CSDB: Search results

Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)

NCBI PubMed ID: 21954138
Publication DOI: 10.1002/pmic.201100300
Journal NLM ID: 101092707
Publisher: Wiley-VCH
Correspondence: david.harvey

bioch.ox.ac.uk
Institutions: Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX, UK

This Viewpoint article addresses comments made on our original article describing a symbolic system for the depiction of N- and O-linked carbohydrate structures and proposes a method for extending the symbol set to include monosaccharides commonly found in carbohydrates present in bacteria and plants. As before, basic monosaccharides are shown by shape with one or more additions such as solid fill or additions of lines, crosses or dots to represent functional groups. The use of colour to differentiate constituent monosaccharides is avoided, thus enabling the system to be used in a variety of formats. Linkage and anomericity are shown by the angle and type of line connecting the symbols. In this extended version, new symbols are proposed for additional hexoses and it is proposed that pyranose and furanose forms of the monosaccharides could be shown by solid or broken outlines to the symbols. Conventions for depicting the presence of multiple functional groups such as deoxy-(NH(2))(2) are also discussed. It is hoped that these proposals will stimulate discussion so that a consensus can be reached as to how the glycobiology community can best convey complex information in a simple manner.

carbohydrates, structure, linkage, Glycoproteomics, Symbols

Structure type: oligomer
Location inside paper: p.4294, fig.1
Compound class: core oligosaccharide with O-unit
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130422,IEDB_130650,IEDB_130659,IEDB_130667,IEDB_135394,IEDB_136105,IEDB_137340,IEDB_137473,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_189517,IEDB_2189047,IEDB_225177,IEDB_885823,IEDB_983931,SB_192

Methods: rules for constructing symbols
Comments, role: adapted structure from ref. [8] (Knirel et al., J. Endotoxin Res. 2006, 12, 324–336).

NCBI Taxonomy refs (TaxIDs): 287
Show glycosyltransferases

There is only one chemically distinct structure:

CCCCCCCCCC[C@H](O)C(=O)O[C@H](CCCCCCCCC)CC(=O)N[C@H]1[C@@H](OP(=O)(O)O)O[C@H](CO[C@@H]2O[C@H](CO[C@]3(C(=O)O)C[C@@H](O[C@]4(C(=O)O)C[C@@H](O)[C@@H](O)[C@@H]([C@H](O)CO)O4)[C@@H](O[C@H]4O[C@H]([C@@H](O)CO)[C@@H](OP(=O)(O)O)[C@H](O[C@H]5O[C@H]([C@H](CNC(=O)O)OP(=O)(O)O)[C@@H](O)[C@H](O[C@H]6O[C@H](CO)[C@H](O[C@H]7O[C@H](CO)[C@@H](O)[C@H](O)[C@H]7O)[C@H](O[C@@H]7O[C@H](CO[C@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@H]8O)[C@@H](O)[C@H](O[C@@H]8O[C@@H](C)[C@H](O)[C@@H](O[C@@H]9O[C@H](C)[C@@H](O)[C@H](O[C@@H]%10O[C@@H](C(=O)O)[C@@H](O[C@@H]%11O[C@@H](C)[C@H](O)[C@@H](O)[C@H]%11OC(C)=O)[C@@H](O)[C@@H]%10NC(C)=O)[C@H]9NC(C)=O)[C@H]8O)[C@H]7O)[C@H]6NC(=O)[C@H](C)N)[C@@H]5O)[C@@H]4OP(=O)(O)OP(=O)(O)OCCN)[C@@H]([C@H](O)CO)O3)[C@@H](OP(=O)(O)O)[C@H](OC(=O)C[C@H](O)CCCCCCC)[C@H]2NC(=O)C[C@@H](CCCCCCCCC)OC(=O)[C@@H](O)CCCCCCCCCC)[C@@H](O)[C@@H]1OC(=O)C[C@H](O)CCCCCCC

SVG MW SMILES 3D mol Ionize