ID VPE1_ORYSJ Reviewed; 497 AA.
AC Q84LM2; A0A0P0WCV4;
DT 04-MAR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 24-JAN-2024, entry version 119.
DE RecName: Full=Vacuolar-processing enzyme beta-isozyme 1 {ECO:0000303|PubMed:19154227};
DE Short=Beta-VPE 1 {ECO:0000303|PubMed:19154227};
DE Short=OsVPE1 {ECO:0000303|PubMed:19154227};
DE EC=3.4.22.34 {ECO:0000269|PubMed:19154227};
DE AltName: Full=Asparaginyl endopeptidase VPE1 {ECO:0000305};
DE Flags: Precursor;
GN Name=VPE1 {ECO:0000303|PubMed:19154227};
GN Synonyms=Glup3 {ECO:0000303|Ref.1};
GN OrderedLocusNames=Os04g0537900 {ECO:0000312|EMBL:BAF15342.1};
GN ORFNames=OsJ_15605 {ECO:0000312|EMBL:EEE61412.1};
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 {ECO:0000312|EMBL:BAC76418.1};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Kinmaze;
RA Kumamaru T., Uemura U., Takemoto Y., Ogawa M., Satoh H.;
RT "High-resolution mapping of glup3 gene accumulating high amount of glutelin
RT precursor.";
RL Rice Genet. Newsl. 19:62-63(2002).
RN [2]
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 [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP FUNCTION, MUTAGENESIS OF CYS-269, SUBCELLULAR LOCATION, SITE, CATALYTIC
RP ACTIVITY, AND AUTO-CATALYTIC ACTIVATION.
RX PubMed=19154227; DOI=10.1111/j.1365-313x.2009.03801.x;
RA Wang Y., Zhu S., Liu S., Jiang L., Chen L., Ren Y., Han X., Liu F., Ji S.,
RA Liu X., Wan J.;
RT "The vacuolar processing enzyme OsVPE1 is required for efficient glutelin
RT processing in rice.";
RL Plant J. 58:606-617(2009).
RN [7]
RP FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF CYS-269 AND GLY-333, AND
RP TISSUE SPECIFICITY.
RX PubMed=19933265; DOI=10.1093/pcp/pcp165;
RA Kumamaru T., Uemura Y., Inoue Y., Takemoto Y., Siddiqui S.U., Ogawa M.,
RA Hara-Nishimura I., Satoh H.;
RT "Vacuolar processing enzyme plays an essential role in the crystalline
RT structure of glutelin in rice seed.";
RL Plant Cell Physiol. 51:38-46(2010).
CC -!- FUNCTION: Asparagine-specific endopeptidase that may be involved in
CC processing of proteins targeted to vacuoles. Cysteine protease required
CC for post-translational proteolysis of seed storage proteins in the
CC protein storage vacuole (PSV) of developing seeds, by processing of
CC proglutelin precursor to mature glutelin subunits, thus contributing to
CC the formation of protein crystalline structures in PSV (Ref.1,
CC PubMed:19154227, PubMed:19933265). {ECO:0000269|PubMed:19154227,
CC ECO:0000269|PubMed:19933265, ECO:0000269|Ref.1}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of proteins and small molecule substrates at
CC -Asn-|-Xaa- bonds.; EC=3.4.22.34;
CC Evidence={ECO:0000269|PubMed:19154227};
CC -!- SUBCELLULAR LOCATION: Protein storage vacuole
CC {ECO:0000269|PubMed:19154227}.
CC -!- TISSUE SPECIFICITY: Expressed in developing seeds.
CC {ECO:0000269|PubMed:19933265}.
CC -!- PTM: Auto-catalytic activation. {ECO:0000269|PubMed:19154227}.
CC -!- DISRUPTION PHENOTYPE: In PAK22, higher quantities of 57 kDa
CC polypeptides and lower levels of 40 kDa acidic and 20 kDa basic
CC glutelin subunits in seeds due to reduced vacuolar processing enzyme
CC (VPE) activity and leading to non-crystalline lattice structure of
CC protein storage vacuoles (PSVs). Seedlings growth retardation.
CC {ECO:0000269|PubMed:19933265, ECO:0000269|Ref.1}.
CC -!- SIMILARITY: Belongs to the peptidase C13 family. {ECO:0000305}.
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DR EMBL; AB109637; BAC76418.1; -; mRNA.
DR EMBL; AP008210; BAF15342.1; -; Genomic_DNA.
DR EMBL; AP014960; BAS90261.1; -; Genomic_DNA.
DR EMBL; CM000141; EEE61412.1; -; Genomic_DNA.
DR RefSeq; XP_015636414.1; XM_015780928.1.
DR AlphaFoldDB; Q84LM2; -.
DR SMR; Q84LM2; -.
DR STRING; 39947.Q84LM2; -.
DR MEROPS; C13.001; -.
DR GlyCosmos; Q84LM2; 2 sites, No reported glycans.
DR PaxDb; 39947-Q84LM2; -.
DR EnsemblPlants; Os04t0537900-01; Os04t0537900-01; Os04g0537900.
DR GeneID; 4336523; -.
DR Gramene; Os04t0537900-01; Os04t0537900-01; Os04g0537900.
DR KEGG; osa:4336523; -.
DR eggNOG; KOG1348; Eukaryota.
DR HOGENOM; CLU_024160_0_0_1; -.
DR InParanoid; Q84LM2; -.
DR OMA; CGRYNSA; -.
DR OrthoDB; 2951493at2759; -.
DR PlantReactome; R-OSA-9626305; Regulatory network of nutrient accumulation.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000007752; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 4.
DR Genevisible; Q84LM2; OS.
DR GO; GO:0000326; C:protein storage vacuole; IDA:UniProtKB.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IMP:UniProtKB.
DR GO; GO:0045735; F:nutrient reservoir activity; IEA:UniProtKB-KW.
DR GO; GO:1990019; P:protein storage vacuole organization; IMP:UniProtKB.
DR GO; GO:0051603; P:proteolysis involved in protein catabolic process; IBA:GO_Central.
DR GO; GO:0006624; P:vacuolar protein processing; IMP:UniProtKB.
DR CDD; cd21115; legumain_C; 1.
DR Gene3D; 1.10.132.130; -; 1.
DR Gene3D; 3.40.50.1460; -; 1.
DR InterPro; IPR043577; AE.
DR InterPro; IPR048501; Legum_prodom.
DR InterPro; IPR046427; Legumain_prodom_sf.
DR InterPro; IPR001096; Peptidase_C13.
DR PANTHER; PTHR12000; HEMOGLOBINASE FAMILY MEMBER; 1.
DR PANTHER; PTHR12000:SF25; VACUOLAR-PROCESSING ENZYME BETA-ISOZYME 1; 1.
DR Pfam; PF20985; Legum_prodom; 1.
DR Pfam; PF01650; Peptidase_C13; 1.
DR PIRSF; PIRSF500139; AE; 1.
DR PIRSF; PIRSF019663; Legumain; 1.
DR PRINTS; PR00776; HEMOGLOBNASE.
PE 1: Evidence at protein level;
KW Disulfide bond; Glycoprotein; Hydrolase; Protease; Reference proteome;
KW Seed storage protein; Signal; Storage protein; Thiol protease; Vacuole.
FT SIGNAL 1..23
FT /evidence="ECO:0000255"
FT CHAIN 24..497
FT /note="Vacuolar-processing enzyme beta-isozyme 1"
FT /evidence="ECO:0000255"
FT /id="PRO_0000431974"
FT ACT_SITE 180
FT /evidence="ECO:0000250|UniProtKB:O89017"
FT ACT_SITE 222
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:O89017"
FT SITE 269
FT /note="Required for post-translational maturation and
FT enzyme activity"
FT /evidence="ECO:0000269|PubMed:19154227"
FT CARBOHYD 153
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 340
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT DISULFID 255..269
FT /evidence="ECO:0000250|UniProtKB:P49046"
FT DISULFID 432..462
FT /evidence="ECO:0000250|UniProtKB:P49046"
FT DISULFID 444..479
FT /evidence="ECO:0000250|UniProtKB:P49046"
FT MUTAGEN 269
FT /note="C->G: In W379; loss of enzyme activity probably due
FT to an incorrectly post-translational maturation by cleavage
FT leading to the accumulation of the 57-kDa glutelin
FT precursor. Reduced vacuolar processing enzyme (VPE)
FT activity leading to non-crystalline lattice structure of
FT protein storage vacuoles (PSVs)."
FT /evidence="ECO:0000269|PubMed:19154227,
FT ECO:0000269|PubMed:19933265"
FT MUTAGEN 333
FT /note="G->D: In EM856; reduced vacuolar processing enzyme
FT (VPE) activity leading to non-crystalline lattice structure
FT of protein storage vacuoles (PSVs)."
FT /evidence="ECO:0000269|PubMed:19933265"
SQ SEQUENCE 497 AA; 54886 MW; 763ADC8F30380A6D CRC64;
MAARCWVWGF VVALLAVAAA ADGEEEEGKW EPLIRMPTEE GDDAEAAAPA PAPAAADYGG
TRWAVLVAGS SGYGNYRHQA DVCHAYQILQ KGGVKEENIV VFMYDDIAHN ILNPRPGTII
NHPKGGDVYA GVPKDYTGHQ VTTENFFAVL LGNKTAVTGG SGKVIDSKPE DHIFIYYSDH
GGPGVLGMPN LPYLYAGDFI KVLQKKHASN SYSKMVIYVE ACESGSIFEG LMPENLNIYV
TTASNAVENS WGTYCPGEEP SPPPEYITCL GDMYSVAWME DSETHNLKKE TIEDQYELVK
KRTSNANKLN EGSHVMEYGD KTFKDEKLFL YQGFNPANGN ITNELIWPVP KATVNQRDAD
LLFMWKRYEQ LNGVSEDKLR ALREIEDTIA HRKHLDSSID FIGKLVFGFE NGPLALEAAR
SSGQPLVDNW DCLKKMVRIF ESQCGSLTQY GMKYMRAFAN ICNNGVSEAK MMEASINACG
RYNSARWSPM TEGGHSA
//
