UBP12_ARATH
ID UBP12_ARATH Reviewed; 1116 AA.
AC Q9FPT1; Q9C5K1; Q9FG10;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Ubiquitin C-terminal hydrolase 12 {ECO:0000303|PubMed:11115897};
DE EC=3.4.19.12 {ECO:0000255|PROSITE-ProRule:PRU10092, ECO:0000255|PROSITE-ProRule:PRU10093};
DE AltName: Full=Deubiquitinating enzyme 12 {ECO:0000303|PubMed:11115897};
DE Short=AtUBP12 {ECO:0000303|PubMed:11115897};
DE AltName: Full=Ubiquitin thioesterase 12 {ECO:0000303|PubMed:11115897};
DE AltName: Full=Ubiquitin-specific-processing protease 12 {ECO:0000303|PubMed:11115897};
GN Name=UBP12 {ECO:0000303|PubMed:11115897};
GN OrderedLocusNames=At5g06600 {ECO:0000312|Araport:AT5G06600};
GN ORFNames=F15M7.13 {ECO:0000312|EMBL:BAB11409.1};
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] (ISOFORM 1), GENE FAMILY ORGANIZATION, AND
RP 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;
RA Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
RL Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases.
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] (ISOFORM 2).
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 INTERACTION WITH SIC/RON3.
RC STRAIN=cv. Columbia, and cv. Landsberg erecta;
RX PubMed=26888284; DOI=10.1073/pnas.1501343112;
RA Karampelias M., Neyt P., De Groeve S., Aesaert S., Coussens G., Rolcik J.,
RA Bruno L., De Winne N., Van Minnebruggen A., Van Montagu M., Ponce M.R.,
RA Micol J.L., Friml J., De Jaeger G., Van Lijsebettens M.;
RT "ROTUNDA3 function in plant development by phosphatase 2A-mediated
RT regulation of auxin transporter recycling.";
RL Proc. Natl. Acad. Sci. U.S.A. 113:2768-2773(2016).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=29339500; DOI=10.1073/pnas.1714177115;
RA An Z., Liu Y., Ou Y., Li J., Zhang B., Sun D., Sun Y., Tang W.;
RT "Regulation of the stability of RGF1 receptor by the ubiquitin-specific
RT proteases UBP12/UBP13 is critical for root meristem maintenance.";
RL Proc. Natl. Acad. Sci. U.S.A. 115:1123-1128(2018).
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 Positive regulator of root meristem development that, together with
CC UBP13, prevents the ubiquitination and turnover of RGFR1 induced by the
CC RGF1 hormone peptide, thus influencing PLT1 and PLT2 expression
CC (PubMed:29339500). {ECO:0000250|UniProtKB:Q9FPT5,
CC ECO:0000269|PubMed:29339500}.
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:0000255|PROSITE-
CC ProRule:PRU10092, ECO:0000255|PROSITE-ProRule:PRU10093};
CC -!- SUBUNIT: Interacts with SIC/RON3. {ECO:0000269|PubMed:26888284}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9FPT1-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9FPT1-2; Sequence=VSP_029989;
CC -!- DISRUPTION PHENOTYPE: The double mutant ubp12 ubp13 roots are
CC completely insensitive to exogenous applied hormone peptide RGF1
CC associated with an accelerated RGF1-induced ubiquitination and turnover
CC of RGFR1 and are characterized by a reduced number of cortical meristem
CC cells and disturbed PLT1 and PLT2 expression.
CC {ECO:0000269|PubMed:29339500}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB11409.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF302663; AAG42754.1; -; mRNA.
DR EMBL; AP002543; BAB11409.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91039.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91040.1; -; Genomic_DNA.
DR EMBL; AF360198; AAK25908.1; -; mRNA.
DR EMBL; AY142616; AAN13185.1; -; mRNA.
DR RefSeq; NP_568171.1; NM_120743.3. [Q9FPT1-1]
DR RefSeq; NP_850783.1; NM_180452.1. [Q9FPT1-2]
DR AlphaFoldDB; Q9FPT1; -.
DR SMR; Q9FPT1; -.
DR BioGRID; 15827; 5.
DR IntAct; Q9FPT1; 1.
DR STRING; 3702.AT5G06600.1; -.
DR MEROPS; C19.A73; -.
DR iPTMnet; Q9FPT1; -.
DR PaxDb; Q9FPT1; -.
DR PRIDE; Q9FPT1; -.
DR ProteomicsDB; 228466; -. [Q9FPT1-1]
DR EnsemblPlants; AT5G06600.1; AT5G06600.1; AT5G06600. [Q9FPT1-1]
DR EnsemblPlants; AT5G06600.2; AT5G06600.2; AT5G06600. [Q9FPT1-2]
DR GeneID; 830548; -.
DR Gramene; AT5G06600.1; AT5G06600.1; AT5G06600. [Q9FPT1-1]
DR Gramene; AT5G06600.2; AT5G06600.2; AT5G06600. [Q9FPT1-2]
DR KEGG; ath:AT5G06600; -.
DR Araport; AT5G06600; -.
DR TAIR; locus:2144118; AT5G06600.
DR eggNOG; KOG1863; Eukaryota.
DR InParanoid; Q9FPT1; -.
DR OMA; KMKGTCL; -.
DR OrthoDB; 77113at2759; -.
DR PhylomeDB; Q9FPT1; -.
DR PRO; PR:Q9FPT1; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FPT1; baseline and differential.
DR Genevisible; Q9FPT1; AT.
DR GO; GO:0005737; C:cytoplasm; IPI:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IPI:TAIR.
DR GO; GO:0004843; F:cysteine-type deubiquitinase activity; IDA:TAIR.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IBA:GO_Central.
DR GO; GO:0009867; P:jasmonic acid mediated signaling pathway; IMP:TAIR.
DR GO; GO:0010078; P:maintenance of root meristem identity; IMP:UniProtKB.
DR GO; GO:0016579; P:protein deubiquitination; IDA:TAIR.
DR GO; GO:0070646; P:protein modification by small protein removal; IMP:UniProtKB.
DR GO; GO:0031647; P:regulation of protein stability; IMP:UniProtKB.
DR GO; GO:2000280; P:regulation of root development; IMP:UniProtKB.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IEA:InterPro.
DR CDD; cd00121; MATH; 1.
DR Gene3D; 2.60.210.10; -; 1.
DR InterPro; IPR002083; MATH/TRAF_dom.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR001394; Peptidase_C19_UCH.
DR InterPro; IPR008974; TRAF-like.
DR InterPro; IPR024729; USP7_ICP0-binding_dom.
DR InterPro; IPR029346; USP_C.
DR InterPro; IPR018200; USP_CS.
DR InterPro; IPR028889; USP_dom.
DR Pfam; PF00917; MATH; 1.
DR Pfam; PF00443; UCH; 1.
DR Pfam; PF14533; USP7_C2; 1.
DR Pfam; PF12436; USP7_ICP0_bdg; 1.
DR SMART; SM00061; MATH; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS50144; MATH; 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 Alternative splicing; Hydrolase; Protease; Reference proteome;
KW Thiol protease; Ubl conjugation pathway.
FT CHAIN 1..1116
FT /note="Ubiquitin C-terminal hydrolase 12"
FT /id="PRO_0000313039"
FT DOMAIN 54..179
FT /note="MATH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00129"
FT DOMAIN 199..524
FT /note="USP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT REGION 1..52
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 35..49
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 208
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035,
FT ECO:0000255|PROSITE-ProRule:PRU10092, ECO:0000255|PROSITE-
FT ProRule:PRU10093"
FT ACT_SITE 455
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035,
FT ECO:0000255|PROSITE-ProRule:PRU10092, ECO:0000255|PROSITE-
FT ProRule:PRU10093"
FT VAR_SEQ 11
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_029989"
FT CONFLICT 840
FT /note="L -> F (in Ref. 1; AAG42754)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1116 AA; 130607 MW; E1FD0B84E6D5EC68 CRC64;
MTMMTPPPVD QPEDEEMLVP NSDLVDGPAQ PMEVTQPETA ASTVENQPAE DPPTLKFTWT
IPNFSRQNTR KHYSDVFVVG GYKWRILIFP KGNNVDHLSM YLDVSDAASL PYGWSRYAQF
SLAVVNQIHT RYTVRKETQH QFNARESDWG FTSFMPLSEL YDPSRGYLVN DTVLVEAEVA
VRKVLDYWSY DSKKETGFVG LKNQGATCYM NSLLQTLYHI PYFRKAVYHM PTTENDAPTA
SIPLALQSLF YKLQYNDTSV ATKELTKSFG WDTYDSFMQH DVQELNRVLC EKLEDKMKGT
VVEGTIQQLF EGHHMNYIEC INVDFKSTRK ESFYDLQLDV KGCKDVYASF DKYVEVERLE
GDNKYHAEGH GLQDAKKGVL FIDFPPVLQL QLKRFEYDFM RDTMVKINDR YEFPLELDLD
REDGKYLSPD ADRSVRNLYT LHSVLVHSGG VHGGHYYAFI RPTLSDQWYK FDDERVTKED
LKRALEEQYG GEEELPQTNP GFNNNPPFKF TKYSNAYMLV YIRESDKDKI ICNVDEKDIA
EHLRVRLKKE QEEKEDKRRY KAQAHLYTII KVARDEDLKE QIGKDIYFDL VDHDKVRSFR
IQKQTPFQQF KEEVAKEFGV PVQLQRFWIW AKRQNHTYRP NRPLTPQEEL QPVGQIREAS
NKANTAELKL FLEVEHLDLR PIPPPEKSKE DILLFFKLYD PEKAVLSYAG RLMVKSSSKP
MDITGKLNEM VGFAPDEEIE LFEEIKFEPC VMCEHLDKKT SFRLCQIEDG DIICFQKPLV
NKEIECLYPA VPSFLEYVQN RQLVRFRALE KPKEDEFVLE LSKQHTYDDV VEKVAEKLGL
DDPSKLRLTS HNCYSQQPKP QPIKYRGVDH LSDMLVHYNQ TSDILYYEVL DIPLPELQGL
KTLKVAFHHA TKEEVVIHNI RLPKQSTVGD VINELKTKVE LSHPDAELRL LEVFYHKIYK
IFPSTERIEN INDQYWTLRA EEIPEEEKNI GPNDRLILVY HFAKETGQNQ QVQNFGEPFF
LVIHEGETLE EIKNRIQKKL HVSDEDFAKW KFAFMSMGRP EYLQDTDVVY NRFQRRDVYG
AFEQYLGLEH ADTTPKRAYA ANQNRHAYEK PVKIYN
