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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Associated disease: infection due to Escherichia coli [ICD11: XN6P4

]

The structure was elucidated in this paper
NCBI PubMed ID: 12124846
Journal NLM ID: 0372525
Publisher: Wiley Interscience
Correspondence: G. Widmalm <gw

organ.su.se>
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden

Conformational studies have been performed of a pentasaccharide derived from the O-polysaccharide from Escherichia coli O142. The polymer was selectively degraded by anhydrous hydrogen fluoride and reduced to yield an oligosaccharide model of its repeating unit, which in the branching region consists of four aminosugars. A comparison of (1)H and (13)C chemical shifts between the pentasaccharide and the polymer showed only minor differences, except where the cleavage had taken place, indicating that the oligomer is a good model of the repeating unit. Langevin dynamics and molecular dynamics simulations with explicit water molecules were carried out to sample the conformational space of the pentasaccharide. For the glycosidic linkages between the hexopyranoside residues, small but significant changes were observed between the simulation techniques. One-dimensional (1D) (1)H,(1)H double pulsed field gradient spin echo (DPFGSE) transverse rotating- frame Overhauser effect spectroscopy (T-ROESY) experiments were performed, and homonuclear cross-relaxation rates were obtained. Subsequently, a comparison of interproton distances from NMR experiment and the two simulation approaches showed that in all cases the use of explicit water in the simulations resulted in better agreement. Hydrogen-bond analysis of the trajectories from the molecular dynamics simulation revealed interresidue interactions to be important as a cluster of different hydrogen bonds and as a distinct highly populated hydrogen bond. NMR data are consistent with the presence of hydrogen bonding within the model of the repeating unit

NMR, oligosaccharide, structure, chemistry, polysaccharide, O-antigen, repeating unit, analysis, O antigen, hydrogen, hydrogen bond, molecular, molecule, polymer, water, Escherichia, Escherichia coli, glycosidic linkage, conformational, dynamics, molecular dynamics, NMR spectroscopy, cluster, O-polysaccharide, O polysaccharide, linkage, chemical, region, reduced, spectroscopy, interaction, difference, pentasaccharide, comparison, solution, case, change, simulation, effect, Overhauser effect, organic, model, use, cleavage, approach, chemical shift, chemical shifts, distance, Hydrogen Bonding, hydrogen fluoride, Langevin dynamics, rotating frame, shift

Structure type: suggested polymer biological repeating unit
Location inside paper: fig.1
Trivial name: O-polysaccharide
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_1391965,IEDB_141582,IEDB_141584,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_423113,IEDB_885822,IEDB_885823

Methods: NMR-2D, NMR, MS, MD simulations, solvolysis
Comments, role: biological repeat frame was based on GT homology analysis; chemical repeat frame is different in the paper
3D data: 3D data

Related record ID(s): 3110, 3209, 20685, 30056
NCBI Taxonomy refs (TaxIDs): 562
Reference(s) to other database(s): GTC:G40436AU, GlycomeDB:28126
Show glycosyltransferases

There is only one chemically distinct structure:

*O[C@H]1[C@H](OC[C@H]2O[C@H](O[C@@H]3[C@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4NC(C)=O)[C@@H](NC(C)=O)[C@@H](O[C@H]4[C@@H](O)[C@@H](CO)O[C@H](*)[C@@H]4NC(C)=O)O[C@@H]3CO)[C@H](NC(C)=O)[C@@H](O)[C@H]2O)O[C@@H](C)[C@H](O)[C@H]1O

SVG MW SMILES 3D mol Ionize