UBP24_ARATH
ID UBP24_ARATH Reviewed; 551 AA.
AC Q9FPS3; O65560; Q8L7U2;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 24;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 24;
DE Short=AtUBP24;
DE AltName: Full=Ubiquitin thioesterase 24;
DE AltName: Full=Ubiquitin-specific-processing protease 24;
GN Name=UBP24; OrderedLocusNames=At4g30890; ORFNames=F6I18.200;
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], GENE FAMILY ORGANIZATION, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
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 [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] OF 274-551.
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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA Rathjen J.P., Peck S.C.;
RT "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT thaliana.";
RL J. Proteomics 72:439-451(2009).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
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 (By similarity).
CC {ECO:0000250}.
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 -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM83229.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAA18204.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79807.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF302672; AAG42762.1; -; mRNA.
DR EMBL; AL022198; CAA18204.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161577; CAB79807.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE85824.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85825.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85826.1; -; Genomic_DNA.
DR EMBL; AY127002; AAM83229.1; ALT_INIT; mRNA.
DR EMBL; BT000568; AAN18137.1; -; mRNA.
DR PIR; F85361; F85361.
DR RefSeq; NP_001190875.1; NM_001203946.1.
DR RefSeq; NP_567860.1; NM_119236.4.
DR RefSeq; NP_974644.1; NM_202915.2.
DR AlphaFoldDB; Q9FPS3; -.
DR SMR; Q9FPS3; -.
DR BioGRID; 14500; 2.
DR STRING; 3702.AT4G30890.3; -.
DR MEROPS; C19.A14; -.
DR iPTMnet; Q9FPS3; -.
DR PaxDb; Q9FPS3; -.
DR PRIDE; Q9FPS3; -.
DR ProteomicsDB; 228489; -.
DR EnsemblPlants; AT4G30890.1; AT4G30890.1; AT4G30890.
DR EnsemblPlants; AT4G30890.2; AT4G30890.2; AT4G30890.
DR EnsemblPlants; AT4G30890.3; AT4G30890.3; AT4G30890.
DR GeneID; 829213; -.
DR Gramene; AT4G30890.1; AT4G30890.1; AT4G30890.
DR Gramene; AT4G30890.2; AT4G30890.2; AT4G30890.
DR Gramene; AT4G30890.3; AT4G30890.3; AT4G30890.
DR KEGG; ath:AT4G30890; -.
DR Araport; AT4G30890; -.
DR TAIR; locus:2126649; AT4G30890.
DR eggNOG; KOG1865; Eukaryota.
DR eggNOG; KOG1871; Eukaryota.
DR HOGENOM; CLU_008279_7_3_1; -.
DR InParanoid; Q9FPS3; -.
DR OMA; PPQSHKE; -.
DR OrthoDB; 1078977at2759; -.
DR PhylomeDB; Q9FPS3; -.
DR PRO; PR:Q9FPS3; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9FPS3; baseline and differential.
DR Genevisible; Q9FPS3; 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; Protease; Reference proteome; Thiol protease;
KW Ubl conjugation pathway.
FT CHAIN 1..551
FT /note="Ubiquitin carboxyl-terminal hydrolase 24"
FT /id="PRO_0000313050"
FT DOMAIN 197..551
FT /note="USP"
FT REGION 51..104
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 163..188
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 329..349
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 81..102
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 163..181
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 206
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 510
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
SQ SEQUENCE 551 AA; 60440 MW; C4211FEC7E931AD9 CRC64;
MSEKKVFVFG SFTEHETRSF FEQKPTKDPQ NSKDKCVGSI QFGSLNLAAE NSSVNTNGEL
KKGEADGTVK SAGSQERLDA SRPASSDKNN DSDAKLPRKN SLRVPEHVVQ NGIIKEISES
NKSLNNGVAV KTDPIGLDNL SMSDGESDPV YKASSSKFQA LDNEDFSSDS SSGSIQRKKN
LKVPTESVPP VKDFTPRGLI NAGNLCFLNA TLQALLSCSP FVQLLQKIQL QDIPKADSPT
LAAFSEFISE LDVPSSSSIR NNVTVVEAGR PFRPAMFEGV LRNFTPDVLN NMSGRPRQED
AQEFLSFIMD QMHDELLKLK EQSPKVTASK SSVISSANDD GDEWETVGPK NKSAVTRTQS
FVPSELSEIF GGQLKSVVKA KGTKASATVQ PYLLLHLDIH PDGVQGIEDA LHLFSAQEDL
EGYRASVTGK TGVVSASKSI KIQKLSKIMI LHLMRFSYGS QGSTKLRKGV KFPLELNLNR
SHLVSLSNES LRYELVATIT HHGWDPSKGH YTTDARRKNG QWLRFDDASV TPIGTKLVLH
DQAYVLFYKQ V
