CSDB: Search results

Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: (Actinopterygii); Homo sapiens
Associated disease: edwardsiellosis; gastroenteritis [ICD11: 1A40.0

]; meningitis [ICD11: 1D01

]; osteomyelitis [ICD11: FB84

]; cholecystitis [ICD11: DC12

]

The structure was elucidated in this paper
NCBI PubMed ID: 28561753
Publication DOI: 10.3390/ijms18061163
Journal NLM ID: 101092791
Publisher: Basel, Switzerland: MDPI
Correspondence: Marta Kaszowska <marta.kaszowska

iitd.pan.wroc.pl>
Institutions: Department of Biotechnology and Molecular Biology, University of Opole, PL-Opole, Poland, Department of Immunochemistry, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland, Department of Microbiology, University of Barcelona, Diagonal 643, 08071 Barcelona, Spain

The chemical structure and genomics of the lipopolysaccharide (LPS) core oligosaccharide of pathogenic Edwardsiella tarda strain EIB 202 were studied for the first time. The complete gene assignment for all LPS core biosynthesis gene functions was acquired. The complete structure of core oligosaccharide was investigated by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy, electrospray ionization mass spectrometry MSn, and matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. The following structure of the undecasaccharide was established: The heterogeneous appearance of the core oligosaccharide structure was due to the partial lack of β-d-Galp and the replacement of α-d-GlcpNAcGly by α-d-GlcpNGly. The glycine location was identified by mass spectrometry.

NMR, core oligosaccharide, MALDI-TOF MS, Edwardsiella tarda, ESI MSn, genomic

Structure type: oligomer ; 933.7 [M+Gly-2H]2-
Location inside paper: abstract, table 1, fig.3, fraction OSVIII
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130670,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_151531,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192

Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, sugar analysis, 31P NMR, ESI-MS, mild acid hydrolysis, MALDI-TOF MS, function analysis of gene clusters
Comments, role: the NMR solution was not indicated; The positions of glycine in OSVIII and OSVII were not determined. In OS glycoform terminal α-D-GlcpN residue was partial replacement by α-D-GlcpNAc residue.

Related record ID(s): 12108
NCBI Taxonomy refs (TaxIDs): 498217
Show glycosyltransferases

NMR conditions: at 303 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
5,3,2	bDGlcp	103.2	74.5	76.3	71.6	76.5	62.7
5,3,3,4,?	xXGly	168.0	41.8
5,3,3,4	aDGlcpN	97.0	55.1	70.5	70.5	72.8	62.5
5,3,3	aDGalpA	102.5	69.6	72.2	80.9	72.5	175.6
5,3,7,7,4	aDGlcpN	95.6	55.1	70.4	76.6	73.2	60.0
5,3,7,7	aDGalpA	99.8	69.0	69.9	77.9	70.9	176.7
5,3,7	aXLDmanHepp	103.2	71.1	72.3	71.4	73.4	69.1	72.0
5,3	aXLDmanHepp	99.6	78.6	80.0	66.6	73.4	69.3	73.3
5,4	bDGlcp	103.3	73.9	76.2	69.9	76.2	61.5
5	aXLDmanHepp	101.7	71.3	74.7	74.4	72.2	69.4	63.9
	aXKdo?	?	97.7	34.7	66.5	75.7	70.1	66.9	64.3


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
5,3,2	bDGlcp	4.63	3.40	3.56	3.33	3.60	3.69-3.98
5,3,3,4,?	xXGly	-	3.90-4.09
5,3,3,4	aDGlcpN	5.29	3.39	3.99	3.63	4.27	3.69-3.97
5,3,3	aDGalpA	5.47	3.93	4.26	4.48	4.67	-
5,3,7,7,4	aDGlcpN	5.33	3.34	4.02	3.60	4.19	3.90-3.91
5,3,7,7	aDGalpA	5.12	4.05	4.16	4.62	4.41	-
5,3,7	aXLDmanHepp	4.98	4.05	3.95	3.93	3.72	4.23	3.69-4.88
5,3	aXLDmanHepp	5.44	4.34	4.19	4.12	3.67	4.28	3.62-4.01
5,4	bDGlcp	4.51	3.36	3.55	3.56	3.55	3.87-3.95
5	aXLDmanHepp	5.19	4.15	4.25	4.35	4.26	4.18	3.80
	aXKdo?	-	-	1.96-2.29	4.21	4.25	3.81	3.97	3.69-3.92


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8
5,3,2	bDGlcp	103.2/4.63	74.5/3.40	76.3/3.56	71.6/3.33	76.5/3.60	62.7/3.69-3.98
5,3,3,4,?	xXGly		41.8/3.90-4.09
5,3,3,4	aDGlcpN	97.0/5.29	55.1/3.39	70.5/3.99	70.5/3.63	72.8/4.27	62.5/3.69-3.97
5,3,3	aDGalpA	102.5/5.47	69.6/3.93	72.2/4.26	80.9/4.48	72.5/4.67	
5,3,7,7,4	aDGlcpN	95.6/5.33	55.1/3.34	70.4/4.02	76.6/3.60	73.2/4.19	60.0/3.90-3.91
5,3,7,7	aDGalpA	99.8/5.12	69.0/4.05	69.9/4.16	77.9/4.62	70.9/4.41	
5,3,7	aXLDmanHepp	103.2/4.98	71.1/4.05	72.3/3.95	71.4/3.93	73.4/3.72	69.1/4.23	72.0/3.69-4.88
5,3	aXLDmanHepp	99.6/5.44	78.6/4.34	80.0/4.19	66.6/4.12	73.4/3.67	69.3/4.28	73.3/3.62-4.01
5,4	bDGlcp	103.3/4.51	73.9/3.36	76.2/3.55	69.9/3.56	76.2/3.55	61.5/3.87-3.95
5	aXLDmanHepp	101.7/5.19	71.3/4.15	74.7/4.25	74.4/4.35	72.2/4.26	69.4/4.18	63.9/3.80
	aXKdo?			34.7/1.96-2.29	66.5/4.21	75.7/4.25	70.1/3.81	66.9/3.97	64.3/3.69-3.92

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
5,3,2	bDGlcp	4.63	3.40	3.56	3.33	3.60	3.69 3.98
5,3,3,4,?	xXGly		3.90 4.09
5,3,3,4	aDGlcpN	5.29	3.39	3.99	3.63	4.27	3.69 3.97
5,3,3	aDGalpA	5.47	3.93	4.26	4.48	4.67
5,3,7,7,4	aDGlcpN	5.33	3.34	4.02	3.60	4.19	3.90 3.91
5,3,7,7	aDGalpA	5.12	4.05	4.16	4.62	4.41
5,3,7	aXLDmanHepp	4.98	4.05	3.95	3.93	3.72	4.23	3.69 4.88
5,3	aXLDmanHepp	5.44	4.34	4.19	4.12	3.67	4.28	3.62 4.01
5,4	bDGlcp	4.51	3.36	3.55	3.56	3.55	3.87 3.95
5	aXLDmanHepp	5.19	4.15	4.25	4.35	4.26	4.18	3.80
	aXKdo?			1.96 2.29	4.21	4.25	3.81	3.97	3.69 3.92

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
5,3,2	bDGlcp	103.2	74.5	76.3	71.6	76.5	62.7
5,3,3,4,?	xXGly	168.0	41.8
5,3,3,4	aDGlcpN	97.0	55.1	70.5	70.5	72.8	62.5
5,3,3	aDGalpA	102.5	69.6	72.2	80.9	72.5	175.6
5,3,7,7,4	aDGlcpN	95.6	55.1	70.4	76.6	73.2	60.0
5,3,7,7	aDGalpA	99.8	69.0	69.9	77.9	70.9	176.7
5,3,7	aXLDmanHepp	103.2	71.1	72.3	71.4	73.4	69.1	72.0
5,3	aXLDmanHepp	99.6	78.6	80.0	66.6	73.4	69.3	73.3
5,4	bDGlcp	103.3	73.9	76.2	69.9	76.2	61.5
5	aXLDmanHepp	101.7	71.3	74.7	74.4	72.2	69.4	63.9
	aXKdo?	?	97.7	34.7	66.5	75.7	70.1	66.9	64.3

The spectrum also has 1 signal at unknown position (not plotted).

There are 4 chemically distinct structures. Please, select:

N[C@H]1[C@@H](O[C@H]2[C@@H](C(=O)O)O[C@H](OC[C@H](O)[C@H]3O[C@H](OC[C@H](O)[C@H]4O[C@H](O[C@@H]5[C@H](O)[C@@H](O[C@@H]6[C@H](O)C[C@](O)(C(=O)O)O[C@@H]6[C@H](O)CO)O[C@H]([C@@H](O)CO)[C@H]5O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)[C@@H](O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)[C@@H](O[C@H]5O[C@H](C(=O)O)[C@H](O[C@H]6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6NCC(=O)O)[C@H](O)[C@H]5O)[C@@H]4O)[C@@H](O)[C@@H](O)[C@@H]3O)[C@H](O)[C@H]2O)O[C@H](CO)[C@@H](O)[C@@H]1O

SVG MW SMILES 3D mol Ionize