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 2, 7B
Trivial name: poly(glycosyl phosphate)
Compound class: CPS
Contained glycoepitopes: IEDB_133754,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_145002,IEDB_146664,IEDB_149136,IEDB_151531,IEDB_225177,IEDB_885823,IEDB_983931,SB_192
Methods: 13C NMR, 1H NMR, DNA sequencing, 31P NMR, bioinformatic analysis, serotyping, DNA extraction
Comments, role: novel variant: Streptococcus pneumoniae 7D; the structure of the CPS was determined to be an approximately 5:1 combination of the structures of 7C and 7B, respectively (see ID 12639).
Related record ID(s): 12636, 12637, 12639, 12924
NCBI Taxonomy refs (TaxIDs): 1313Reference(s) to other database(s): GTC:G97384WN, GlycomeDB:
34748
Show glycosyltransferases
NMR conditions: in D2O at 313 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
0,4,4,2,2,2 Ac 174.96 22.56
0,4,4,2,2 aDGlcpN 95.56 54.35 71.11 70.13 71.67 64.99
0,4,4,2 aLRhap 99.42 76.98 69.96 72.53 69.53 17.47
0,4,4 bLRhap 101.24 77.87 73.90 72.64 73.14 17.54
0,4 bDGlcp 102.00 74.05 76.59 79.54 76.01 62.61
0,3,4 bDRibf 108.85 75.61 71.61 83.10 63.89
0,3 aLRhap 100.89 71.17 71.28 79.64 67.50 17.61
0 aDGlcp 95.95 73.26 75.29 72.81 72.86 59.90
P
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
0,4,4,2,2,2 Ac - 2.048
0,4,4,2,2 aDGlcpN 4.968 3.933 3.804 3.596 4.145 4.119-4.188
0,4,4,2 aLRhap 5.046 4.087 3.967 3.506 4.062 1.331
0,4,4 bLRhap 4.881 4.130 3.657 3.385 3.421 1.330
0,4 bDGlcp 4.473 3.237 3.586 3.292 3.433 3.687-4.066
0,3,4 bDRibf 5.330 4.062 4.146 4.022 3.699-3.837
0,3 aLRhap 5.222 3.999 3.989 3.524 4.401 1.290
0 aDGlcp 5.493 3.746 4.003 3.869 3.967 3.893
P
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
0,4,4,2,2,2 Ac 22.56/2.048
0,4,4,2,2 aDGlcpN 95.56/4.968 54.35/3.933 71.11/3.804 70.13/3.596 71.67/4.145 64.99/4.119-4.188
0,4,4,2 aLRhap 99.42/5.046 76.98/4.087 69.96/3.967 72.53/3.506 69.53/4.062 17.47/1.331
0,4,4 bLRhap 101.24/4.881 77.87/4.130 73.90/3.657 72.64/3.385 73.14/3.421 17.54/1.330
0,4 bDGlcp 102.00/4.473 74.05/3.237 76.59/3.586 79.54/3.292 76.01/3.433 62.61/3.687-4.066
0,3,4 bDRibf 108.85/5.330 75.61/4.062 71.61/4.146 83.10/4.022 63.89/3.699-3.837
0,3 aLRhap 100.89/5.222 71.17/3.999 71.28/3.989 79.64/3.524 67.50/4.401 17.61/1.290
0 aDGlcp 95.95/5.493 73.26/3.746 75.29/4.003 72.81/3.869 72.86/3.967 59.90/3.893
P
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 0,4,4,2,2,2 | Ac |
| 2.048 | |
| 0,4,4,2,2 | aDGlcpN | 4.968 | 3.933 | 3.804 | 3.596 | 4.145 | 4.119
4.188 |
| 0,4,4,2 | aLRhap | 5.046 | 4.087 | 3.967 | 3.506 | 4.062 | 1.331 |
| 0,4,4 | bLRhap | 4.881 | 4.130 | 3.657 | 3.385 | 3.421 | 1.330 |
| 0,4 | bDGlcp | 4.473 | 3.237 | 3.586 | 3.292 | 3.433 | 3.687
4.066 |
| 0,3,4 | bDRibf | 5.330 | 4.062 | 4.146 | 4.022 | 3.699
3.837 | |
| 0,3 | aLRhap | 5.222 | 3.999 | 3.989 | 3.524 | 4.401 | 1.290 |
| 0 | aDGlcp | 5.493 | 3.746 | 4.003 | 3.869 | 3.967 | 3.893 |
| | P | |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 0,4,4,2,2,2 | Ac | 174.96 | 22.56 | |
| 0,4,4,2,2 | aDGlcpN | 95.56 | 54.35 | 71.11 | 70.13 | 71.67 | 64.99 |
| 0,4,4,2 | aLRhap | 99.42 | 76.98 | 69.96 | 72.53 | 69.53 | 17.47 |
| 0,4,4 | bLRhap | 101.24 | 77.87 | 73.90 | 72.64 | 73.14 | 17.54 |
| 0,4 | bDGlcp | 102.00 | 74.05 | 76.59 | 79.54 | 76.01 | 62.61 |
| 0,3,4 | bDRibf | 108.85 | 75.61 | 71.61 | 83.10 | 63.89 | |
| 0,3 | aLRhap | 100.89 | 71.17 | 71.28 | 79.64 | 67.50 | 17.61 |
| 0 | aDGlcp | 95.95 | 73.26 | 75.29 | 72.81 | 72.86 | 59.90 |
| | P | |
|
There is only one chemically distinct structure:
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Found 1 record.
Displayed record 1
