UBP15_ORYSJ
ID UBP15_ORYSJ Reviewed; 975 AA.
AC Q0E2F9; A0A0P0VH87; Q6ESV0;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=Ubiquitin C-terminal hydrolase 15 {ECO:0000305};
DE EC=3.4.19.12 {ECO:0000269|PubMed:30796160};
DE AltName: Full=Deubiquitinating enzyme 15 {ECO:0000305};
DE AltName: Full=Protein LARGE GRAIN 1 {ECO:0000303|PubMed:30796160};
DE AltName: Full=Ubiquitin thioesterase 15 {ECO:0000305};
DE AltName: Full=Ubiquitin-specific protease 15 {ECO:0000303|PubMed:30796160};
DE Short=OsUBP15 {ECO:0000303|PubMed:30796160};
GN Name=UBP15 {ECO:0000303|PubMed:30796160};
GN Synonyms=LG1 {ECO:0000303|PubMed:30796160};
GN OrderedLocusNames=Os02g0244300 {ECO:0000312|EMBL:BAS77856.1},
GN LOC_Os02g14730 {ECO:0000305};
GN ORFNames=P0503B05.35 {ECO:0000312|EMBL:BAD28270.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP GENE FAMILY.
RX PubMed=30498503; DOI=10.3389/fpls.2018.01636;
RA Wang D.H., Song W., Wei S.W., Zheng Y.F., Chen Z.S., Han J.D., Zhang H.T.,
RA Luo J.C., Qin Y.M., Xu Z.H., Bai S.N.;
RT "Characterization of the ubiquitin C-terminal hydrolase and ubiquitin-
RT specific protease families in rice (Oryza sativa).";
RL Front. Plant Sci. 9:1636-1636(2018).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=30796160; DOI=10.1104/pp.19.00065;
RA Shi C., Ren Y., Liu L., Wang F., Zhang H., Tian P., Pan T., Wang Y.,
RA Jing R., Liu T., Wu F., Lin Q., Lei C., Zhang X., Zhu S., Guo X., Wang J.,
RA Zhao Z., Wang J., Zhai H., Cheng Z., Wan J.;
RT "Ubiquitin specific protease 15 has an important role in regulating grain
RT width and size in rice.";
RL Plant Physiol. 180:381-391(2019).
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 grain size (PubMed:30796160). Acts as
CC positive regulator of grain width and size by influencing cell
CC proliferation (PubMed:30796160). Functions partially antagonistically
CC with GW2 in the regulation of grain width (PubMed:30796160). Possesses
CC deubiquitinating enzyme activity in vitro (PubMed:30796160).
CC {ECO:0000269|PubMed:30796160, ECO:0000305|PubMed:30796160}.
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:30796160};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:30796160}. Nucleus
CC {ECO:0000269|PubMed:30796160}.
CC -!- TISSUE SPECIFICITY: Highly expressed in young panicles
CC (PubMed:30796160). Expressed in roots, leaf blades, leaf sheaths and
CC stems (PubMed:30796160). Expressed at low levels in brown grains
CC (PubMed:30796160). {ECO:0000269|PubMed:30796160}.
CC -!- MISCELLANEOUS: The dominant gain-of-function large grain1-D (lg1-D)
CC develops significantly enlarged grains. {ECO:0000269|PubMed:30796160}.
CC -!- SIMILARITY: Belongs to the peptidase C19 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD28270.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP005004; BAD28270.1; ALT_INIT; Genomic_DNA.
DR EMBL; AP008208; BAF08329.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS77856.1; -; Genomic_DNA.
DR RefSeq; XP_015627057.1; XM_015771571.1.
DR AlphaFoldDB; Q0E2F9; -.
DR SMR; Q0E2F9; -.
DR STRING; 4530.OS02T0244300-01; -.
DR MEROPS; C19.096; -.
DR PRIDE; Q0E2F9; -.
DR EnsemblPlants; Os02t0244300-01; Os02t0244300-01; Os02g0244300.
DR GeneID; 4328857; -.
DR Gramene; Os02t0244300-01; Os02t0244300-01; Os02g0244300.
DR KEGG; osa:4328857; -.
DR eggNOG; KOG1865; Eukaryota.
DR HOGENOM; CLU_007397_1_0_1; -.
DR InParanoid; Q0E2F9; -.
DR OMA; HECARCS; -.
DR OrthoDB; 561804at2759; -.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
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:0051301; P:cell division; IEA:EnsemblPlants.
DR GO; GO:0009908; P:flower development; IEA:EnsemblPlants.
DR GO; GO:0010154; P:fruit development; IEA:EnsemblPlants.
DR GO; GO:0048366; P:leaf development; IEA:EnsemblPlants.
DR GO; GO:0016579; P:protein deubiquitination; IBA:GO_Central.
DR GO; GO:0048364; P:root development; IEA:EnsemblPlants.
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 2: Evidence at transcript level;
KW Cytoplasm; Hydrolase; Metal-binding; Nucleus; Protease; Reference proteome;
KW Thiol protease; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..975
FT /note="Ubiquitin C-terminal hydrolase 15"
FT /id="PRO_0000454380"
FT DOMAIN 441..747
FT /note="USP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT ZN_FING 88..125
FT /note="MYND-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT REGION 301..378
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 764..783
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 308..323
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 335..349
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 350..366
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 450
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT ACT_SITE 706
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01035"
FT BINDING 88
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 102
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 108
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 121
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
FT BINDING 125
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00134"
SQ SEQUENCE 975 AA; 108072 MW; DFCD345331411379 CRC64;
MLQPRESDVP VLFVVFIVLP VIAYFLLGRW HDAVSKKARV SVLAQRAAEE TFKVETMATP
DVILPGPSLR PMPYMRSAPS ARPEYHECAT CHGPAKTRCS RCKSVRYCSG KCQIIHWRQG
HKQTCQQWNG FGTSSSGGLP PTENTEQMPF LSNLNSPLRG SDVHLHDMDF DTMSEPSFVT
TDSYNLDTSP FLSDRSNMNK PNQFLHTSEN GAAIGSYEKN DYSIDGEVPS SEILSGNKGL
NNSSGSGENC GNRDVIYPLN SVVHQPNNYA PEIRKRPKAS ITVYESDKGV YLTSDMISSG
EGPYASAAES LQRSNSSGNV TGKGNMIHKK PPYPSGKVSS SQKSQEKVLT SHQYDGHEKN
PHNKNEQRST KTAVSTNSSL QGCNGISKAG ASKVEALKKP SKFLKTSLVG LINDNKRSKV
LFPYEDLVKF FQYEVRGISP RGLFNCGNSC YANAVLQCLM CTKPLMIYLL LRLHSKDCCS
KNWCLMCELE QYASTLRESG GPVSPSRILS NLRNIGCRLG GGSQEDAHEF LRHLVMSMQG
ACLDGLGGEK QVEASLQETT LIQQMFGGRL KSKVKCLRCY HESERYENIM DLTLEIHGWV
ESLQDALTQF TAPEDLDGEN MYKCGRCSAY VKARKQLSVH EVPNILTVVL KRFQTGKYGK
INKCVTFPDM LDMVPFVTGA GDNPPLYFLY AVVVHVDTEN ASFSGHYISY VKDMQGTWLR
IDDSEVQAVS LNQVMSEGAY MLFYMRSFPR PPKIYIEKGL SSVPTCSKRH SSKSSKGSKQ
DLNHTESLFA SSDQTYGIYD FRPDNGYIQD QHAALRTRNF YHTDDAFADS ISTDFSDATS
SEWSLFTSSD ESSFTTESTR DSFSVVDYGD NAGLDPISSI FGPYYAQDHP PGSFASCTRL
SPSNPQTRYF QENTGFVSDS SMPAHLPGNV HRGRYPDRAC SSSAEPPASA NPRSVYGRYG
LSREGFVQTS GFCQM
