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Structure type: oligomer
Compound class: N-glycan, glucomannan, oligosaccharide
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_148491,IEDB_148492,IEDB_148493,IEDB_150092,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153212,IEDB_167188,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: 10309
  Qasba PK, Balaji PV, Rao VSR "Molecular dynamics simulations of oligosaccharides and their conformation in the crystal structure of lectin-carbohydrate complex: importance of the torsion angle psi for the orientation of α-1,6-arm" - Glycobiology 4 (1994) 805-815
  

  The conformation of the heptasaccharide Man-α1,6-(Man-α1,3)(Xyl-β1,2)-Man-β1,4-GlcNAc2-β1,4-(L- Fuc-α1,3)-GlcNAc1, the carbohydrate moiety of Erythrina corallodendron lectin (EcorL), the hexasaccharide Man-α1,6-(Man-α1,3) (GlcNAc-β1,4)-Man-β1,4-GlcNAc-β1,4-GlcNAc and their disaccharide fragments have been studied by molecular dynamics (MD) simulations for 1000 ps with different initial conformations. In the isolated heptasaccharide, the most frequently accessed conformation during MD has a psi value of 180 degrees around Man-α1,6-Man linkage. This conformation is stabilized by the formation of a hydrogen bond between the carbonyl oxygen of GlcNAc2 with the O3/O4 hydroxyls of the α1,6-linked mannose residue. The conformation of the heptasaccharide found in the crystal structure of the EcorL-lactose complex (Shaanan et al., Science, 254, 862, 1991), that has a psi value of approximately 76 degrees around Man-α1,6-Man linkage, is accessed, although less frequently, during MD of the isolated oligosaccharide. The phi, psi, chi = 58 degrees, -134 degrees, -60 degrees conformation around Man-α1,6-Man fragment observed in the crystal structure of the Lathyrus ochrus lectin complexed with a biantennary octasaccharide (Table I in Homans, S.W., Glycobiology, 3, 551, 1993) has also been accessed in the present MD simulations. These psi values for the α1,6-linkage, which are observed in the protein-carbohydrate crystal structures and are accessed in the MD simulations, though occasionally, have not been predicted from NMR studies. Furthermore, these different values of psi lead to significantly different orientations of the α1,6-arm for the same value of chi. This contrasts with the earlier predictions that only different values of chi can bring about significant changes in the orientation of the α1,6-arm. The MD simulations also show that the effects of bisecting GlcNAc or β1,2-xylose are very similar on the α1,3-arm and slightly different on the α1,6-arm.

  NCBI PubMed ID: 7734844
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Institutions: Laboratory of Mathematical Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
  
   
  
  Erythrina corallodendron
  CSDB ID 127276 (all data & tools)
• Article ID: 11711
  Bardor M, Cabanes-Macheteau M, Faye L, Lerouge P "Monitoring of N-glycosylation of plant glycoproteins by fluorophore-assisted carbohydrate electrophoresis" - Electrophoresis 21(12) (2000) 2550-2556
  

  We have evaluated the efficiency of a fast, simple and efficient method, fluorophore-assisted carbohydrate electrophoresis (FACE), for the characterization of plant N-linked glycans. After their enzymatic release from plant glycoproteins, N-glycans were reductively aminated to the charged fluorophore 8-aminonaphthalene-1, 3, 6-trisulfonic acid (ANTS) and separated using high resolution polyacrylamide gel electrophoresis. In addition, an affinity purification procedure using concanavalin A was developed for separation of ANTS-labeled high-mannose-type N-glycans from other plant oligosaccharides.

  3, plant glycoproteins, 8-aminonaphthalene-1, 6-trisulfonic acid labeled plant N-glycans, fluorophore-assisted carbohydrate electrophoresis

  NCBI PubMed ID: 10939471
  Publication DOI: 10.1002/1522-2683(20000701)21:12<2550::AID-ELPS2550>3.0.CO;2-G
  Journal NLM ID: 8204476
  Publisher: Wiley-VCH
  Correspondence: plerouge@crihan.fr
  Institutions: Laboratoire des Transports Intracellulaires, CNRS ESA, Université de Rouen, Faculté des Sciences, Mont Saint Aignan, France
  Methods: MALDI-TOF MS, electrophoresis, FACE, PAGE, binding assays, fluorescence microscopy, fluorescence labeling, centrifugation
  
   
  
  Arabidopsis thaliana
  CSDB ID 64823 (all data & tools)
• Article ID: 11783
  Choi KH, Laursen RA "Amino-acid sequence and glycan structures of cysteine proteases with proline specificity from ginger rhizome Zingiber officinale" - European Journal of Biochemistry 267(5) (2000) 1516-1526
  

  The ginger proteases (GP-I and GP-II), isolated from the ginger rhizome Zingiber officinale, have an unusual substrate specificity preference for cleaving peptides with a proline residue at the P2 position. The complete amino-acid sequence of GP-II, a glycoprotein containing 221 amino acids, and about 98% that of GP-I have been determined. Both proteases, which are 82% similar, have cysteine residues at positions 27 and histidines at position 161, corresponding to the essential cysteine-histidine diads found in the papain family of cysteine proteases, and six corresponding cysteine residues that form the three invariant disulfide linkages seen in this family of proteins. The sequence homology with other members (papain, bromelain, actinidin, protease omega, etc.) of this family is approximately 50%. GP-II has two predicted glycosylation sites at Asn99 and Asn156. Analyisis by electrospray and collision-induced dissociation MS showed that both sites were occupied by the glycans (Man)3(Xyl)1(Fuc)1(GlcNAc)2 and (Man)3(Xyl)1(Fuc)1(GlcNAc)3, in a ratio of approximately 7 : 1. Both glycans are xylose containing biantennary complex types that share the common core structural unit, Man1→6(Man1→3)(Xyl1→2)Man1→4GlcNAc1→4(Fuc1→3)GlcNAc for the major form, with an additional N-acetylglucosamine residue being linked, in the minor form, to one of the terminal mannose units of the core structure.

  mass spectrometry, glycoprotein, amino-acid sequence, cysteine protease, ginger, glycosylation site, proline peptidase, proteinase

  NCBI PubMed ID: 10691991
  Publication DOI: 10.1046/j.1432-1327.2000.01152.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: laursen@bu.edu
  Institutions: Department of Chemistry, Boston University, Boston, USA
  Methods: methylation, chemical analysis, ESI-MS, acid hydrolysis, GLC, MALDI-TOF MS, HPLC, UV, enzymatic digestion, extraction, CID-MS, acetylation, reduction, column chromatography, RP-HPLC, dialysis, enzymatic assay, precipitation, derivatization, centrifugation, amino acid sequence analysis
  
   
  
  Ananas comosus
  CSDB ID 65147 (all data & tools)
• Article ID: 11984
  Kimura Y, Matsuo S "Free N-glycans already occur at an early stage of seed development" - Journal of Biochemistry 127(6) (2000) 1013-1019
  

  As a part of our studies to elucidate the physiological significance of free N-glycans in differentiating or growing plant cells, we first demonstrate that two kinds of free N-glycans already occur at an early stage of seed development. In this report, we used the developing Ginkgo biloba seeds as a model plant, since we have already revealed a functional feature of the Ginkgo endo-β-N-acetylghicosaminidase and structural features of N-glycans linked to storage glycoproteins in the developing seeds [Kimura, Y. et al. (1998) Biosci. Biotechnol. Biochem. 62, 253–261; Kimura, Y. and Matsuo, S. (2000) Biosci. Biotechnol. Biochem. 64, 562–568]. The structures of free N-glycans, which were determined by a combination of ESI-MS, sequential α-mannosidase digestions, partial acetolysis, and two dimensional sugar chain map, fell into two categories. One dominant species is a high-mannose type structure having one GlcNAc residue at the reducing end (Man9-5GlcNAc1). The concentration of this type of free glycan (as the pyridylaminated derivatives) is about 2.2 nmol in 1 g fresh weight. The detailed structural analysis revealed that the high-mannose type structures have a common core unit; Manα1–6(Man1–3)Mana1–6(Manα1–3)Manβ1–4GlcNAc The other minor species of free N-glycans is the plant complex type structure having an N-acetylchitobiose unit at the reducing end (Man3Xyl1Fuc1GlcNAc2). The concentration of this type of free glycan (as the pyridylaminated derivative) was about 75 pmol in 1 g fresh weight.

  Ginkgo biloba, free N-glycan, N-glycan metabolism, plant endo-β-N-acetylglucosaminidase, seed development

  NCBI PubMed ID: 10833269
  Publication DOI: 10.1093/oxfordjournals.jbchem.a022692
  Journal NLM ID: 0376600
  Publisher: Japanese Biochemical Society
  Correspondence: Kimura Y
  Institutions: Department of Bioresources Chemistry, Faculty of Agriculture, Okayama University, Okayama, Japan
  Methods: gel filtration, ESI-MS, acid hydrolysis, MS/MS, HPLC, enzymatic digestion, affinity chromatography, acetylation, column chromatography, RP-HPLC, derivatization
  
   
  
  Ginkgo biloba
  CSDB ID 66006 (all data & tools)
• Article ID: 11986
  Kimura Y, Matsuo S "Changes in N-linked oligosaccharides during seed development of Ginkgo biloba" - Bioscience, Biotechnology, and Biochemistry 64(3) (2000) 562-568
  

  Structural changes in N-linked oligosaccharides of glycoproteins during seed development of Ginkgo biloba have been explored to discover possible endogenous substrate(s) for the Ginko endo-β-N-acetylglucosaminidase (endo-GB; Kimura, Y., et al. (1998) Biosci. Biotechnol. Biochem., 62, 253-261), which should be involved in the production of high-mannose type free N-glycans. The structural analysis of the pyridylaminated oligosaccharides with a 2D sugar chain map, by ESI-MS/MS spectroscopy, showed that all N-glycans expressed on glycoproteins through the developmental stage of the Ginkgo seeds have the xylose-containing type (GlcNAc2~0Man3Xyl1Fuc1~0GlcNAc2) but no high-mannose type structure. Man3Xyl1Fuc1GlcNAc2, a typical plant complex type structure especially found in vacuolar glycoproteins, was a dominant structure through the seed development, while the amount of expression of GlcNAc2Man3Xyl1Fuc1GlcNAc2 and GlcNAc1Man3Xyl1Fuc1GlcNAc2 decreased as the seeds developed. The dominantly occurrence of xylose-containing type structures and the absence of the high-mannose type structures on Ginkgo glycoproteins were also shown by lectin-blotting and immunoblotting of SDS-soluble glycoproteins extracted from the developing seeds at various developmental stages. Concerning the endogenous substrates for plant endo-β-N-acetylglucosaminidase, these results suggested that the endogenous substrates might be the dolicol-oligosaccharide intermediates or some glycopeptides with the high-mannose type N-glycan(s) derived from misfolded glycoproteins in the quality control system for newly synthesized glycoproteins.

  Ginkgo biloba, endo-β-N-acetylglucosaminidase, seed development, plant N-glycan, storage glycoprotein

  NCBI PubMed ID: 10803954
  Publication DOI: 10.1271/bbb.64.562
  Journal NLM ID: 9205717
  Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
  Correspondence: Kimura Y
  Institutions: Department of Bioresources Chemistry, Faculty of Agriculture, Okayama University, Okayama, Japan
  Methods: SDS-PAGE, ESI-MS, acid hydrolysis, HPLC, immunoblotting, enzymatic digestion, extraction, acetylation, dialysis, precipitation, derivatization, centrifugation, binding assay
  
   
  
  Ginkgo biloba
  CSDB ID 66020 (all data & tools)
• Article ID: 12005
  Kolarich D, Altmann F "N-glycan analysis by matrix-assisted laser desorption/ionization mass spectrometry of electrophoretically separated nonmammalian proteins: application to peanut allergen Ara h 1 and olive pollen allergen Ole e 1" - Analytical Biochemistry 285(1) (2000) 64-75
  

  A method has been developed which allows the analysis of glycoproteins separated by SDS-PAGE. The procedure, though applicable to N-glycosylated glycoproteins of any origin, is particularly devised for glycoproteins potentially containing fucose in α1,3-linkage to the reducing GlcNAc as may be found in plants and invertebrates, e.g., insects and parasitic helminths. Starting with an established procedure for mass spectrometric peptide mapping, the analysis of N-glycans by matrix-assisted laser desorption/ionization mass spectrometry involved the use of peptide:N-glycosidase A, a triphasic microcolumn for sample cleanup, and a new matrix mixture consisting of 2,5-dihyhydroxybenzoic acid, 1-hydroxyisoquinoline, and arabinosazone. The method was tested on proteins with N-glycans of known structure, i.e., as horseradish peroxidase, zucchini ascorbate oxidase, soybean agglutinin, honeybee venom hyaluronidase, bovine ribonuclease B, and bovine fetuin. An electrophoretic band corresponding to 4 μg of glycoprotein was generally sufficient to allow detection of the major N-glycan species. As an additional benefit, a peptide mass map is generated which serves to identify the analyzed protein. The method was applied to glycoprotein allergens whose glycan structures were unknown. Ara h 1 and Ole e 1, major allergens from peanut and olive pollen, respectively, contained mainly xylosylated N-glycans with the composition Man3(−4)XylGlcNAc2 in the case of Ara h 1 and GlcNAc1–2Man3XylGlcNAc2 in the case of Ole e 1 where also some GlcNAc0–2Man3XylFucGlcNAc2 was found.

  MALDI-MS, electrophoresis, allergy, N-glycan, olive pollen, peanut

  NCBI PubMed ID: 10998264
  Publication DOI: 10.1006/abio.2000.4737
  Journal NLM ID: 0370535
  Publisher: Academic Press
  Correspondence: faltmann@edv2.boku.ac.at
  Institutions: Glycobiology Division, Institute of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
  
   
  
  Arachis hypogaea, Olea europaea
  CSDB ID 66110 (all data & tools)
• Article ID: 12256
  Olczak M, Watorek W "Structural analysis of N-glycans from yellow lupin (Lupinus luteus) seed diphosphonucleotide phosphatase/phosphodiesterase" - Biochimica et Biophysica Acta 1523(2-3) (2000) 236-245
  

  N-linked oligosaccharide chains released by hydrazinolysis from yellow lupin seed diphosphonucleotide phosphatase/phosphodiesterase were fluorescence labeled and separated by high performance liquid chromatography (GlycoSep N and GlycoSep H columns). Exoglycosidase sequencing elucidated the structures of 24 separated N-glycans. Thirty percent of isolated glycans were found to be of high-mannose type (three to eight mannosyl residues), 42% were complex type and 26% belonged to paucimannosidic type. Among complex type glycans, structures with Lewis(a) epitope were identified. It is very unusual to find all types of plant N-glycans in one protein. Possible reasons for such a broad spectrum of N-glycan structures are discussed.

  N-glycan, exoglycosidase sequencing, diphosphonucleotide phosphatase/phosphodiesterase, yellow lupin

  NCBI PubMed ID: 11042390
  Publication DOI: 10.1016/s0304-4165(00)00128-8
  Journal NLM ID: 0217513
  Publisher: Elsevier
  Correspondence: watorek@bf.uni.wroc.pl
  Institutions: Institute of Biochemistry and Molecular Biology, Wroclaw University, Wroclaw, Poland
  Methods: HPLC, enzymatic digestion, extraction, fluorescence labeling, spectrometry
  
   
  
  Lupinus luteus
  CSDB ID 67231 (all data & tools)