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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Associated disease: infection due to Escherichia coli [ICD11: XN6P4

]

The structure was elucidated in this paper
NCBI PubMed ID: 10215878
Journal NLM ID: 0107600
Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst

fz-borstel.de
Institutions: Center for Medicine and Biosciences, Borstel Research Center, Germany, Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands, Institute of Chemical Physics, Russian Academy of Sciences, Moscow, Russia

The lipopolysaccharides (LPS) from Escherichia coli rough mutant strains F470 (R1 core type) and F576 (R2 core type) were deacylated yielding in each case a mixture of oligosaccharides with one predominant product which was isolated using high-performance anion-exchange chromatography. In addition, one oligosaccharide present in minor quantities was isolated from LPS of E. coli strain F576 (R2 core type). The structures of the oligosaccharides were determined by chemical analyses and NMR spectroscopic experiments. Furthermore, de-O-acylated and dephosphorylated LPS preparations were investigated by fast-atom bombardment and collision induced dissociation tandem mass spectrometry. The combined data allow us to deduce the following carbohydrate backbones of the E. coli R1 and R2 core types which share the following structure (Scheme 1 [see formula in text], but differ in the substituents R1 and R2 which for the R1 core type are predominantly: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]a-Glc-(1→3)-a-Glc-, R2 = H and to a minor extent: R1 = a-Gal-(1→2)-a-Gal-(1→2)-[b-Glc-(1→3)]-a-Glc-(1→3)-a-Glc-, R2 = a-GlcN and for the R2 core type predominantly: R1 = a-GlcNAc-(1→2)-a-Glc-(1→2)-a-Glc-(1→3)-[a-Gal-(1→6)]-a-Glc-, R2 = H and to a minor extent: R1 = a-GlcNAc-[b-Gal-(1→4)]-(1→2)-a-Glc-(1→2)-a-Glc-[a-Gal-(1→6)]-(1→3)-a-Glc-, R2 = H in which all sugars are d-pyranoses (L,D-Hep, L-glycero-D-manno-heptopyranose; P, phosphate).

Escherichia coli; lipopolysaccharide; core types R1 and R2; structural analysis

Structure type: oligomer
Location inside paper: abstract, p.633, fig.3, table 5, table 6, oligosaccharide 1
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135394,IEDB_135818,IEDB_136906,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_153543,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

Methods: NMR-2D, NMR, chemical analysis, MS
Comments, role: R1 core type, major structure

Related record ID(s): 5695, 5696, 5697, 21500
NCBI Taxonomy refs (TaxIDs): 562
Reference(s) to other database(s): GlycomeDB:26680
Show glycosyltransferases

NMR conditions: in D2O at 300 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
0,6,6,4	aXKdop	175.4	100.9	35.8	66.9	67.7	72.7	71.7	63.9
0,6,6,5,3,3,3,2,2	aDGalp	96.9	69.3	70.5	70.5	72.3	62.3
0,6,6,5,3,3,3,2	aDGalp	92.4	73.6	69.1	71.0	72.3	62.3
0,6,6,5,3,3,3,3	bDGlcp	103.4	74.3	76.9	70.8	76.9	61.7
0,6,6,5,3,3,3	aDGlcp	95.3	73.6	79.4	69.5	72.3	61.7
0,6,6,5,3,3	aDGlcp	102.1	71.6	76.9	71.8	73.3	61.1
0,6,6,5,3,4	P
0,6,6,5,3,7	aXLDmanHepp	101.1	70.5	71.8	67.5	73.4	70.5	64.2
0,6,6,5,3	aXLDmanHepp	103.5	71.0	80.1	69.6	73.6	68.3	69.5
0,6,6,5,4	P
0,6,6,5	aXLDmanHepp	100.1	71.9	79.0	71.0	73.8	70.1	64.3
0,6,6	aXKdop	175.3	100.6	35.3	71.6	70.8	73.2	70.8	65.0
0,6,4	P
0,6	bDGlcpN	100.4	56.6	73.5	75.1	75.1	63.5
0	aDGlcpN	91.8	55.5	71.8	70.8	73.7	70.8
	P


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
0,6,6,4	aXKdop	-	-	1.78-2.14	4.11	4.05	3.65	3.98	3.71-3.95
0,6,6,5,3,3,3,2,2	aDGalp	5.30	3.84	3.94	3.99	4.12	3.75-3.75
0,6,6,5,3,3,3,2	aDGalp	5.59	3.98	4.17	3.98	4.12	3.75-3.75
0,6,6,5,3,3,3,3	bDGlcp	4.74	3.33	3.52	3.41	3.45	3.73-3.91
0,6,6,5,3,3,3	aDGlcp	5.81	3.87	4.19	3.53	4.15	3.75-3.96
0,6,6,5,3,3	aDGlcp	5.21	3.64	4.09	3.75	3.85	3.76-3.89
0,6,6,5,3,4	P
0,6,6,5,3,7	aXLDmanHepp	4.94	3.97	3.86	3.85	3.63	4.00	3.72-3.74
0,6,6,5,3	aXLDmanHepp	5.09	4.40	4.12	4.42	3.85	4.24	3.71-3.79
0,6,6,5,4	P
0,6,6,5	aXLDmanHepp	5.31	4.07	4.13	4.42	4.21	4.11	3.79-3.91
0,6,6	aXKdop	-	-	1.94-2.13	4.14	4.28	3.74	3.88	?
0,6,4	P
0,6	bDGlcpN	4.87	3.07	3.84	3.78	3.73	3.44-3.65
0	aDGlcpN	5.66	3.42	3.87	3.61	4.14	3.77-4.29
	P


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8
0,6,6,4	aXKdop			35.8/1.78-2.14	66.9/4.11	67.7/4.05	72.7/3.65	71.7/3.98	63.9/3.71-3.95
0,6,6,5,3,3,3,2,2	aDGalp	96.9/5.30	69.3/3.84	70.5/3.94	70.5/3.99	72.3/4.12	62.3/3.75-3.75
0,6,6,5,3,3,3,2	aDGalp	92.4/5.59	73.6/3.98	69.1/4.17	71.0/3.98	72.3/4.12	62.3/3.75-3.75
0,6,6,5,3,3,3,3	bDGlcp	103.4/4.74	74.3/3.33	76.9/3.52	70.8/3.41	76.9/3.45	61.7/3.73-3.91
0,6,6,5,3,3,3	aDGlcp	95.3/5.81	73.6/3.87	79.4/4.19	69.5/3.53	72.3/4.15	61.7/3.75-3.96
0,6,6,5,3,3	aDGlcp	102.1/5.21	71.6/3.64	76.9/4.09	71.8/3.75	73.3/3.85	61.1/3.76-3.89
0,6,6,5,3,4	P
0,6,6,5,3,7	aXLDmanHepp	101.1/4.94	70.5/3.97	71.8/3.86	67.5/3.85	73.4/3.63	70.5/4.00	64.2/3.72-3.74
0,6,6,5,3	aXLDmanHepp	103.5/5.09	71.0/4.40	80.1/4.12	69.6/4.42	73.6/3.85	68.3/4.24	69.5/3.71-3.79
0,6,6,5,4	P
0,6,6,5	aXLDmanHepp	100.1/5.31	71.9/4.07	79.0/4.13	71.0/4.42	73.8/4.21	70.1/4.11	64.3/3.79-3.91
0,6,6	aXKdop			35.3/1.94-2.13	71.6/4.14	70.8/4.28	73.2/3.74	70.8/3.88	65.0/?
0,6,4	P
0,6	bDGlcpN	100.4/4.87	56.6/3.07	73.5/3.84	75.1/3.78	75.1/3.73	63.5/3.44-3.65
0	aDGlcpN	91.8/5.66	55.5/3.42	71.8/3.87	70.8/3.61	73.7/4.14	70.8/3.77-4.29
	P

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
0,6,6,4	aXKdop			1.78 2.14	4.11	4.05	3.65	3.98	3.71 3.95
0,6,6,5,3,3,3,2,2	aDGalp	5.30	3.84	3.94	3.99	4.12	3.75 3.75
0,6,6,5,3,3,3,2	aDGalp	5.59	3.98	4.17	3.98	4.12	3.75 3.75
0,6,6,5,3,3,3,3	bDGlcp	4.74	3.33	3.52	3.41	3.45	3.73 3.91
0,6,6,5,3,3,3	aDGlcp	5.81	3.87	4.19	3.53	4.15	3.75 3.96
0,6,6,5,3,3	aDGlcp	5.21	3.64	4.09	3.75	3.85	3.76 3.89
0,6,6,5,3,4	P
0,6,6,5,3,7	aXLDmanHepp	4.94	3.97	3.86	3.85	3.63	4.00	3.72 3.74
0,6,6,5,3	aXLDmanHepp	5.09	4.40	4.12	4.42	3.85	4.24	3.71 3.79
0,6,6,5,4	P
0,6,6,5	aXLDmanHepp	5.31	4.07	4.13	4.42	4.21	4.11	3.79 3.91
0,6,6	aXKdop			1.94 2.13	4.14	4.28	3.74	3.88	?
0,6,4	P
0,6	bDGlcpN	4.87	3.07	3.84	3.78	3.73	3.44 3.65
0	aDGlcpN	5.66	3.42	3.87	3.61	4.14	3.77 4.29
	P

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
0,6,6,4	aXKdop	175.4	100.9	35.8	66.9	67.7	72.7	71.7	63.9
0,6,6,5,3,3,3,2,2	aDGalp	96.9	69.3	70.5	70.5	72.3	62.3
0,6,6,5,3,3,3,2	aDGalp	92.4	73.6	69.1	71.0	72.3	62.3
0,6,6,5,3,3,3,3	bDGlcp	103.4	74.3	76.9	70.8	76.9	61.7
0,6,6,5,3,3,3	aDGlcp	95.3	73.6	79.4	69.5	72.3	61.7
0,6,6,5,3,3	aDGlcp	102.1	71.6	76.9	71.8	73.3	61.1
0,6,6,5,3,4	P
0,6,6,5,3,7	aXLDmanHepp	101.1	70.5	71.8	67.5	73.4	70.5	64.2
0,6,6,5,3	aXLDmanHepp	103.5	71.0	80.1	69.6	73.6	68.3	69.5
0,6,6,5,4	P
0,6,6,5	aXLDmanHepp	100.1	71.9	79.0	71.0	73.8	70.1	64.3
0,6,6	aXKdop	175.3	100.6	35.3	71.6	70.8	73.2	70.8	65.0
0,6,4	P
0,6	bDGlcpN	100.4	56.6	73.5	75.1	75.1	63.5
0	aDGlcpN	91.8	55.5	71.8	70.8	73.7	70.8
	P

There is only one chemically distinct structure:

N[C@H]1[C@@H](OP(=O)(O)O)O[C@H](CO[C@@H]2O[C@H](CO[C@]3(C(=O)O)C[C@@H](O[C@]4(C(=O)O)C[C@@H](O)[C@@H](O)[C@@H]([C@H](O)CO)O4)[C@@H](O[C@H]4O[C@H]([C@@H](O)CO)[C@@H](OP(=O)(O)O)[C@H](O[C@H]5O[C@H]([C@@H](O)CO[C@H]6O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]6O)[C@@H](OP(=O)(O)O)[C@H](O[C@H]6O[C@H](CO)[C@@H](O)[C@H](O[C@H]7O[C@H](CO)[C@@H](O)[C@H](O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@H]8O)[C@H]7O[C@H]7O[C@H](CO)[C@H](O)[C@H](O)[C@H]7O[C@H]7O[C@H](CO)[C@H](O)[C@H](O)[C@H]7O)[C@H]6O)[C@@H]5O)[C@@H]4O)[C@@H]([C@H](O)CO)O3)[C@@H](OP(=O)(O)O)[C@H](O)[C@H]2N)[C@@H](O)[C@@H]1O

SVG MW SMILES 3D mol Ionize