CSDB: Search results

Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: Homo sapiens
Associated disease: gastritis [ICD11: DA42

]; peptic ulcer [ICD11: DA61

, ICD11: XN3DY

]; infection due to Helicobacter pylori [ICD11: XN3DY

]

The structure was elucidated in this paper
NCBI PubMed ID: 23541029
Publication DOI: 10.1016/j.carres.2013.03.008
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: E. Vinogradov <evguenii.vinogradov

nrc-cnrc.gc.ca>
Institutions: National Research Council Canada, 100 Sussex Drive, Ottawa, ON, Canada K1A 0R6

In this study, we describe a re-investigation of the lipopolysaccharide structure of Helicobacter pylori serogroup O:3. Application of NMR and MS approaches to the analysis of oligosaccharides obtained through degradation of LPS from H. pylori serogroup O:3 by various methods confirmed that its general architecture was identical to that of LPS from H. pylori strains 26695 and SS1 and followed a sequential linear assembly of the α-1,6-glucan, dd-heptan, and O-chain components. Additionally, MALDI-MS analysis demonstrated that a significant proportion of H. pylori serogroup O:3 LPS was terminated with α-1,6-glucan and was not further substituted by dd-heptan and the O-chain polysaccharide.

NMR, LPS, structure, Helicobacter pylori, MS

Structure type: oligomer
Location inside paper: p.141, fig.1, 1
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_136045,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144998,IEDB_146664,IEDB_152214,IEDB_158538,IEDB_174333,IEDB_2189046,IEDB_2346541,IEDB_983931,SB_192,SB_86

Methods: 13C NMR, 1H NMR, methylation, NMR-2D, sugar analysis, alkaline deacylation, alkaline deamination, MALDI-TOF/TOF MS
Comments, role: product of deamination of the alkaline deacylated product of the LPS

Related record ID(s): 29415, 29416, 29417, 29418, 29420, 29421, 29422, 29903
NCBI Taxonomy refs (TaxIDs): 210
Show glycosyltransferases

NMR conditions: at 298 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
3,3,6,6,6,3,3,3,3	aXDDmanHepp	103.3	71.0	71.8	68.6	75.0	72.7	62.8
3,3,6,6,6,3,3,3	aXDDmanHepp	103.3	70.7	79.1	68.0	75.1	72.5	62.8
3,3,6,6,6,3,3	aXDDmanHepp	103.3	70.7	79.1	68.0	75.1	72.5	62.8
3,3,6,6,6,3	aXDDmanHepp	102.0	70.8	79.3	67.7	74.1	73.8	63.5
3,3,6,6,6	aDGlcp	99.0	71.4	80.8	71.1	71.8	61.4
3,3,6,6	aDGlcp	98.9	72.6	74.6	70.7	71.4	66.8
3,3,6	aDGlcp	98.9	72.5	74.5	70.7	71.7	66.6
3,3	aXDDmanHepp	103.0	70.9	71.4	68.8	72.6	79.9	62.1
3	aLFucp	99.9	68.7	77.7	72.7	68.3	16.5
	x?Suga	62.3	82.6	84.4	76.5	83.8	61.9


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
3,3,6,6,6,3,3,3,3	aXDDmanHepp	5.13	4.06	3.85	3.75	3.86	4.06	3.73-3.82
3,3,6,6,6,3,3,3	aXDDmanHepp	5.11	4.25	3.99	3.88	3.90	4.07	3.73-3.82
3,3,6,6,6,3,3	aXDDmanHepp	5.10	4.25	3.99	3.89	3.89	4.07	3.73-3.82
3,3,6,6,6,3	aXDDmanHepp	5.22	4.22	3.95	3.93	4.06	4.03	3.74-3.77
3,3,6,6,6	aDGlcp	4.98	3.64	3.85	3.58	3.84	3.77-3.84
3,3,6,6	aDGlcp	4.97-4.99	3.59	3.73	3.52	3.92	3.75-3.98
3,3,6	aDGlcp	5.16	3.60	3.75	3.52	4.12	3.75-4.00
3,3	aXDDmanHepp	5.11	4.05	3.90	3.83	3.96	4.08	3.88-3.91
3	aLFucp	4.95	3.91	3.97	4.01	4.21	1.22
	x?Suga	3.71-3.76	4.08	4.08	4.20	3.94	3.72-3.80


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7
3,3,6,6,6,3,3,3,3	aXDDmanHepp	103.3/5.13	71.0/4.06	71.8/3.85	68.6/3.75	75.0/3.86	72.7/4.06	62.8/3.73-3.82
3,3,6,6,6,3,3,3	aXDDmanHepp	103.3/5.11	70.7/4.25	79.1/3.99	68.0/3.88	75.1/3.90	72.5/4.07	62.8/3.73-3.82
3,3,6,6,6,3,3	aXDDmanHepp	103.3/5.10	70.7/4.25	79.1/3.99	68.0/3.89	75.1/3.89	72.5/4.07	62.8/3.73-3.82
3,3,6,6,6,3	aXDDmanHepp	102.0/5.22	70.8/4.22	79.3/3.95	67.7/3.93	74.1/4.06	73.8/4.03	63.5/3.74-3.77
3,3,6,6,6	aDGlcp	99.0/4.98	71.4/3.64	80.8/3.85	71.1/3.58	71.8/3.84	61.4/3.77-3.84
3,3,6,6	aDGlcp	98.9/4.97-4.99	72.6/3.59	74.6/3.73	70.7/3.52	71.4/3.92	66.8/3.75-3.98
3,3,6	aDGlcp	98.9/5.16	72.5/3.60	74.5/3.75	70.7/3.52	71.7/4.12	66.6/3.75-4.00
3,3	aXDDmanHepp	103.0/5.11	70.9/4.05	71.4/3.90	68.8/3.83	72.6/3.96	79.9/4.08	62.1/3.88-3.91
3	aLFucp	99.9/4.95	68.7/3.91	77.7/3.97	72.7/4.01	68.3/4.21	16.5/1.22
	x?Suga	62.3/3.71-3.76	82.6/4.08	84.4/4.08	76.5/4.20	83.8/3.94	61.9/3.72-3.80

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
3,3,6,6,6,3,3,3,3	aXDDmanHepp	5.13	4.06	3.85	3.75	3.86	4.06	3.73 3.82
3,3,6,6,6,3,3,3	aXDDmanHepp	5.11	4.25	3.99	3.88	3.90	4.07	3.73 3.82
3,3,6,6,6,3,3	aXDDmanHepp	5.10	4.25	3.99	3.89	3.89	4.07	3.73 3.82
3,3,6,6,6,3	aXDDmanHepp	5.22	4.22	3.95	3.93	4.06	4.03	3.74 3.77
3,3,6,6,6	aDGlcp	4.98	3.64	3.85	3.58	3.84	3.77 3.84
3,3,6,6	aDGlcp	4.97 4.99	3.59	3.73	3.52	3.92	3.75 3.98
3,3,6	aDGlcp	5.16	3.60	3.75	3.52	4.12	3.75 4.00
3,3	aXDDmanHepp	5.11	4.05	3.90	3.83	3.96	4.08	3.88 3.91
3	aLFucp	4.95	3.91	3.97	4.01	4.21	1.22
	x?Suga	3.71 3.76	4.08	4.08	4.20	3.94	3.72 3.80

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
3,3,6,6,6,3,3,3,3	aXDDmanHepp	103.3	71.0	71.8	68.6	75.0	72.7	62.8
3,3,6,6,6,3,3,3	aXDDmanHepp	103.3	70.7	79.1	68.0	75.1	72.5	62.8
3,3,6,6,6,3,3	aXDDmanHepp	103.3	70.7	79.1	68.0	75.1	72.5	62.8
3,3,6,6,6,3	aXDDmanHepp	102.0	70.8	79.3	67.7	74.1	73.8	63.5
3,3,6,6,6	aDGlcp	99.0	71.4	80.8	71.1	71.8	61.4
3,3,6,6	aDGlcp	98.9	72.6	74.6	70.7	71.4	66.8
3,3,6	aDGlcp	98.9	72.5	74.5	70.7	71.7	66.6
3,3	aXDDmanHepp	103.0	70.9	71.4	68.8	72.6	79.9	62.1
3	aLFucp	99.9	68.7	77.7	72.7	68.3	16.5
	x?Suga	62.3	82.6	84.4	76.5	83.8	61.9

There is only one chemically distinct structure:

[1*]O[C@@H]1O[C@@H](C)[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]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

R1 = x?Suga, Sug = anhMan-ol