UBP9_ARATH
ID UBP9_ARATH Reviewed; 910 AA.
AC Q93Y01; Q9T0B8; Q9ZSB6;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 9;
DE EC=3.4.19.12;
DE AltName: Full=Deubiquitinating enzyme 9;
DE Short=AtUBP9;
DE AltName: Full=Ubiquitin thioesterase 9;
DE AltName: Full=Ubiquitin-specific-processing protease 9;
GN Name=UBP9; OrderedLocusNames=At4g10590; ORFNames=F3H7.7, T4F9.50;
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 [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 [2]
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 [3]
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 [4]
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).
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=AAD03434.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB40025.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78182.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF118222; AAD03434.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL049523; CAB40025.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161517; CAB78182.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE82901.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE82902.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66517.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM66518.1; -; Genomic_DNA.
DR EMBL; AY054463; AAK96655.1; -; mRNA.
DR EMBL; BT010363; AAQ56806.1; -; mRNA.
DR PIR; T04194; T04194.
DR RefSeq; NP_001328408.1; NM_001340677.1.
DR RefSeq; NP_001328409.1; NM_001340676.1.
DR RefSeq; NP_567363.1; NM_117127.2.
DR RefSeq; NP_849356.1; NM_179025.2.
DR AlphaFoldDB; Q93Y01; -.
DR SMR; Q93Y01; -.
DR STRING; 3702.AT4G10590.2; -.
DR MEROPS; C19.A03; -.
DR PaxDb; Q93Y01; -.
DR PRIDE; Q93Y01; -.
DR ProteomicsDB; 228477; -.
DR EnsemblPlants; AT4G10590.1; AT4G10590.1; AT4G10590.
DR EnsemblPlants; AT4G10590.2; AT4G10590.2; AT4G10590.
DR EnsemblPlants; AT4G10590.3; AT4G10590.3; AT4G10590.
DR EnsemblPlants; AT4G10590.4; AT4G10590.4; AT4G10590.
DR GeneID; 826651; -.
DR Gramene; AT4G10590.1; AT4G10590.1; AT4G10590.
DR Gramene; AT4G10590.2; AT4G10590.2; AT4G10590.
DR Gramene; AT4G10590.3; AT4G10590.3; AT4G10590.
DR Gramene; AT4G10590.4; AT4G10590.4; AT4G10590.
DR KEGG; ath:AT4G10590; -.
DR Araport; AT4G10590; -.
DR TAIR; locus:2139222; AT4G10590.
DR eggNOG; KOG1870; Eukaryota.
DR HOGENOM; CLU_001060_7_1_1; -.
DR InParanoid; Q93Y01; -.
DR OMA; ELPCHAQ; -.
DR OrthoDB; 1283205at2759; -.
DR PhylomeDB; Q93Y01; -.
DR PRO; PR:Q93Y01; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q93Y01; baseline and differential.
DR Genevisible; Q93Y01; AT.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IEA:UniProtKB-EC.
DR GO; GO:0016579; P:protein deubiquitination; IEA:InterPro.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR Gene3D; 3.30.2230.10; -; 1.
DR InterPro; IPR035927; DUSP-like_sf.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR006615; Pept_C19_DUSP.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR Pfam; PF06337; DUSP; 1.
DR Pfam; PF00443; UCH; 1.
DR SMART; SM00695; DUSP; 1.
DR SUPFAM; SSF143791; SSF143791; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS51283; DUSP; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS00973; USP_2; 1.
DR PROSITE; PS50235; USP_3; 1.
PE 2: Evidence at transcript level;
KW Hydrolase; Protease; Reference proteome; Thiol protease;
KW Ubl conjugation pathway.
FT CHAIN 1..910
FT /note="Ubiquitin carboxyl-terminal hydrolase 9"
FT /id="PRO_0000313036"
FT DOMAIN 19..134
FT /note="DUSP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00613"
FT DOMAIN 303..894
FT /note="USP"
FT REGION 68..89
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 312
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
FT ACT_SITE 852
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092,
FT ECO:0000255|PROSITE-ProRule:PRU10093"
SQ SEQUENCE 910 AA; 102649 MW; E01B0AD928A8EE71 CRC64;
MTIPNSDFMI ENGVCDFPTT PEEEKRIVSE LITESEDNLK EGNLYFVISK RWYTSWEKYV
EQSTKEYISG ESSEASRPGP IDNHDIIESE SDVNDPQLRR LLMERVDYVL VPQEVWKRLV
EWYSGGPPIE RKLICQGFYT RSYSVEVYPL CLMLTDGRDE SRTVIRLGKQ ASIRELYEKV
CALTGVPQEK AHIWDYFDKR KNGLLDSLSY KSLEESSLHM DQDILLEVDG SSSSQSAMSS
TGNELALVPL EPSRSSVTIA GGPTLSNGHS TTSNFSLFPR ITSEDDGSNS LSILGKGEKG
GLAGLSNLGN TCFMNSALQC LAHTPPIVEY FLQDYSDDIN RDNPLGMCGE LAIAFGDLLK
KLWSSGRNSV APRAFKTKLA RFAPQFSGYN QHDSQELLAF LLDGLHEDLN KVKRKPYIEL
KDSDSRPDDE VAEELWNYHK ARNDSVIVDV CQGQYKSTLV CPACGKISIT FDPFMYLSVP
LPSTLTRSMT VTVFYCDGSH LPMPYTVIVP KNGSIRDLIT ALGTACLLAE DESLLLAEVY
DHKIFKYFEN PLDSLSSIKD DEHIVAYRLN QMPKGSGKAK LEILHGGQKR PILESVRGRD
VKLFGTPFVT YVNTEPLSGA DIDAVLSRFL SPLHKVHAPS KIHNGSENGH LPDATVDEAS
EILSSPDTEI DDASDRELSF RIFLTDERGL NFKPLQSESS ISLGIATRVL VEWNEGEHER
YDSSYLSDLP EVHKTSFSAK KTRQESISLF SCLEAFLAEE PLGPDDMWFC PSCKEHRQAN
KKLDLWKLPD ILVFHLKRFT YSRYLKNKID TFVNFPVHDL DLSKYVKNKN DQSYLYELYA
VSNHYGGLGG GHYTAYAKLI DDNEWYHFDD SHVSSVNESE IKNSAAYVLF YRRVRSETET
QTVEMSTDMD
