Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: meningitis [ICD11:
1D01 
];
pneumonia [ICD11:
CA40 ]
The structure was elucidated in this paperNCBI PubMed ID: 20539880Publication DOI: 10.1039/c004090hJournal NLM ID: 101154995Publisher: The Royal Society of Chemistry
Correspondence: annakond
gmail.com
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Russian Federation, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, Institute of Molecular Genetics, Russian Academy of Sciences, Russian Federation
We established a peculiar structure of the O-specific polysaccharide (O-antigen) of a psychrotrophic strain of Acinetobacter lwoffii, EK30A, isolated from a 1.6-1.8 million-year-old Siberian permafrost subsoil sediment sample. The polysaccharide was released by mild acid degradation of the lipopolysaccharide and studied using chemical analyses, Smith degradation, (1)H and (13)C NMR spectroscopy and mass spectrometry. It was found to contain d-homoserine, which is N-linked to 4-amino-4,6-dideoxy-d-glucose (Qui4N) and is N-acylated itself with acetyl in about half of the repeating units or (S)-3-hydroxybutanoyl group in the other half. The following is the structure of the tetrasaccharide repeating unit of the polysaccharide: →3)-β-D-Quip4NAcyl-(1→6)-α-D-Galp-(1→4)-α-D-GalpNAc-(1→3)-α-D-FucpNAc-(1→ where Acyl stands for either N-acetyl- or N-[(S)-3-hydroxybutanoyl]-d-homoseryl.
structure, O-antigen, identification, Acinetobacter lwoffii, D-homoserine
Structure type: polymer chemical repeating unit
Location inside paper: abstract, p.3575
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_141794,IEDB_144989,IEDB_151528,IEDB_190606,IEDB_885822,SB_7
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, Smith degradation, mild acid degradation
Comments, role: NMR data for D-homoserine in 50%lS3HOBut(1-2)xDHSer residue are 1H: - 4.35 1.78-1.88 3.69, 13C ? 52.6 34.5 59.2 (as specified in NMRC & NMRH); NMR data for D-homoserine in 50%Ac(1-2)xDHSer residue are 1H - 4.30 1.75-1.88 3.62, 13C ? 52.7 34.4 59.2;
Related record ID(s): 25507
NCBI Taxonomy refs (TaxIDs): 28090
Show glycosyltransferases
NMR conditions: in D2O at 303 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,4,6,4 xDHSer ? 52.6 34.5 59.2
3,4,6 bDQuip4N 103.7 74.0 78.9 58.1 72.3 17.8
3,4 aDGalp 102.3 70.0 70.4 70.4 71.0 69.8
3,2 Ac 175.4-175.9 23.6
3 aDGalpN 94.5 51.2 68.8 79.9 73.0 61.7
2 Ac 175.4-175.9 24.0
aDFucpN 98.8 48.5 74.2 68.3 68.3 16.9
3,4,6,4,2 50%Ac 175.4-175.9 23.0
3,4,6,4,2 50%lS3HOBut ? 45.9 66.5 23.5
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,4,6,4 xDHSer - 4.35 1.78-1.88 3.69
3,4,6 bDQuip4N 4.43 3.36 3.71 3.82 3.58 1.17
3,4 aDGalp 5.00 3.87 3.97 4.05-4.08 4.48 3.71-3.98
3,2 Ac - 2.07
3 aDGalpN 5.12 4.27 3.82-3.83 4.12 3.84 3.87-3.91
2 Ac - 2.06
aDFucpN 4.96-4.98 4.32 3.93 3.98 4.42 1.21
3,4,6,4,2 50%Ac - 2.03
3,4,6,4,2 50%lS3HOBut - 2.46 4.18 1.23
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,4,6,4 xDHSer 52.6/4.35 34.5/1.78-1.88 59.2/3.69
3,4,6 bDQuip4N 103.7/4.43 74.0/3.36 78.9/3.71 58.1/3.82 72.3/3.58 17.8/1.17
3,4 aDGalp 102.3/5.00 70.0/3.87 70.4/3.97 70.4/4.05-4.08 71.0/4.48 69.8/3.71-3.98
3,2 Ac 23.6/2.07
3 aDGalpN 94.5/5.12 51.2/4.27 68.8/3.82-3.83 79.9/4.12 73.0/3.84 61.7/3.87-3.91
2 Ac 24.0/2.06
aDFucpN 98.8/4.96-4.98 48.5/4.32 74.2/3.93 68.3/3.98 68.3/4.42 16.9/1.21
3,4,6,4,2 50%Ac 23.0/2.03
3,4,6,4,2 50%lS3HOBut 45.9/2.46 66.5/4.18 23.5/1.23
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,4,6,4 | xDHSer |
| 4.35 | 1.78
1.88 | 3.69 | |
| 3,4,6 | bDQuip4N | 4.43 | 3.36 | 3.71 | 3.82 | 3.58 | 1.17 |
| 3,4 | aDGalp | 5.00 | 3.87 | 3.97 | 4.05
4.08 | 4.48 | 3.71
3.98 |
| 3,2 | Ac |
| 2.07 | |
| 3 | aDGalpN | 5.12 | 4.27 | 3.82
3.83 | 4.12 | 3.84 | 3.87
3.91 |
| 2 | Ac |
| 2.06 | |
| | aDFucpN | 4.96
4.98 | 4.32 | 3.93 | 3.98 | 4.42 | 1.21 |
| 3,4,6,4,2 | 50%Ac |
| 2.03 | |
| 3,4,6,4,2 | 50%lS3HOBut |
| 2.46 | 4.18 | 1.23 | |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,4,6,4 | xDHSer | ? | 52.6 | 34.5 | 59.2 | |
| 3,4,6 | bDQuip4N | 103.7 | 74.0 | 78.9 | 58.1 | 72.3 | 17.8 |
| 3,4 | aDGalp | 102.3 | 70.0 | 70.4 | 70.4 | 71.0 | 69.8 |
| 3,2 | Ac | 175.4
175.9 | 23.6 | |
| 3 | aDGalpN | 94.5 | 51.2 | 68.8 | 79.9 | 73.0 | 61.7 |
| 2 | Ac | 175.4
175.9 | 24.0 | |
| | aDFucpN | 98.8 | 48.5 | 74.2 | 68.3 | 68.3 | 16.9 |
| 3,4,6,4,2 | 50%Ac | 175.4
175.9 | 23.0 | |
| 3,4,6,4,2 | 50%lS3HOBut | ? | 45.9 | 66.5 | 23.5 | |
|
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The spectrum also has 2 signals at unknown positions (not plotted). |
There is only one chemically distinct structure:
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