CSDB: Search results

Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: Homo sapiens
Associated disease: septicemia [ICD11: MA15.Y

]; infection due to Vibrio vulnificus [ICD11: XN44G

]

The structure was elucidated in this paper
NCBI PubMed ID: 19185290
Publication DOI: 10.1016/j.carres.2008.12.017
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: D.A. Rowe-Magnus <dean.rowe-magnus

sri.utoronto.ca>
Institutions: Institute for Biological Sciences, National Research Council, 100 Sussex Dr., Ottawa, Ont., Canada K1A 0R6, Department of Molecular and Cellular Biology, University of Guelph, 488 Gordon Street, New Science Complex, Guelph, ON, Canada N1G 2W1, Division of Clinical Integrative Biology, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, S1-26A, Toronto, Ontario, Canada M4N 3N5, Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada

The structure of the lipopolysaccharide core of Vibrio vulnificus type strain 27562 is presented. LPS hydrolysis gave two oligosaccharides, OS-1 and OS-2, as well as lipid A. NMR spectroscopic data corresponded to the presence of one Kdo residue, one β-glucopyranose, three heptoses, one glyceric acid, one acetate, three PEtN, and one 5,7-diacylamido-3,5,7,9-tetradeoxynonulosonic acid residue (pseudaminic acid, Pse) in OS1. OS2 differed form OS 1 by the absence of glyceric acid, acetate, and Pse residues. Lipid A was analyzed for fatty acid composition and the following fatty acids were found: C14:0, C12:0-3OH, C16:0, C16:1, C14:0-3OH, C18:0, C18:1 in a ratio of 1:3:3:1:2.5:0.6:0.8.

Lipopolysaccharide, structure, core, Vibrio vulnificus

Structure type: oligomer
Location inside paper: p.487, scheme 1, 7
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_135394,IEDB_137777,IEDB_140956,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_151531,IEDB_2189046,IEDB_2189047,IEDB_983931,SB_192

Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, sugar analysis, dephosphorylation, 31P NMR, ESI-MS, mild acid hydrolysis, alkaline degradation, GC, NMR-1D, immunoblotting, PAGE, N-acetylation, partial de-O-acylation
Comments, role: extracted from seafood. NMR assignment of #0,6_bDGlcpN H2 (4.15) might be erroneous.

Related record ID(s): 23871, 24249, 24250, 24251, 24252, 24253, 24255
NCBI Taxonomy refs (TaxIDs): 672
Show glycosyltransferases

NMR conditions: in D2O at 298 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
0,6,6,5,3,2	aXLDmanHepp
0,6,6,5,3	aXLDmanHepp
0,6,6,5,2,0	xXEtN
0,6,6,5,2	P
0,6,6,5,4,6	bXPsep
0,6,6,5,4	bDGlcp
0,6,6,5,7,0	xXEtN
0,6,6,5,7	P
0,6,6,5	aXDDmanHepp
0,6,6,4	P
0,6,6,8	P
0,6,6	?XKdop	?	?	36.0	71.9	74.2	73.3	69.9	68.8
0,6,4	P
0,6	bDGlcpN	100.7	57.6	73.7	76.3	75.9	64.6
0	aDGlcpN
	P


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
0,6,6,5,3,2	aXLDmanHepp
0,6,6,5,3	aXLDmanHepp
0,6,6,5,2,0	xXEtN
0,6,6,5,2	P
0,6,6,5,4,6	bXPsep
0,6,6,5,4	bDGlcp
0,6,6,5,7,0	xXEtN
0,6,6,5,7	P
0,6,6,5	aXDDmanHepp
0,6,6,4	P
0,6,6,8	P
0,6,6	?XKdop	-	-	2.12-2.38	4.63	4.37	3.97	3.88	4.11-4.19
0,6,4	P
0,6	bDGlcpN	4.90	4.15	3.89	3.90	3.76	3.63-3.78
0	aDGlcpN
	P


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8
0,6,6,5,3,2	aXLDmanHepp
0,6,6,5,3	aXLDmanHepp
0,6,6,5,2,0	xXEtN
0,6,6,5,2	P
0,6,6,5,4,6	bXPsep
0,6,6,5,4	bDGlcp
0,6,6,5,7,0	xXEtN
0,6,6,5,7	P
0,6,6,5	aXDDmanHepp
0,6,6,4	P
0,6,6,8	P
0,6,6	?XKdop			36.0/2.12-2.38	71.9/4.63	74.2/4.37	73.3/3.97	69.9/3.88	68.8/4.11-4.19
0,6,4	P
0,6	bDGlcpN	100.7/4.90	57.6/4.15	73.7/3.89	76.3/3.90	75.9/3.76	64.6/3.63-3.78
0	aDGlcpN
	P

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
0,6,6,5,3,2	aXLDmanHepp
0,6,6,5,3	aXLDmanHepp
0,6,6,5,2,0	xXEtN
0,6,6,5,2	P
0,6,6,5,4,6	bXPsep
0,6,6,5,4	bDGlcp
0,6,6,5,7,0	xXEtN
0,6,6,5,7	P
0,6,6,5	aXDDmanHepp
0,6,6,4	P
0,6,6,8	P
0,6,6	?XKdop			2.12 2.38	4.63	4.37	3.97	3.88	4.11 4.19
0,6,4	P
0,6	bDGlcpN	4.90	4.15	3.89	3.90	3.76	3.63 3.78
0	aDGlcpN
	P

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
0,6,6,5,3,2	aXLDmanHepp
0,6,6,5,3	aXLDmanHepp
0,6,6,5,2,0	xXEtN
0,6,6,5,2	P
0,6,6,5,4,6	bXPsep
0,6,6,5,4	bDGlcp
0,6,6,5,7,0	xXEtN
0,6,6,5,7	P
0,6,6,5	aXDDmanHepp
0,6,6,4	P
0,6,6,8	P
0,6,6	?XKdop	?	?	36.0	71.9	74.2	73.3	69.9	68.8
0,6,4	P
0,6	bDGlcpN	100.7	57.6	73.7	76.3	75.9	64.6
0	aDGlcpN
	P

The spectrum also has 2 signals at unknown positions (not plotted).

There is only one chemically distinct structure:

C[C@H](O)[C@H](N)[C@@H]1O[C@@](OC[C@H]2O[C@@H](O[C@H]3[C@H](O[C@H]4O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]4O[C@H]4O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@H](OP(=O)(O)OCCN)[C@@H](O[C@@H]4[C@H](OP(=O)(O)O)CC(OC[C@H]5O[C@@H](OC[C@H]6O[C@H](OP(=O)(O)O)[C@H](N)[C@@H](O)[C@@H]6O)[C@H](N)[C@@H](O)[C@@H]5OP(=O)(O)O)(C(=O)O)O[C@@H]4[C@H](O)COP(=O)(O)O)O[C@@H]3[C@H](O)COP(=O)(O)OCCN)[C@H](O)[C@@H](O)[C@@H]2O)(C(=O)O)C[C@H](O)[C@@H]1N

SVG MW SMILES 3D mol Ionize