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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: Homo sapiens
Associated disease: bacteremia [ICD11: MA15.0

]; gastroenteritis [ICD11: 1A40.0

]

The structure was elucidated in this paper
NCBI PubMed ID: 23643833
Publication DOI: 10.1016/j.carres.2013.03.029
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: W. Jachymek <jachymek

iitd.pan.wroc.pl>
Institutions: Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland

Hafnia alvei strain PCM 2670 is a clinical isolate from a patient with chronic reproductive tract infection. The novel structure of the semi-rough lipopolysaccharide was established with the use of NMR spectroscopy and mass spectrometry as well as immunochemical techniques. According to the mass spectrometry data, heptose in the oligosaccharide is partially substituted by glycine. H. alvei PCM 2670 core structure encompasses the common core of H. alvei which is modified with two additional galactose units. The 6-substituted galactose is the O-antigen repeating unit substitution residue. The repeating unit consists of five monosaccharide residues and has the following structure: →2)-β-Galp-(1→6)-α-Glcp-(1→6)-α-GlcpNAc3OAc-(1→4)-α-GalpA-(1→3)-β-GlcpNAc6OAc-(1→6)-core.

NMR, Hafnia alvei, glycine, ESIMS, semi-rough lipopolysaccharide

Structure type: fragment of a bigger structure
Location inside paper: abstract, p.71, fig.5, table 1, OS2
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130670,IEDB_133751,IEDB_135813,IEDB_136044,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88

Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, SDS-PAGE, sugar analysis, 31P NMR, ESI-MS, NMR-1D, immunoblotting
Comments, role: In the high molecular weight PS terminal bGalp is substituted on C2 and RU is O-acetylated on GlcpNAc residues. NMR data are for core oligosaccharide with single O-unit; error in the paper: incorrect O-acetylation positions in fig.5 (corrected from text at p.70)

Related record ID(s): 29430, 29431, 29432, 29433, 29434
NCBI Taxonomy refs (TaxIDs): 569
Show glycosyltransferases

NMR conditions: in D2O at 278 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
5,3,3,3,2	aDGalp	96.7	71.6	70.1	70.0	70.9	62.1
5,3,3,3,4,6,3,4,6,6	bDGalp	104.1	71.7	73.5	69.5	76.2	61.6
5,3,3,3,4,6,3,4,6	aDGlcp	98.9	72.4	73.8	70.1	71.7	69.0
5,3,3,3,4,6,3,4,2	Ac
5,3,3,3,4,6,3,4,3	Ac
5,3,3,3,4,6,3,4	aDGlcpN	99.7	54.5	71.9	70.6	71.8	66.3
5,3,3,3,4,6,3	aDGalpA	101.3	69.1	69.2	80.1	71.4	173.3
5,3,3,3,4,6,2	Ac
5,3,3,3,4,6,6	Ac
5,3,3,3,4,6	bDGlcpN	102.1	54.9	82.8	76.1	76.3	61.2
5,3,3,3,4	bDGalp	104.1	71.7	73.3	69.0	72.0	68.3
5,3,3,3	aDGlcp	96.9	75.6	70.9	79.2	70.9	60.3
5,3,3	aDGlcp	102.2	70.9	80.2	69.5	72.9	60.9
5,3,4	P
5,3,7	aXLDmanHepp	100.2	70.8	71.2	67.1	69.0	69.5	63.9
5,3	aXLDmanHepp	103.7	70.6	80.1	69.5	72.9	68.7	68.5
5,4,0,0	xXEtN	62.8	40.8
5,4,0	P
5,4	P
5	aXLDmanHepp	100.2	71.8	78.6	72.4	71.8	70.0	63.7
	?XKdo?	?	96.2	34.2	66.4	73.3	73.6	69.9	64.9
5,3,2	%xXGly
5,3,6	%xXGly


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
5,3,3,3,2	aDGalp	5.25	3.87	3.97	4.02	3.98	3.74-3.80
5,3,3,3,4,6,3,4,6,6	bDGalp	4.42	3.55	3.65	3.92	3.73	3.73-3.75
5,3,3,3,4,6,3,4,6	aDGlcp	4.96	3.56	3.78	3.54	3.85	3.87-4.17
5,3,3,3,4,6,3,4,2	Ac
5,3,3,3,4,6,3,4,3	Ac
5,3,3,3,4,6,3,4	aDGlcpN	4.93	3.91	3.71	3.62	4.33	3.65-4.05
5,3,3,3,4,6,3	aDGalpA	5.38	3.89	3.99	4.38	4.37	-
5,3,3,3,4,6,2	Ac
5,3,3,3,4,6,6	Ac
5,3,3,3,4,6	bDGlcpN	4.61	3.78	3.74	3.69	3.49	3.77-3.92
5,3,3,3,4	bDGalp	4.46	3.53	3.63	3.88	3.63	3.89-3.93
5,3,3,3	aDGlcp	5.56	3.76	3.95	3.72	4.16	3.91-3.95
5,3,3	aDGlcp	5.20	3.65	3.97	4.05	3.93	3.80-3.93
5,3,4	P
5,3,7	aXLDmanHepp	5.00	3.93	3.68	3.85	3.86	4.11	3.72-3.74
5,3	aXLDmanHepp	5.10	4.40	4.12	4.42	3.81	4.24	3.60-3.77
5,4,0,0	xXEtN	3.29	4.12
5,4,0	P
5,4	P
5	aXLDmanHepp	5.21	4.02	4.08	4.62	4.24	4.03	3.65-3.75
	?XKdo?	-	-	1.91-2.27	4.12	4.17	3.81	3.70	3.47-3.95
5,3,2	%xXGly
5,3,6	%xXGly


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8
5,3,3,3,2	aDGalp	96.7/5.25	71.6/3.87	70.1/3.97	70.0/4.02	70.9/3.98	62.1/3.74-3.80
5,3,3,3,4,6,3,4,6,6	bDGalp	104.1/4.42	71.7/3.55	73.5/3.65	69.5/3.92	76.2/3.73	61.6/3.73-3.75
5,3,3,3,4,6,3,4,6	aDGlcp	98.9/4.96	72.4/3.56	73.8/3.78	70.1/3.54	71.7/3.85	69.0/3.87-4.17
5,3,3,3,4,6,3,4,2	Ac
5,3,3,3,4,6,3,4,3	Ac
5,3,3,3,4,6,3,4	aDGlcpN	99.7/4.93	54.5/3.91	71.9/3.71	70.6/3.62	71.8/4.33	66.3/3.65-4.05
5,3,3,3,4,6,3	aDGalpA	101.3/5.38	69.1/3.89	69.2/3.99	80.1/4.38	71.4/4.37	
5,3,3,3,4,6,2	Ac
5,3,3,3,4,6,6	Ac
5,3,3,3,4,6	bDGlcpN	102.1/4.61	54.9/3.78	82.8/3.74	76.1/3.69	76.3/3.49	61.2/3.77-3.92
5,3,3,3,4	bDGalp	104.1/4.46	71.7/3.53	73.3/3.63	69.0/3.88	72.0/3.63	68.3/3.89-3.93
5,3,3,3	aDGlcp	96.9/5.56	75.6/3.76	70.9/3.95	79.2/3.72	70.9/4.16	60.3/3.91-3.95
5,3,3	aDGlcp	102.2/5.20	70.9/3.65	80.2/3.97	69.5/4.05	72.9/3.93	60.9/3.80-3.93
5,3,4	P
5,3,7	aXLDmanHepp	100.2/5.00	70.8/3.93	71.2/3.68	67.1/3.85	69.0/3.86	69.5/4.11	63.9/3.72-3.74
5,3	aXLDmanHepp	103.7/5.10	70.6/4.40	80.1/4.12	69.5/4.42	72.9/3.81	68.7/4.24	68.5/3.60-3.77
5,4,0,0	xXEtN	62.8/3.29	40.8/4.12
5,4,0	P
5,4	P
5	aXLDmanHepp	100.2/5.21	71.8/4.02	78.6/4.08	72.4/4.62	71.8/4.24	70.0/4.03	63.7/3.65-3.75
	?XKdo?			34.2/1.91-2.27	66.4/4.12	73.3/4.17	73.6/3.81	69.9/3.70	64.9/3.47-3.95
5,3,2	%xXGly
5,3,6	%xXGly

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
5,3,3,3,2	aDGalp	5.25	3.87	3.97	4.02	3.98	3.74 3.80
5,3,3,3,4,6,3,4,6,6	bDGalp	4.42	3.55	3.65	3.92	3.73	3.73 3.75
5,3,3,3,4,6,3,4,6	aDGlcp	4.96	3.56	3.78	3.54	3.85	3.87 4.17
5,3,3,3,4,6,3,4,2	Ac
5,3,3,3,4,6,3,4,3	Ac
5,3,3,3,4,6,3,4	aDGlcpN	4.93	3.91	3.71	3.62	4.33	3.65 4.05
5,3,3,3,4,6,3	aDGalpA	5.38	3.89	3.99	4.38	4.37
5,3,3,3,4,6,2	Ac
5,3,3,3,4,6,6	Ac
5,3,3,3,4,6	bDGlcpN	4.61	3.78	3.74	3.69	3.49	3.77 3.92
5,3,3,3,4	bDGalp	4.46	3.53	3.63	3.88	3.63	3.89 3.93
5,3,3,3	aDGlcp	5.56	3.76	3.95	3.72	4.16	3.91 3.95
5,3,3	aDGlcp	5.20	3.65	3.97	4.05	3.93	3.80 3.93
5,3,4	P
5,3,7	aXLDmanHepp	5.00	3.93	3.68	3.85	3.86	4.11	3.72 3.74
5,3	aXLDmanHepp	5.10	4.40	4.12	4.42	3.81	4.24	3.60 3.77
5,4,0,0	xXEtN	3.29	4.12
5,4,0	P
5,4	P
5	aXLDmanHepp	5.21	4.02	4.08	4.62	4.24	4.03	3.65 3.75
	?XKdo?			1.91 2.27	4.12	4.17	3.81	3.70	3.47 3.95
5,3,2	%xXGly
5,3,6	%xXGly

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
5,3,3,3,2	aDGalp	96.7	71.6	70.1	70.0	70.9	62.1
5,3,3,3,4,6,3,4,6,6	bDGalp	104.1	71.7	73.5	69.5	76.2	61.6
5,3,3,3,4,6,3,4,6	aDGlcp	98.9	72.4	73.8	70.1	71.7	69.0
5,3,3,3,4,6,3,4,2	Ac
5,3,3,3,4,6,3,4,3	Ac
5,3,3,3,4,6,3,4	aDGlcpN	99.7	54.5	71.9	70.6	71.8	66.3
5,3,3,3,4,6,3	aDGalpA	101.3	69.1	69.2	80.1	71.4	173.3
5,3,3,3,4,6,2	Ac
5,3,3,3,4,6,6	Ac
5,3,3,3,4,6	bDGlcpN	102.1	54.9	82.8	76.1	76.3	61.2
5,3,3,3,4	bDGalp	104.1	71.7	73.3	69.0	72.0	68.3
5,3,3,3	aDGlcp	96.9	75.6	70.9	79.2	70.9	60.3
5,3,3	aDGlcp	102.2	70.9	80.2	69.5	72.9	60.9
5,3,4	P
5,3,7	aXLDmanHepp	100.2	70.8	71.2	67.1	69.0	69.5	63.9
5,3	aXLDmanHepp	103.7	70.6	80.1	69.5	72.9	68.7	68.5
5,4,0,0	xXEtN	62.8	40.8
5,4,0	P
5,4	P
5	aXLDmanHepp	100.2	71.8	78.6	72.4	71.8	70.0	63.7
	?XKdo?	?	96.2	34.2	66.4	73.3	73.6	69.9	64.9
5,3,2	%xXGly
5,3,6	%xXGly

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

There are 2 chemically distinct structures. Please, select:

CC(=O)N[C@H]1[C@@H](O[C@H]2[C@@H](C(=O)O)O[C@H](O[C@H]3[C@H](O)[C@@H](COC(C)=O)O[C@@H](OC[C@H]4O[C@@H](O[C@H]5[C@H](O)[C@@H](O[C@H]6O[C@H](CO)[C@H](O)[C@H](O)[C@H]6O)[C@@H](O[C@H]6[C@H](O)[C@@H](CO)O[C@H](O[C@@H]7[C@H](O)[C@@H](O[C@@H]8[C@H](O)[C@@H](O[C@@H]9[C@H](O)CC(O)(C(=O)O)O[C@@H]9[C@H](O)CO)O[C@H]([C@@H](O)CO)[C@H]8OP(=O)(O)OP(=O)(O)OCCN)O[C@H]([C@@H](O)CO[C@H]8O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]8O)[C@H]7OP(=O)(O)O)[C@@H]6O)O[C@@H]5CO)[C@H](O)[C@@H](O)[C@H]4O)[C@@H]3NC(C)=O)[C@H](O)[C@H]2O)O[C@H](CO[C@H]2O[C@H](CO[C@@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@H]2O)[C@@H](O)[C@@H]1OC(C)=O

SVG MW SMILES 3D mol Ionize