Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: infection due to Escherichia coli [ICD11:
XN6P4 
]
The structure was elucidated in this paperNCBI PubMed ID: 36239409Publication DOI: 10.1093/glycob/cwac069бJournal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: G. Widmalm <goran.widmalm
su.se>
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden, Department of Aquatic Sciences and Assessment, Swedish University of Agriculture, P.O. Box 7050, Uppsala, Sweden
The structure of the O-antigen from the international reference strain Escherichia coli O93:-:H16 has been determined. A nonrandom modal chain-length distribution was observed for the lipopolysaccharide, a pattern which is typical when long O-specific polysaccharides are expressed. By a combination of (i) bioinformatics information on the gene cluster related to O-antigen synthesis including putative function on glycosyl transferases, (ii) the magnitude of NMR coupling constants of anomeric protons and (iii) unassigned 2D 1H,13C-HSQC and 1H,1H-TOCSY NMR spectra it was possible to efficiently elucidate the structure of the carbohydrate polymer in an automated fashion using the computer program CASPER. The polysaccharide also carries O-acetyl groups and their locations were determined by 2D NMR experiments showing that ~½ of the population was 2,6-di-O-acetylated, ~¼ was 2-O-acetylated, whereas ~¼ did not carry O-acetyl group(s) in the 3-O-substituted mannosyl residue of the repeating unit. The structure of the tetrasaccharide repeating unit of the O-antigen is given by: →2)-β-d-Manp-(1→3)-β-d-Manp2Ac6Ac-(1→4)-β-d-GlcpA-(1→3)-α-d-GlcpNAc-(1→, which should also be the biological repeating unit and it shares structural elements with capsular polysaccharides from E. coli K84 and K50. The structure of the acidic O-specific polysaccharide from Cellulophaga baltica strain NN015840T differs to that of the O-antigen from E. coli O93 by lacking the O-acetyl group at O6 of the O-acetylated mannosyl residue.
Lipopolysaccharide, NMR spectroscopy, bioinformatics, CASPER, CarbBuilder
Structure type: polymer chemical repeating unit
Location inside paper: abstract, Fig. 7, table 1
Compound class: O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_137340,IEDB_137485,IEDB_140630,IEDB_141807,IEDB_144983,IEDB_151531,IEDB_152206,IEDB_423153,IEDB_983930,SB_44,SB_72
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, sugar analysis, GLC, de-O-acetylation, computer analysis with CASPER, bioinformatic analysis, CarbBuilder
Comments, role: O-deacetylated polysaccharide; O-antigen polysaccharide consisting of three populations, viz., ~½ of them are 2,6-di-O-acetylated, ~¼ are 2-O-acetylated and ~¼ do not carry O-acetyl groups on the -3)bDManp residue.
3D data: 3D data
Related record ID(s): 8456, 20936
NCBI Taxonomy refs (TaxIDs): 562
Show glycosyltransferases
NMR conditions: in D2O at 343 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,4,3 bDManp 97.55 77.33 74.37 68.04 77.54 61.78
3,4 bDManp 100.66 68.50 80.11 65.80 77.21 61.82
3 bDGlcpA 103.27 73.41 74.78 81.26 76.45 ?
2 Ac ? 22.87
aDGlcpN 98.78 53.70 81.15 69.31 72.04 61.14
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,4,3 bDManp 4.85 4.16 3.80 3.72 3.42 3.79-3.94
3,4 bDManp 4.62 4.17 3.85 3.62 3.39 3.75-3.92
3 bDGlcpA 4.59 3.40 3.65 3.74 3.81 -
2 Ac - 2.04
aDGlcpN 5.25 4.06 4.06 3.61 4.21 3.83-3.85
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,4,3 bDManp 97.55/4.85 77.33/4.16 74.37/3.80 68.04/3.72 77.54/3.42 61.78/3.79-3.94
3,4 bDManp 100.66/4.62 68.50/4.17 80.11/3.85 65.80/3.62 77.21/3.39 61.82/3.75-3.92
3 bDGlcpA 103.27/4.59 73.41/3.40 74.78/3.65 81.26/3.74 76.45/3.81
2 Ac 22.87/2.04
aDGlcpN 98.78/5.25 53.70/4.06 81.15/4.06 69.31/3.61 72.04/4.21 61.14/3.83-3.85
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,4,3 | bDManp | 4.85 | 4.16 | 3.80 | 3.72 | 3.42 | 3.79
3.94 |
| 3,4 | bDManp | 4.62 | 4.17 | 3.85 | 3.62 | 3.39 | 3.75
3.92 |
| 3 | bDGlcpA | 4.59 | 3.40 | 3.65 | 3.74 | 3.81 |
|
| 2 | Ac |
| 2.04 | |
| | aDGlcpN | 5.25 | 4.06 | 4.06 | 3.61 | 4.21 | 3.83
3.85 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,4,3 | bDManp | 97.55 | 77.33 | 74.37 | 68.04 | 77.54 | 61.78 |
| 3,4 | bDManp | 100.66 | 68.50 | 80.11 | 65.80 | 77.21 | 61.82 |
| 3 | bDGlcpA | 103.27 | 73.41 | 74.78 | 81.26 | 76.45 | ? |
| 2 | Ac | ? | 22.87 | |
| | aDGlcpN | 98.78 | 53.70 | 81.15 | 69.31 | 72.04 | 61.14 |
|
![](nmr_drawer.py?width=750&height=130&nucleus=C&rotate_labels=false&spectrum=[{"s":97.55,"l":"1","c":[0,0,225]},{"s":77.33,"l":"2","c":[0,0,225]},{"s":74.37,"l":"3","c":[0,0,225]},{"s":68.04,"l":"4","c":[0,0,225]},{"s":77.54,"l":"5","c":[0,0,225]},{"s":61.78,"l":"6","c":[0,0,225]},{"s":100.66,"l":"1","c":[230,0,30]},{"s":68.5,"l":"2","c":[230,0,30]},{"s":80.11,"l":"3","c":[230,0,30]},{"s":65.8,"l":"4","c":[230,0,30]},{"s":77.21,"l":"5","c":[230,0,30]},{"s":61.82,"l":"6","c":[230,0,30]},{"s":103.27,"l":"1","c":[0,165,0]},{"s":73.41,"l":"2","c":[0,165,0]},{"s":74.78,"l":"3","c":[0,165,0]},{"s":81.26,"l":"4","c":[0,165,0]},{"s":76.45,"l":"5","c":[0,165,0]},{"s":22.87,"l":"2","c":[0,0,0]},{"s":98.78,"l":"1","c":[120,0,225]},{"s":53.7,"l":"2","c":[120,0,225]},{"s":81.15,"l":"3","c":[120,0,225]},{"s":69.31,"l":"4","c":[120,0,225]},{"s":72.04,"l":"5","c":[120,0,225]},{"s":61.14,"l":"6","c":[120,0,225]}])
The spectrum also has 2 signals at unknown positions (not plotted). |
There is only one chemically distinct structure:
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Displayed record 1
