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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide

• Article ID: 1778
  Knirel YA, Kochetkov NK "The structure of lipopolysaccharides of gram-negative bacteria. III. The structure of O-antigens: A review" - Biochemistry (Moscow) 59(12) (1994) 1325-1383
  

  This review summarizes data on the composition and structure of the O-antigens, the polysaccharide chains of the outer-membrane lipopolysaccharides (LPS) of Gram-negative bacteria defining the immunospecificity of these microbial cells. Special reference is given to some structural features of the O-antigens, such as the presence of unique monosaccharides and noncarbohydrate components, masked regularity, and the occurrence in one microorganism of LPS with structurally different polysaccharide chains. Antigenic relationships between microorganisms belonging to different taxonomic groups are discussed.

  structure, O-antigen, chemical composition, bacterial lipopolysaccharides, Salmonella livingstone C1

  NCBI PubMed ID: 7533007
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Pseudomonas aeruginosa O12
  CSDB ID 108470 (all data & tools)
• Article ID: 2402
  Knirel YA, Vinogradov EV, Shashkov AS, Dmitriev BA, Kochetkov NK, Stanislavsky ES, Mashilova GM "Somatic antigens of Pseudomonas aeruginosa. The structure of the O-specific polysaccharide chain of the lipopolysaccharide from P. aeruginosa O13 (Lányi)" - European Journal of Biochemistry 163 (1987) 627-637
  

  The O-specific polysaccharide, obtained on mild acid degradation of lipopolysaccharide of Pseudomonas aeruginosa O13 (Lányi classification), is built up of trisaccharide repeating units involving 2-acetamidino-2,6-dideoxy-D-glucose (N-acetyl-D-quinovosamine, D-QuiNAc), 2-acetamidino-2,6-dideoxy-L-galactose (L-fucosacetamidine, L-FucAm), and a new sialic-acid-like sugar, 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-L-galacto-nonulosonic acid (Sug), and thus contains simultaneously both acidic and basic functions. Cleavage of the polysaccharide with hydrogen fluoride in methanol revealed the high stability of the glycosidic linkage of the ulosonic acid and afforded methyl glycosides of a disaccharide and a trisaccharide. The structures of the new ulosonic acid and acetamidino group were established by analysing the oligosaccharide fragments by 1H, 13C nuclear magnetic resonance spectrometry, as well as on the basis of their chemical conversions: alkaline hydrolysis of the acetamidino group into acetamido group, reductive deamination with lithium borohydride into the ethylamino group and acetylation with acetic anhydride in pyridine accompanied by intramolecular acylation of the acetamidino function by the ulosonic acid to form a six-membered lactam ring. Identification of the oligosaccharide fragments and comparative analysis of the 13C nuclear magnetic resonance spectra of the oligosaccharides and polysaccharide revealed the following structure of the repeating unit: →3)D-QuiNAcp(α1→3)Sugp(α2→3)L-FucAmp(α1→.

  NCBI PubMed ID: 3104040
  Publication DOI: 10.1111/j.1432-1033.1987.tb10912.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Methods: 13C NMR
  
   
  
  Pseudomonas aeruginosa O13, Pseudomonas aeruginosa Lányi
  CSDB ID 123023 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudomonas aeruginosa O13
  CSDB ID 1443 (all data & tools)
• Article ID: 6301
  Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" - Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
  

  Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.

  chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal

  NCBI PubMed ID: 35750381
  Publication DOI: 10.1016/S1875-5364(22)60177-8
  Journal NLM ID: 101504416
  Publisher: Beijing: Science Press; Elsevier
  Correspondence: J. Yin
  Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
  
   
  
  Pseudomonas aeruginosa O13
  CSDB ID 9105 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 1778
  Knirel YA, Kochetkov NK "The structure of lipopolysaccharides of gram-negative bacteria. III. The structure of O-antigens: A review" - Biochemistry (Moscow) 59(12) (1994) 1325-1383
  

  This review summarizes data on the composition and structure of the O-antigens, the polysaccharide chains of the outer-membrane lipopolysaccharides (LPS) of Gram-negative bacteria defining the immunospecificity of these microbial cells. Special reference is given to some structural features of the O-antigens, such as the presence of unique monosaccharides and noncarbohydrate components, masked regularity, and the occurrence in one microorganism of LPS with structurally different polysaccharide chains. Antigenic relationships between microorganisms belonging to different taxonomic groups are discussed.

  structure, O-antigen, chemical composition, bacterial lipopolysaccharides, Salmonella livingstone C1

  NCBI PubMed ID: 7533007
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Salmonella arizonae O61
  CSDB ID 108596 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide, O-antigen

• Article ID: 1831
  Knirel YA, Vinogradov EV, Shashkov AS, Dmitriev BA, Kochetkov NK "Structure of Pseudomonas aeruginosa O13 O-specific polysaccharide containing 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-L-galacto-nonulosonic acid and 2-acetamidino-2,6-dideoxy-L-galactose" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 12 (1986) 848-851
  

  O-Specific polysaccharide chain of P. aeruginosa 013 (Lányi) lipopolysaccharide is composed of N-acetyl-D-quinovosamine (QuiNAc), acetamidino derivative of L-fucosamine (FucNAm), and 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-L-galacto-nonulosonic acid (Sug). On solvolysis with HF in methanol, the polysaccharide afforded methylglycosides of a disaccharide and a trisaccharide both containing fucosamine and ulosonic acid derivatives. Chemical transformations (alkaline hydrolysis, reductive deamination, acetylation accompanied by intramolecular acylation of acetamidino group by ulosonic acid), 1H and 13C NMR analysis and mass spectral data proved the following structure of the trisaccharide unit of the polysaccharide: -8)-β-Sug-(1-3)-α-L-FucNAm-(1-3)-α-D-QuiNAc -(1-

  NCBI PubMed ID: 2430578
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: 13C NMR
  
   
  
  Pseudomonas aeruginosa 13, Pseudomonas aeruginosa Lanyi
  CSDB ID 110525 (all data & tools)
• Article ID: 2213
  Vinogradov EV, Shashkov AS, Knirel YA, Kochetkov NK, Dabrowski J, Grosskurth H, Stanislavsky ES, Kholodkova EV "The structure of the O-specific polysaccharide chain of the lipopolysaccharide of Salmonella arizonae O61" - Carbohydrate Research 231 (1992) 1-11
  

  The O-specific polysaccharide was obtained by mild degradation of the Salmonella arizonae O61 lipopolysaccharide with acid. It contained 2-acetamido-2-deoxy-D-glucose, 2-acetamidino-2,6-dideoxy-L-galactose (FucAm), and 7-acetamido-3,5,7,9-tetradeoxy-5-[(R)-3-hydroxybutyramido]-D- glycero-L-galacto-nonulosonic acid (Sug). On the basis of partial acid hydrolysis with 0.1 M HCl, solvolysis with anhydrous HF in methanol, and 1H- and 13C-NMR analysis (including 1H/13C inversely correlated spectroscopy for localisation of N-acyl substituents), it was concluded that the O-specific polysaccharide had the following structure. →3)-α-L-FucAm-(1→3)-α-D-GlcNAc-(1→8)-β-Sug-(2→. The O-antigen of S. arizonae O61 is structurally related to that of Pseudomonas aeruginosa O12, thus explaining the known serological cross-reactivity between these micro-organisms.

  NCBI PubMed ID: 1394306
  Publication DOI: 10.1016/0008-6215(92)84002-A
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Max Planck Institute for Medical Research, Heidelberg Germany, I.I. Mechnikov Institute of Vaccines and Sera, Moscow Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, partial acid hydrolysis, HF solvolysis, sugar analysis, acid hydrolysis, GPC
  
   
  
  Pseudomonas aeruginosa O12
  CSDB ID 2668 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide, O-antigen

• Article ID: 1843
  Elkin YN, Knirel YA, Vinogradov EV, Paramonov NA, Troshkov ML, Aminev "Fast-atom-bombardment mass-spectra of aminooligosaccharides" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 12 (1986) 1658-1661
  
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: FAB-MS
  
   
  
  Pseudomonas aeruginosa
  CSDB ID 110587 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudomonas aeruginosa O13
  CSDB ID 1444 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide, O-antigen

• Article ID: 1843
  Elkin YN, Knirel YA, Vinogradov EV, Paramonov NA, Troshkov ML, Aminev "Fast-atom-bombardment mass-spectra of aminooligosaccharides" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 12 (1986) 1658-1661
  
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: FAB-MS
  
   
  
  Pseudomonas aeruginosa
  CSDB ID 110588 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudomonas aeruginosa O13
  CSDB ID 1445 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136095,IEDB_137340,IEDB_137472,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_190606,IEDB_983931,SB_192

• Article ID: 2812
  Knirel YA "New sialic acid-like sugars: components of bacterial lipopolysaccharides" - Proceedings of Sialic acids 1998: Japanese-German Symposium on Sialic Acids (1st : 1988 : Berlin) (1988) 160-161
  
  Book NLM ID: 9012728
  Publisher: Kiel: Kieler Verlag Wissenschaft + Bildung
  Editors: Schauer R, Yamakawa T
  
   
  
  Shigella boydii 7
  CSDB ID 148517 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen

• Article ID: 2812
  Knirel YA "New sialic acid-like sugars: components of bacterial lipopolysaccharides" - Proceedings of Sialic acids 1998: Japanese-German Symposium on Sialic Acids (1st : 1988 : Berlin) (1988) 160-161
  
  Book NLM ID: 9012728
  Publisher: Kiel: Kieler Verlag Wissenschaft + Bildung
  Editors: Schauer R, Yamakawa T
  
   
  
  Pseudomonas aeruginosa O13
  CSDB ID 148514 (all data & tools)