VPEB_ARATH
ID VPEB_ARATH Reviewed; 486 AA.
AC Q39044; Q93VS7; Q9SI79;
DT 11-JUL-2002, integrated into UniProtKB/Swiss-Prot.
DT 11-JUL-2002, sequence version 3.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Vacuolar-processing enzyme beta-isozyme {ECO:0000303|PubMed:7579169};
DE EC=3.4.22.34 {ECO:0000250|UniProtKB:Q84LM2};
DE AltName: Full=Asparaginyl endopeptidase beta-VPE {ECO:0000305};
DE AltName: Full=Beta-VPE {ECO:0000303|PubMed:7579169};
DE Flags: Precursor;
GN Name=bVPE {ECO:0000303|PubMed:7579169};
GN OrderedLocusNames=At1g62710 {ECO:0000312|Araport:AT1G62710};
GN ORFNames=F23N19.7 {ECO:0000312|EMBL:AAF19550.1};
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 [GENOMIC DNA], TISSUE SPECIFICITY, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=7579169; DOI=10.1007/bf00019120;
RA Kinoshita T., Nishimura M., Hara-Nishimura I.;
RT "Homologues of a vacuolar processing enzyme that are expressed in different
RT organs in Arabidopsis thaliana.";
RL Plant Mol. Biol. 29:81-89(1995).
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 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 TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=10417725; DOI=10.1046/j.1365-313x.1999.00497.x;
RA Kinoshita T., Yamada K., Hiraiwa N., Kondo M., Nishimura M.,
RA Hara-Nishimura I.;
RT "Vacuolar processing enzyme is up-regulated in the lytic vacuoles of
RT vegetative tissues during senescence and under various stressed
RT conditions.";
RL Plant J. 19:43-53(1999).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
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 [7]
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).
CC -!- FUNCTION: Asparagine-specific endopeptidase involved in the processing
CC of vacuolar seed protein precursors into the mature forms (By
CC similarity). Probably involved in post-translational proteolysis of
CC seed storage proteins in the protein storage vacuole of developing
CC seeds (PubMed:12417707, PubMed:14688293).
CC {ECO:0000250|UniProtKB:P49043, ECO:0000269|PubMed:12417707,
CC ECO:0000269|PubMed:14688293}.
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 -!- SUBCELLULAR LOCATION: Vacuole {ECO:0000269|PubMed:7579169}. Protein
CC storage vacuole {ECO:0000269|PubMed:10417725}.
CC -!- TISSUE SPECIFICITY: Seed specific. Also expressed in the flowers and
CC buds. {ECO:0000269|PubMed:10417725, ECO:0000269|PubMed:14688293,
CC ECO:0000269|PubMed:7579169}.
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). Slight
CC differences in polypeptide accumulation in seeds with an increased
CC amount of propolypeptide forms of legumin-type globulins
CC (PubMed:12417707). In plants lacking all vacuolar-processing enzyme
CC isozymes (e.g. alpha, beta, gamma and delta) shift of storage protein
CC accumulation from normally processed polypeptides to a finite number of
CC prominent alternatively processed polypeptides cleaved at sites other
CC than the conserved Asn residues targeted by VPE (PubMed:14688293).
CC {ECO:0000269|PubMed:12417707, ECO:0000269|PubMed:14688293}.
CC -!- SIMILARITY: Belongs to the peptidase C13 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF19550.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; D61394; BAA09615.1; -; Genomic_DNA.
DR EMBL; AC007190; AAF19550.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE33996.1; -; Genomic_DNA.
DR EMBL; AY059156; AAL15381.1; -; mRNA.
DR EMBL; AF367254; AAK56243.1; -; mRNA.
DR PIR; C96652; C96652.
DR PIR; S60050; S60050.
DR RefSeq; NP_176458.1; NM_104948.4.
DR PDB; 6YSA; X-ray; 2.01 A; A/B/C/D/E/F/G/H/I/J/K/L=47-486.
DR PDBsum; 6YSA; -.
DR AlphaFoldDB; Q39044; -.
DR SMR; Q39044; -.
DR BioGRID; 27790; 1.
DR STRING; 3702.AT1G62710.1; -.
DR MEROPS; C13.001; -.
DR PaxDb; Q39044; -.
DR PRIDE; Q39044; -.
DR ProteomicsDB; 242627; -.
DR EnsemblPlants; AT1G62710.1; AT1G62710.1; AT1G62710.
DR GeneID; 842569; -.
DR Gramene; AT1G62710.1; AT1G62710.1; AT1G62710.
DR KEGG; ath:AT1G62710; -.
DR Araport; AT1G62710; -.
DR TAIR; locus:2026242; AT1G62710.
DR eggNOG; KOG1348; Eukaryota.
DR HOGENOM; CLU_024160_0_0_1; -.
DR InParanoid; Q39044; -.
DR OMA; MLHRQHL; -.
DR OrthoDB; 826971at2759; -.
DR PhylomeDB; Q39044; -.
DR PRO; PR:Q39044; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q39044; baseline and differential.
DR Genevisible; Q39044; AT.
DR GO; GO:0000326; C:protein storage vacuole; ISS:UniProtKB.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; ISS:UniProtKB.
DR GO; GO:0051603; P:proteolysis involved in protein catabolic process; IBA:GO_Central.
DR GO; GO:0006624; P:vacuolar protein processing; ISS:TAIR.
DR InterPro; IPR043577; AE.
DR InterPro; IPR033165; Legumain_beta.
DR InterPro; IPR001096; Peptidase_C13.
DR PANTHER; PTHR12000; PTHR12000; 1.
DR PANTHER; PTHR12000:SF25; PTHR12000:SF25; 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 3D-structure; Glycoprotein; Hydrolase; Protease; Reference proteome;
KW Signal; Thiol protease; Vacuole.
FT SIGNAL 1..21
FT /evidence="ECO:0000255"
FT CHAIN 22..486
FT /note="Vacuolar-processing enzyme beta-isozyme"
FT /id="PRO_0000026527"
FT ACT_SITE 169
FT /evidence="ECO:0000255"
FT ACT_SITE 211
FT /evidence="ECO:0000255"
FT SITE 258
FT /note="Required for post-translational maturation and
FT enzyme activity"
FT /evidence="ECO:0000250|UniProtKB:Q84LM2"
FT CARBOHYD 309
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT CONFLICT 288..289
FT /note="Missing (in Ref. 1; BAA09615)"
FT /evidence="ECO:0000305"
FT CONFLICT 324
FT /note="D -> E (in Ref. 1; BAA09615)"
FT /evidence="ECO:0000305"
FT CONFLICT 337
FT /note="V -> A (in Ref. 1; BAA09615)"
FT /evidence="ECO:0000305"
FT CONFLICT 358
FT /note="Y -> H (in Ref. 1; BAA09615)"
FT /evidence="ECO:0000305"
FT STRAND 51..57
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 65..80
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 88..91
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 132..140
FT /evidence="ECO:0007829|PDB:6YSA"
FT TURN 143..145
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 161..167
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 178..181
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 185..198
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 202..208
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 213..216
FT /evidence="ECO:0007829|PDB:6YSA"
FT TURN 217..220
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 223..233
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 235..237
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 240..243
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 262..271
FT /evidence="ECO:0007829|PDB:6YSA"
FT TURN 276..278
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 281..292
FT /evidence="ECO:0007829|PDB:6YSA"
FT TURN 293..297
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 305..308
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 310..314
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 318..321
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 325..327
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 332..334
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 343..345
FT /evidence="ECO:0007829|PDB:6YSA"
FT TURN 346..348
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 349..359
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 367..397
FT /evidence="ECO:0007829|PDB:6YSA"
FT STRAND 399..401
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 403..405
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 418..432
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 438..442
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 443..451
FT /evidence="ECO:0007829|PDB:6YSA"
FT HELIX 456..467
FT /evidence="ECO:0007829|PDB:6YSA"
SQ SEQUENCE 486 AA; 53828 MW; 8B3EFD53CDAEC9C3 CRC64;
MAKSCYFRPA LLLLLVLLVH AESRGRFEPK ILMPTEEANP ADQDEDGVGT RWAVLVAGSS
GYGNYRHQAD VCHAYQILRK GGLKEENIVV LMYDDIANHP LNPRPGTLIN HPDGDDVYAG
VPKDYTGSSV TAANFYAVLL GDQKAVKGGS GKVIASKPND HIFVYYADHG GPGVLGMPNT
PHIYAADFIE TLKKKHASGT YKEMVIYVEA CESGSIFEGI MPKDLNIYVT TASNAQESSY
GTYCPGMNPS PPSEYITCLG DLYSVAWMED SETHNLKKET IKQQYHTVKM RTSNYNTYSG
GSHVMEYGNN SIKSEKLYLY QGFDPATVNL PLNELPVKSK IGVVNQRDAD LLFLWHMYRT
SEDGSRKKDD TLKELTETTR HRKHLDASVE LIATILFGPT MNVLNLVREP GLPLVDDWEC
LKSMVRVFEE HCGSLTQYGM KHMRAFANVC NNGVSKELME EASTAACGGY SEARYTVHPS
ILGYSA
