Taxonomic group: bacteria / Firmicutes
(Phylum: Firmicutes)
Host organism: Homo sapiens
Associated disease: pneumonia [ICD11:
CA40 
];
infection due to Streptococcus pneumoniae [ICD11:
XN3PW ]
The structure was elucidated in this paperNCBI PubMed ID: 29715685Publication DOI: 10.1016/j.carres.2018.04.011Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: jduus
kemi.dtu.dk
Institutions: Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark, SSI Diagnostica A/S, Hilleroed, Denmark, Respiratory and Vaccine Preventable Bacterial Reference Unit, Public Health England - National Infection Service, Colindale, London, UK
Streptococcus pneumoniae is characterised into 92 serotypes based on antigenic reactions of commercial rabbit sera to the capsular polysaccharides. During development of a bioinformatic serotyping tool (PneumoCaT), an isolate exhibited a novel codon at residue 385 of the glycosyltransferase gene wcwK encoding a distinct amino acid, which differentiates genogroup 7. Investigation by repeat serotyping and Quellung reaction revealed a novel pattern of factor sera with the isolate reacting very strongly with 7f, but also with 7e factor sera. The structure of the capsular polysaccharide was determined by NMR spectroscopy to be an approximately 5:1 combination of the structures of 7C and 7B, respectively, and the structure of 7C was also elucidated. All data from whole genome sequencing, NMR spectroscopy, production of antisera and serotyping of the novel 7 strain shows that it is a new serotype, which will be named in the Danish nomenclature as 7D.
Streptococcus pneumoniae, NMR spectroscopy, structure elucidation, Hybrid serotype, Whole genome sequence
Structure type: polymer chemical repeating unit
Location inside paper: p.25, fig.1, table S3, 7A
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_136105,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983931,SB_192,SB_7
Methods: 13C NMR, 1H NMR, DNA sequencing, 31P NMR, bioinformatic analysis, serotyping, DNA extraction
Related record ID(s): 12636, 12638, 12639, 12924
NCBI Taxonomy refs (TaxIDs): 1313Reference(s) to other database(s): GTC:G60134AP, GlycomeDB:
16860
Show glycosyltransferases
NMR conditions: in D2O at 313 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,4,3 aDGalp 95.57 68.46 69.79 69.14 74.14 68.18
3,4,2 Ac 174.21 22.82
3,4 bLRhap 99.98 69.04 75.26 71.57 72.99 17.70
3 bDGlcp 105.56 73.72 76.17 78.12 75.12 61.77
2 Ac 175.40 23.10
4,2,2 Ac 174.46 22.86
4,2 aDGlcpN 94.30 54.30 71.33 70.35 72.50 60.70
4 aLRhap 99.03 74.14 69.99 72.35 70.41 17.46
bDGalpN 102.20 52.20 80.99 78.18 75.38 61.96
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,4,3 aDGalp 5.022 3.781 3.850 3.952 4.199 3.663-3.997
3,4,2 Ac - 2.159
3,4 bLRhap 5.055 5.637 3.826 3.485 3.568 1.404
3 bDGlcp 4.400 3.423 3.520 3.561 3.390 3.652-3.891
2 Ac - 2.078
4,2,2 Ac - 2.049
4,2 aDGlcpN 5.009 3.918 3.835 3.538 3.921 3.826
4 aLRhap 5.149 4.199 3.973 3.587 3.807 1.324
bDGalpN 4.497 3.967 3.859 4.199 3.735 3.763
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,4,3 aDGalp 95.57/5.022 68.46/3.781 69.79/3.850 69.14/3.952 74.14/4.199 68.18/3.663-3.997
3,4,2 Ac 22.82/2.159
3,4 bLRhap 99.98/5.055 69.04/5.637 75.26/3.826 71.57/3.485 72.99/3.568 17.70/1.404
3 bDGlcp 105.56/4.400 73.72/3.423 76.17/3.520 78.12/3.561 75.12/3.390 61.77/3.652-3.891
2 Ac 23.10/2.078
4,2,2 Ac 22.86/2.049
4,2 aDGlcpN 94.30/5.009 54.30/3.918 71.33/3.835 70.35/3.538 72.50/3.921 60.70/3.826
4 aLRhap 99.03/5.149 74.14/4.199 69.99/3.973 72.35/3.587 70.41/3.807 17.46/1.324
bDGalpN 102.20/4.497 52.20/3.967 80.99/3.859 78.18/4.199 75.38/3.735 61.96/3.763
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,4,3 | aDGalp | 5.022 | 3.781 | 3.850 | 3.952 | 4.199 | 3.663
3.997 |
| 3,4,2 | Ac |
| 2.159 | |
| 3,4 | bLRhap | 5.055 | 5.637 | 3.826 | 3.485 | 3.568 | 1.404 |
| 3 | bDGlcp | 4.400 | 3.423 | 3.520 | 3.561 | 3.390 | 3.652
3.891 |
| 2 | Ac |
| 2.078 | |
| 4,2,2 | Ac |
| 2.049 | |
| 4,2 | aDGlcpN | 5.009 | 3.918 | 3.835 | 3.538 | 3.921 | 3.826 |
| 4 | aLRhap | 5.149 | 4.199 | 3.973 | 3.587 | 3.807 | 1.324 |
| | bDGalpN | 4.497 | 3.967 | 3.859 | 4.199 | 3.735 | 3.763 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,4,3 | aDGalp | 95.57 | 68.46 | 69.79 | 69.14 | 74.14 | 68.18 |
| 3,4,2 | Ac | 174.21 | 22.82 | |
| 3,4 | bLRhap | 99.98 | 69.04 | 75.26 | 71.57 | 72.99 | 17.70 |
| 3 | bDGlcp | 105.56 | 73.72 | 76.17 | 78.12 | 75.12 | 61.77 |
| 2 | Ac | 175.40 | 23.10 | |
| 4,2,2 | Ac | 174.46 | 22.86 | |
| 4,2 | aDGlcpN | 94.30 | 54.30 | 71.33 | 70.35 | 72.50 | 60.70 |
| 4 | aLRhap | 99.03 | 74.14 | 69.99 | 72.35 | 70.41 | 17.46 |
| | bDGalpN | 102.20 | 52.20 | 80.99 | 78.18 | 75.38 | 61.96 |
|
There is only one chemically distinct structure:
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