIVPSPISKL FGGQFRSVLD IPNNKESQSI
TLDPFQTIQL DISDAGVNDL ETAFKKFSEY ELLPFKSSSG NDVEAKKQTF IDKLPQVLLI
QFKRFSFINN VNKDNAMTNY NAYNGRIEKI RKKIKYGHEL IIPEESMSSI TLKNNTSGID
DRRYKLTGVI YHHGVSSDGG HYTADVYHSE HNKWYRIDDV NITELEDDDV LKGGEEASDS
RTAYILMYQK RN
