Taxonomic group: bacteria / Firmicutes
(Phylum: Firmicutes)
Associated disease: infection due to Streptococcus pneumoniae [ICD11:
XN3PW 
]
The structure was elucidated in this paperNCBI PubMed ID: 31221321Publication DOI: 10.1016/j.carbpol.2019.03.070Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: W. Zou <wei.zou
nrc-cnrc.gc.ca>
Institutions: Human Health Therapeutic Research Center, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
Pneumococcal cell wall polysaccharide (C-PS), a contaminant in pneumococcal capsular polysaccharide (Pn-PS) vaccines is degraded by mild deamination of the 4-amino-2-acetamido-2,4,6-tri-deoxy-galactose (AAT) in C-PS, which was carried out by addition of 5% aqueous sodium nitrite to a solution of polysaccharide in 5% aqueous acetic acid. Glycosidic linkage and functional groups such as O-acetates, phosphodiesters, and pyruvates were preserved under the conditions. The small fragments from degraded C-PS were removed by ultrafiltration or dialysis to provide essentially C-PS free Pn-PS. Because of the presence of AAT in its structure the deamination is not suitable for the purification of type 1 Pn-PS. Meanwhile, the mass and NMR spectroscopic analysis on the deamination products suggests that both type 1 Pn-PS and C-PS degraded following a major pathway of 5,4-hydride shift, cleavage of AAT O5-C1 bond, C1 hemiacetal formation, and its hydrolysis to release neighboring GalA- in type 1 Pn-PS and GalNAc(6-O-PCho)- in C-PS
mechanism, degradation, deamination, cell wall polysaccharide, pneumococcal capsular polysaccharide
Structure type: oligomer ; 369.0 [M-H]-
Location inside paper: p.200, p.S005, table 1
Compound class: CPS
Methods: 13C NMR, 1H NMR, gel filtration, sugar analysis, MS/MS, MS, dialysis, SEC-HPLC, ultrafiltration, mild deamination
Comments, role: major oligosaccharide was obtained by mild deamination of the type 1 pneumococcal CPS (Pn-PS)
Related record ID(s): 1070, 1938, 1939, 1940, 1942, 1943, 1944, 1945, 1946, 1947, 1948, 1949, 1950, 1951, 1952, 1953, 1954, 1955, 1956, 1957, 1958, 1959, 1960, 1961, 1962, 1963, 1964, 1965, 1966
NCBI Taxonomy refs (TaxIDs): 1313Reference(s) to other database(s): GTC:G02037ZM
Show glycosyltransferases
NMR conditions: in D2O at 298 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3 aDGalpA 97.0 68.9 70.1 71.3 72.1 180.3
aDGalpA 93.6 67.3 75.4 68.1 71.3 180.3
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3 aDGalpA 5.25 3.90 4.03 4.37 4.85 -
aDGalpA 5.34 3.94 4.05 4.58 4.70 -
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3 aDGalpA 97.0/5.25 68.9/3.90 70.1/4.03 71.3/4.37 72.1/4.85
aDGalpA 93.6/5.34 67.3/3.94 75.4/4.05 68.1/4.58 71.3/4.70
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3 | aDGalpA | 5.25 | 3.90 | 4.03 | 4.37 | 4.85 |
|
| | aDGalpA | 5.34 | 3.94 | 4.05 | 4.58 | 4.70 |
|
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3 | aDGalpA | 97.0 | 68.9 | 70.1 | 71.3 | 72.1 | 180.3 |
| | aDGalpA | 93.6 | 67.3 | 75.4 | 68.1 | 71.3 | 180.3 |
|
There is only one chemically distinct structure:
Found 
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