Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85,SB_86

• Article ID: 9546
  Takahashi N, Hotta T, Ishihara H, Mori M, Tejima S, Bligny R, Akazawa T, Endo S, Arata Y "Xylose-containing common structural unit in N-linked oligosaccharides of laccase from sycamore cells" - Biochemistry 25(2) (1986) 388-395
  

  The structures of asparagine-linked oligosaccharides of laccase excreted by sycamore (Acer pseudoplatanus L.) cells are reported. Peptic glycopeptides obtained from the laccase were treated with N-oligosaccharide glycopeptidase (EC 3.5.1.52) to release the oligosaccharide moieties. The oligosaccharides thus obtained were fractionated into six components by gel filtration, thin-layer chromatography, and high-performance liquid chromatography. The structures of the isolated oligosaccharides were determined by sugar analysis, exoglycosidase digestion, and methylation analysis in combination with high-resolution proton nuclear magnetic resonance spectroscopy. It was found that (1) the six oligosaccharides are a series of compounds of xylose-containing biantennary complex types that share as the core a common structural unit, i.e., Xyl-β(l-2)[Man-α(l-6)]Man-β(l-4)GlcNAc-β(l-4)[Fuc-α(1-3)]GlcNAc, and (2) mannose, N-acetylglucosamine, galactose, and fucose residues are additionally linked to the core as the outer chain moieties.

  Publication DOI: 10.1021/bi00350a018
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Institutions: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan, Department of Biochemistry, Nagoya City University Medical School, Nagoya, Japan, Centre National de la Recherche Scientifique, CENG, Grenoble, France, Research Institute for Biological Regulation School of Agriculture, Nagoya University, Nagoya, Japan, Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Tokyo, Japan
  Methods: 1H NMR, TLC, acid hydrolysis, HPLC, enzymatic digestion, methylation analysis
  
   
  
  Acer pseudoplatanus
  CSDB ID 107209 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130646,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_140108,IEDB_140122,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_423128,IEDB_548907,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_30,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 9546
  Takahashi N, Hotta T, Ishihara H, Mori M, Tejima S, Bligny R, Akazawa T, Endo S, Arata Y "Xylose-containing common structural unit in N-linked oligosaccharides of laccase from sycamore cells" - Biochemistry 25(2) (1986) 388-395
  

  The structures of asparagine-linked oligosaccharides of laccase excreted by sycamore (Acer pseudoplatanus L.) cells are reported. Peptic glycopeptides obtained from the laccase were treated with N-oligosaccharide glycopeptidase (EC 3.5.1.52) to release the oligosaccharide moieties. The oligosaccharides thus obtained were fractionated into six components by gel filtration, thin-layer chromatography, and high-performance liquid chromatography. The structures of the isolated oligosaccharides were determined by sugar analysis, exoglycosidase digestion, and methylation analysis in combination with high-resolution proton nuclear magnetic resonance spectroscopy. It was found that (1) the six oligosaccharides are a series of compounds of xylose-containing biantennary complex types that share as the core a common structural unit, i.e., Xyl-β(l-2)[Man-α(l-6)]Man-β(l-4)GlcNAc-β(l-4)[Fuc-α(1-3)]GlcNAc, and (2) mannose, N-acetylglucosamine, galactose, and fucose residues are additionally linked to the core as the outer chain moieties.

  Publication DOI: 10.1021/bi00350a018
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Institutions: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan, Department of Biochemistry, Nagoya City University Medical School, Nagoya, Japan, Centre National de la Recherche Scientifique, CENG, Grenoble, France, Research Institute for Biological Regulation School of Agriculture, Nagoya University, Nagoya, Japan, Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Tokyo, Japan
  Methods: 1H NMR, TLC, acid hydrolysis, HPLC, enzymatic digestion, methylation analysis
  
   
  
  Acer pseudoplatanus
  CSDB ID 107210 (all data & tools)
• Article ID: 10560
  Hino K, Yamamoto S, Sano O, Taniguchi Y, Kohno K, Usui M, Fukuda S, Hanzawa H, Haruyama H, Kurimoto M "Carbohydrate structures of the glycoprotein allergen Cry j I from Japanese cedar (Cryptomeria japonica) pollen" - Journal of Biochemistry 117 (1995) 289-295
  

  The glycoprotein allergen Cry j I from Japanese cedar (Cryptomeria japonica) pollen was treated with pepsin and glycopeptidase A to release asparagine-linked oligosaccharides. The reducing ends of the oligosaccharides were aminated with the fluorescent reagent 2-aminopyridine. The oligosaccharide derivatives were purified by gel permeation chromatography and reversed-phase HPLC. Their structures were determined by sequential exoglycosidase digestion and 500 MHz 1H-NMR spectroscopy. Four oligosaccharide structures, A, B, C, and D, were identified as the xylose-containing complex-type. They were present at a molar ratio of 8:1:6:1. By amino acid sequence analyses of the tryptic peptides, Asn-170 and Asn-333 of Cry j I were found to carry asparagine-linked oligosaccharides.

  glycoprotein, carbohydrate structure, 1H-NMR, allergen, Cry j I

  NCBI PubMed ID: 7608114
  Publication DOI: 10.1093/jb/117.2.289
  Journal NLM ID: 0376600
  Publisher: Japanese Biochemical Society
  Institutions: Fujisaki Institute, Hayashibara Biochemical Laboratories, Inc., Okayama
  Methods: 1H NMR, HPLC, enzymatic digestion, CC, amino acid sequencing
  
   
  
  Cryptomeria japonica
  CSDB ID 132984 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130646,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_140108,IEDB_140122,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_423128,IEDB_540672,IEDB_548907,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_30,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 9546
  Takahashi N, Hotta T, Ishihara H, Mori M, Tejima S, Bligny R, Akazawa T, Endo S, Arata Y "Xylose-containing common structural unit in N-linked oligosaccharides of laccase from sycamore cells" - Biochemistry 25(2) (1986) 388-395
  

  The structures of asparagine-linked oligosaccharides of laccase excreted by sycamore (Acer pseudoplatanus L.) cells are reported. Peptic glycopeptides obtained from the laccase were treated with N-oligosaccharide glycopeptidase (EC 3.5.1.52) to release the oligosaccharide moieties. The oligosaccharides thus obtained were fractionated into six components by gel filtration, thin-layer chromatography, and high-performance liquid chromatography. The structures of the isolated oligosaccharides were determined by sugar analysis, exoglycosidase digestion, and methylation analysis in combination with high-resolution proton nuclear magnetic resonance spectroscopy. It was found that (1) the six oligosaccharides are a series of compounds of xylose-containing biantennary complex types that share as the core a common structural unit, i.e., Xyl-β(l-2)[Man-α(l-6)]Man-β(l-4)GlcNAc-β(l-4)[Fuc-α(1-3)]GlcNAc, and (2) mannose, N-acetylglucosamine, galactose, and fucose residues are additionally linked to the core as the outer chain moieties.

  Publication DOI: 10.1021/bi00350a018
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Institutions: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan, Department of Biochemistry, Nagoya City University Medical School, Nagoya, Japan, Centre National de la Recherche Scientifique, CENG, Grenoble, France, Research Institute for Biological Regulation School of Agriculture, Nagoya University, Nagoya, Japan, Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Tokyo, Japan
  Methods: 1H NMR, TLC, acid hydrolysis, HPLC, enzymatic digestion, methylation analysis
  
   
  
  Acer pseudoplatanus
  CSDB ID 107211 (all data & tools)
• Article ID: 10560
  Hino K, Yamamoto S, Sano O, Taniguchi Y, Kohno K, Usui M, Fukuda S, Hanzawa H, Haruyama H, Kurimoto M "Carbohydrate structures of the glycoprotein allergen Cry j I from Japanese cedar (Cryptomeria japonica) pollen" - Journal of Biochemistry 117 (1995) 289-295
  

  The glycoprotein allergen Cry j I from Japanese cedar (Cryptomeria japonica) pollen was treated with pepsin and glycopeptidase A to release asparagine-linked oligosaccharides. The reducing ends of the oligosaccharides were aminated with the fluorescent reagent 2-aminopyridine. The oligosaccharide derivatives were purified by gel permeation chromatography and reversed-phase HPLC. Their structures were determined by sequential exoglycosidase digestion and 500 MHz 1H-NMR spectroscopy. Four oligosaccharide structures, A, B, C, and D, were identified as the xylose-containing complex-type. They were present at a molar ratio of 8:1:6:1. By amino acid sequence analyses of the tryptic peptides, Asn-170 and Asn-333 of Cry j I were found to carry asparagine-linked oligosaccharides.

  glycoprotein, carbohydrate structure, 1H-NMR, allergen, Cry j I

  NCBI PubMed ID: 7608114
  Publication DOI: 10.1093/jb/117.2.289
  Journal NLM ID: 0376600
  Publisher: Japanese Biochemical Society
  Institutions: Fujisaki Institute, Hayashibara Biochemical Laboratories, Inc., Okayama
  Methods: 1H NMR, HPLC, enzymatic digestion, CC, amino acid sequencing
  
   
  
  Cryptomeria japonica
  CSDB ID 132985 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85,SB_86

• Article ID: 9884
  Kimura Y, Nakagawa Y, Tokuda T, Yamai M, Nakajima S, Higashide E, Takagi S, Takagi SS "Structures of N-linked oligosaccharides of microsomal glycoproteins from developing castor bean endosperms" - Bioscience, Biotechnology, and Biochemistry 56 (1992) 215-222
  

  The structures of sugar chains of the glycoproteins from the microsomal fraction of developing castor bean endosperms have been analyzed. The structural analyses were done by a fluorescence method combined with component analysis, exoglycosidase digestions, partial acetolysis, Smith degradation, and 1H-NMR spectroscopy. The estimated structures fell into three categories; the first was oligomannose-type, the second xylomannose-type, the third complex-type. Among these oligosaccharides, Man3Fuc1Xyl1GlcNAc2 (M3FX) and Man6GlcNAc2 (M6B) were the major structures. The structures of Man4GlcNAc2 (M4C) and Man4Xyl1GlcNAc2 (M4X) have also been found in the microsomal glycoproteins of the developing bean endosperms. These results could indicate that the structures of M4C, M4X, and M3FX are formed in the stage of sugar chain processing in the microsomal fraction, in which oligomannose-type sugar chains are modified into complex-type ones by several kinds of processing enzymes.

  NCBI PubMed ID: 1368297
  Journal NLM ID: 9205717
  Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
  Institutions: Division of Bio-resource Science, Graduate School of Natural Science and Technology, Okayama University, Japan
  Methods: 1H NMR, Smith degradation, enzymatic digestion, partial acetolysis
  
   
  
  Ricinus communis
  CSDB ID 111156 (all data & tools)
• Article ID: 10211
  Stahl B, Klabunde T, Witzel H, Krebs B, Steup M, Karas M, Hillenkamp F "The oligosaccharides of the Fe(III)-Zn(II) purple acid phosphatase of the red kidney bean. Determination of the structure by a combination of matrix-assisted laser desorption/ionization mass spectrometry and selective enzymic degradation" - European Journal of Biochemistry 220 (1994) 321-330
  

  Purple acid phosphatase of the common bean Phaseolus vulgaris (KBPase), a dimeric 110-kDa glycoprotein related to the mammalian purple acid phosphatases with a two-metal cluster at the active site contains five oligosaccharide side chains/monomer. The N-linked glycan structures were characterized by selective enzymic degradation in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The purified protein was cleaved by cyanogen bromide. One 30-kDa large methionine-free fragment required a further tryptic digest. The peptides were separated by HPLC and the glycosylated species were identified both by their heterogeneous mass spectra and by an immunoassay. None of the glycopeptides proved to have more than one glycosylation site. The composition of the carbohydrate moieties were calculated by comparing the mass spectra of the glycopeptides before and after enzymic deglycosylation. These results were complemented by data from a carbohydrate composition analysis. In four of the five peptides an α1-3 fucose attached to the asparagine-linked N-acetylglucosamine prevented removal of the glycan by peptide N-glycosidase F; peptide N-glycosidase A removed all carbohydrates from the peptides. To reveal the sequence of the carbohydrate moiety including the linkage positions between the different saccharides, one of the glycopeptides was degraded by specific exoglycosidases. The enzymic degradations by these hydrolases were monitored by mass spectrometry of small aliquots taken at intervals during the reaction. The detailed structure of this one glycan in conjunction with the respective mass spectra and the composition analysis were used to infer the structure of the other four glycans. All glycans of the KBPase have a complex-type xylose-containing structure with four of the five having an additional fucose.

  NCBI PubMed ID: 8125089
  Publication DOI: 10.1111/j.1432-1033.1994.tb18628.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Institut für Botanik, Westfälische Wilhelms-Universität, Münster, Germany, Institut für Anorganische Chemie, Westfälische Wilhelms-Universität, Münster, Germany, Institut für Biochemie, Westfälische Wilhelms-Universität, Münster, Germany, Institut fur Medizinische Physik, Westfälische Wilhelms-Universität, Münster, Germany
  Methods: GC-MS, GC, MALDI-MS, enzymatic digestion, RP-HPLC, trypsinolysis
  
   
  
  Phaseolus vulgaris
  CSDB ID 124453 (all data & tools)
• Article ID: 10223
  Kamerling JP "Xylose-containing carbohydrate chains derived from N-glycoproteins" - Pure and Applied Chemistry 63 (1991) 465-472
  

  Xylose-containing N-linked carbohydrate chains are integral parts of certain plant and animal glycoproteins. In all of the known structures, p-D-xylose is 1-2-linked to p-D-mannose of the trimannosyl-N,N'-diacetylchitobiose unit. If a-L-fucose is present at the asparagine-linked N-acetyl-D-glucosamine, then there are differences in the sites of its attachment, namely, a1-3- or a1-6-linked, depending on the biological origin. The a-D-mannose residues can be substituted with additional monosaccharides or 3-0-methylated. The state of the art with respect to structural analysis, organic synthesis, conformational analysis, biosynthesis, lectin binding, and immunological aspects is reviewed.

  Publication DOI: 10.1351/pac199163040465
  Journal NLM ID: 0376514
  Publisher: Oxford: Blackwell Scientific Publications
  Institutions: Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Utrecht, The Netherlands
  
   
  
  Acer pseudoplatanus
  CSDB ID 148090 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130646,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_140108,IEDB_140122,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_423128,IEDB_540672,IEDB_548907,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_30,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 9938
  Takahashi N, Hitotsuya H, Hanzawa H, Arata Y, Kurihara Y "Structural study of asparagine-linked oligosaccharide moiety of taste- modifying protein, miraculin" - Journal of Biological Chemistry 265 (1990) 7793-7798
  

  The structures of the N-linked oligosaccharides of miraculin, which is a taste modifying glycoprotein isolated from miracle fruits, berries of Richadella dulcifica, are reported. Asparagine-linked oligosaccharides were released from the protein by glycopeptidase (almond) digestion. The reducing ends of the oligosaccharide chains thus obtained were aminated with a fluorescent reagent, 2-aminopyridine, and the mixture of pyridylamino derivatives of the oligosaccharides was separated by high performance liquid chromatography (HPLC) on an ODS-silica column. More than five kinds of oligosaccharide fractions were separated by the one chromatographic run. The structure of each oligosaccharide thus isolated was analyzed by a combination of sequential exoglycosidase digestion and another kind of HPLC with an amidesilica column. Furthermore, high resolution proton nuclear magnetic resonance (1H NMR) measurements were carried out. It was found that 1) five oligosaccharides obtained are a series of compounds with xylose-containing common structural core, Xyl β1----2 (Man α1----6) Man β1----4-GlcNAc β1----4 (Fuca1----3)GlcNAc, 2) a variety of oligosaccharide structures are significant for two glycosylation sites, Asn-42 and Asn-186, and 3) two new oligosaccharides, B and D, with unusual structures containing monoantennary complex-type were characterized. (formula; see text)

  NCBI PubMed ID: 2335505
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Institutions: Faculty of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan, Department of Biochemistry, Nagoya City University College of Nursing, Japan, Department of Chemistry, Faculty of Education, Yokohama National University, Yokohama, Japan
  Methods: gel filtration, 1H NMR, HPLC, enzymatic digestion
  
   
  
  Richadella dulcifica
  CSDB ID 135866 (all data & tools)
• Article ID: 10223
  Kamerling JP "Xylose-containing carbohydrate chains derived from N-glycoproteins" - Pure and Applied Chemistry 63 (1991) 465-472
  

  Xylose-containing N-linked carbohydrate chains are integral parts of certain plant and animal glycoproteins. In all of the known structures, p-D-xylose is 1-2-linked to p-D-mannose of the trimannosyl-N,N'-diacetylchitobiose unit. If a-L-fucose is present at the asparagine-linked N-acetyl-D-glucosamine, then there are differences in the sites of its attachment, namely, a1-3- or a1-6-linked, depending on the biological origin. The a-D-mannose residues can be substituted with additional monosaccharides or 3-0-methylated. The state of the art with respect to structural analysis, organic synthesis, conformational analysis, biosynthesis, lectin binding, and immunological aspects is reviewed.

  Publication DOI: 10.1351/pac199163040465
  Journal NLM ID: 0376514
  Publisher: Oxford: Blackwell Scientific Publications
  Institutions: Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Utrecht, The Netherlands
  
   
  
  Acer pseudoplatanus, Richadella dulcifica
  CSDB ID 148081 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130646,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_140108,IEDB_140122,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_423128,IEDB_548907,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_30,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 10127
  Tezuka K, Hayashi M, Ishihara H, Onozaki K, Nishimura M, Takahashi N "Occurrence of heterogeneity of N-linked oligosaccharides attached to sycamore (Acer pseudoplatanus L.) laccase after excretion" - Biochemistry and Molecular Biology International 29 (1993) 395-402
  

  The N-linked oligosaccharide moieties of sycamore (Acer pseudoplatanus L.) laccase are known to be highly heterogeneous. We confirmed that this oligosaccharide heterogeneity was caused not only during the oligosaccharide biosynthesis in Golgi apparatus, but also after the excretion of laccase protein into a culture medium. The culture medium for the sycamore cells (Acer pseudoplatanus L.) contained β-galactosidase, α-L-fucosidase, β-N-acetylglucosaminidase, α-mannosidase and β-xylosidase activities. We showed that the largest sugar chain in laccase, oligosaccharide F, [formula: see text] was degraded to [formula: see text] by a crude exoglycosidase mixture in the culture medium.

  NCBI PubMed ID: 8485457
  Journal NLM ID: 9306673
  Institutions: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences, Nagoya City University, Japan
  
   
  
  Acer pseudoplatanus
  CSDB ID 106488 (all data & tools)
• Article ID: 10223
  Kamerling JP "Xylose-containing carbohydrate chains derived from N-glycoproteins" - Pure and Applied Chemistry 63 (1991) 465-472
  

  Xylose-containing N-linked carbohydrate chains are integral parts of certain plant and animal glycoproteins. In all of the known structures, p-D-xylose is 1-2-linked to p-D-mannose of the trimannosyl-N,N'-diacetylchitobiose unit. If a-L-fucose is present at the asparagine-linked N-acetyl-D-glucosamine, then there are differences in the sites of its attachment, namely, a1-3- or a1-6-linked, depending on the biological origin. The a-D-mannose residues can be substituted with additional monosaccharides or 3-0-methylated. The state of the art with respect to structural analysis, organic synthesis, conformational analysis, biosynthesis, lectin binding, and immunological aspects is reviewed.

  Publication DOI: 10.1351/pac199163040465
  Journal NLM ID: 0376514
  Publisher: Oxford: Blackwell Scientific Publications
  Institutions: Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Utrecht, The Netherlands
  
   
  
  Acer pseudoplatanus
  CSDB ID 148096 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_548907,IEDB_983930,SB_137,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_29,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 10211
  Stahl B, Klabunde T, Witzel H, Krebs B, Steup M, Karas M, Hillenkamp F "The oligosaccharides of the Fe(III)-Zn(II) purple acid phosphatase of the red kidney bean. Determination of the structure by a combination of matrix-assisted laser desorption/ionization mass spectrometry and selective enzymic degradation" - European Journal of Biochemistry 220 (1994) 321-330
  

  Purple acid phosphatase of the common bean Phaseolus vulgaris (KBPase), a dimeric 110-kDa glycoprotein related to the mammalian purple acid phosphatases with a two-metal cluster at the active site contains five oligosaccharide side chains/monomer. The N-linked glycan structures were characterized by selective enzymic degradation in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The purified protein was cleaved by cyanogen bromide. One 30-kDa large methionine-free fragment required a further tryptic digest. The peptides were separated by HPLC and the glycosylated species were identified both by their heterogeneous mass spectra and by an immunoassay. None of the glycopeptides proved to have more than one glycosylation site. The composition of the carbohydrate moieties were calculated by comparing the mass spectra of the glycopeptides before and after enzymic deglycosylation. These results were complemented by data from a carbohydrate composition analysis. In four of the five peptides an α1-3 fucose attached to the asparagine-linked N-acetylglucosamine prevented removal of the glycan by peptide N-glycosidase F; peptide N-glycosidase A removed all carbohydrates from the peptides. To reveal the sequence of the carbohydrate moiety including the linkage positions between the different saccharides, one of the glycopeptides was degraded by specific exoglycosidases. The enzymic degradations by these hydrolases were monitored by mass spectrometry of small aliquots taken at intervals during the reaction. The detailed structure of this one glycan in conjunction with the respective mass spectra and the composition analysis were used to infer the structure of the other four glycans. All glycans of the KBPase have a complex-type xylose-containing structure with four of the five having an additional fucose.

  NCBI PubMed ID: 8125089
  Publication DOI: 10.1111/j.1432-1033.1994.tb18628.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Institut für Botanik, Westfälische Wilhelms-Universität, Münster, Germany, Institut für Anorganische Chemie, Westfälische Wilhelms-Universität, Münster, Germany, Institut für Biochemie, Westfälische Wilhelms-Universität, Münster, Germany, Institut fur Medizinische Physik, Westfälische Wilhelms-Universität, Münster, Germany
  Methods: GC-MS, GC, MALDI-MS, enzymatic digestion, RP-HPLC, trypsinolysis
  
   
  
  Phaseolus vulgaris
  CSDB ID 124454 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_548907,IEDB_983930,SB_137,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_29,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 10211
  Stahl B, Klabunde T, Witzel H, Krebs B, Steup M, Karas M, Hillenkamp F "The oligosaccharides of the Fe(III)-Zn(II) purple acid phosphatase of the red kidney bean. Determination of the structure by a combination of matrix-assisted laser desorption/ionization mass spectrometry and selective enzymic degradation" - European Journal of Biochemistry 220 (1994) 321-330
  

  Purple acid phosphatase of the common bean Phaseolus vulgaris (KBPase), a dimeric 110-kDa glycoprotein related to the mammalian purple acid phosphatases with a two-metal cluster at the active site contains five oligosaccharide side chains/monomer. The N-linked glycan structures were characterized by selective enzymic degradation in combination with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The purified protein was cleaved by cyanogen bromide. One 30-kDa large methionine-free fragment required a further tryptic digest. The peptides were separated by HPLC and the glycosylated species were identified both by their heterogeneous mass spectra and by an immunoassay. None of the glycopeptides proved to have more than one glycosylation site. The composition of the carbohydrate moieties were calculated by comparing the mass spectra of the glycopeptides before and after enzymic deglycosylation. These results were complemented by data from a carbohydrate composition analysis. In four of the five peptides an α1-3 fucose attached to the asparagine-linked N-acetylglucosamine prevented removal of the glycan by peptide N-glycosidase F; peptide N-glycosidase A removed all carbohydrates from the peptides. To reveal the sequence of the carbohydrate moiety including the linkage positions between the different saccharides, one of the glycopeptides was degraded by specific exoglycosidases. The enzymic degradations by these hydrolases were monitored by mass spectrometry of small aliquots taken at intervals during the reaction. The detailed structure of this one glycan in conjunction with the respective mass spectra and the composition analysis were used to infer the structure of the other four glycans. All glycans of the KBPase have a complex-type xylose-containing structure with four of the five having an additional fucose.

  NCBI PubMed ID: 8125089
  Publication DOI: 10.1111/j.1432-1033.1994.tb18628.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Institut für Botanik, Westfälische Wilhelms-Universität, Münster, Germany, Institut für Anorganische Chemie, Westfälische Wilhelms-Universität, Münster, Germany, Institut für Biochemie, Westfälische Wilhelms-Universität, Münster, Germany, Institut fur Medizinische Physik, Westfälische Wilhelms-Universität, Münster, Germany
  Methods: GC-MS, GC, MALDI-MS, enzymatic digestion, RP-HPLC, trypsinolysis
  
   
  
  Phaseolus vulgaris
  CSDB ID 124455 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85,SB_86

• Article ID: 10560
  Hino K, Yamamoto S, Sano O, Taniguchi Y, Kohno K, Usui M, Fukuda S, Hanzawa H, Haruyama H, Kurimoto M "Carbohydrate structures of the glycoprotein allergen Cry j I from Japanese cedar (Cryptomeria japonica) pollen" - Journal of Biochemistry 117 (1995) 289-295
  

  The glycoprotein allergen Cry j I from Japanese cedar (Cryptomeria japonica) pollen was treated with pepsin and glycopeptidase A to release asparagine-linked oligosaccharides. The reducing ends of the oligosaccharides were aminated with the fluorescent reagent 2-aminopyridine. The oligosaccharide derivatives were purified by gel permeation chromatography and reversed-phase HPLC. Their structures were determined by sequential exoglycosidase digestion and 500 MHz 1H-NMR spectroscopy. Four oligosaccharide structures, A, B, C, and D, were identified as the xylose-containing complex-type. They were present at a molar ratio of 8:1:6:1. By amino acid sequence analyses of the tryptic peptides, Asn-170 and Asn-333 of Cry j I were found to carry asparagine-linked oligosaccharides.

  glycoprotein, carbohydrate structure, 1H-NMR, allergen, Cry j I

  NCBI PubMed ID: 7608114
  Publication DOI: 10.1093/jb/117.2.289
  Journal NLM ID: 0376600
  Publisher: Japanese Biochemical Society
  Institutions: Fujisaki Institute, Hayashibara Biochemical Laboratories, Inc., Okayama
  Methods: 1H NMR, HPLC, enzymatic digestion, CC, amino acid sequencing
  
   
  
  Cryptomeria japonica
  CSDB ID 132982 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_115015,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130653,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_1394182,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_149135,IEDB_149556,IEDB_150092,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_241116,IEDB_423096,IEDB_461723,IEDB_490029,IEDB_548907,IEDB_983930,SB_137,SB_155,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_29,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 10774
  Fitchette-Laine AC, Gomord V, Cabanes M, Michalski JC, Foucher B, Cavelier B, Hawes C, Lerouge P, Faye L "N-glycans harboring the Lewis a epitope are expressed at the surface of plant cells" - Plant Journal: for Cell and Molecular Biology 12(6) (1997) 1411-1417
  

  In plants, N-linked glycans are processed in the Golgi apparatus to complex-type N-glycans of limited size containing a β(1,2)-xylose and/or an α(1,3)-fucose residue. Larger mono-and bi-antennary N-linked complex glycans have not often been described. This study has re-examined the structure of such plant N-linked glycans, and, through both immunological and structural data, it is shown that the antennae are composed of Lewis a (Le(a)) antigens, comprising the carbohydrate sequence Gal β 1-3[Fuc α 1-4]GlcNAc. Furthermore, a fucosyltransferase activity involved in the biosynthesis of this antigen was detected in sycamore cells. This is the first characterization in plants of a Lewis antigen that is usually found on cell-surface glycoconjugates in mammals and involved in recognition and adhesion processes. Le(a)-containing N-linked glycans are widely distributed in plants and highly expressed at the cell surface, which may suggest a putative function in cell/cell communication.

  NCBI PubMed ID: 9450345
  Publication DOI: 10.1046/j.1365-313x.1997.12061411.x
  Journal NLM ID: 9207397
  Publisher: Oxford: Blackwell Scientific Publishers and BIOS Scientific Publishers for the Society for Experimental Biology
  Correspondence: lfaye@crihan.fr
  Institutions: Laboratoire des Transports Intracellulaires, ESA-CNRS 6037, Université de Rouen, Faculté des Sciences, Mont Saint Aignan, France
  Methods: methylation, GLC-MS, SDS-PAGE, glycosyltransferase assays, ELISA, ESI-MS, immunoblotting
  
   
  
  Platanus
  CSDB ID 60030 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_115015,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130653,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_1394182,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_149135,IEDB_149556,IEDB_150092,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_423096,IEDB_461723,IEDB_490029,IEDB_548907,IEDB_983930,SB_137,SB_155,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_29,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 10794
  Melo NS, Nimtz M, Conradt HS, Fevereiro PS, Costa J "Identification of the human Lewis(a) carbohydrate motif in a secretory peroxidase from a plant cell suspension culture (Vaccinium myrtillus L.)" - FEBS Letters 415(2) (1997) 186-191
  

  This paper reports for the first time the presence of the human Lewis(a) type determinant in glycoproteins secreted by plant cells. A single glycopeptide was identified in the tryptic hydrolysis of the peroxidase VMPxC1 from Vaccinium myrtillus L. by HPLC/ESI-MS. The oligosaccharide structures were elucidated by ESI-MS-MS and by methylation analysis before and after removal of fucose by mild acid hydrolysis. The major structure determined is of the biantennary plant complex type containing the outer chain motif Lewis(a) [structure in text]. A corresponding fucosyltransferase activity catalyzing the formation of Lewis(a) type structures in vitro was identified in cellular extracts of the suspension culture

  Extracellular glycoprotein, Lewisa, Peroxidase, Plant complex oligosaccharide, Vaccinium myrtillus

  NCBI PubMed ID: 9350993
  Publication DOI: 10.1016/S0014-5793(97)01121-6
  Journal NLM ID: 0155157
  Publisher: Elsevier
  Correspondence: jcosta@itqb.unl.pt
  Institutions: ITQBIIBET, Apartado 12, P-2780 Oeiras, Portugal
  Methods: methylation, SDS-PAGE, glycosyltransferase assays, ESI-MS, MALDI-TOF MS, HPLC, enzymatic digestion, hydrazinolysis
  
   
  
  Vaccinium myrtillus L
  CSDB ID 60090 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_115015,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130653,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_1394182,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_149135,IEDB_149556,IEDB_150092,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_423096,IEDB_461723,IEDB_490029,IEDB_548907,IEDB_983930,SB_137,SB_155,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_29,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 10794
  Melo NS, Nimtz M, Conradt HS, Fevereiro PS, Costa J "Identification of the human Lewis(a) carbohydrate motif in a secretory peroxidase from a plant cell suspension culture (Vaccinium myrtillus L.)" - FEBS Letters 415(2) (1997) 186-191
  

  This paper reports for the first time the presence of the human Lewis(a) type determinant in glycoproteins secreted by plant cells. A single glycopeptide was identified in the tryptic hydrolysis of the peroxidase VMPxC1 from Vaccinium myrtillus L. by HPLC/ESI-MS. The oligosaccharide structures were elucidated by ESI-MS-MS and by methylation analysis before and after removal of fucose by mild acid hydrolysis. The major structure determined is of the biantennary plant complex type containing the outer chain motif Lewis(a) [structure in text]. A corresponding fucosyltransferase activity catalyzing the formation of Lewis(a) type structures in vitro was identified in cellular extracts of the suspension culture

  Extracellular glycoprotein, Lewisa, Peroxidase, Plant complex oligosaccharide, Vaccinium myrtillus

  NCBI PubMed ID: 9350993
  Publication DOI: 10.1016/S0014-5793(97)01121-6
  Journal NLM ID: 0155157
  Publisher: Elsevier
  Correspondence: jcosta@itqb.unl.pt
  Institutions: ITQBIIBET, Apartado 12, P-2780 Oeiras, Portugal
  Methods: methylation, SDS-PAGE, glycosyltransferase assays, ESI-MS, MALDI-TOF MS, HPLC, enzymatic digestion, hydrazinolysis
  
   
  
  Vaccinium myrtillus L
  CSDB ID 60091 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_115015,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130653,IEDB_130701,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_1391962,IEDB_1394182,IEDB_141793,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142489,IEDB_143794,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_149135,IEDB_149556,IEDB_150092,IEDB_150899,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_190606,IEDB_241116,IEDB_423096,IEDB_461723,IEDB_490029,IEDB_548907,IEDB_983930,SB_137,SB_155,SB_165,SB_166,SB_187,SB_195,SB_197,SB_198,SB_29,SB_33,SB_44,SB_67,SB_7,SB_72,SB_73,SB_74,SB_85,SB_86,SB_88

• Article ID: 10794
  Melo NS, Nimtz M, Conradt HS, Fevereiro PS, Costa J "Identification of the human Lewis(a) carbohydrate motif in a secretory peroxidase from a plant cell suspension culture (Vaccinium myrtillus L.)" - FEBS Letters 415(2) (1997) 186-191
  

  This paper reports for the first time the presence of the human Lewis(a) type determinant in glycoproteins secreted by plant cells. A single glycopeptide was identified in the tryptic hydrolysis of the peroxidase VMPxC1 from Vaccinium myrtillus L. by HPLC/ESI-MS. The oligosaccharide structures were elucidated by ESI-MS-MS and by methylation analysis before and after removal of fucose by mild acid hydrolysis. The major structure determined is of the biantennary plant complex type containing the outer chain motif Lewis(a) [structure in text]. A corresponding fucosyltransferase activity catalyzing the formation of Lewis(a) type structures in vitro was identified in cellular extracts of the suspension culture

  Extracellular glycoprotein, Lewisa, Peroxidase, Plant complex oligosaccharide, Vaccinium myrtillus

  NCBI PubMed ID: 9350993
  Publication DOI: 10.1016/S0014-5793(97)01121-6
  Journal NLM ID: 0155157
  Publisher: Elsevier
  Correspondence: jcosta@itqb.unl.pt
  Institutions: ITQBIIBET, Apartado 12, P-2780 Oeiras, Portugal
  Methods: methylation, SDS-PAGE, glycosyltransferase assays, ESI-MS, MALDI-TOF MS, HPLC, enzymatic digestion, hydrazinolysis
  
   
  
  Vaccinium myrtillus L
  CSDB ID 60092 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: Gn2M3FX
Contained glycoepitopes: IEDB_114701,IEDB_115005,IEDB_115015,IEDB_116644,IEDB_122244,IEDB_123886,IEDB_123887,IEDB_123888,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_1394182,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_146665,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_149135,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_167188,IEDB_167189,IEDB_174332,IEDB_174333,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85,SB_86

• Article ID: 10931
  Kajiura H, Seki T, Fujiyama K "Arabidopsis thaliana ALG3 mutant synthesizes immature oligosaccharides in the ER and accumulates unique N-glycans" - Glycobiology 20 (2010) 736-751
  

  The core oligosaccharide Glc3Man9GlcNAc2 is assembled by a series of membrane-bound glycosyltransferases as the lipid carrier dolichylpyrophosphate-linked glycan in the endoplasmic reticulum (ER). The first step of this assembly pathway on the ER luminal side is mediated by ALG3 (asparagine-linked glycosylation 3), which is a highly conserved reaction among eukaryotic cells. Complementary genetics compared with Saccharomyces cerevisiae ALG gene families and bioinformatic approaches have enabled the identification of ALG3 from other species. In Arabidopsis thaliana, AtALG3 (At2g47760) was identified as α1,3-mannosyltransferase. Complementation analysis showed that AtALG3 rescued the temperature-sensitive phenotype, that lipid-linked oligosaccharide assemblies and that protein underglycosylation of S. cerevisiae ALG3-deficient mutant. In Arabidopsis ALG3 mutant, an immature lipid-linked oligosaccharide structure, M5ER, was synthesized, and used for protein N-glycosylation, resulting in the blockade of subsequent maturation with the concanavalin A affinoactive and Endo H-insensitive structure. N-Glycan profiling of total proteins from alg3 mutants exhibited a unique structural profile, alg3 has rare N-glycan structures including Man3GlcNAc2, M4ER, M5ER and GlcM5ER, which are not usually detected in Arabidopsis, and a much less amount of complex-type N-glycan than that in wild type. Interestingly, despite protein N-glycosylation differences compared with wild type, alg3 showed no obvious phenotype under normal and high temperature or salt/osmotic stress conditions. These results indicate that AtALG3 is a critical factor for mature N-glycosylation of proteins, but not essential for cell viability and growth in Arabidopsis.

  Arabidopsis thaliana, N-glycosylation, endoplasmic reticulum, α1, lipid-linked oligosaccharide, 3-mannosyltransferase

  Publication DOI: 10.1093/glycob/cwq028
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: fujiyama@icb.osaka-u.ac.jp
  Institutions: The International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita-shi, Osaka 565, Japan
  Methods: biological assays, HPLC, RP-HPLC, LC-MS/MS, confocal microscopy, genetic manipulations
  
   
  
  Arabidopsis thaliana
  CSDB ID 60972 (all data & tools)
• Article ID: 10932
  Yoo JY, Ko KS, Seo H-K, Park S, Fanata WID, Harmoko R, Ramasamy NK, Thulasinathan T, Mengiste T, Lim J-M, Lee SY, Lee KO "Limited addition of the 6-arm β1,2-linked N-acetylglucosamine (GlcNAc) residue facilitates the formation of the largest N-glycan in plants" - Journal of Biological Chemistry 290 (2015) 16560-16572
  

  The most abundant N-glycan in plants is the paucimannosidic N-glycan with core β1,2-xylose and α1,3-fucose residues (Man3XylFuc(GlcNAc)2). Here, we report a mechanism in Arabidopsis thaliana that efficiently produces the largest N-glycan in plants. Genetic and biochemical evidence indicates that the addition of the 6-arm β1,2-GlcNAc residue by N-acetylglucosaminyltransferase II (GnTII) is less effective than additions of the core β1,2-xylose and α1,3-fucose residues by XylT, FucTA, and FucTB in Arabidopsis. Furthermore, analysis of gnt2 mutant and 35S:GnTII transgenic plants shows that the addition of the 6-arm non-reducing GlcNAc residue to the common N-glycan acceptor GlcNAcMan3(GlcNAc)2 inhibits additions of the core β1,2-xylose and α1,3-fucose residues. Our findings indicate that plants limit the rate of the addition of the 6-arm GlcNAc residue to the common N-glycan acceptor as a mechanism to facilitate formation of the prevalent N-glycans with Man3XylFuc(GlcNAc)2 and (GlcNAc)2Man3XylFuc(GlcNAc)2 structures.

  glycosyltransferase, glycosylation, plant, post-translational modification (PTM), carbohydrate processing

  Publication DOI: 10.1074/jbc.M115.653162
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: leeko@gnu.ac.kr
  Institutions: Division of Applied Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 660-701, Korea, Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
  Methods: biological assays, MALDI-TOF-MS, genetic manipulations, prediction
  
   
  
  Arabidopsis thaliana
  CSDB ID 60988 (all data & tools)
• Article ID: 10936
  Kajiura H, Okamoto T, Misaki R, Matsuura Y, Fujiyama K "Arabidopsis β1,2-xylosyltransferase: substrate specificity and participation in the plant-specific N-glycosylation pathway" - Journal of Bioscience and Bioengineering 113 (2012) 48-54
  

  β1,2-Xylosyltransferase (XYLT) is a plant-specific glycosyltransferase that contributes to the biosynthesis of N-glycoproteins in plants. However, the specificity of XYLT for N-glycans has not yet been completely clarified. To gain insights into the function of XYLT in the plant N-glycosylation pathway, we examined the acceptor substrate specificity of recombinant Arabidopsis XYLT (AtXYLT) using 2-aminopyridine-labeled N-glycans as the substrates and confirmed the N-glycans of Arabidopsis xylt mutant. Recombinant AtXYLT expressed in insect cells required the β1,2-linked N-acetylglucosamine (GlcNAc) residue at the nonreducing terminus of the α1,3-branched mannose (Man) residue (GlcNAcβ1,2-Manα1,3-Man; GNM3B) for activity. However, AtXYLT showed decreased activity with substrates that contained α1,3-fucose at the chitobiose core-GlcNAc or a terminal GlcNAc at the α1,6-branched Man residue of GlcNAcβ1,2-Man (GlcNAcβ1,2-Manα1,6-Man; GNM3A), whose ratios were 10% and 50% of the optimal substrate, GNM3B, respectively. Moreover, AtXYLT did not show any activity in the transfer of the Xyl residue to N-glycans that contained a mammalian-type β1,4-linked galactose (Gal) residue at the nonreducing terminus of GlcNAcβ1,2-Man. These results indicate that a β1,2-linked GlcNAc residue at the nonreducing terminus of an α1,3-branched Man residue is necessary for AtXYLT activity and that mammalian-type β1,4-linked Gal residue(s) on the same branch completely inhibit(s) the activity. Furthermore, N-glycan analysis showed that approximately 30% of the N-glycans carry the Xyl residue in the wild type. These findings suggest that AtXYLT acts on protein-bound N-glycans prior to α1,3-fucosyltransferase and mannosidase II in planta.

  N-glycan, plant N-glycosylation, Arabidopsis β1, 2-xylosyltransferase, β1, 2-xylosylation, baculovirus

  Publication DOI: 10.1016/j.jbiosc.2011.09.011
  Journal NLM ID: 100888800
  Publisher: Osaka, Japan, Amsterdam, The Netherlands: Society for Bioscience and Bioengineering
  Correspondence: fujiyama@icb.osaka-u.ac.jp
  Institutions: International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan, Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
  Methods: biological assays, HPLC, LC-MS/MS, genetic manipulations
  
   
  
  Arabidopsis thaliana
  CSDB ID 61029 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: Gn2M3F
Contained glycoepitopes: IEDB_115015,IEDB_123886,IEDB_123888,IEDB_130701,IEDB_135813,IEDB_136045,IEDB_137340,IEDB_137485,IEDB_1394182,IEDB_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145669,IEDB_148493,IEDB_149135,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167186,IEDB_174333,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85,SB_86

• Article ID: 10932
  Yoo JY, Ko KS, Seo H-K, Park S, Fanata WID, Harmoko R, Ramasamy NK, Thulasinathan T, Mengiste T, Lim J-M, Lee SY, Lee KO "Limited addition of the 6-arm β1,2-linked N-acetylglucosamine (GlcNAc) residue facilitates the formation of the largest N-glycan in plants" - Journal of Biological Chemistry 290 (2015) 16560-16572
  

  The most abundant N-glycan in plants is the paucimannosidic N-glycan with core β1,2-xylose and α1,3-fucose residues (Man3XylFuc(GlcNAc)2). Here, we report a mechanism in Arabidopsis thaliana that efficiently produces the largest N-glycan in plants. Genetic and biochemical evidence indicates that the addition of the 6-arm β1,2-GlcNAc residue by N-acetylglucosaminyltransferase II (GnTII) is less effective than additions of the core β1,2-xylose and α1,3-fucose residues by XylT, FucTA, and FucTB in Arabidopsis. Furthermore, analysis of gnt2 mutant and 35S:GnTII transgenic plants shows that the addition of the 6-arm non-reducing GlcNAc residue to the common N-glycan acceptor GlcNAcMan3(GlcNAc)2 inhibits additions of the core β1,2-xylose and α1,3-fucose residues. Our findings indicate that plants limit the rate of the addition of the 6-arm GlcNAc residue to the common N-glycan acceptor as a mechanism to facilitate formation of the prevalent N-glycans with Man3XylFuc(GlcNAc)2 and (GlcNAc)2Man3XylFuc(GlcNAc)2 structures.

  glycosyltransferase, glycosylation, plant, post-translational modification (PTM), carbohydrate processing

  Publication DOI: 10.1074/jbc.M115.653162
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: leeko@gnu.ac.kr
  Institutions: Division of Applied Life Science and Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 660-701, Korea, Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
  Methods: biological assays, MALDI-TOF-MS, genetic manipulations, prediction
  
   
  
  Arabidopsis thaliana
  CSDB ID 60986 (all data & tools)