Found 8 structures.
Displayed structures from 1 to 8
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1. Compound ID: 70
Structure type: oligomer
Trivial name: raffinose
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_164059,IEDB_190606,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 17
Blixt O, Van Die I, Norberg T, van den Eijnden DH "High-level expression of the Neisseria meningitidis lgtA gene in Escherichia coli and characterization of the encoded N-acetylglucosaminyltransferase as a useful catalyst in the synthesis of GlcNAcb1→3Gal and GalNAcb1-3Gal linkages" -
Glycobiology 9(10) (1999) 1061-1071
We have expressed the Neisseria meningitidis lgtA gene at a high level in Escherichia coli. The encoded β-N-acetylglucosaminyltransferase, referred to as LgtA, which in the bacterium is involved in the synthesis of the lacto-N-neo-tetraose structural element of the bacterial lipooligosaccharide, was obtained in an enzymatically highly active form. This glycosyltransferase appeared to be unusual in that it displays a broad acceptor specificity toward both α- and β-galactosides, whether structurally related to N- or O-protein-, or lipid-linked oligosaccharides. Product analysis by one- and two-dimensional 400 MHz 1H- and 13C NMR spectroscopy reveals that LgtA catalyzes the introduction of GlcNAc from UDP-GlcNAc in a β1→3-linkage to accepting Gal residues. The enzyme can thus be characterized as a UDP-GlcNAc:Gal α/β-R β 3-N-acetylglucosaminyltransferase. Although lactose is a highly preferred acceptor substrate the recombinant enzyme also acts efficiently on monomeric and dimeric N-acetyllactosamine revealing its potential value in the synthesis of polylactosaminoglycan structures in enzyme assisted procedures. Furthermore, LgtA shows a high donor promiscuity toward UDP-GalNAc, but not toward other UDP-sugars, and can catalyze the introduction of GalNAc in β1→3-linkage to α- or β-Gal in the acceptor structures at moderate rates. LgtA therefore shows promise to be a useful catalyst in the preparative synthesis of both GlcNAc β1→3 Gal and GalNAc β1→3 Gal linkages.
oligosaccharide, enzyme-assisted-synthesis, recombinant glycosyltransferase, glycosidic linkage, polylactosaminoglycan, recombinant glycosyltrasferase
NCBI PubMed ID: 10521543Publication DOI: 10.1093/glycob/9.10.1061Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Institutions: Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden, Department of Medical Chemistry, Vrije Universiteit, Van der Boechorstraat 7, 1081 BT Amsterdam, The Netherlands
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, enzyme-assisted synthesis, DNA techniques, glycosyltransferase assays, kinetics assays
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2. Compound ID: 71
Structure type: oligomer
Trivial name: stachyose
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_164059,IEDB_190606,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 17
Blixt O, Van Die I, Norberg T, van den Eijnden DH "High-level expression of the Neisseria meningitidis lgtA gene in Escherichia coli and characterization of the encoded N-acetylglucosaminyltransferase as a useful catalyst in the synthesis of GlcNAcb1→3Gal and GalNAcb1-3Gal linkages" -
Glycobiology 9(10) (1999) 1061-1071
We have expressed the Neisseria meningitidis lgtA gene at a high level in Escherichia coli. The encoded β-N-acetylglucosaminyltransferase, referred to as LgtA, which in the bacterium is involved in the synthesis of the lacto-N-neo-tetraose structural element of the bacterial lipooligosaccharide, was obtained in an enzymatically highly active form. This glycosyltransferase appeared to be unusual in that it displays a broad acceptor specificity toward both α- and β-galactosides, whether structurally related to N- or O-protein-, or lipid-linked oligosaccharides. Product analysis by one- and two-dimensional 400 MHz 1H- and 13C NMR spectroscopy reveals that LgtA catalyzes the introduction of GlcNAc from UDP-GlcNAc in a β1→3-linkage to accepting Gal residues. The enzyme can thus be characterized as a UDP-GlcNAc:Gal α/β-R β 3-N-acetylglucosaminyltransferase. Although lactose is a highly preferred acceptor substrate the recombinant enzyme also acts efficiently on monomeric and dimeric N-acetyllactosamine revealing its potential value in the synthesis of polylactosaminoglycan structures in enzyme assisted procedures. Furthermore, LgtA shows a high donor promiscuity toward UDP-GalNAc, but not toward other UDP-sugars, and can catalyze the introduction of GalNAc in β1→3-linkage to α- or β-Gal in the acceptor structures at moderate rates. LgtA therefore shows promise to be a useful catalyst in the preparative synthesis of both GlcNAc β1→3 Gal and GalNAc β1→3 Gal linkages.
oligosaccharide, enzyme-assisted-synthesis, recombinant glycosyltransferase, glycosidic linkage, polylactosaminoglycan, recombinant glycosyltrasferase
NCBI PubMed ID: 10521543Publication DOI: 10.1093/glycob/9.10.1061Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Institutions: Department of Chemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden, Department of Medical Chemistry, Vrije Universiteit, Van der Boechorstraat 7, 1081 BT Amsterdam, The Netherlands
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, enzyme-assisted synthesis, DNA techniques, glycosyltransferase assays, kinetics assays
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3. Compound ID: 15975
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b-D-Xylp-(1-4)-+
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a-D-Xylp-(1-2)-a-D-Glcp-(1-6)-b-D-Glcp-(1-5)-+ |
| |
-1)-b-D-Frup-(2-2)-b-D-Xylp-(1-6)-b-D-Fruf-(2-4)-b-D-Ribp-(1- |
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Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_114701,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_164059,IEDB_167188,IEDB_174332,IEDB_581504,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 6195
Andrew M, Jayaraman G "Molecular Characterization and Biocompatibility of Exopolysaccharide Produced by Moderately Halophilic Bacterium Virgibacillus dokdonensis from the Saltern of Kumta Coast" -
Polymers 14(9) (2022) 3986
The use of natural polysaccharides as biomaterials is gaining importance in tissue engineering due to their inherent biocompatibility. In this direction, the present study aims to explore the structure and biocompatibility of the EPS produced by Virgibacillus dokdonensis VITP14. This marine bacterium produces 17.3 g/L of EPS at 96 h of fermentation. The EPS was purified using ion exchange and gel permeation chromatographic methods. The porous web-like structure and elemental composition (C, O, Na, Mg, P, S) of the EPS were inferred from SEM and EDX analysis. AFM analysis revealed spike-like lumps with a surface roughness of 84.85 nm. The zeta potential value of -10 mV indicates the anionic nature of the EPS. Initial molecular characterization showed that the EPS is a heteropolysaccharide composed of glucose (25.8%), ribose (18.6%), fructose (31.5%), and xylose (24%), which are the monosaccharide units in the HPLC analysis. The FTIR spectrum indicates the presence of functional groups/bonds typical of EPSs (O-H, C-H, C-O-H, C-O, S=O, and P=O). The polymer has an average molecular weight of 555 kDa. Further, NMR analysis revealed the monomer composition, the existence of two α- and six β-glycosidic linkages, and the branched repeating unit as →1)[α-D-Xylp-(1→2)-α-D-Glcp-(1→6)-β-D-Glcp-(1→5)]-β-D-Frup-(2→2)[β-D-Xylp-(1→4)]-β-D-Xylp-(1→6)-β-D-Fruf-(2→4)-β-D-Ribp-(1→. The EPS is thermally stable till 251.4 °C. X-ray diffraction analysis confirmed the semicrystalline (54.2%) nature of the EPS. Further, the EPS exhibits significant water solubility (76.5%), water-holding capacity (266.8%), emulsifying index (66.8%), hemocompatibility (erythrocyte protection > 87%), and cytocompatibility (cell viability > 80% on RAW264.7 and keratinocyte HaCaT cells) at higher concentrations and prolongs coagulation time in APTT and PT tests. Our research unveils the significant biocompatibility of VITP14 EPS for synthesizing a variety of biomaterials.
exopolysaccharides, fermentation, Marine bacteria, anticoagulant activity, Structural characterization, halophiles, biomaterial, cytocompatibility, hemocompatibility
NCBI PubMed ID: 36235941Publication DOI: 10.3390/polym14193986Journal NLM ID: 101545357Publisher: Basel: MDPI
Correspondence: G. Jayaraman
Institutions: School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
Methods: 13C NMR, 1H NMR, NMR-2D, X-ray, FTIR, HPLC, GPC, statistical analysis, zeta potential measurement, cell viability assay, SEM, AFM, emulsifying activity determination, TGA, WHC, X-ray EDX, hemolytic activity, hemolysis activity, anticoagulant activity
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4. Compound ID: 18692
Structure type: oligomer
; 527 [M+Na]+
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_164059,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 7328
Okada H, Fukushi E, Yamamori A, Kawazoe N, Onodera S, Kawabata J, Shiomi N "Isolation and structural confirmation of the oligosaccharides containing α-D-fructofuranoside linkages isolated from fermented beverage of plant extracts" -
Carbohydrate Research 346(16) (2011) 2633-2637
Fermented beverage of plant extracts was prepared from the extracts of approximately 50 types of vegetables and fruits. Natural fermentation was carried out mainly by lactic acid bacteria (Leuconostoc spp.) and yeast (Zygosaccharomyces spp. and Pichia spp.). Two oligosaccharides containing an α-fructofuranoside linkage were detected in this beverage and isolated using carbon-Celite column chromatography and preparative HPLC. The structural confirmation of the saccharides was determined by methylation analysis, MALDI-TOF-MS, and NMR measurements. These saccharides were identified as α-D-fructofuranosyl-(2→6)-D-glucopyranose, which was isolated from a natural source for the first time, and a novel saccharide β-D-fructopyranosyl-(2→6)-α-D-fructofuranosyl-(2↔1)-α-D-glucopyranoside
oligosaccharide, Fermented beverage of plant extracts, a-D-Fructofuranoside, Natural fructopyranoside
NCBI PubMed ID: 21996604Publication DOI: 10.1016/j.carres.2011.09.002Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: Okada H
Institutions: General Institute of Ohtakakohso Co., Otaru, Japan, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan, Department of Food and Nutrition Sciences, Graduate School of Dairy Science Research, Rakuno Gakuen University, Ebetsu, Japan
Methods: 13C NMR, 1H NMR, methylation, acid hydrolysis, GLC, HPAEC, MALDI-TOF MS, methanolysis, HPLC, extraction, HMBC, COSY, HSQC-TOCSY
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5. Compound ID: 19532
Structure type: oligomer
; 517 [M-H]-
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_164059,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 7699
Andberg M, Mollerup F, Parikka K, Koutaniemi S, Boer H, Juvonen M, Master E, Tenkanen M, Kruus K "A Novel Colletotrichum graminicola Raffinose Oxidase in the AA5 Family" -
Applied and Environmental Microbiology 83(20) (2017) e01383-17
We describe here the identification and characterization of a copper radical oxidase from auxiliary activities family 5 (AA5_2) that was distinguished by showing preferential activity toward raffinose. Despite the biotechnological potential of carbohydrate oxidases from family AA5, very few members have been characterized. The gene encoding raffinose oxidase from Colletotrichum graminicola (CgRaOx; EC 1.1.3.-) was identified utilizing a bioinformatics approach based on the known modular structure of a characterized AA5_2 galactose oxidase. CgRaOx was expressed in Pichia pastoris, and the purified enzyme displayed the highest activity on the trisaccharide raffinose, whereas the activity on the disaccharide melibiose was three times lower and more than ten times lower activity was detected on d-galactose at a 300 mM substrate concentration. Thus, the substrate preference of CgRaOx was distinguished clearly from the substrate preferences of the known galactose oxidases. The site of oxidation for raffinose was studied by 1H nuclear magnetic resonance and mass spectrometry, and we confirmed that the hydroxyl group at the C-6 position was oxidized to an aldehyde and that in addition uronic acid was produced as a side product. A new electrospray ionization mass spectrometry method for the identification of C-6 oxidized products was developed, and the formation mechanism of the uronic acid was studied. CgRaOx presented a novel activity pattern in the AA5 family.IMPORTANCE Currently, there are only a few characterized members of the CAZy AA5 protein family. These enzymes are interesting from an application point of view because of their ability to utilize the cheap and abundant oxidant O2 without the requirement of complex cofactors such as FAD or NAD(P). Here, we present the identification and characterization of a novel AA5 member from Colletotrichum graminicola As discussed in the present study, the bioinformatics approach using the modular structure of galactose oxidase was successful in finding a C-6 hydroxyl carbohydrate oxidase having substrate preference for the trisaccharide raffinose. By the discovery of this activity, the diversity of the CAZy AA5 family is increasing.
CAZy AA5; EC 1.1.3.−; NMR; carbohydrate; galactose oxidase; nuclear magnetic resonance
NCBI PubMed ID: 28778886Publication DOI: 10.1128/AEM.01383-17Journal NLM ID: 7605801Publisher: American Society for Microbiology
Correspondence: martina.andberg@vtt.fi
Institutions: Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland, VTT, Technical Research Centre of Finland, Espoo, Finland, Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
Methods: 1H NMR, DNA techniques, ESI-MS, ESI-MS/MS, enzymatic digestion
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6. Compound ID: 19533
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Subst-(1-6)-a-D-Glcp-(1-2)-b-D-Frup
Subst = water elimination product of the aldehyde = SMILES O=C/C1=C/[C@H](O)[C@@H](O){1}[C@@H](O)O1 |
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Structure type: oligomer
; 519 [M+Cl]-
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_164059,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 7700
Andberg M, Mollerup F, Parikka K, Koutaniemi S, Boer H, Juvonen M, Master E, Tenkanen M, Kruus K "A novel Colletotrichum graminicola raffinose oxidase in the AA5 Family" -
Applied and Environmental Microbiology 83(20) (2017) ID 01383-17
We describe here the identification and characterization of a copper radical oxidase from auxiliary activities family 5 (AA5_2) that was distinguished by showing preferential activity toward raffinose. Despite the biotechnological potential of carbohydrate oxidases from family AA5, very few members have been characterized. The gene encoding raffinose oxidase from Colletotrichum graminicola (CgRaOx; EC 1.1.3.-) was identified utilizing a bioinformatics approach based on the known modular structure of a characterized AA5_2 galactose oxidase. CgRaOx was expressed in Pichia pastoris, and the purified enzyme displayed the highest activity on the trisaccharide raffinose, whereas the activity on the disaccharide melibiose was three times lower and more than ten times lower activity was detected on d-galactose at a 300 mM substrate concentration. Thus, the substrate preference of CgRaOx was distinguished clearly from the substrate preferences of the known galactose oxidases. The site of oxidation for raffinose was studied by 1H nuclear magnetic resonance and mass spectrometry, and we confirmed that the hydroxyl group at the C-6 position was oxidized to an aldehyde and that in addition uronic acid was produced as a side product. A new electrospray ionization mass spectrometry method for the identification of C-6 oxidized products was developed, and the formation mechanism of the uronic acid was studied. CgRaOx presented a novel activity pattern in the AA5 family.IMPORTANCE Currently, there are only a few characterized members of the CAZy AA5 protein family. These enzymes are interesting from an application point of view because of their ability to utilize the cheap and abundant oxidant O2 without the requirement of complex cofactors such as FAD or NAD(P). Here, we present the identification and characterization of a novel AA5 member from Colletotrichum graminicola As discussed in the present study, the bioinformatics approach using the modular structure of galactose oxidase was successful in finding a C-6 hydroxyl carbohydrate oxidase having substrate preference for the trisaccharide raffinose. By the discovery of this activity, the diversity of the CAZy AA5 family is increasing.
CAZy AA5; EC 1.1.3.−; NMR; carbohydrate; galactose oxidase; nuclear magnetic resonance
NCBI PubMed ID: 28778886Publication DOI: 10.1128/AEM.01383-17Journal NLM ID: 7605801Publisher: American Society for Microbiology
Correspondence: martina.andberg@vtt.fi
Institutions: Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland, VTT, Technical Research Centre of Finland, Espoo, Finland, Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
Methods: 1H NMR, DNA techniques, ESI-MS, ESI-MS/MS, enzymatic digestion
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7. Compound ID: 19534
|
Subst-(1-6)-a-D-Glcp-(1-2)-b-D-Frup
Subst = raffinose aldehyde in hydrate form = SMILES OC(O)[C@H]1O[C@H](O)[C@H](O){1}[C@@H](O)[C@H]1O |
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Structure type: oligomer
; 555 [M+Cl]-
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_164059,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 7701
Andberg M, Mollerup F, Parikka K, Koutaniemi S, Boer H, Juvonen M, Master E, Tenkanen M, Kruus K "A novel Colletotrichum graminicola raffinose oxidase in the AA5 Family" -
Applied and Environmental Microbiology 83(20) (2017) ID e01383-17
We describe here the identification and characterization of a copper radical oxidase from auxiliary activities family 5 (AA5_2) that was distinguished by showing preferential activity toward raffinose. Despite the biotechnological potential of carbohydrate oxidases from family AA5, very few members have been characterized. The gene encoding raffinose oxidase from Colletotrichum graminicola (CgRaOx; EC 1.1.3.-) was identified utilizing a bioinformatics approach based on the known modular structure of a characterized AA5_2 galactose oxidase. CgRaOx was expressed in Pichia pastoris, and the purified enzyme displayed the highest activity on the trisaccharide raffinose, whereas the activity on the disaccharide melibiose was three times lower and more than ten times lower activity was detected on d-galactose at a 300 mM substrate concentration. Thus, the substrate preference of CgRaOx was distinguished clearly from the substrate preferences of the known galactose oxidases. The site of oxidation for raffinose was studied by 1H nuclear magnetic resonance and mass spectrometry, and we confirmed that the hydroxyl group at the C-6 position was oxidized to an aldehyde and that in addition uronic acid was produced as a side product. A new electrospray ionization mass spectrometry method for the identification of C-6 oxidized products was developed, and the formation mechanism of the uronic acid was studied. CgRaOx presented a novel activity pattern in the AA5 family.IMPORTANCE Currently, there are only a few characterized members of the CAZy AA5 protein family. These enzymes are interesting from an application point of view because of their ability to utilize the cheap and abundant oxidant O2 without the requirement of complex cofactors such as FAD or NAD(P). Here, we present the identification and characterization of a novel AA5 member from Colletotrichum graminicola As discussed in the present study, the bioinformatics approach using the modular structure of galactose oxidase was successful in finding a C-6 hydroxyl carbohydrate oxidase having substrate preference for the trisaccharide raffinose. By the discovery of this activity, the diversity of the CAZy AA5 family is increasing.
CAZy AA5; EC 1.1.3.−; NMR; carbohydrate; galactose oxidase; nuclear magnetic resonance
NCBI PubMed ID: 28778886Publication DOI: 10.1128/AEM.01383-17Journal NLM ID: 7605801Publisher: American Society for Microbiology
Correspondence: martina.andberg@vtt.fi
Institutions: Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland, VTT, Technical Research Centre of Finland, Espoo, Finland, Department of Biotechnology and Chemical Technology, Aalto University, Espoo, Finland, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
Methods: 1H NMR, DNA techniques, ESI-MS, ESI-MS/MS, enzymatic digestion
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8. Compound ID: 19569
Structure type: oligomer
; 527 [M+Na]+
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_164059,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 7721
Yamamori A, Takata Y, Fukushi E, Kawabata J, Okada H, Kawazoe N, Ueno K, Onodera S, Shiomi N "Structural analysis of a novel oligosaccharide isolated from fermented beverage of plant extracts" -
Journal of Applied Glycoscience 64(4) (2017) 123-127
A fermented beverage of plant extracts (Super Ohtaka) was prepared from about 50 kinds of fruits and vegetables. This natural fermentation was performed by yeast (Zygosaccharomyces spp. and Pichia spp.) and lactic acid bacteria (Leuconostoc spp.) and resulted in the production of a novel fructopyranose-containing saccharide, which was subsequently isolated using carbon-Celite column chromatography and preparative-HPLC. The structure of the saccharide was determined using MALDI-TOF MS and NMR, and the saccharide was identified as β-D-fructopyranosyl-(2→6)-β-D-fructofuranosyl-(2→1)-α-D-glucopyranoside. This is the first description of this novel saccharide and its isolation from a natural source.
trisaccharide, structural analysis, pyrano-6-kestose, fructopyranosyl sucrose, fructopyranose, fermented beverage
Publication DOI: 10.5458/jag.jag.JAG-2017_014Journal NLM ID: 101167786Publisher: Hitotsubashi, Chiyoda-ku: Japanese Society of Applied Glycoscience
Correspondence: Yamamori A
Institutions: Graduate School of Agriculture, Hokkaido University, Sapporo, Japan, Department of Food and Nutrition Sciences, Graduate School of Dairy Science Research, Rakuno Gakuen University, Ebetsu, Japan, General Institute of Ohtakakohso Co., Ltd., Otaru, Japan
Methods: 13C NMR, 1H NMR, HPAEC, MALDI-TOF MS, HPLC, TOCSY, HMBC, COSY, HSQC, HCl acid hydrolysis
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