UBP13_ARATH
ID UBP13_ARATH Reviewed; 1115 AA.
AC Q84WU2; Q0WVD3; Q9FU99; Q9SF08;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Ubiquitin C-terminal hydrolase 13 {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 13 {ECO:0000303|PubMed:11115897};
DE Short=AtUBP13 {ECO:0000303|PubMed:11115897};
DE AltName: Full=Ubiquitin thioesterase 13 {ECO:0000303|PubMed:11115897};
DE AltName: Full=Ubiquitin-specific-processing protease 13 {ECO:0000303|PubMed:11115897};
GN Name=UBP13 {ECO:0000303|PubMed:11115897};
GN OrderedLocusNames=At3g11910 {ECO:0000312|Araport:AT3G11910};
GN ORFNames=F26K24.20 {ECO:0000312|EMBL:AAF23207.1},
GN MEC18.1 {ECO:0000312|EMBL:BAB17021.1};
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(2000).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-545.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
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 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 [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH RGI1 AND RGI2.
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 UBP12, 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 (PubMed:26888284). Interacts with RGI1
CC and RGI2 (PubMed:29339500). {ECO:0000269|PubMed:26888284,
CC ECO:0000269|PubMed:29339500}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q84WU2-1; Sequence=Displayed;
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 -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF23207.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAB17021.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC016795; AAF23207.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP002040; BAB17021.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE75116.1; -; Genomic_DNA.
DR EMBL; CP002686; ANM64251.1; -; Genomic_DNA.
DR EMBL; BT002760; AAO22588.1; -; mRNA.
DR EMBL; AK226819; BAE98915.1; -; mRNA.
DR RefSeq; NP_001326292.1; NM_001337962.1. [Q84WU2-1]
DR RefSeq; NP_187797.3; NM_112024.6. [Q84WU2-1]
DR AlphaFoldDB; Q84WU2; -.
DR SMR; Q84WU2; -.
DR BioGRID; 5698; 3.
DR STRING; 3702.AT3G11910.1; -.
DR MEROPS; C19.A53; -.
DR PaxDb; Q84WU2; -.
DR PRIDE; Q84WU2; -.
DR ProteomicsDB; 233060; -. [Q84WU2-1]
DR EnsemblPlants; AT3G11910.1; AT3G11910.1; AT3G11910. [Q84WU2-1]
DR EnsemblPlants; AT3G11910.3; AT3G11910.3; AT3G11910. [Q84WU2-1]
DR GeneID; 820364; -.
DR Gramene; AT3G11910.1; AT3G11910.1; AT3G11910. [Q84WU2-1]
DR Gramene; AT3G11910.3; AT3G11910.3; AT3G11910. [Q84WU2-1]
DR KEGG; ath:AT3G11910; -.
DR Araport; AT3G11910; -.
DR TAIR; locus:2081501; AT3G11910.
DR eggNOG; KOG1863; Eukaryota.
DR HOGENOM; CLU_003532_0_1_1; -.
DR InParanoid; Q84WU2; -.
DR PhylomeDB; Q84WU2; -.
DR PRO; PR:Q84WU2; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q84WU2; baseline and differential.
DR Genevisible; Q84WU2; 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:0009506; C:plasmodesma; HDA: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..1115
FT /note="Ubiquitin C-terminal hydrolase 13"
FT /id="PRO_0000313040"
FT DOMAIN 53..178
FT /note="MATH"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00129"
FT DOMAIN 198..522
FT /note="USP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT REGION 1..51
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 207
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 454
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035,
FT ECO:0000255|PROSITE-ProRule:PRU10092, ECO:0000255|PROSITE-
FT ProRule:PRU10093"
SQ SEQUENCE 1115 AA; 130649 MW; 29D3A53A60CCDFF1 CRC64;
MTMMTPPPLD QQEDEEMLVP NPDLVEGPQP MEVAQTDPAA TAVENPPPED PPSLKFTWTI
PMFTRLNTRK HYSDVFVVGG YKWRILIFPK GNNVDHLSMY LDVADAANLP YGWSRYSQFS
LAVVNQVNNR YSIRKETQHQ FNARESDWGF TSFMPLSELY EPTRGYLVND TVLIEAEVAV
RKVLDYWSYD SKKETGFVGL KNQGATCYMN SLLQTLYHIP YFRKAVYHMP TTENDAPTAS
IPLALQSLFY KLQYNDTSVA TKELTKSFGW DTYDSFMQHD VQELNRVLCE KLEDKMKGTV
VEGTIQKLFE GHHMNYIECI NVDYKSTRKE SFYDLQLDVK GCKDVYASFD KYVEVERLEG
DNKYHAEGHD LQDAKKGVLF IDFPPVLQLQ LKRFEYDFMR DTMVKINDRY EFPLQLDLDR
EDGRYLSPDA DKSVRNLYTL HSVLVHSGGV HGGHYYAFIR PTLSDQWYKF DDERVTKEDV
KRALEEQYGG EEELPQNNPG FNNPPFKFTK YSNAYMLVYI RESDKDKIIC NVDEKDIAEH
LRVRLKKEQE EKEDKRKYKA QAHLFTTIKV ARDDDITEQI GKNIYFDLVD HEKVRSFRIQ
KQTPFQQFKE EVAKEFGVPV QLQRFWIWAK RQNHTYRPNR PLSPNEELQT VGQIREASNK
ANNAELKLFL EIERGPDDLP IPPPEKTSED ILLFFKLYDP ENAVLRYVGR LMVKSSSKPM
DIVGQLNKMA GFAPDEEIEL FEEIKFEPCV MCEQIDKKTS FRLCQIEDGD IICYQKPLSI
EESEFRYPDV PSFLEYVQNR ELVRFRTLEK PKEDEFTMEL SKLHTYDDVV ERVAEKLGLD
DPSKLRLTSH NCYSQQPKPQ PIKYRGVDHL SDMLVHYNQT SDILYYEVLD IPLPELQGLK
TLKVAFHSAT KDEVIIHNIR LPKQSTVGDV INELKTKVEL SHQDAELRLL EVFFHKIYKI
FPSTERIENI NDQYWTLRAE EIPEEEKNIG PNDRLIHVYH FTKEAGQNQQ VQNFGEPFFL
VIHEGETLEE IKTRIQKKLH VPDEDFAKWK FASFSMGRPD YLLDTDVVYN RFQRRDVYGA
WEQYLGLEHI DNAPKRAYAA NQNRHAYEKP VKIYN
