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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Associated disease: chronic gastritis [ICD11: DA42.Z

, ICD11: XT8W

]; peptic ulcer [ICD11: DA61

, ICD11: XN3DY

]; gastric cancer [ICD11: 2B72.Z

]; infection due to Helicobacter pylori [ICD11: XN3DY

]

The structure was elucidated in this paper
NCBI PubMed ID: 21790998
Publication DOI: 10.1111/j.1742-4658.2011.08270.x
Journal NLM ID: 101229646
Publisher: Blackwell Publishing
Correspondence: evguenii.vinogradov

nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council Canada, Ottawa, ON, Canada

In this study, we describe a reinvestigation of the lipopolysaccharide (LPS) structure of Helicobacter pylori strain Sydney (SS1) based on the NMR analysis of oligosaccharides obtained through the use of various degradations of the LPS as well as capillary electrophoresis-MS data. The results of the analysis indicated that the core region of a major H. pylori SS1 LPS glycoform consists of a backbone core oligosaccharide substituted at the d-glycero-d-manno-heptose (dd-Hep) residue by a linear chain composed of a trisaccharide fragment α-ddHep-3-α-L-Fuc-3-β-GlcNAc, as previously demonstrated for H. pylori strain 26695, further elongated by consecutively added α-Glc and β-Gal residues, and terminating in a novel linear chain consisting of 1,2-linked β-ribofuranosyl residues, where the last β-ribofuranosyl residue provides a point of attachment for the O-chain polysaccharide: [Formula: see text] where [2-β-Ribf-](n) is a short (three to five residues) oligomer of 1,2-linked β-ribofuranose (riban), and PS is a polysaccharide chain consisting of N-acetyllactosamine, substituted with α-Fuc to form Lewis (Le)-type structures. In addition to the previously identified LacNAc, Le(y) and Le(x) components, the O-chain polysaccharide of H. pylori SS1 LPS was found to contain a novel LacNAc unit carrying a phosphoethanolamine substituent at the O-6 position of β-GlcNAc residues.

Lipopolysaccharide, NMR, core region, Helicobacter pylori

Structure type: oligomer
Location inside paper: p.3486, fig.1, PS2
Contained glycoepitopes: IEDB_114709,IEDB_120354,IEDB_123890,IEDB_130646,IEDB_130655,IEDB_130697,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_137776,IEDB_140108,IEDB_140122,IEDB_141794,IEDB_141807,IEDB_149136,IEDB_150939,IEDB_151531,IEDB_158550,IEDB_190606,SB_165,SB_166,SB_173,SB_187,SB_195,SB_30,SB_7,SB_88

Methods: 13C NMR, 1H NMR, methylation, periodate oxidation, GLC-MS, NMR-2D, sugar analysis, 31P NMR, deacylation, deamination, NMR-1D, CE-MS
Comments, role: O-unit is in ID 26557. Product of periodate oxidation - reduction - acid hydrolysis of LPS.

Related record ID(s): 26128, 26543, 26544, 26545, 26546, 26547, 26548, 26549, 26550, 26551, 26552, 26553, 26554, 26555, 26557
NCBI Taxonomy refs (TaxIDs): 102617
Show glycosyltransferases

NMR conditions: at 298 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6
2,2,2,2,4,3,4,3,4	bDGalp	104.1	71.2	83.4	69.5	76.1	62.2
2,2,2,2,4,3,4,3,2	Ac	?	23.5
2,2,2,2,4,3,4,3	bDGlcpN	103.9	56.3	73.3	79.3	75.7	61.0
2,2,2,2,4,3,4	bDGalp	103.7	71.2	83.4	69.5	76.1	62.2
2,2,2,2,4,3,2	Ac	?	23.5
2,2,2,2,4,3,6,0,2	Me	43.7
2,2,2,2,4,3,6,0	xXEtN	60.6	58.5
2,2,2,2,4,3,6	P
2,2,2,2,4,3	bDGlcpN	103.9	56.3	73.3	78.5	74.4	65.1
2,2	bDRibf	107.6	82.1	71.4	84.2	63.7
2,2,2,2,4,3,4,3,4,3,2	Ac	?	23.5
2,2,2,2,4,3,4,3,4,3	bDGlcpN	103.9	56.5	75.8	70.8	76.8	61.7
2,2,2,2,4	bDGalp	104.1	71.2	83.4	69.5	76.1	62.2
2,2,2,2,2	Ac	?	23.5
2,2,2,2	bDGlcpN	103.1	56.8	73.3	79.3	75.7	61.0
2,2,2	bDRibf	107.6	83.7	71.4	84.2	63.7
2	bDRibf	106.2	82.4	70.7	84.2	63.7
	xDThre-ol	?	79.6	?	?


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6
2,2,2,2,4,3,4,3,4	bDGalp	4.47	3.58	3.73	4.15	3.72	3.74-3.78
2,2,2,2,4,3,4,3,2	Ac	-	2.04
2,2,2,2,4,3,4,3	bDGlcpN	4.71	3.81	3.74	3.73	3.59	3.84-3.95
2,2,2,2,4,3,4	bDGalp	4.53	3.56	3.75	4.15	3.72	3.74-3.78
2,2,2,2,4,3,2	Ac	-	2.04
2,2,2,2,4,3,6,0,2	Me	2.96
2,2,2,2,4,3,6,0	xXEtN	4.21	3.45
2,2,2,2,4,3,6	P
2,2,2,2,4,3	bDGlcpN	4.71	3.81	3.74	3.81	3.72	4.21
2,2	bDRibf	5.40	4.21	4.32	4.00	3.66-3.83
2,2,2,2,4,3,4,3,4,3,2	Ac	-	2.04
2,2,2,2,4,3,4,3,4,3	bDGlcpN	4.69	3.76	3.54	3.46	3.46	3.76-3.90
2,2,2,2,4	bDGalp	4.47	3.58	3.73	4.15	3.72	3.74-3.78
2,2,2,2,2	Ac	-	2.04
2,2,2,2	bDGlcpN	4.76	3.78	3.73	3.73	3.61	3.84-3.97
2,2,2	bDRibf	5.42	4.24	4.30	4.00	3.66-3.83
2	bDRibf	5.38	4.16	4.34	4.00	3.66-3.83
	xDThre-ol	?	3.75	?	?


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6
2,2,2,2,4,3,4,3,4	bDGalp	104.1/4.47	71.2/3.58	83.4/3.73	69.5/4.15	76.1/3.72	62.2/3.74-3.78
2,2,2,2,4,3,4,3,2	Ac		23.5/2.04
2,2,2,2,4,3,4,3	bDGlcpN	103.9/4.71	56.3/3.81	73.3/3.74	79.3/3.73	75.7/3.59	61.0/3.84-3.95
2,2,2,2,4,3,4	bDGalp	103.7/4.53	71.2/3.56	83.4/3.75	69.5/4.15	76.1/3.72	62.2/3.74-3.78
2,2,2,2,4,3,2	Ac		23.5/2.04
2,2,2,2,4,3,6,0,2	Me	43.7/2.96
2,2,2,2,4,3,6,0	xXEtN	60.6/4.21	58.5/3.45
2,2,2,2,4,3,6	P
2,2,2,2,4,3	bDGlcpN	103.9/4.71	56.3/3.81	73.3/3.74	78.5/3.81	74.4/3.72	65.1/4.21
2,2	bDRibf	107.6/5.40	82.1/4.21	71.4/4.32	84.2/4.00	63.7/3.66-3.83
2,2,2,2,4,3,4,3,4,3,2	Ac		23.5/2.04
2,2,2,2,4,3,4,3,4,3	bDGlcpN	103.9/4.69	56.5/3.76	75.8/3.54	70.8/3.46	76.8/3.46	61.7/3.76-3.90
2,2,2,2,4	bDGalp	104.1/4.47	71.2/3.58	83.4/3.73	69.5/4.15	76.1/3.72	62.2/3.74-3.78
2,2,2,2,2	Ac		23.5/2.04
2,2,2,2	bDGlcpN	103.1/4.76	56.8/3.78	73.3/3.73	79.3/3.73	75.7/3.61	61.0/3.84-3.97
2,2,2	bDRibf	107.6/5.42	83.7/4.24	71.4/4.30	84.2/4.00	63.7/3.66-3.83
2	bDRibf	106.2/5.38	82.4/4.16	70.7/4.34	84.2/4.00	63.7/3.66-3.83
	xDThre-ol	?/?	79.6/3.75	?/?	?/?

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6
2,2,2,2,4,3,4,3,4	bDGalp	4.47	3.58	3.73	4.15	3.72	3.74 3.78
2,2,2,2,4,3,4,3,2	Ac		2.04
2,2,2,2,4,3,4,3	bDGlcpN	4.71	3.81	3.74	3.73	3.59	3.84 3.95
2,2,2,2,4,3,4	bDGalp	4.53	3.56	3.75	4.15	3.72	3.74 3.78
2,2,2,2,4,3,2	Ac		2.04
2,2,2,2,4,3,6,0,2	Me	2.96
2,2,2,2,4,3,6,0	xXEtN	4.21	3.45
2,2,2,2,4,3,6	P
2,2,2,2,4,3	bDGlcpN	4.71	3.81	3.74	3.81	3.72	4.21
2,2	bDRibf	5.40	4.21	4.32	4.00	3.66 3.83
2,2,2,2,4,3,4,3,4,3,2	Ac		2.04
2,2,2,2,4,3,4,3,4,3	bDGlcpN	4.69	3.76	3.54	3.46	3.46	3.76 3.90
2,2,2,2,4	bDGalp	4.47	3.58	3.73	4.15	3.72	3.74 3.78
2,2,2,2,2	Ac		2.04
2,2,2,2	bDGlcpN	4.76	3.78	3.73	3.73	3.61	3.84 3.97
2,2,2	bDRibf	5.42	4.24	4.30	4.00	3.66 3.83
2	bDRibf	5.38	4.16	4.34	4.00	3.66 3.83
	xDThre-ol	?	3.75	?	?

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6
2,2,2,2,4,3,4,3,4	bDGalp	104.1	71.2	83.4	69.5	76.1	62.2
2,2,2,2,4,3,4,3,2	Ac	?	23.5
2,2,2,2,4,3,4,3	bDGlcpN	103.9	56.3	73.3	79.3	75.7	61.0
2,2,2,2,4,3,4	bDGalp	103.7	71.2	83.4	69.5	76.1	62.2
2,2,2,2,4,3,2	Ac	?	23.5
2,2,2,2,4,3,6,0,2	Me	43.7
2,2,2,2,4,3,6,0	xXEtN	60.6	58.5
2,2,2,2,4,3,6	P
2,2,2,2,4,3	bDGlcpN	103.9	56.3	73.3	78.5	74.4	65.1
2,2	bDRibf	107.6	82.1	71.4	84.2	63.7
2,2,2,2,4,3,4,3,4,3,2	Ac	?	23.5
2,2,2,2,4,3,4,3,4,3	bDGlcpN	103.9	56.5	75.8	70.8	76.8	61.7
2,2,2,2,4	bDGalp	104.1	71.2	83.4	69.5	76.1	62.2
2,2,2,2,2	Ac	?	23.5
2,2,2,2	bDGlcpN	103.1	56.8	73.3	79.3	75.7	61.0
2,2,2	bDRibf	107.6	83.7	71.4	84.2	63.7
2	bDRibf	106.2	82.4	70.7	84.2	63.7
	xDThre-ol	?	79.6	?	?

The spectrum also has 7 signals at unknown positions (not plotted).

There is only one chemically distinct structure:

CNCCOP(=O)(O)OC[C@H]1O[C@@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H](O[C@@H]3[C@@H](CO)O[C@@H](O[C@H]4[C@@H](O)[C@@H](CO)O[C@@H](O[C@@H]5[C@@H](COP(=O)(O)OCCNC)O[C@@H](O[C@H]6[C@@H](O)[C@@H](CO)O[C@@H](O[C@@H]7[C@@H](CO)O[C@@H](O[C@H]8[C@@H](O)[C@@H](CO)O[C@@H](O[C@@H]9[C@@H](COP(=O)(O)OCCNC)O[C@@H](O[C@H]%10[C@@H](O)[C@@H](CO)O[C@@H](O[C@@H]%11[C@@H](CO)O[C@@H](O[C@H]%12[C@H](O[C@H]%13[C@H](O[C@H]%14[C@H](O[C@H](CO)[C@H](O)CO)O[C@H](CO)[C@H]%14O)O[C@H](CO)[C@H]%13O)O[C@H](CO)[C@H]%12O)[C@H](NC(C)=O)[C@H]%11O)[C@@H]%10O)[C@H](NC(C)=O)[C@H]9O)[C@@H]8O)[C@H](NC(C)=O)[C@H]7O)[C@@H]6O)[C@H](NC(C)=O)[C@H]5O)[C@@H]4O)[C@H](NC(C)=O)[C@H]3O)[C@@H]2O)[C@H](NC(C)=O)[C@@H](O)[C@@H]1O[C@@H]1O[C@H](CO)[C@H](O)[C@H](O[C@@H]2O[C@H](CO)[C@@H](O[C@@H]3O[C@H](CO)[C@H](O)[C@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4NC(C)=O)[C@H]3O)[C@H](O)[C@H]2NC(C)=O)[C@H]1O

SVG MW SMILES 3D mol Ionize

Warning = sub-repeat ending at bDRibf: variable unit count (1-3) was assumed to be 1
Warning = sub-repeat ending at bDGlcpN: unknown unit count was assumed to be 3