UBP15_ARATH
ID UBP15_ARATH Reviewed; 924 AA.
AC Q9FPS9; Q9SHG9;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Ubiquitin carboxyl-terminal hydrolase 15 {ECO:0000305};
DE EC=3.4.19.12 {ECO:0000269|PubMed:18485060};
DE AltName: Full=Deubiquitinating enzyme 15 {ECO:0000305};
DE AltName: Full=Protein SUPPRESSOR 2 OF DA1 {ECO:0000303|PubMed:24585836};
DE AltName: Full=Ubiquitin thioesterase 15 {ECO:0000305};
DE AltName: Full=Ubiquitin-specific protease 15 {ECO:0000303|PubMed:11115897};
DE Short=AtUBP15 {ECO:0000303|PubMed:11115897};
GN Name=UBP15 {ECO:0000303|PubMed:11115897};
GN Synonyms=SOD2 {ECO:0000303|PubMed:24585836}; OrderedLocusNames=At1g17110;
GN ORFNames=F20D23.20;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY,
RP DISRUPTION PHENOTYPE, AND MUTAGENESIS OF CYS-447.
RX PubMed=18485060; DOI=10.1111/j.1365-313x.2008.03557.x;
RA Liu Y., Wang F., Zhang H., He H., Ma L., Deng X.W.;
RT "Functional characterization of the Arabidopsis ubiquitin-specific protease
RT gene family reveals specific role and redundancy of individual members in
RT development.";
RL Plant J. 55:844-856(2008).
RN [5]
RP FUNCTION, INTERACTION WITH DA1, AND DISRUPTION PHENOTYPE.
RX PubMed=24585836; DOI=10.1105/tpc.114.122663;
RA Du L., Li N., Chen L., Xu Y., Li Y., Zhang Y., Li C., Li Y.;
RT "The ubiquitin receptor DA1 regulates seed and organ size by modulating the
RT stability of the ubiquitin-specific protease UBP15/SOD2 in Arabidopsis.";
RL Plant Cell 26:665-677(2014).
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 (Probable).
CC Involved in the regulation of organ size. Acts as positive regulator of
CC cell proliferation. Possesses deubiquitinating enzyme activity in
CC vitro. The enzyme activity of UBP15 is required for its function in
CC regulation of cell proliferation (PubMed:18485060). Functions
CC antagonistically in a common pathway with DA1 to regulate seed size.
CC Acts maternally to regulate seed size by promoting cell proliferation
CC in the integuments of ovules and developing seeds. Functions
CC independently of DA2 and BB (PubMed:24585836).
CC {ECO:0000269|PubMed:18485060, ECO:0000269|PubMed:24585836,
CC ECO:0000305|PubMed:18485060}.
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:0000269|PubMed:18485060};
CC -!- SUBUNIT: Interacts with DA1. {ECO:0000269|PubMed:24585836}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:18485060}. Nucleus
CC {ECO:0000269|PubMed:18485060}.
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=Q9FPS9-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Highly expressed in rosette leaves and
CC inflorescence. Expressed at low levels in cotyledons, stems, cauline
CC leaves and siliques. {ECO:0000269|PubMed:18485060}.
CC -!- DISRUPTION PHENOTYPE: Narrow, serrated and flat rosette leaves, early
CC flowering, weak apical dominance and reduced fertility, partially due
CC to defect in cell proliferation (PubMed:18485060). Reduced seed weight
CC (PubMed:24585836). {ECO:0000269|PubMed:18485060,
CC ECO:0000269|PubMed:24585836}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD50020.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF302665; AAG42756.1; -; mRNA.
DR EMBL; AC007651; AAD50020.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE29542.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM60192.1; -; Genomic_DNA.
DR PIR; H86306; H86306.
DR RefSeq; NP_001322494.1; NM_001332280.1. [Q9FPS9-1]
DR RefSeq; NP_564014.1; NM_101571.2. [Q9FPS9-1]
DR AlphaFoldDB; Q9FPS9; -.
DR SMR; Q9FPS9; -.
DR BioGRID; 23521; 3.
DR STRING; 3702.AT1G17110.2; -.
DR MEROPS; C19.096; -.
DR PaxDb; Q9FPS9; -.
DR PRIDE; Q9FPS9; -.
DR ProteomicsDB; 233048; -. [Q9FPS9-1]
DR EnsemblPlants; AT1G17110.1; AT1G17110.1; AT1G17110. [Q9FPS9-1]
DR EnsemblPlants; AT1G17110.3; AT1G17110.3; AT1G17110. [Q9FPS9-1]
DR GeneID; 838281; -.
DR Gramene; AT1G17110.1; AT1G17110.1; AT1G17110. [Q9FPS9-1]
DR Gramene; AT1G17110.3; AT1G17110.3; AT1G17110. [Q9FPS9-1]
DR KEGG; ath:AT1G17110; -.
DR Araport; AT1G17110; -.
DR eggNOG; KOG1865; Eukaryota.
DR InParanoid; Q9FPS9; -.
DR OMA; HECARCS; -.
DR PhylomeDB; Q9FPS9; -.
DR PRO; PR:Q9FPS9; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9FPS9; baseline and differential.
DR Genevisible; Q9FPS9; 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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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 InterPro; IPR002893; Znf_MYND.
DR Pfam; PF00443; UCH; 1.
DR Pfam; PF01753; zf-MYND; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS00972; USP_1; 1.
DR PROSITE; PS50235; USP_3; 1.
DR PROSITE; PS01360; ZF_MYND_1; 1.
DR PROSITE; PS50865; ZF_MYND_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cytoplasm; Hydrolase; Metal-binding; Nucleus;
KW Protease; Reference proteome; Thiol protease; Ubl conjugation pathway;
KW Zinc; Zinc-finger.
FT CHAIN 1..924
FT /note="Ubiquitin carboxyl-terminal hydrolase 15"
FT /id="PRO_0000313041"
FT DOMAIN 438..744
FT /note="USP"
FT ZN_FING 130..167
FT /note="MYND-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT REGION 226..301
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 317..366
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 750..793
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 226..241
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 243..260
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 285..301
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 327..366
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 750..788
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 447
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT ACT_SITE 703
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10092"
FT BINDING 130
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 133
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 141
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 144
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 154
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 163
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 167
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT MUTAGEN 447
FT /note="C->A,S: Abolishes deubiquitination enzyme activity."
FT /evidence="ECO:0000269|PubMed:18485060"
FT CONFLICT 106
FT /note="R -> K (in Ref. 1; AAG42756)"
FT /evidence="ECO:0000305"
FT CONFLICT 390
FT /note="I -> V (in Ref. 1; AAG42756)"
FT /evidence="ECO:0000305"
FT CONFLICT 536
FT /note="Q -> P (in Ref. 1; AAG42756)"
FT /evidence="ECO:0000305"
FT CONFLICT 568
FT /note="R -> H (in Ref. 1; AAG42756)"
FT /evidence="ECO:0000305"
FT CONFLICT 599..600
FT /note="SL -> FF (in Ref. 1; AAG42756)"
FT /evidence="ECO:0000305"
FT CONFLICT 605
FT /note="T -> I (in Ref. 1; AAG42756)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 924 AA; 103677 MW; 32BD93822243271C CRC64;
MLEPRGADIP ILFLVLVVLP VVAYILLGKW SNISEKRVRA NLLAQMAAEE ALRAETVVNA
DRGVRFESVA TENRAQRTRT KTVSAGGGAV RAEFDAGARE TVAEQRSDSV TATCGVTVVA
PVNNNELHVC ARCFGPAKTR CSRCKSVRYC SGKCQIIHWR VAHKDECVPV ESCSSSSERV
SFEKDSVLYD HGMDSTMYSN NTTQAAKGKT SKSSVDFASL GISQNDITPQ INTQGRKSVG
KQHSSKANRE SCRRDSATVF DSSDEAASAG GDNKTSHIKH KSRGNSYAAE TNPRRHSVDS
SAVQMNGQSF VSGMQESHKH ENNLGVRSSF GCPNTQYPSN GTRTATLPRT GINKSGEQSC
TETSKKGQVA AVSKTVRSKD TGISEESNGI SSTMGIMKMM GLRNSTKHDD RYKNLKMLFP
YEEFLKFFQC EVFDLSPRGL VNCGNSCYAN AVLQSLTCTK PLVAYLLRRS HSRSCSGKDW
CLMCELEQHV MMLRESGGPL SASRILSHMR SINCQIGDGS QEDAHEFLRL LVASMQSICL
ERLGGETKVD PRLQETTLVQ HMFGGRLRSK VKCLRCDHES ERYENIMDLT LEIYGWVESL
QDALTQFTRP EDLDGENMYR CSRCAGYVRA RKELSIHEAP NILTIVLKRF QEGRYGKINK
CISFPEMLDM IPFMTRTGDV PPLYMLYAVI VHLDTLNASF SGHYISYVKD LRGNWYRIDD
SEIHPVPMTQ VMSEGAYMLF YMRSYPRPQR GEHNGKAPVH HSQPRNEMKE QRKPVNRFKP
RADHKNTESS SSEWSLFTSS DEASFTTEST RDSFSTIDYT DVCHVVDSSS PFAIFNNVYH
NVEPSPHNTV ACRMFSGTKP ETRYFVEQET NHNNTVVLDA TPSLYPIPAP YPPHDYYDQS
MYVNYETNPE FNNGQDQDRT YSYW
