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Taxonomic group: plant / Streptophyta (Phylum: Streptophyta)
Organ / tissue: seed

The structure was elucidated in this paper
NCBI PubMed ID: 9532781
Publication DOI: 10.1271/bbb.62.253
Journal NLM ID: 9205717
Publisher: Japan Society for Bioscience, Biotechnology, and Agrochemistry
Institutions: Department of Bioresources Chemistry, Faculty of Agriculture, Okayama University, Okayama, Japan

An endo-beta-N-acetylglucosaminidase has been purified to homogeneity from mature seeds of Ginkgo biloba. The molecular mass of the endo-beta-N-acetylglucosaminidase, named Endo-GB, was estimated to be around 63 kDa by SDS-PAGE and around 62 kDa by Hiprep S-200 chromatography, respectively. The substrate specificity has been explored with regard to the pyridylaminated N-glycans. Several high mannose-type sugar chains bearing alpha-1,2-mannosyl residue(s), Man9-6GlcNAc2-PA, were the most favored substrates followed by Man5GlcNAc2-PA and a typical hybrid-type structure (GlcNAc1Man5Glc NAc2-PA) which does not bear an alpha-1,2-mannosyl residue. On the contrary, endo-GB could hardly hydrolyze the common core pentasaccharide of N-glycan (Man3GlcNAc2-PA) and the xylose-containing sugar chains (Man4-3Xyl1Glc NAc2-PA, Man3Fuc1Xyl1GlcNAc2-PA) being widely distributed in plant glycoproteins. Furthermore, we analyzed the structures of N-glycans conjugated to storage glycoproteins in the mature Ginkgo seeds to see the occurrence of endogenous substrates for Endo-GB. The structural analysis showed, however, only xylose-containing type N-glycans (Man3Fuc1Xyl1GlcNAc2 (95%) and Man3Xyl1 GlcNAc2 (5%)), which can not be substrate for Endo-GB, predominantly occur in the storage glycoproteins.

N-glycan structure, Ginkgo biloba, plant glycoprotein, endo-beta-N-acetylglucosaminidase, N-glycan releasing enzyme

Structure type: oligomer ; 1268 [M+H]+
Location inside paper: p. 257, column 2, paragraph 2, M3FX, table 1
Aglycon: (->4) Asn-X-Ser/Thr (protein)
Compound class: N-glycan
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_141793,IEDB_141807,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_145668,IEDB_145669,IEDB_148491,IEDB_148492,IEDB_148493,IEDB_149135,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

Methods: 1H NMR, GLC, HPLC, centrifugation, fluorescent labeling with 2-aminopyridine, carbohydrate analysis, IS-MS

Related record ID(s): 61376
NCBI Taxonomy refs (TaxIDs): 3311
Reference(s) to other database(s): GTC:G80306BI
Show glycosyltransferases

NMR conditions: in D2O [as TSV]

13C NMR data:
missing...
1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6
3	a?Fucp	5.064	?	?	?	?	1.210
2	Ac	-	1.944
4,4,2	b?Xylp	4.448	?	?	?	?
4,4,3	aDManp	5.139	4.047	?	?	?	?
4,4,6	aDManp	4.927	3.930	?	?	?	?
4,4	bDManp	?	4.277	?	?	?	?
4,2	Ac
4	bDGlcpN
	bDGlcpN

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6
3	a?Fucp	5.064	?	?	?	?	1.210
2	Ac		1.944
4,4,2	b?Xylp	4.448	?	?	?	?
4,4,3	aDManp	5.139	4.047	?	?	?	?
4,4,6	aDManp	4.927	3.930	?	?	?	?
4,4	bDManp	?	4.277	?	?	?	?
4,2	Ac
4	bDGlcpN
	bDGlcpN

There are 4 chemically distinct structures. Please, select:

CC(=O)N[C@H]1[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@H](NC(C)=O)[C@H]2O[C@H]2O[C@H](C)[C@H](O)[C@H](O)[C@H]2O)O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H](O)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H]2O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1O

SVG MW SMILES 3D mol Ionize

N-glycan structure, Ginkgo biloba, plant glycoprotein, endo-beta-N-acetylglucosaminidase, N-glycan releasing enzyme

Structure type: oligomer ; 1122 [M+H]+
Location inside paper: p. 257, column 2, paragraph 3, M3X, table 1
Aglycon: (->4) Asn-X-Ser/Thr (protein)
Compound class: N-glycan
Contained glycoepitopes: IEDB_114701,IEDB_123886,IEDB_123887,IEDB_130701,IEDB_135813,IEDB_137340,IEDB_137485,IEDB_141793,IEDB_141807,IEDB_144983,IEDB_145668,IEDB_148491,IEDB_148492,IEDB_151531,IEDB_152206,IEDB_153212,IEDB_167188,IEDB_174332,IEDB_548907,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_85

Methods: 1H NMR, GLC, HPLC, centrifugation, fluorescent labeling with 2-aminopyridine, carbohydrate analysis, IS-MS

Related record ID(s): 61375
NCBI Taxonomy refs (TaxIDs): 3311
Reference(s) to other database(s): GTC:G37075ZM
Show glycosyltransferases

NMR conditions: in D2O [as TSV]

13C NMR data:
missing...
1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6
4,4,2	b?Xylp	4.425	?	?	?	?
4,4,3	aDManp	5.112	4.033	?	?	?	?
4,4,6	aDManp	4.904	3.980	?	?	?	?
4,4	bDManp	?	4.240	?	?	?	?
4,2	Ac	-	?
4	bDGlcpN
2	Ac	-	1.934
	bDGlcpN

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6
4,4,2	b?Xylp	4.425	?	?	?	?
4,4,3	aDManp	5.112	4.033	?	?	?	?
4,4,6	aDManp	4.904	3.980	?	?	?	?
4,4	bDManp	?	4.240	?	?	?	?
4,2	Ac		?
4	bDGlcpN
2	Ac		1.934
	bDGlcpN

There are 2 chemically distinct structures. Please, select:

CC(=O)N[C@H]1[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@H](NC(C)=O)[C@H]2O)O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H](O)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H]2O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1O

SVG MW SMILES 3D mol Ionize