VPED_ARATH
ID VPED_ARATH Reviewed; 466 AA.
AC Q9LJX8; F4JDJ3; Q56X37; Q8LGK2;
DT 04-MAR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Vacuolar-processing enzyme delta-isozyme {ECO:0000303|PubMed:12417707};
DE Short=Delta-VPE {ECO:0000303|PubMed:12417707};
DE EC=3.4.22.34 {ECO:0000250|UniProtKB:Q84LM2};
DE AltName: Full=Asparaginyl endopeptidase delta-VPE {ECO:0000305};
DE Flags: Precursor;
GN Name=dVPE {ECO:0000303|PubMed:12417707};
GN OrderedLocusNames=At3g20210 {ECO:0000312|Araport:AT3G20210};
GN ORFNames=MAL21.23 {ECO:0000312|EMBL:BAB01880.1};
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 {ECO:0000312|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE
RP SPECIFICITY.
RC STRAIN=cv. Columbia; TISSUE=Green siliques;
RX PubMed=12417707; DOI=10.1105/tpc.005009;
RA Gruis D.F., Selinger D.A., Curran J.M., Jung R.;
RT "Redundant proteolytic mechanisms process seed storage proteins in the
RT absence of seed-type members of the vacuolar processing enzyme family of
RT cysteine proteases.";
RL Plant Cell 14:2863-2882(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia; TISSUE=Green siliques;
RA Nakaune S., Yamada K., Mikio N., Hara-Nishimura I.;
RT "Isolation and characterization of delta vacuolar processing enzyme(dVPE)
RT from Arabidopsis thaliana.";
RL Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
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 [4]
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 [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 237-466.
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 (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=14688293; DOI=10.1105/tpc.016378;
RA Gruis D., Schulze J., Jung R.;
RT "Storage protein accumulation in the absence of the vacuolar processing
RT enzyme family of cysteine proteases.";
RL Plant Cell 16:270-290(2004).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE,
RP TISSUE SPECIFICITY, AND ACTIVITY REGULATION.
RX PubMed=15705955; DOI=10.1105/tpc.104.026872;
RA Nakaune S., Yamada K., Kondo M., Kato T., Tabata S., Nishimura M.,
RA Hara-Nishimura I.;
RT "A vacuolar processing enzyme, deltaVPE, is involved in seed coat formation
RT at the early stage of seed development.";
RL Plant Cell 17:876-887(2005).
CC -!- FUNCTION: Asparagine-specific endopeptidase that may be involved in
CC processing of proteins targeted to vacuoles (By similarity). Probably
CC involved in post-translational proteolysis of seed storage proteins in
CC the protein storage vacuole of developing seeds (PubMed:12417707,
CC PubMed:14688293). Exhibits a caspase-1-like activity in extracellular
CC granules. At the early stage of seed development, required for the
CC formation of the seed coat, by regulating cell death of specific cell
CC layers in inner integument (PubMed:15705955).
CC {ECO:0000250|UniProtKB:P49043, ECO:0000269|PubMed:12417707,
CC ECO:0000269|PubMed:14688293, ECO:0000269|PubMed:15705955}.
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:0000250|UniProtKB:Q84LM2};
CC -!- ACTIVITY REGULATION: Strongly inhibited by biotin-YVAD-fmk (a caspase-1
CC inhibitor) and by Ac-DEVD-fmk. {ECO:0000269|PubMed:15705955}.
CC -!- SUBCELLULAR LOCATION: Secreted, extracellular space
CC {ECO:0000269|PubMed:15705955}. Secreted, cell wall
CC {ECO:0000269|PubMed:15705955}. Vacuole {ECO:0000250|UniProtKB:Q39119}.
CC Note=Localized to electron-dense structures inside and outside the
CC walls of seed coat cells that undergo cell death.
CC {ECO:0000269|PubMed:15705955}.
CC -!- TISSUE SPECIFICITY: Seed specific. Restricted to developing seeds at 7
CC days after anthesis, and, at lower levels, detected in flowers
CC (PubMed:12417707, PubMed:14688293). Detected in siliques, specifically
CC in seed coats (at protein level) (PubMed:15705955).
CC {ECO:0000269|PubMed:12417707, ECO:0000269|PubMed:14688293,
CC ECO:0000269|PubMed:15705955}.
CC -!- DEVELOPMENTAL STAGE: Specifically and transiently expressed in two cell
CC layers of the seed coat (ii2 and ii3) at an early stage of seed
CC development (at protein level). {ECO:0000269|PubMed:15705955}.
CC -!- PTM: Auto-catalytic activation. {ECO:0000250|UniProtKB:Q84LM2}.
CC -!- DISRUPTION PHENOTYPE: No macroscopic phenotype, probably due to
CC functional redundancy (PubMed:12417707, PubMed:14688293). In plants
CC lacking all vacuolar-processing enzyme isozymes (e.g. alpha, beta,
CC gamma and delta) shift of storage protein accumulation from normally
CC processed polypeptides to a finite number of prominent alternatively
CC processed polypeptides cleaved at sites other than the conserved Asn
CC residues targeted by VPE (PubMed:14688293). Delayed cell death of the
CC two layers of the seed coat (PubMed:15705955).
CC {ECO:0000269|PubMed:12417707, ECO:0000269|PubMed:14688293,
CC ECO:0000269|PubMed:15705955}.
CC -!- SIMILARITY: Belongs to the peptidase C13 family. {ECO:0000305}.
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DR EMBL; AB105106; BAC65233.1; -; mRNA.
DR EMBL; AF521661; AAN64910.1; -; mRNA.
DR EMBL; AP000383; BAB01880.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76347.1; -; Genomic_DNA.
DR EMBL; AY120765; AAM53323.1; -; mRNA.
DR EMBL; BT000949; AAN41349.1; -; mRNA.
DR EMBL; AY084227; AAM60827.1; -; mRNA.
DR EMBL; AK221840; BAD94082.1; -; mRNA.
DR RefSeq; NP_188656.1; NM_112912.3.
DR AlphaFoldDB; Q9LJX8; -.
DR SMR; Q9LJX8; -.
DR STRING; 3702.AT3G20210.2; -.
DR MEROPS; C13.A01; -.
DR PaxDb; Q9LJX8; -.
DR PRIDE; Q9LJX8; -.
DR ProteomicsDB; 242736; -.
DR EnsemblPlants; AT3G20210.1; AT3G20210.1; AT3G20210.
DR GeneID; 821565; -.
DR Gramene; AT3G20210.1; AT3G20210.1; AT3G20210.
DR KEGG; ath:AT3G20210; -.
DR Araport; AT3G20210; -.
DR TAIR; locus:2087625; AT3G20210.
DR eggNOG; KOG1348; Eukaryota.
DR HOGENOM; CLU_024160_0_0_1; -.
DR OMA; VMQYGNM; -.
DR OrthoDB; 826971at2759; -.
DR PhylomeDB; Q9LJX8; -.
DR PRO; PR:Q9LJX8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LJX8; baseline and differential.
DR Genevisible; Q9LJX8; AT.
DR GO; GO:0005615; C:extracellular space; IDA:TAIR.
DR GO; GO:0009505; C:plant-type cell wall; IDA:UniProtKB.
DR GO; GO:0000326; C:protein storage vacuole; ISS:UniProtKB.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IDA:TAIR.
DR GO; GO:0012501; P:programmed cell death; IMP:TAIR.
DR GO; GO:0051603; P:proteolysis involved in protein catabolic process; IBA:GO_Central.
DR GO; GO:0010214; P:seed coat development; IMP:TAIR.
DR GO; GO:0006624; P:vacuolar protein processing; ISS:TAIR.
DR InterPro; IPR043577; AE.
DR InterPro; IPR001096; Peptidase_C13.
DR PANTHER; PTHR12000; PTHR12000; 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 Cell wall; Glycoprotein; Hydrolase; Protease; Reference proteome; Secreted;
KW Signal; Thiol protease; Vacuole.
FT SIGNAL 1..24
FT /evidence="ECO:0000255"
FT CHAIN 25..466
FT /note="Vacuolar-processing enzyme delta-isozyme"
FT /evidence="ECO:0000255"
FT /id="PRO_0000431976"
FT ACT_SITE 164
FT /evidence="ECO:0000255"
FT ACT_SITE 206
FT /evidence="ECO:0000255"
FT SITE 253
FT /note="Required for post-translational maturation and
FT enzyme activity"
FT /evidence="ECO:0000250|UniProtKB:Q84LM2"
FT CARBOHYD 137
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CARBOHYD 322
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CONFLICT 195
FT /note="K -> I (in Ref. 6; AAM60827)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 466 AA; 52085 MW; 3192DD88972324CC CRC64;
MSSPLGHFQI LVFLHALLIF SAESRKTQLL NDNDVESSDK SAKGTRWAVL VAGSNEYYNY
RHQADICHAY QILRKGGLKD ENIIVFMYDD IAFSSENPRP GVIINKPDGE DVYKGVPKDY
TKEAVNVQNF YNVLLGNESG VTGGNGKVVK SGPNDNIFIY YADHGAPGLI AMPTGDEVMA
KDFNEVLEKM HKRKKYNKMV IYVEACESGS MFEGILKKNL NIYAVTAANS KESSWGVYCP
ESYPPPPSEI GTCLGDTFSI SWLEDSDLHD MSKETLEQQY HVVKRRVGSD VPETSHVCRF
GTEKMLKDYL SSYIGRNPEN DNFTFTESFS SPISNSGLVN PRDIPLLYLQ RKIQKAPMGS
LESKEAQKKL LDEKNHRKQI DQSITDILRL SVKQTNVLNL LTSTRTTGQP LVDDWDCFKT
LVNSFKNHCG ATVHYGLKYT GALANICNMG VDVKQTVSAI EQACSM
