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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: 21903201
Publication DOI: 10.1016/j.carres.2011.06.036
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: evguenii.vinogradov

nrc-cnrc.gc.ca; evguenii.vinogradov

nrc.ca
Institutions: Institute for Biological Sciences, National Research Council Canada, Ottawa, Canada

We describe a re-investigation of the structure of the lipopolysaccharide (LPS) from Helicobacter pylori genomic strain 26695 and its corresponding HP0826::Kan mutant lacking the O-chain component based on the in-depth NMR analysis of the oligosaccharide products obtained through the use of various degradation procedures performed on the purified LPS from both strains, as well as CE-MS data. New structural evidence indicates the presence of the linear arrangement of glucan and heptan portions of the LPS attached through -6-α-ddHep-3-α-L-Fuc-3-β-GlcNAc- fragment to the inner core dd-heptose residue. This structure differs from previously reported structures of the H. pylori 26695 LPS in several aspects

Lipopolysaccharide, NMR, LPS, structure, Helicobacter pylori

Structure type: oligomer
Location inside paper: p.2439, fig.1, 4
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_136044,IEDB_136045,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_152214,IEDB_158538,IEDB_174333,IEDB_190606,IEDB_2189046,IEDB_2189047,IEDB_2346541,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_86,SB_88

Methods: 13C NMR, 1H NMR, methylation, periodate oxidation, GLC-MS, NMR-2D, sugar analysis, 31P NMR, deacylation, deamination, de-O-acylation with hydrazine, NMR-1D, CE-MS
Comments, role: products of KOH deacylation of the LPS

Related record ID(s): 26129, 26558, 26559, 26560, 26561, 26562, 26563, 26565, 26566, 26567, 26568, 26569, 26570
NCBI Taxonomy refs (TaxIDs): 85962
Show glycosyltransferases

NMR conditions: at 298 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3,2	bDGlcpN	98.2	56.3	73.1	70.8	77.6	61.5
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3	aXDDmanHepp	100.8	77.1	70.7	68.7	74.6	72.8	63.0
6,6,5,3,2,2,3,3,6,6,6,3,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6	aDGlcp
6,6,5,3,2,2,3,3,6,6	aDGlcp
6,6,5,3,2,2,3,3,6	aDGlcp	98.9	72.5	74.5	70.7	71.6	66.7
6,6,5,3,2,2,3,3	aXDDmanHepp	102.8	71.1	71.3	68.7	74.5	79.8	62.0
6,6,5,3,2,2,3	aLFucp	103.0	69.5	77.7	72.5	69.0	16.3
6,6,5,3,2,2	bDGlcpN	97.8	56.4	83.7	69.6	77.6	61.5
6,6,5,3,2,7,4	aDGlcp
6,6,5,3,2,7	bDGalp
6,6,5,3,2	aXDDmanHepp	100.5	77.1	70.6	68.7	74.7	70.7	72.0
6,6,5,3	aXLDmanHepp
6,6,5	aXLDmanHepp
6,6	aXKdop
6	bDGlcpN
	xDGlcN-ol
6,6,5,6	P
6,6,5,7	P


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3,2	bDGlcpN	4.86	3.17	3.68	3.52	3.52	3.78-3.93
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3	aXDDmanHepp	5.26	4.34	3.96	3.84	3.87	4.06	3.74-3.81
6,6,5,3,2,2,3,3,6,6,6,3,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6	aDGlcp
6,6,5,3,2,2,3,3,6,6	aDGlcp
6,6,5,3,2,2,3,3,6	aDGlcp	5.15	3.61	3.74	3.52	4.11	3.76-3.99
6,6,5,3,2,2,3,3	aXDDmanHepp	5.15	4.05	3.91	3.84	3.84	4.08	3.90
6,6,5,3,2,2,3	aLFucp	5.05	4.05	4.02	4.01	4.28	1.21
6,6,5,3,2,2	bDGlcpN	4.91	3.36	3.78	3.64	3.52	3.79-3.95
6,6,5,3,2,7,4	aDGlcp
6,6,5,3,2,7	bDGalp
6,6,5,3,2	aXDDmanHepp	5.19	4.35	3.95	3.83	3.85	4.24	3.78-4.14
6,6,5,3	aXLDmanHepp
6,6,5	aXLDmanHepp
6,6	aXKdop
6	bDGlcpN
	xDGlcN-ol
6,6,5,6	P
6,6,5,7	P


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3,2	bDGlcpN	98.2/4.86	56.3/3.17	73.1/3.68	70.8/3.52	77.6/3.52	61.5/3.78-3.93
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3	aXDDmanHepp	100.8/5.26	77.1/4.34	70.7/3.96	68.7/3.84	74.6/3.87	72.8/4.06	63.0/3.74-3.81
6,6,5,3,2,2,3,3,6,6,6,3,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6	aDGlcp
6,6,5,3,2,2,3,3,6,6	aDGlcp
6,6,5,3,2,2,3,3,6	aDGlcp	98.9/5.15	72.5/3.61	74.5/3.74	70.7/3.52	71.6/4.11	66.7/3.76-3.99
6,6,5,3,2,2,3,3	aXDDmanHepp	102.8/5.15	71.1/4.05	71.3/3.91	68.7/3.84	74.5/3.84	79.8/4.08	62.0/3.90
6,6,5,3,2,2,3	aLFucp	103.0/5.05	69.5/4.05	77.7/4.02	72.5/4.01	69.0/4.28	16.3/1.21
6,6,5,3,2,2	bDGlcpN	97.8/4.91	56.4/3.36	83.7/3.78	69.6/3.64	77.6/3.52	61.5/3.79-3.95
6,6,5,3,2,7,4	aDGlcp
6,6,5,3,2,7	bDGalp
6,6,5,3,2	aXDDmanHepp	100.5/5.19	77.1/4.35	70.6/3.95	68.7/3.83	74.7/3.85	70.7/4.24	72.0/3.78-4.14
6,6,5,3	aXLDmanHepp
6,6,5	aXLDmanHepp
6,6	aXKdop
6	bDGlcpN
	xDGlcN-ol
6,6,5,6	P
6,6,5,7	P

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3,2	bDGlcpN	4.86	3.17	3.68	3.52	3.52	3.78 3.93
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3	aXDDmanHepp	5.26	4.34	3.96	3.84	3.87	4.06	3.74 3.81
6,6,5,3,2,2,3,3,6,6,6,3,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6	aDGlcp
6,6,5,3,2,2,3,3,6,6	aDGlcp
6,6,5,3,2,2,3,3,6	aDGlcp	5.15	3.61	3.74	3.52	4.11	3.76 3.99
6,6,5,3,2,2,3,3	aXDDmanHepp	5.15	4.05	3.91	3.84	3.84	4.08	3.90
6,6,5,3,2,2,3	aLFucp	5.05	4.05	4.02	4.01	4.28	1.21
6,6,5,3,2,2	bDGlcpN	4.91	3.36	3.78	3.64	3.52	3.79 3.95
6,6,5,3,2,7,4	aDGlcp
6,6,5,3,2,7	bDGalp
6,6,5,3,2	aXDDmanHepp	5.19	4.35	3.95	3.83	3.85	4.24	3.78 4.14
6,6,5,3	aXLDmanHepp
6,6,5	aXLDmanHepp
6,6	aXKdop
6	bDGlcpN
	xDGlcN-ol
6,6,5,6	P
6,6,5,7	P

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3,2	bDGlcpN	98.2	56.3	73.1	70.8	77.6	61.5
6,6,5,3,2,2,3,3,6,6,6,3,3,3,3	aXDDmanHepp	100.8	77.1	70.7	68.7	74.6	72.8	63.0
6,6,5,3,2,2,3,3,6,6,6,3,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6,3	aXDDmanHepp
6,6,5,3,2,2,3,3,6,6,6	aDGlcp
6,6,5,3,2,2,3,3,6,6	aDGlcp
6,6,5,3,2,2,3,3,6	aDGlcp	98.9	72.5	74.5	70.7	71.6	66.7
6,6,5,3,2,2,3,3	aXDDmanHepp	102.8	71.1	71.3	68.7	74.5	79.8	62.0
6,6,5,3,2,2,3	aLFucp	103.0	69.5	77.7	72.5	69.0	16.3
6,6,5,3,2,2	bDGlcpN	97.8	56.4	83.7	69.6	77.6	61.5
6,6,5,3,2,7,4	aDGlcp
6,6,5,3,2,7	bDGalp
6,6,5,3,2	aXDDmanHepp	100.5	77.1	70.6	68.7	74.7	70.7	72.0
6,6,5,3	aXLDmanHepp
6,6,5	aXLDmanHepp
6,6	aXKdop
6	bDGlcpN
	xDGlcN-ol
6,6,5,6	P
6,6,5,7	P

There is only one chemically distinct structure:

C[C@@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](CO)O[C@@H](O[C@H]3[C@@H](O)[C@H](O)[C@@H]([C@H](O)CO[C@@H]4O[C@H](CO)[C@H](O[C@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)[C@H](O)[C@H]4O)O[C@@H]3O[C@H]3[C@@H](O)[C@H](O)[C@@H]([C@@H](O)CO)O[C@@H]3O[C@@H]3[C@H](O)[C@@H](O[C@@H]4[C@H](O)C[C@](OC[C@H]5O[C@@H](OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](N)CO)[C@H](N)[C@@H](O)[C@@H]5O)(C(=O)O)O[C@@H]4[C@H](O)CO)O[C@H]([C@H](CO)OP(=O)(O)O)[C@H]3O)[C@@H]2N)[C@@H](O)[C@H](O[C@H]2O[C@H]([C@@H](CO)O[C@H]3O[C@H](CO[C@H]4O[C@H](CO[C@H]5O[C@H](CO)[C@@H](O)[C@H](O[C@H]6O[C@H]([C@H](O)CO)[C@@H](O)[C@H](O[C@H]7O[C@H]([C@H](O)CO)[C@@H](O)[C@H](O[C@H]8O[C@H]([C@H](O)CO)[C@@H](O)[C@H](O[C@H]9O[C@H]([C@H](O)CO)[C@@H](O)[C@H](O)[C@@H]9O[C@@H]9O[C@H](CO)[C@@H](O)[C@H](O)[C@H]9N)[C@@H]8O)[C@@H]7O)[C@@H]6O)[C@H]5O)[C@@H](O)[C@H](O)[C@H]4O)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@@H]2O)[C@@H]1O

SVG MW SMILES 3D mol Ionize