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Zdorovenko EL, Besarab NV, Shashkov AS, Novik GI, Shirokov AA, Burov AM, Knirel YA
Investigation of O-polysaccharides from bacterial strains of Pseudomonas genus as potential receptors of bacteriophage BIM BV-45.
International Journal of Biological Macromolecules 118 (2018)
1065-1072
Pseudomonas fluorescens BIM B-582
(Ancestor NCBI TaxID 294,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Publication DOI: 10.1016/j.ijbiomac.2018.06.165Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: zdorovenkoe
mail.ru
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049, Saratov, Russian Federation
The structure of potential bacteriophage receptors located on cell walls of Gram-negative bacteria deposited at Belarusian collection of microorganisms was investigated. Studies by 1D and 2D 1H and 13C NMR spectroscopy enabled to elucidate the structure of the O-specific polysaccharides (OPS) constituting lipopolysaccharide (LPS) of some Pseudomonas species. The capacity of bacteriophage to adsorb to LPS molecules was tested.
Pseudomonas, NMR spectroscopy, Bacteriophages, electron microscopy, Adsorption, O-polysaccharides (OPS)
Structure type: polymer chemical repeating unit
Location inside paper: p.1069
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, mild acid hydrolysis, GC, GPC, analysis of bacteriophage morphology, analysis of the bacteriophages adsorption
Related record ID(s): 12849, 13009
NCBI Taxonomy refs (TaxIDs): 294Reference(s) to other database(s): GTC:G89479ZL
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There is only one chemically distinct structure:
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Zdorovenko EL, Besarab NV, Shashkov AS, Novik GI, Shirokov AA, Burov AM, Knirel YA
Investigation of O-polysaccharides from bacterial strains of Pseudomonas genus as potential receptors of bacteriophage BIM BV-45.
International Journal of Biological Macromolecules 118 (2018)
1065-1072
|
-3)-b-D-Quip4NAc-(1-3)-a-L-Rhap2Ac-(1-3)-a-D-Quip4NAc-(1-3)-b-D-Quip4NAc-(1-3)-a-L-Rhap-(1- |
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Pseudomonas fluorescens BIM B-186
(Ancestor NCBI TaxID 294,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
The structure was elucidated in this paperPublication DOI: 10.1016/j.ijbiomac.2018.06.165Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: zdorovenkoe
mail.ru
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049, Saratov, Russian Federation
The structure of potential bacteriophage receptors located on cell walls of Gram-negative bacteria deposited at Belarusian collection of microorganisms was investigated. Studies by 1D and 2D 1H and 13C NMR spectroscopy enabled to elucidate the structure of the O-specific polysaccharides (OPS) constituting lipopolysaccharide (LPS) of some Pseudomonas species. The capacity of bacteriophage to adsorb to LPS molecules was tested.
Pseudomonas, NMR spectroscopy, Bacteriophages, electron microscopy, Adsorption, O-polysaccharides (OPS)
Structure type: polymer chemical repeating unit
Location inside paper: table 2, p.1071
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_130422,IEDB_136105,IEDB_225177,IEDB_885823
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, mild acid hydrolysis, GC, GPC, analysis of bacteriophage morphology, analysis of the bacteriophages adsorption
Related record ID(s): 12848, 13009
NCBI Taxonomy refs (TaxIDs): 294Reference(s) to other database(s): GTC:G33760XZ
Show glycosyltransferases
NMR conditions: in D2O at 333 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,3,3,3,4 Ac 175.3-175.8 23.5
3,3,3,3 bDQuip4N 103.9 76.0 80.9 56.2 72.0 18.1
3,3,3,2 Ac 174.2 21.7
3,3,3 aLRhap 99.1 72.9 79.5 72.3 70.2 18.1
3,3,4 Ac 175.3-175.8 23.5
3,3 aDQuip4N 101.0 73.9 79.0 56.3 68.1 17.9
3,4 Ac 175.3-175.8 23.5
3 bDQuip4N 105.0 74.1 82.1 57.4 72.3 18.1
aLRhap 102.0 71.6 81.2 72.2 70.3 18.2
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,3,3,3,4 Ac - 1.95-2.04
3,3,3,3 bDQuip4N 4.60 3.48 3.63 3.63 3.57 1.23
3,3,3,2 Ac - 2.14
3,3,3 aLRhap 5.16 5.26 3.98 3.64 3.69 1.32
3,3,4 Ac - 1.95-2.04
3,3 aDQuip4N 4.97 3.68 3.76 3.66 4.17 1.13
3,4 Ac - 1.95-2.04
3 bDQuip4N 4.65 3.49 3.63 3.73 3.58 1.21
aLRhap 5.17 4.20 3.83 3.60 3.65 1.29
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,3,3,3,4 Ac 23.5/1.95-2.04
3,3,3,3 bDQuip4N 103.9/4.60 76.0/3.48 80.9/3.63 56.2/3.63 72.0/3.57 18.1/1.23
3,3,3,2 Ac 21.7/2.14
3,3,3 aLRhap 99.1/5.16 72.9/5.26 79.5/3.98 72.3/3.64 70.2/3.69 18.1/1.32
3,3,4 Ac 23.5/1.95-2.04
3,3 aDQuip4N 101.0/4.97 73.9/3.68 79.0/3.76 56.3/3.66 68.1/4.17 17.9/1.13
3,4 Ac 23.5/1.95-2.04
3 bDQuip4N 105.0/4.65 74.1/3.49 82.1/3.63 57.4/3.73 72.3/3.58 18.1/1.21
aLRhap 102.0/5.17 71.6/4.20 81.2/3.83 72.2/3.60 70.3/3.65 18.2/1.29
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,3,3,3,4 | Ac |
| 1.95
2.04 | |
| 3,3,3,3 | bDQuip4N | 4.60 | 3.48 | 3.63 | 3.63 | 3.57 | 1.23 |
| 3,3,3,2 | Ac |
| 2.14 | |
| 3,3,3 | aLRhap | 5.16 | 5.26 | 3.98 | 3.64 | 3.69 | 1.32 |
| 3,3,4 | Ac |
| 1.95
2.04 | |
| 3,3 | aDQuip4N | 4.97 | 3.68 | 3.76 | 3.66 | 4.17 | 1.13 |
| 3,4 | Ac |
| 1.95
2.04 | |
| 3 | bDQuip4N | 4.65 | 3.49 | 3.63 | 3.73 | 3.58 | 1.21 |
| | aLRhap | 5.17 | 4.20 | 3.83 | 3.60 | 3.65 | 1.29 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,3,3,3,4 | Ac | 175.3
175.8 | 23.5 | |
| 3,3,3,3 | bDQuip4N | 103.9 | 76.0 | 80.9 | 56.2 | 72.0 | 18.1 |
| 3,3,3,2 | Ac | 174.2 | 21.7 | |
| 3,3,3 | aLRhap | 99.1 | 72.9 | 79.5 | 72.3 | 70.2 | 18.1 |
| 3,3,4 | Ac | 175.3
175.8 | 23.5 | |
| 3,3 | aDQuip4N | 101.0 | 73.9 | 79.0 | 56.3 | 68.1 | 17.9 |
| 3,4 | Ac | 175.3
175.8 | 23.5 | |
| 3 | bDQuip4N | 105.0 | 74.1 | 82.1 | 57.4 | 72.3 | 18.1 |
| | aLRhap | 102.0 | 71.6 | 81.2 | 72.2 | 70.3 | 18.2 |
|
There is only one chemically distinct structure:
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Zdorovenko EL, Besarab NV, Shashkov AS, Novik GI, Shirokov AA, Burov AM, Knirel YA
Investigation of O-polysaccharides from bacterial strains of Pseudomonas genus as potential receptors of bacteriophage BIM BV-45.
International Journal of Biological Macromolecules 118 (2018)
1065-1072
|
b-D-GlcpNAc-(1-4)-+
|
-3)-a-D-Rhap-(1-3)-a-D-Rhap-(1-2)-a-D-Rhap-(1-2)-a-D-Rhap-(1- |
← revised structure
Show graphically |
Pseudomonas syringae BIM B-240
(Ancestor NCBI TaxID 317,
species name lookup)
Pseudomonas wieringae
(Ancestor NCBI TaxID 286,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
The structure was elucidated in this paperPublication DOI: 10.1016/j.ijbiomac.2018.06.165Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: zdorovenkoe
mail.ru
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology, National Academy of Sciences of Belarus, 220141 Minsk, Belarus, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049, Saratov, Russian Federation
The structure of potential bacteriophage receptors located on cell walls of Gram-negative bacteria deposited at Belarusian collection of microorganisms was investigated. Studies by 1D and 2D 1H and 13C NMR spectroscopy enabled to elucidate the structure of the O-specific polysaccharides (OPS) constituting lipopolysaccharide (LPS) of some Pseudomonas species. The capacity of bacteriophage to adsorb to LPS molecules was tested.
Pseudomonas, NMR spectroscopy, Bacteriophages, electron microscopy, Adsorption, O-polysaccharides (OPS)
Structure type: polymer chemical repeating unit
Location inside paper: p.1069, table 1
The structure in this paper was incorrect:
Trivial name: D-rhamnan
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_1394181,IEDB_141807,IEDB_144827,IEDB_144829,IEDB_145005,IEDB_145006,IEDB_145008,IEDB_145010,IEDB_151531
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, mild acid hydrolysis, GC, GPC, analysis of bacteriophage morphology, analysis of the bacteriophages adsorption
Comments, role: errors in structure on p.1069
Related record ID(s): 12848, 12849
NCBI Taxonomy refs (TaxIDs): 317,
286Reference(s) to other database(s): GTC:G83557OQ, GlycomeDB:
4066
Show glycosyltransferases
NMR conditions: in D2O at 333 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
2,2,3,4,2 Ac
2,2,3,4 bDGlcpN 103.3 57.5 75.1 72.1 77.4 63.0
2,2,3 aDRhap 102.6 71.7 77.3 80.7 69.9 18.1
2,2 aDRhap 102.7 71.3 79.2 72.7 71.7 18.1
2 aDRhap 101.8 79.8 71.5 73.9 70.5 18.1
aDRhap 102.9 78.4 71.7 73.9 71.5 18.1
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
2,2,3,4,2 Ac
2,2,3,4 bDGlcpN 4.57 3.76 3.58 3.33 3.44 3.71-3.99
2,2,3 aDRhap 5.03 4.10 4.39 3.71 3.86 1.31
2,2 aDRhap 5.03 4.12 3.87 3.57 3.73 1.31
2 aDRhap 5.16 4.17 3.95 3.49 3.80 1.31
aDRhap 5.07 4.12 3.91 3.46 3.78 1.31
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
2,2,3,4,2 Ac
2,2,3,4 bDGlcpN 103.3/4.57 57.5/3.76 75.1/3.58 72.1/3.33 77.4/3.44 63.0/3.71-3.99
2,2,3 aDRhap 102.6/5.03 71.7/4.10 77.3/4.39 80.7/3.71 69.9/3.86 18.1/1.31
2,2 aDRhap 102.7/5.03 71.3/4.12 79.2/3.87 72.7/3.57 71.7/3.73 18.1/1.31
2 aDRhap 101.8/5.16 79.8/4.17 71.5/3.95 73.9/3.49 70.5/3.80 18.1/1.31
aDRhap 102.9/5.07 78.4/4.12 71.7/3.91 73.9/3.46 71.5/3.78 18.1/1.31
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 2,2,3,4,2 | Ac | |
| 2,2,3,4 | bDGlcpN | 4.57 | 3.76 | 3.58 | 3.33 | 3.44 | 3.71
3.99 |
| 2,2,3 | aDRhap | 5.03 | 4.10 | 4.39 | 3.71 | 3.86 | 1.31 |
| 2,2 | aDRhap | 5.03 | 4.12 | 3.87 | 3.57 | 3.73 | 1.31 |
| 2 | aDRhap | 5.16 | 4.17 | 3.95 | 3.49 | 3.80 | 1.31 |
| | aDRhap | 5.07 | 4.12 | 3.91 | 3.46 | 3.78 | 1.31 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 2,2,3,4,2 | Ac | |
| 2,2,3,4 | bDGlcpN | 103.3 | 57.5 | 75.1 | 72.1 | 77.4 | 63.0 |
| 2,2,3 | aDRhap | 102.6 | 71.7 | 77.3 | 80.7 | 69.9 | 18.1 |
| 2,2 | aDRhap | 102.7 | 71.3 | 79.2 | 72.7 | 71.7 | 18.1 |
| 2 | aDRhap | 101.8 | 79.8 | 71.5 | 73.9 | 70.5 | 18.1 |
| | aDRhap | 102.9 | 78.4 | 71.7 | 73.9 | 71.5 | 18.1 |
|
There is only one chemically distinct structure:
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