GLCB1_SOYBN
ID GLCB1_SOYBN Reviewed; 439 AA.
AC P25974; I1NGF4;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 16-JAN-2019, sequence version 2.
DT 25-MAY-2022, entry version 111.
DE RecName: Full=Beta-conglycinin beta subunit 1 {ECO:0000305};
DE Short=CG-beta-1 {ECO:0000305};
DE AltName: Full=Beta-conglycinin beta subunit {ECO:0000303|PubMed:2562562};
DE AltName: Allergen=Gly m 5 {ECO:0000305};
DE Flags: Precursor;
GN Name=CG-4 {ECO:0000303|PubMed:2562562};
GN ORFNames=GLYMA_20G146200 {ECO:0000312|EMBL:KRG91303.1};
OS Glycine max (Soybean) (Glycine hispida).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine;
OC Glycine subgen. Soja.
OX NCBI_TaxID=3847;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Dare, and cv. Forrest;
RX PubMed=2562562; DOI=10.2307/3869102;
RA Harada J.J., Barker S.J., Goldberg R.B.;
RT "Soybean beta-conglycinin genes are clustered in several DNA regions and
RT are regulated by transcriptional and posttranscriptional processes.";
RL Plant Cell 1:415-425(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Williams 82;
RX PubMed=20075913; DOI=10.1038/nature08670;
RA Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W.,
RA Hyten D.L., Song Q., Thelen J.J., Cheng J., Xu D., Hellsten U., May G.D.,
RA Yu Y., Sakurai T., Umezawa T., Bhattacharyya M.K., Sandhu D.,
RA Valliyodan B., Lindquist E., Peto M., Grant D., Shu S., Goodstein D.,
RA Barry K., Futrell-Griggs M., Abernathy B., Du J., Tian Z., Zhu L., Gill N.,
RA Joshi T., Libault M., Sethuraman A., Zhang X.-C., Shinozaki K.,
RA Nguyen H.T., Wing R.A., Cregan P., Specht J., Grimwood J., Rokhsar D.,
RA Stacey G., Shoemaker R.C., Jackson S.A.;
RT "Genome sequence of the palaeopolyploid soybean.";
RL Nature 463:178-183(2010).
RN [3]
RP PROTEIN SEQUENCE OF 24-38.
RX PubMed=16663129; DOI=10.1104/pp.72.4.1114;
RA Staswick P.E., Broue P., Nielsen N.C.;
RT "Glycinin composition of several perennial species related to soybean.";
RL Plant Physiol. 72:1114-1118(1983).
RN [4]
RP PROTEIN SEQUENCE OF 24-50.
RC STRAIN=cv. Raiden;
RX DOI=10.1016/S0031-9422(00)81477-6;
RA Hirano H., Kagawa H., Kamata Y., Yamauchi F.;
RT "Structural homology among the major 7s globulin subunits of soybean seed
RT storage proteins.";
RL Phytochemistry 26:41-45(1987).
RN [5]
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=15447650; DOI=10.1111/j.1365-313x.2004.02204.x;
RA Mori T., Maruyama N., Nishizawa K., Higasa T., Yagasaki K., Ishimoto M.,
RA Utsumi S.;
RT "The composition of newly synthesized proteins in the endoplasmic reticulum
RT determines the transport pathways of soybean seed storage proteins.";
RL Plant J. 40:238-249(2004).
RN [6]
RP SUBCELLULAR LOCATION.
RX DOI=10.1016/j.plantsci.2004.06.004;
RA Nishizawa K., Maruyama N., Satoh R., Higasa T., Utsumi S.;
RT "A vacuolar sorting determinant of soybean beta-conglycinin beta subunit
RT resides in a C-terminal sequence.";
RL Plant Sci. 167:937-947(2004).
RN [7]
RP ALLERGEN.
RX PubMed=18996574; DOI=10.1016/j.jaci.2008.09.034;
RA Holzhauser T., Wackermann O., Ballmer-Weber B.K., Bindslev-Jensen C.,
RA Scibilia J., Perono-Garoffo L., Utsumi S., Poulsen L.K., Vieths S.;
RT "Soybean (Glycine max) allergy in Europe: Gly m 5 (beta-conglycinin) and
RT Gly m 6 (glycinin) are potential diagnostic markers for severe allergic
RT reactions to soy.";
RL J. Allergy Clin. Immunol. 123:452-458(2009).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 24-439 OF WILD-TYPE PROTEIN, AND
RP GLYCOSYLATION AT ASN-351.
RX PubMed=11422391; DOI=10.1046/j.1432-1327.2001.02268.x;
RA Maruyama N., Adachi M., Takahashi K., Yagasaki K., Kohno M., Takenaka Y.,
RA Okuda E., Nakagawa S., Mikami B., Utsumi S.;
RT "Crystal structures of recombinant and native soybean beta-conglycinin beta
RT homotrimers.";
RL Eur. J. Biochem. 268:3595-3604(2001).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 24-439 OF MUTANT PROTEIN, AND
RP MUTAGENESIS OF ILE-145 AND LYS-147.
RX PubMed=12758152; DOI=10.1016/s1570-9639(03)00113-4;
RA Maruyama N., Maruyama Y., Tsuruki T., Okuda E., Yoshikawa M., Utsumi S.;
RT "Creation of soybean beta-conglycinin beta with strong phagocytosis-
RT stimulating activity.";
RL Biochim. Biophys. Acta 1648:99-104(2003).
CC -!- FUNCTION: Seed storage protein. Accumulates during seed development and
CC is hydrolyzed after germination to provide a carbon and nitrogen source
CC for the developing seedling. {ECO:0000305|PubMed:2562562}.
CC -!- SUBUNIT: The alpha-, alpha'-, and beta-subunits associate in various
CC combinations to form trimeric proteins. {ECO:0000305|PubMed:15447650}.
CC -!- SUBCELLULAR LOCATION: Vacuole, aleurone grain {ECO:0000305}.
CC Endoplasmic reticulum {ECO:0000269|PubMed:15447650}. Protein storage
CC vacuole {ECO:0000269|PubMed:15447650, ECO:0000269|Ref.6}.
CC Note=Localizes in protein storage vacuoles in cotyledons of developing
CC and mature beans (PubMed:15447650, Ref.6). Synthesized and assembled
CC into trimers in the endoplasmic reticulum, and transported to the
CC protein storage vacuoles by the dense vesicles (PubMed:15447650).
CC {ECO:0000269|PubMed:15447650, ECO:0000269|Ref.6}.
CC -!- TISSUE SPECIFICITY: Expressed in seeds. Not detected in cotyledons or
CC in mature plants. {ECO:0000305|PubMed:2562562}.
CC -!- DEVELOPMENTAL STAGE: Expressed early in embryogenesis, with a high
CC transcription rate at midmaturation and then decreases prior to seed
CC dormancy. {ECO:0000269|PubMed:2562562}.
CC -!- PTM: The N-linked glycans are not essential for the folding and
CC assembly into trimers. {ECO:0000269|PubMed:11422391}.
CC -!- ALLERGEN: Causes an allergic reaction in human (PubMed:18996574). Binds
CC to IgE of patients with severe allergic reactions (anaphylaxis) to
CC soybean (PubMed:18996574). {ECO:0000269|PubMed:18996574}.
CC -!- MISCELLANEOUS: Mutagenesis of Ile-145 and Lys-147 allow the creation of
CC a beta-conglycinin beta chain containing a phagocytosis-stimulating
CC peptide, soymetide, found normally only in the alpha' chain. The three
CC mutants created exhibit phagocytosis activities after digestion by
CC trypsin and the order is wild type < I145M/K147T < I145M/K147F <
CC I145M/K147W. {ECO:0000269|PubMed:12758152}.
CC -!- SIMILARITY: Belongs to the 7S seed storage protein family.
CC {ECO:0000305}.
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DR EMBL; S44893; AAB23463.1; -; Genomic_DNA.
DR EMBL; CM000853; KRG91303.1; -; Genomic_DNA.
DR EMBL; ACUP02012674; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; JQ0969; FWSYCB.
DR PDB; 1IPJ; X-ray; 2.70 A; A/B/C=24-439.
DR PDB; 1IPK; X-ray; 2.70 A; A/B/C=24-439.
DR PDB; 1UIJ; X-ray; 2.50 A; A/B/C/D/E/F=24-439.
DR PDBsum; 1IPJ; -.
DR PDBsum; 1IPK; -.
DR PDBsum; 1UIJ; -.
DR AlphaFoldDB; P25974; -.
DR SMR; P25974; -.
DR STRING; 3847.GLYMA20G28460.1; -.
DR Allergome; 5816; Gly m 5.
DR Allergome; 5819; Gly m 5.0301.
DR Allergome; 5820; Gly m 5.0302.
DR iPTMnet; P25974; -.
DR EnsemblPlants; KRG91303; KRG91303; GLYMA_20G146200.
DR Gramene; KRG91303; KRG91303; GLYMA_20G146200.
DR eggNOG; ENOG502QQEP; Eukaryota.
DR HOGENOM; CLU_018703_0_1_1; -.
DR InParanoid; P25974; -.
DR OMA; NDFGRYH; -.
DR EvolutionaryTrace; P25974; -.
DR Proteomes; UP000008827; Chromosome 20.
DR GO; GO:0033095; C:aleurone grain; IEA:UniProtKB-SubCell.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:UniProtKB.
DR GO; GO:0000326; C:protein storage vacuole; IDA:UniProtKB.
DR GO; GO:0045735; F:nutrient reservoir activity; IEA:UniProtKB-KW.
DR Gene3D; 2.60.120.10; -; 2.
DR InterPro; IPR006045; Cupin_1.
DR InterPro; IPR013096; Cupin_2.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR Pfam; PF00190; Cupin_1; 1.
DR Pfam; PF07883; Cupin_2; 1.
DR SMART; SM00835; Cupin_1; 2.
DR SUPFAM; SSF51182; SSF51182; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Allergen; Direct protein sequencing; Endoplasmic reticulum;
KW Glycoprotein; Reference proteome; Seed storage protein; Signal;
KW Storage protein; Vacuole.
FT SIGNAL 1..23
FT /evidence="ECO:0000305|Ref.4"
FT CHAIN 24..439
FT /note="Beta-conglycinin beta subunit 1"
FT /evidence="ECO:0000269|PubMed:16663129, ECO:0000269|Ref.4"
FT /id="PRO_0000032191"
FT DOMAIN 34..193
FT /note="Cupin type-1 1"
FT /evidence="ECO:0000255"
FT DOMAIN 240..401
FT /note="Cupin type-1 2"
FT /evidence="ECO:0000255"
FT REGION 411..439
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 430..439
FT /note="Necessary for sorting to protein storage vacuole"
FT /evidence="ECO:0000269|Ref.6"
FT CARBOHYD 351
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|PubMed:11422391"
FT MUTAGEN 145
FT /note="I->M: Little or no effect on the secondary structure
FT and strong phagocytosis-stimulating activity; when
FT associated with T-147; F-147 or W-147."
FT /evidence="ECO:0000269|PubMed:12758152"
FT MUTAGEN 147
FT /note="K->T,F,W: Little or no effect on the secondary
FT structure and strong phagocytosis-stimulating activity;
FT when associated with M-145."
FT /evidence="ECO:0000269|PubMed:12758152"
FT CONFLICT 36
FT /note="L -> F (in Ref. 1; AAB23463)"
FT /evidence="ECO:0000305"
FT CONFLICT 39
FT /note="S -> V (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 44
FT /note="T -> G (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 50
FT /note="N -> D (in Ref. 4; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 51
FT /note="G -> V (in Ref. 1; AAB23463)"
FT /evidence="ECO:0000305"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:1IPK"
FT HELIX 38..40
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 41..47
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 49..56
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 64..69
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 73..79
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 83..101
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 113..118
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 122..126
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 131..136
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 143..154
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 160..164
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 172..175
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 178..185
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 189..196
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 205..212
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 215..221
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 230..234
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 242..244
FT /evidence="ECO:0007829|PDB:1IPK"
FT STRAND 248..250
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 252..259
FT /evidence="ECO:0007829|PDB:1UIJ"
FT TURN 261..263
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 265..270
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 272..279
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 283..292
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 294..311
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 327..335
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 339..342
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 348..363
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 370..376
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 381..383
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 386..392
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 393..395
FT /evidence="ECO:0007829|PDB:1UIJ"
FT HELIX 397..403
FT /evidence="ECO:0007829|PDB:1UIJ"
FT STRAND 411..414
FT /evidence="ECO:0007829|PDB:1UIJ"
SQ SEQUENCE 439 AA; 50476 MW; 86D20314FC21D9E7 CRC64;
MMRVRFPLLV LLGTVFLASV CVSLKVREDE NNPFYLRSSN SFQTLFENQN GRIRLLQRFN
KRSPQLENLR DYRIVQFQSK PNTILLPHHA DADFLLFVLS GRAILTLVNN DDRDSYNLHP
GDAQRIPAGT TYYLVNPHDH QNLKIIKLAI PVNKPGRYDD FFLSSTQAQQ SYLQGFSHNI
LETSFHSEFE EINRVLFGEE EEQRQQEGVI VELSKEQIRQ LSRRAKSSSR KTISSEDEPF
NLRSRNPIYS NNFGKFFEIT PEKNPQLRDL DIFLSSVDIN EGALLLPHFN SKAIVILVIN
EGDANIELVG IKEQQQKQKQ EEEPLEVQRY RAELSEDDVF VIPAAYPFVV NATSNLNFLA
FGINAENNQR NFLAGEKDNV VRQIERQVQE LAFPGSAQDV ERLLKKQRES YFVDAQPQQK
EEGSKGRKGP FPSILGALY
