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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: Homo sapiens
Associated disease: functional gastrointestinal disorders [ICD11: DD9Y

]; infection due to Escherichia coli [ICD11: XN6P4

]

The structure was elucidated in this paper
NCBI PubMed ID: 24607538
Publication DOI: 10.1016/j.carres.2014.02.013
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: A.V. Perepelov <perepel

ioc.ac.ru>
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, Institute of Immunology, Federal Medical-Biological Agency, Moscow, Russia

O-Polysaccharide (O-antigen) accompanied by a minor mannan was isolated from the lipopolysaccharide of Escherichia coli O39 and studied by component analyses, methylation, Smith degradation, mass spectrometry, and 1D and 2D NMR spectroscopy. In addition, a new approach, solvolysis with anhydrous trifluoroacetic acid, was applied to cleave selectively the rhamnosidic linkage. The following structure of the O-polysaccharide was established: →3)-β-D-Quip4N(R3Hb)-(1→2)[α-D-Galp(l→3)]-α-D-Manp-(l→4)-α-L-Rhap-(1→3)-α-D-GlcpNAc-(1→ where D-Qui4N(R3Hb) indicates 4,6-dideoxy-4-[(R)-3-hydroxybutanoylamino]-D-glucose. The O-antigen gene cluster of E. coli O39 has been sequenced. The gene functions were tentatively assigned by a comparison with sequences in the available databases and found to be in agreement with the O-polysaccharide structure.

Lipopolysaccharide, O-antigen, Escherichia coli, bacterial polysaccharide structure, O-antigen gene cluster

Structure type: oligomer
Location inside paper: p.32, table 1, p.33, chart 1, OS-1
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130701,IEDB_137340,IEDB_141807,IEDB_144983,IEDB_151531,IEDB_152206,IEDB_983930,SB_44,SB_67,SB_72

Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, DNA sequencing, sugar analysis, ESI-MS, mild acid hydrolysis, Smith degradation, NMR-1D, GPC, analysis of gene, solvolysis with trifluoroacetic acid
Biosynthesis and genetic data: genetic data
Comments, role: O-polysaccharide after periodate oxidation, reduction (NaBH4) and mild acid hydrolysis (OS-1).

Related record ID(s): 30116, 30425, 30426, 30428
NCBI Taxonomy refs (TaxIDs): 562
Show glycosyltransferases

NMR conditions: in D2O at 303 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6
3,2,3,2	Ac	175.5	23.5
3,2,3	aDGlcpN	98.4	54.8	72.2	70.7	72.8	61.2
3,2,4	lR3HOBut	174.9	46.2	66.2	23.5
3,2	bDQuip4N	103.1	73.4	78.7	57.7	72.2	17.9
3	aDManp	99.3	79.3	70.9	68.2	74.1	61.7
	x?1dEry-ol	18.3	67.7	83.6	61.9


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6
3,2,3,2	Ac	-	2.06-2.07
3,2,3	aDGlcpN	5.10	3.88	3.74	3.54	4.15	3.80-3.84
3,2,4	lR3HOBut	-	2.36	4.14	1.23
3,2	bDQuip4N	4.48	3.46	3.73	3.79	3.56	1.21
3	aDManp	5.18	4.16	3.93	3.72	3.84	3.82-3.86
	x?1dEry-ol	1.22	4.05	3.72	3.73-3.73


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6
3,2,3,2	Ac		23.5/2.06-2.07
3,2,3	aDGlcpN	98.4/5.10	54.8/3.88	72.2/3.74	70.7/3.54	72.8/4.15	61.2/3.80-3.84
3,2,4	lR3HOBut		46.2/2.36	66.2/4.14	23.5/1.23
3,2	bDQuip4N	103.1/4.48	73.4/3.46	78.7/3.73	57.7/3.79	72.2/3.56	17.9/1.21
3	aDManp	99.3/5.18	79.3/4.16	70.9/3.93	68.2/3.72	74.1/3.84	61.7/3.82-3.86
	x?1dEry-ol	18.3/1.22	67.7/4.05	83.6/3.72	61.9/3.73-3.73

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6
3,2,3,2	Ac		2.06 2.07
3,2,3	aDGlcpN	5.10	3.88	3.74	3.54	4.15	3.80 3.84
3,2,4	lR3HOBut		2.36	4.14	1.23
3,2	bDQuip4N	4.48	3.46	3.73	3.79	3.56	1.21
3	aDManp	5.18	4.16	3.93	3.72	3.84	3.82 3.86
	x?1dEry-ol	1.22	4.05	3.72	3.73 3.73

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6
3,2,3,2	Ac	175.5	23.5
3,2,3	aDGlcpN	98.4	54.8	72.2	70.7	72.8	61.2
3,2,4	lR3HOBut	174.9	46.2	66.2	23.5
3,2	bDQuip4N	103.1	73.4	78.7	57.7	72.2	17.9
3	aDManp	99.3	79.3	70.9	68.2	74.1	61.7
	x?1dEry-ol	18.3	67.7	83.6	61.9

There are 2 chemically distinct structures. Please, select:

CC(=O)N[C@H]1[C@@H](O[C@@H]2[C@@H](O)[C@H](O[C@@H]3[C@@H](O[C@H](CO)[C@H](C)O)O[C@H](CO)[C@@H](O)[C@@H]3O)O[C@H](C)[C@H]2NC(=O)C[C@@H](C)O)O[C@H](CO)[C@@H](O)[C@@H]1O

SVG MW SMILES 3D mol Ionize