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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: Homo sapiens
Associated disease: diarrhea [ICD11: ME05.1

, ICD11: SA55

]; gastroenteritis [ICD11: 1A40.0

]; urinary tract infections (UTI) [ICD11: GC08

]

The structure was elucidated in this paper
NCBI PubMed ID: 21316039
Publication DOI: 10.1016/j.carres.2011.01.011
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: olga.ovchinnikova

gmail.com
Institutions: N D Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia

Opportunistic human pathogens of the genus Providencia from the family Enterobacteriaceae are serotyped by their O-antigens, which represent the O-polysaccharide chains of the lipopolysaccharides (LPSs) on the cell surface. In this work, the O-polysaccharide of Providencia alcalifaciens O9 was obtained by mild acid degradation of a long-chain S-form LPS. The structure of the hexasaccharide repeat (O-unit) of the O-polysaccharide containing one D-Gal, two D-Glc, and three D-GalNAc residues was established by sugar and methylation analyses along with one- and two-dimensional (1)H and (13)C NMR spectroscopy. Another degradation product was derived from a short-chain SR-form LPS and found to consist of a core oligosaccharide bearing one O-unit. Its studies by NMR spectroscopy and electrospray ionization mass spectrometry enabled identification of one of the GalNAc residues as the first monosaccharide of the O-unit, whose glycosidic linkage links the O-units to each other and the first O-unit to the core. The core is distinguished by the occurrence of two glycoforms differing in the nature of a lateral monosaccharide, which is either D-Glc or D-GlcNAc. Although composed of common monosaccharides, the O-polysaccharide of P. alcalifaciens O9 has a unique structure among bacterial polysaccharides, whereas the oligosaccharide region belongs to one of several core types recognized in the LPSs of Providencia.

core oligosaccharide, O-polysaccharide, Providencia, lipopolysaccharide structure, biological repeating unit

Structure type: oligomer
Location inside paper: p.647, fig.2, 2
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130648,IEDB_130650,IEDB_130693,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141582,IEDB_141584,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_885822,IEDB_983931,SB_192,SB_7

Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, sugar analysis, ESI-MS, mild acid hydrolysis, GC
Comments, role: O-unit core oligosaccharide from SR-type LPS glycoform

Related record ID(s): 26299, 26904
NCBI Taxonomy refs (TaxIDs): 126385
Reference(s) to other database(s): GTC:G90209TH
Show glycosyltransferases

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

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6
5,3,3,3,2,2,2	Ac	175.1	23.2
5,3,3,3,2,2	aDGlcpN	94.8	54.5	72.4	71.3	73.7	?
5,3,3,3,2,4,3,3	bDGlcp	106.3	74.3	76.8	71.1	77.4	62.2
5,3,3,3,2,4,3,2	Ac	175.1	23.2
5,3,3,3,2,4,3,4,6,6	bDGlcp	103.9	74.5	77.1	71.1	77.3	62.0
5,3,3,3,2,4,3,4,6	aDGalp	101.7	70.5	70.5	70.7	71.7	69.8
5,3,3,3,2,4,3,4,2	Ac	175.6	23.4
5,3,3,3,2,4,3,4	aDGalpN	98.5	51.5	70.6	68.8	70.0	66.4
5,3,3,3,2,4,3	aDGalpN	95.2	50.0	77.6	75.8	73.6	61.2
5,3,3,3,2,4,2	Ac	176.0	23.9
5,3,3,3,2,4	aDGalpN	102.3	52.3	76.1	64.9	76.7	62.1
5,3,3,3,2	aDGlcp	91.6	74.3	71.9	79.3	72.8	?
5,3,3,3	aDGalp	96.7	73.1	69.5	70.3	71.5	62.2
5,3,3	aDGlcp	101.7	72.0	77.7	72.5	73.7	?
5,3,6,0	%xXEtN
5,3,6	P
5,3,7,7	bDGalpA
5,3,7	a?Hepp
5,3	a?Hepp
5,4,0,0	xXEtN
5,4,0	%xXP?
5,4	P
5	a?Hepp
8	bLArap4N
	?XKdo?


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6
5,3,3,3,2,2,2	Ac	-	2.05
5,3,3,3,2,2	aDGlcpN	5.19	4.02	3.85	3.52	3.90	?
5,3,3,3,2,4,3,3	bDGlcp	4.46	3.35	3.51	3.49	3.42	3.73-3.91
5,3,3,3,2,4,3,2	Ac	-	2.05
5,3,3,3,2,4,3,4,6,6	bDGlcp	4.51	3.36	3.52	3.40	3.50	3.75-3.95
5,3,3,3,2,4,3,4,6	aDGalp	4.99	3.82	3.90	3.99	4.23	3.82-4.12
5,3,3,3,2,4,3,4,2	Ac	-	2.09
5,3,3,3,2,4,3,4	aDGalpN	4.94	4.22	4.13	4.15	4.66	3.76-3.81
5,3,3,3,2,4,3	aDGalpN	5.12	4.54	3.89	4.30	3.91	3.68-3.70
5,3,3,3,2,4,2	Ac	-	2.11
5,3,3,3,2,4	aDGalpN	4.66	4.12	3.84	4.16	3.71	3.76-3.79
5,3,3,3,2	aDGlcp	5.65	3.80	4.07	3.75	3.83	?
5,3,3,3	aDGalp	5.70	3.92	4.00	4.06	4.44	3.74-3.78
5,3,3	aDGlcp	5.33	3.63	4.05	3.45	3.88	?
5,3,6,0	%xXEtN
5,3,6	P
5,3,7,7	bDGalpA
5,3,7	a?Hepp
5,3	a?Hepp
5,4,0,0	xXEtN
5,4,0	%xXP?
5,4	P
5	a?Hepp
8	bLArap4N
	?XKdo?


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6
5,3,3,3,2,2,2	Ac		23.2/2.05
5,3,3,3,2,2	aDGlcpN	94.8/5.19	54.5/4.02	72.4/3.85	71.3/3.52	73.7/3.90	?/?
5,3,3,3,2,4,3,3	bDGlcp	106.3/4.46	74.3/3.35	76.8/3.51	71.1/3.49	77.4/3.42	62.2/3.73-3.91
5,3,3,3,2,4,3,2	Ac		23.2/2.05
5,3,3,3,2,4,3,4,6,6	bDGlcp	103.9/4.51	74.5/3.36	77.1/3.52	71.1/3.40	77.3/3.50	62.0/3.75-3.95
5,3,3,3,2,4,3,4,6	aDGalp	101.7/4.99	70.5/3.82	70.5/3.90	70.7/3.99	71.7/4.23	69.8/3.82-4.12
5,3,3,3,2,4,3,4,2	Ac		23.4/2.09
5,3,3,3,2,4,3,4	aDGalpN	98.5/4.94	51.5/4.22	70.6/4.13	68.8/4.15	70.0/4.66	66.4/3.76-3.81
5,3,3,3,2,4,3	aDGalpN	95.2/5.12	50.0/4.54	77.6/3.89	75.8/4.30	73.6/3.91	61.2/3.68-3.70
5,3,3,3,2,4,2	Ac		23.9/2.11
5,3,3,3,2,4	aDGalpN	102.3/4.66	52.3/4.12	76.1/3.84	64.9/4.16	76.7/3.71	62.1/3.76-3.79
5,3,3,3,2	aDGlcp	91.6/5.65	74.3/3.80	71.9/4.07	79.3/3.75	72.8/3.83	?/?
5,3,3,3	aDGalp	96.7/5.70	73.1/3.92	69.5/4.00	70.3/4.06	71.5/4.44	62.2/3.74-3.78
5,3,3	aDGlcp	101.7/5.33	72.0/3.63	77.7/4.05	72.5/3.45	73.7/3.88	?/?
5,3,6,0	%xXEtN
5,3,6	P
5,3,7,7	bDGalpA
5,3,7	a?Hepp
5,3	a?Hepp
5,4,0,0	xXEtN
5,4,0	%xXP?
5,4	P
5	a?Hepp
8	bLArap4N
	?XKdo?

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6
5,3,3,3,2,2,2	Ac		2.05
5,3,3,3,2,2	aDGlcpN	5.19	4.02	3.85	3.52	3.90	?
5,3,3,3,2,4,3,3	bDGlcp	4.46	3.35	3.51	3.49	3.42	3.73 3.91
5,3,3,3,2,4,3,2	Ac		2.05
5,3,3,3,2,4,3,4,6,6	bDGlcp	4.51	3.36	3.52	3.40	3.50	3.75 3.95
5,3,3,3,2,4,3,4,6	aDGalp	4.99	3.82	3.90	3.99	4.23	3.82 4.12
5,3,3,3,2,4,3,4,2	Ac		2.09
5,3,3,3,2,4,3,4	aDGalpN	4.94	4.22	4.13	4.15	4.66	3.76 3.81
5,3,3,3,2,4,3	aDGalpN	5.12	4.54	3.89	4.30	3.91	3.68 3.70
5,3,3,3,2,4,2	Ac		2.11
5,3,3,3,2,4	aDGalpN	4.66	4.12	3.84	4.16	3.71	3.76 3.79
5,3,3,3,2	aDGlcp	5.65	3.80	4.07	3.75	3.83	?
5,3,3,3	aDGalp	5.70	3.92	4.00	4.06	4.44	3.74 3.78
5,3,3	aDGlcp	5.33	3.63	4.05	3.45	3.88	?
5,3,6,0	%xXEtN
5,3,6	P
5,3,7,7	bDGalpA
5,3,7	a?Hepp
5,3	a?Hepp
5,4,0,0	xXEtN
5,4,0	%xXP?
5,4	P
5	a?Hepp
8	bLArap4N
	?XKdo?

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6
5,3,3,3,2,2,2	Ac	175.1	23.2
5,3,3,3,2,2	aDGlcpN	94.8	54.5	72.4	71.3	73.7	?
5,3,3,3,2,4,3,3	bDGlcp	106.3	74.3	76.8	71.1	77.4	62.2
5,3,3,3,2,4,3,2	Ac	175.1	23.2
5,3,3,3,2,4,3,4,6,6	bDGlcp	103.9	74.5	77.1	71.1	77.3	62.0
5,3,3,3,2,4,3,4,6	aDGalp	101.7	70.5	70.5	70.7	71.7	69.8
5,3,3,3,2,4,3,4,2	Ac	175.6	23.4
5,3,3,3,2,4,3,4	aDGalpN	98.5	51.5	70.6	68.8	70.0	66.4
5,3,3,3,2,4,3	aDGalpN	95.2	50.0	77.6	75.8	73.6	61.2
5,3,3,3,2,4,2	Ac	176.0	23.9
5,3,3,3,2,4	aDGalpN	102.3	52.3	76.1	64.9	76.7	62.1
5,3,3,3,2	aDGlcp	91.6	74.3	71.9	79.3	72.8	?
5,3,3,3	aDGalp	96.7	73.1	69.5	70.3	71.5	62.2
5,3,3	aDGlcp	101.7	72.0	77.7	72.5	73.7	?
5,3,6,0	%xXEtN
5,3,6	P
5,3,7,7	bDGalpA
5,3,7	a?Hepp
5,3	a?Hepp
5,4,0,0	xXEtN
5,4,0	%xXP?
5,4	P
5	a?Hepp
8	bLArap4N
	?XKdo?

The spectrum also has 3 signals at unknown positions (not plotted).

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

SVG MW SMILES 3D mol Ionize

R1 = a?Hepp