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 27-MAR-2024, entry version 131. 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}, MEC18.1 GN {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}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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; 4. DR STRING; 3702.Q84WU2; -. DR MEROPS; C19.A53; -. DR PaxDb; 3702-AT3G11910-1; -. 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; AT3G11910; UBP13. DR eggNOG; KOG1863; Eukaryota. DR HOGENOM; CLU_003532_0_1_1; -. DR InParanoid; Q84WU2; -. DR OrthoDB; 51419at2759; -. DR PhylomeDB; Q84WU2; -. DR PRO; PR:Q84WU2; -. DR Proteomes; UP000006548; Chromosome 3. DR ExpressionAtlas; Q84WU2; baseline and differential. 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: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:0006508; P:proteolysis; IEA:UniProtKB-KW. DR GO; GO:0031647; P:regulation of protein stability; IMP:UniProtKB. DR GO; GO:2000280; P:regulation of root development; IMP:UniProtKB. DR CDD; cd00121; MATH; 1. DR CDD; cd02659; peptidase_C19C; 1. DR Gene3D; 3.90.70.10; Cysteine proteinases; 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 PANTHER; PTHR24006:SF943; UBIQUITIN C-TERMINAL HYDROLASE 13; 1. DR PANTHER; PTHR24006; UBIQUITIN CARBOXYL-TERMINAL HYDROLASE; 1. 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; Cysteine proteinases; 1. DR SUPFAM; SSF49599; TRAF domain-like; 1. DR PROSITE; PS50144; MATH; 1. DR PROSITE; PS00972; USP_1; 1. DR PROSITE; PS00973; USP_2; 1. DR PROSITE; PS50235; USP_3; 1. DR Genevisible; Q84WU2; AT. 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 //