UBP3_ARATH
ID UBP3_ARATH Reviewed; 371 AA.
AC O24454;
DT 26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 3;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 3;
DE Short=AtUBP3;
DE AltName: Full=Ubiquitin thioesterase 3;
DE AltName: Full=Ubiquitin-specific-processing protease 3;
GN Name=UBP3; OrderedLocusNames=At4g39910; ORFNames=T5J17.80;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-32,
RP AND TISSUE SPECIFICITY.
RC STRAIN=cv. Landsberg erecta;
RX PubMed=9268021; DOI=10.1007/s004380050501;
RA Chandler J.S., McArdle B., Callis J.;
RT "AtUBP3 and AtUBP4 are two closely related Arabidopsis thaliana ubiquitin-
RT specific proteases present in the nucleus.";
RL Mol. Gen. Genet. 255:302-310(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP FUNCTION.
RX PubMed=10898935; DOI=10.1006/abbi.2000.1874;
RA Rao-Naik C., Chandler J.S., McArdle B., Callis J.;
RT "Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5
RT and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using
RT Escherichia coli in vivo and in vitro assays.";
RL Arch. Biochem. Biophys. 379:198-208(2000).
RN [6]
RP GENE FAMILY ORGANIZATION, AND NOMENCLATURE.
RX PubMed=11115897; DOI=10.1104/pp.124.4.1828;
RA Yan N., Doelling J.H., Falbel T.G., Durski A.M., Vierstra R.D.;
RT "The ubiquitin-specific protease family from Arabidopsis. AtUBP1 and 2 are
RT required for the resistance to the amino acid analog canavanine.";
RL Plant Physiol. 124:1828-1843(2000).
RN [7]
RP MYRISTOYLATION AT GLY-2.
RX PubMed=12912986; DOI=10.1074/jbc.m307321200;
RA Boisson B., Giglione C., Meinnel T.;
RT "Unexpected protein families including cell defense components feature in
RT the N-myristoylome of a higher eukaryote.";
RL J. Biol. Chem. 278:43418-43429(2003).
RN [8]
RP FUNCTION.
RX PubMed=17905865; DOI=10.1104/pp.106.095323;
RA Doelling J.H., Phillips A.R., Soyler-Ogretim G., Wise J., Chandler J.S.,
RA Callis J., Otegui M.S., Vierstra R.D.;
RT "The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for
RT pollen development and transmission in Arabidopsis.";
RL Plant Physiol. 145:801-813(2007).
CC -!- FUNCTION: Recognizes and hydrolyzes the peptide bond at the C-terminal
CC Gly of ubiquitin. Involved in the processing of poly-ubiquitin
CC precursors as well as that of ubiquitinated proteins. Required for the
CC correct development of pollen. {ECO:0000269|PubMed:10898935,
CC ECO:0000269|PubMed:17905865}.
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 -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9268021}.
CC -!- TISSUE SPECIFICITY: Constitutively and ubiquitously expressed.
CC {ECO:0000269|PubMed:9268021}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
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DR EMBL; U76845; AAB67966.1; -; mRNA.
DR EMBL; AL035708; CAB38904.1; -; Genomic_DNA.
DR EMBL; AL161596; CAB80654.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE87136.1; -; Genomic_DNA.
DR EMBL; AY058889; AAL24275.1; -; mRNA.
DR EMBL; AY079044; AAL79594.1; -; mRNA.
DR PIR; T06097; T06097.
DR RefSeq; NP_568074.1; NM_120154.5.
DR AlphaFoldDB; O24454; -.
DR SMR; O24454; -.
DR STRING; 3702.AT4G39910.1; -.
DR MEROPS; C19.008; -.
DR MEROPS; C19.092; -.
DR iPTMnet; O24454; -.
DR PaxDb; O24454; -.
DR PRIDE; O24454; -.
DR ProteomicsDB; 228474; -.
DR EnsemblPlants; AT4G39910.1; AT4G39910.1; AT4G39910.
DR GeneID; 830150; -.
DR Gramene; AT4G39910.1; AT4G39910.1; AT4G39910.
DR KEGG; ath:AT4G39910; -.
DR Araport; AT4G39910; -.
DR TAIR; locus:2140074; AT4G39910.
DR eggNOG; KOG1864; Eukaryota.
DR HOGENOM; CLU_008279_2_0_1; -.
DR InParanoid; O24454; -.
DR OMA; NKYFCDV; -.
DR OrthoDB; 378361at2759; -.
DR PhylomeDB; O24454; -.
DR PRO; PR:O24454; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O24454; baseline and differential.
DR Genevisible; O24454; AT.
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; IBA:GO_Central.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
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; Lipoprotein; Myristate; Nucleus; Protease; Reference proteome;
KW Thiol protease; Ubl conjugation pathway.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000255"
FT CHAIN 2..371
FT /note="Ubiquitin carboxyl-terminal hydrolase 3"
FT /id="PRO_0000080694"
FT DOMAIN 23..367
FT /note="USP"
FT MOTIF 83..100
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000255"
FT ACT_SITE 32
FT /note="Nucleophile"
FT ACT_SITE 315
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT LIPID 2
FT /note="N-myristoyl glycine"
FT /evidence="ECO:0000269|PubMed:12912986"
FT MUTAGEN 32
FT /note="C->S: Loss of activity."
FT /evidence="ECO:0000269|PubMed:9268021"
SQ SEQUENCE 371 AA; 42447 MW; 2C843280BDF24D3B CRC64;
MGAAGSKLEK ALGDQFPEGE RYFGFENFGN TCYCNSVLQA LYFCVPFREQ LLEYYTSNKS
VADAEENLMT CLADLFSQIS SQKKKTGVIA PKRFVQRLKK QNELFRSYMH QDAHEFLNYL
LNEVVDILEK EAKATKTEHE TSSSSSPEKI ANGLKVPQAN GVVHKEPIVT WVHNIFQGIL
TNETRCLRCE TVTARDETFL DLSLDIEQNS SITSCLKNFS STETLHAEDK FFCDKCCSLQ
EAQKRMKIKK PPHILVIHLK RFKYIEQLGR YKKLSYRVVF PLELKLSNTV EPYADVEYSL
FAVVVHVGSG PNHGHYVSLV KSHNHWLFFD DENVEMIEES AVQTFFGSSQ EYSSNTDHGY
ILFYESLGPT K
