Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_135610,IEDB_135813,IEDB_136105,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_885823,SB_7

• Article ID: 43
  Deng LY, Kasper DL, Krick TP, Wessels MR "Characterization of the linkage between the type III capsular polysaccharide and the bacterial cell wall of group B Streptococcus" - Journal of Biological Chemistry 275(11) (2000) 7497-7504
  

  The capsular polysaccharide of group B Streptococcus is a key virulence factor and an important target for protective immune responses. Until now, the nature of the attachment between the capsular polysaccharide and the bacterial cell has been poorly defined. We isolated insoluble cell wall fragments from lysates of type III group B Streptococcus and showed that the complexes contained both capsular polysaccharide and group B carbohydrate covalently bound to peptidoglycan. Treatment with the endo-N-acetylmuramidase mutanolysin released soluble complexes of capsular polysaccharide linked to group B carbohydrate by peptidoglycan fragments. Capsular polysaccharide could be enzymatically cleaved from group B carbohydrate by treatment of the soluble complexes with β-N-acetylglucosaminidase, which catalyzes hydrolysis of the β-D-GlcNAc(1→4)β-D-MurNAc subunit produced by mutanolysin digestion of peptidoglycan. Evidence from gas chromatography/mass spectrometry and (31)P NMR analysis of the separated polysaccharides supports a model of the group B Streptococcus cell surface in which the group B carbohydrate and the capsular polysaccharide are independently linked to the glycan backbone of cell wall peptidoglycan; group B carbohydrate is linked to N-acetylmuramic acid, and capsular polysaccharide is linked via a phosphodiester bond and an oligosaccharide linker to N-acetylglucosamine

  polysaccharide, Streptococcus, capsular polysaccharide, type, group B Streptococcus, cell wall, linkage

  NCBI PubMed ID: 10713053
  Publication DOI: 10.1074/jbc.275.11.7497
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: mwessels@channing.harvard.edu
  Institutions: Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
  Methods: enzymatic degradation
  
   
  
  Streptococcus sp. B III
  CSDB ID 2104 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885813,IEDB_885823

• Article ID: 279
  Kaji E, Anabuki N, Zen S "Syntheses of three interglycosidic isomers of N-acetyl-b-D-mannosaminyl-L-rhamnoses associated with O-antigens of several gram-negative opportunistic pathogens" - Chemical and Pharmaceutical Bulletin 43 (1995) 1441-1447
  

  We achieved practical, highly stereoselective syntheses of three interglycosidic isomers of N-acetyl-β-D-mannosaminyl-L-rhamnoses, among which a β(1→4)-isomer corresponds to the repeating unit of the O-antigen of lipopolysaccharide (LPS) from the opportunistic pathogens Pseudomonas cepacia O5 and Pseudomonas aeruginosa X (Meitert). The other isomers are a β(1→2)-disaccharide, a constituent of LPS from Escherichia coli O1A, and an artificial β(1→3)-isomer. The disaccharides were obtained by simple three-step reaction sequences from 2-(benzoyloxyimino)-2-deoxyglycosyl halides (mannosamine progenitor). β-Selective glycosylations of appropriately protected L-rhamnosyl acceptors were performed. Subsequent reduction of the 2-acyloxyimino function to an amino group, N-acetylation, and removal of the protecting groups provided the target disaccharides. 13C NMR and nuclear Overhauser effect spectra proved to be useful for structural determination of the positional isomers of the disaccharides.

  Lipopolysaccharide, O-antigen, Gram-negative bacteria, 2-amino-2-deoxy-D-mannose, β-3-D-mannosaminyl-L-rhamnose, 2-uiose oxime, opportunistic infection

  NCBI PubMed ID: 7586068
  Journal NLM ID: 0377775
  Publisher: Pharmaceutical Society Of Japan
  Institutions: School of Pharmaceutical Sciences, Kiiasaw University, Shirokane 5-9-1, Minato-ku, Tokyo IDS, Japan, School of Pharmaceutical Sciences, Kiiasaw University, Shirokane 5-9-1, Minato-ku, Tokyo IDS, Japan.
  
   
  
  Escherichia coli O1A
  CSDB ID 7222 (all data & tools)
• Article ID: 1777
  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
  
   
  
  Escherichia coli O1A
  CSDB ID 108682 (all data & tools)
• Article ID: 1887
  Nifant'ev NE, Shashkov AS, Lipkind GM, Kochetkov NK, Jann B, Jann K "Computer-assisted structural analysis of the Escherichia coli O1A, O1B, and O1C specific polysaccharides" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 19(10) (1993) 981-988
  

  A computer evaluation of 13C-NMR data for the title polysaccharides based on the monosaccharide and methylation analysis data led to the structure of the repeating unit of the O1A polysaccharide as well as to several probable structures of the O1C polysaccharide, of which the correct one was inferred by means of a single NOE experiment. The analysis of the spectrum of the O1B polysaccharide was unsuccessful, due to the presence in its structure of the fragment α-L-Rha-(1→2)-α-D-Gal-(1→3)-D-GlcNAc with the terminal (1→2)-linkage, whose spectral data could not be calculated by additive schemes using only glycosylation effects. However in reevaluation of the O1B spectral data by taking into account the deviations from additivities of the chemical shifts values in spectra of the related trisaccharides, to reveal the most probable structure of the O1B's repeating unit. [formula: see text]

  NCBI PubMed ID: 7506030
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow
  Methods: 13C NMR
  
   
  
  Escherichia coli O1A
  CSDB ID 110886 (all data & tools)
• Article ID: 1936
  Jann B, Shashkov AS, Gupta DS, Panasenko SM, Jann K "The O1 antigen of Escherichia coli: structural characterization of the O1A1-specific polysaccharide" - Carbohydrate Polymers 18(1) (1992) 51-57
  

  The O-specific polysaccharide moiety of the O1A1 antigen (lipopolysaccharide) from E. coli 01:K1 consists of L-rhamnose, N-acetyl-d-glucosamine and N-acetyl-d-mannosamine in the molar ratio of 3:1:1. By using fragmentation procedures, methylation analysis, and NMR spectroscopy, the O1A1 polysaccharide was found to have the structure [formula: see text].

  Publication DOI: 10.1016/0144-8617(92)90187-U
  Journal NLM ID: 8307156
  Publisher: Elsevier
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Max-Planck-Institut für Immunbiologie, D-7800 Freiburg, FRG
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, sugar analysis, Smith degradation, de-N-acetylation/deamination, periodate oxidation
  
   
  
  Escherichia coli O1A1
  CSDB ID 112956 (all data & tools)
• Article ID: 2184
  Baumann H, Jansson PE, Kenne L, Widmalm G "Structural studies of the Escherichia coli O1A O-polysaccharide, using the computer program CASPER" - Carbohydrate Research 211 (1991) 183-190
  

  no abstract available

  NCBI PubMed ID: 1773429
  Publication DOI: 10.1016/0008-6215(91)84159-c
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Sweden
  
   
  
  Escherichia coli O1A
  CSDB ID 116148 (all data & tools)
• Article ID: 3196
  Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" - FEMS Microbiology Reviews 30(3) (2006) 382-403
  

  Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/

  NMR, structure, serotype, O-antigen, Enterobacteriacea, database

  NCBI PubMed ID: 16594963
  Publication DOI: 10.1111/j.1574-6976.2006.00016.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: andrej.weintraub@ki.se
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  
   
  
  Escherichia coli O1A, Escherichia coli O1A1
  CSDB ID 20630 (all data & tools)
• Article ID: 5188
  Micoli F, Costantino P, Adamo R "Potential targets for next generation anti-microbial glycoconjugate vaccines" - FEMS Microbiology Reviews 42(3) (2018) 388-423
  

  Cell surface carbohydrates have been proven optimal targets for vaccine development. Conjugation of polysaccharides to a carrier protein triggers a T-cell dependent immune response to the glycan moiety. Licensed glycoconjugate vaccines are produced by chemical conjugation of capsular polysaccharides to prevent meningitis caused by meningococcus, pneumococcus and Haemophilus influenzae type b. However, other classes of carbohydrates (O-antigens, exopolysaccharides, wall/teichoic acids) represent attractive targets for developing vaccines.Recent analysis from WHO/CHO underpins alarming concern towards antibiotic resistant bacteria, such as the so called ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) and additional pathogens such as Clostridium difficile and Group A Streptococcus. Fungal infections are also becoming increasingly invasive for immunocompromised patients or hospitalized individuals. Other emergencies could derive from bacteria which spread during environmental calamities (Vibrio cholerae) or with potential as bioterrorism weapons (Burkholderia pseudomallei and mallei, Francisella tularensis). Vaccination could aid reducing the use of broad spectrum antibiotics and provide protection by herd immunity also to individuals who are not vaccinated.This review analyses structural and functional differences of the polysaccharides exposed on the surface of emerging pathogenic bacteria, combined with medical need and technological feasibility of corresponding glycoconjugate vaccines.

  carbohydrates, glycoconjugates, vaccines, glycoengineering, antimicrobial resistance

  NCBI PubMed ID: 29547971
  Publication DOI: 10.1093/femsre/fuy011
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: Roberto Adamo
  Institutions: GSK Vaccines Institute for Global Health (GVGH), Via Fiorentina 1, 53100 Siena
  
   
  
  Escherichia coli O1A
  CSDB ID 12690 (all data & tools)
• Article ID: 5472
  Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G "Structure and genetics of Escherichia coli O antigens" - FEMS Microbiology Reviews 44(6) (2020) 655-683
  

  Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and four (O14, O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.

  structure, O antigen, Escherichia coli, gene cluster, serogroup, diversity

  NCBI PubMed ID: 31778182
  Publication DOI: 10.1093/femsre/fuz028
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: G. Widmalm ; Lei Wang
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China, School of Molecular and Microbial Bioscience (G08), University of Sydney, Sydney, Australia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
  
   
  
  Escherichia coli O1A, Escherichia coli O1A1
  CSDB ID 1067 (all data & tools)
• Article ID: 6117
  Nishi N, Seki K, Takahashi D, Toshima K "Synthesis of a Pentasaccharide Repeating Unit of Lipopolysaccharide Derived from Virulent E. coli O1 and Identification of a Glycotope Candidate of Avian Pathogenic E. coli O1" - Angewandte Chemie, International Edition 60(4) (2021) 1789-1796
  

  Avian pathogenic Escherichia coli (APEC) is a common bacterial pathogen infecting chickens, resulting in economic losses to the poultry industry worldwide. In particular, APEC O1, one of the most common serotypes of APEC, is considered problematic due to its zoonotic potential. Therefore, many attempts have been made to develop an effective vaccine against APEC O1. In fact, the lipopolysaccharide (LPS) O-antigen of APEC O1 has been shown to be a potent antigen for inducing specific protective immune responses. However, the detailed structure of the O-antigen of APEC O1 is not clear. The present study demonstrates the first synthesis of a pentasaccharide repeating unit of LPS derived from virulent E. coli O1 and its conjugate with BSA. ELISA tests using the semi-synthetic glycoconjugate and the APEC O1 immune chicken serum revealed that the pentasaccharide is a glycotope candidate of APEC O1, with great potential as an antigen for vaccine development.

  Bacterial, Escherichia coli, glycoconjugate, avian pathogenic Escherichia coli, β-rhamnoside, boron-mediated aglycon delivery, glycotope

  NCBI PubMed ID: 33124093
  Publication DOI: 10.1002/anie.202013729
  Journal NLM ID: 0370543
  Publisher: Weinheim: Wiley-VCH
  Correspondence: dtak@applc.keio.ac.jp; toshima@applc.keio.ac.jp
  Institutions: Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
  Methods: 13C NMR, TLC, ELISA, chemical synthesis, chemical methods, MALDI-TOF MS, conjugation, 1H NMr
  
   
  
  Escherichia coli O1A
  CSDB ID 10914 (all data & tools)
• Article ID: 6249
  Jiang X, Bai J, Zhang H, Yuan J, Lu G, Wang Y, Jiang B, Huang D, Feng L "Development of an O-polysaccharide based recombinant glycoconjugate vaccine in engineered E. coli against ExPEC O1" - Carbohydrate Polymers 277 (2022) 118796
  

  Extraintestinal pathogenic Escherichia coli O1 is a frequently identified serotype that causes serious infections and is often refractory to antimicrobial therapy. Glycoconjugate vaccine represents a promising measure to reduce ExPEC infections. Herein, we designed an O1-specific glyco-optimized chassis strain for manufacture of O-polysaccharide (OPS) antigen and OPS-based bioconjugate. Specifically, OPS and OPS-based glycoprotein were synthesized in glyco-optimized chassis strain, when compared to the unmeasurable level of the parent strain. The optimal expression of oligosaccharyltransferase and carrier protein further improved the titer. MS analysis elucidated the correct structure of resulting bioconjugate at routine and unreported glycosylation sequons of carrier protein, with a higher glycosylation efficiency. Finally, purified bioconjugate stimulated mouse to generate specific IgG antibodies and protected them against virulent ExPEC O1 challenge. The plug-and-play glyco-optimized platform is suitable for bioconjugate synthesis, thus providing a potential platform for future medical applications.

  mass spectrometry, glycoconjugate vaccine, glyco-optimized chassis strain, glycosylation efficiency, glycosylation sequon

  NCBI PubMed ID: 34893224
  Publication DOI: 10.1016/j.carbpol.2021.118796
  Journal NLM ID: 8307156
  Publisher: Elsevier
  Correspondence: Di Huang ; Lu Feng
  Institutions: Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin, PR China, TEDA Institute of Biological Sciences and Biotechnology, Tianjin Key Laboratory of Microbial Functional Genomics, Nankai University, Tianjin, PR China
  Methods: PCR, SDS-PAGE, ELISA, genetic methods, LC-MS/MS, immunization, bioconjugate vaccine production
  
   
  
  Escherichia coli O1A
  CSDB ID 8481 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: CH2CH2CH3
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 387
  Stuike-Prill R, Pinto BM "Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations" - Carbohydrate Research 279 (1995) 59-73
  

  Metropolis Monte Carlo simulations have been performed on four substructures from the call-wall polysaccharide antigen of Streptococcus group A to explore the conformational begaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 2, the hexasacchride, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-bDglucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 4. In general, the conformational flexibility of simular glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a secon conformation found for the b-D-GlcNAc-(1→3)-a-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Futhermore, a conformational locale of the a-L-Rha-(1→3)-a-L-Rha linkage found to by populated in the trisaccaharide 1, tetrasaccahride 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton disances compare favourably with experimental average distances obtained fro mNMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to by a hoghly defined conformational feature. The same unit has been found to by one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

  Oligosaccharides, Metropolis Monte Carlo simulations, Cell-wall polysaccharide, Streptococcus group A

  NCBI PubMed ID: 8593633
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark, Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
  Methods: NMR, conformation analysis
  
   
  
  Streptococcus sp. A
  CSDB ID 8404 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: CH2CH2CH3
Contained glycoepitopes: IEDB_131174,IEDB_131175,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 387
  Stuike-Prill R, Pinto BM "Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations" - Carbohydrate Research 279 (1995) 59-73
  

  Metropolis Monte Carlo simulations have been performed on four substructures from the call-wall polysaccharide antigen of Streptococcus group A to explore the conformational begaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 2, the hexasacchride, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-bDglucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 4. In general, the conformational flexibility of simular glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a secon conformation found for the b-D-GlcNAc-(1→3)-a-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Futhermore, a conformational locale of the a-L-Rha-(1→3)-a-L-Rha linkage found to by populated in the trisaccaharide 1, tetrasaccahride 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton disances compare favourably with experimental average distances obtained fro mNMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to by a hoghly defined conformational feature. The same unit has been found to by one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

  Oligosaccharides, Metropolis Monte Carlo simulations, Cell-wall polysaccharide, Streptococcus group A

  NCBI PubMed ID: 8593633
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark, Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
  Methods: NMR, conformation analysis
  
   
  
  Streptococcus sp. A
  CSDB ID 8405 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: CH2CH2CH3
Contained glycoepitopes: IEDB_127513,IEDB_131174,IEDB_131175,IEDB_131177,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_143254,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 387
  Stuike-Prill R, Pinto BM "Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations" - Carbohydrate Research 279 (1995) 59-73
  

  Metropolis Monte Carlo simulations have been performed on four substructures from the call-wall polysaccharide antigen of Streptococcus group A to explore the conformational begaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 2, the hexasacchride, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-bDglucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 4. In general, the conformational flexibility of simular glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a secon conformation found for the b-D-GlcNAc-(1→3)-a-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Futhermore, a conformational locale of the a-L-Rha-(1→3)-a-L-Rha linkage found to by populated in the trisaccaharide 1, tetrasaccahride 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton disances compare favourably with experimental average distances obtained fro mNMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to by a hoghly defined conformational feature. The same unit has been found to by one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

  Oligosaccharides, Metropolis Monte Carlo simulations, Cell-wall polysaccharide, Streptococcus group A

  NCBI PubMed ID: 8593633
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark, Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
  Methods: NMR, conformation analysis
  
   
  
  Streptococcus sp. A
  CSDB ID 8406 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144825,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 555
  Barone G, Bedini E, Unverzagt C, Parilli M "Synthesis of the pentasaccharide repeating unit of the major O-antigen component from Pseudomonas syringae pv. ribicola NVPPB 1010" - Carbohydrate Research 339(2) (2004) 393-400
  

  The synthesis of the repeating unit of the major O-antigen component from Pseudomonas syringae pv. ribicola NVPPB 1010 is reported. The strategy used was based on the successive coupling of a trisaccharide rhamnosyl trichloroacetimidate with a rhamnosyl acceptor with a free hydroxyl group on C-2. The pentasaccharide was then obtained by coupling with a N-Troc-tri-O-acetyl-glucosamine trichloroacetimidate. The synthesis allowed the oligomerisation of the repeating unit.

  repeating unit, Oligosaccharides, O-chain, glycosylation, Pseudomonas ribicola

  NCBI PubMed ID: 14698898
  Publication DOI: 10.1016/j.carres.2003.10.002
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: parrilli@unina.it
  Institutions: Dipartimento di Chimica Organica e Biochimica, Universita di Napoli ''Federico II'', Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy, Bioorganische Chemie, Gebaude NWI, Universitat Bayreuth,95440 Bayreuth, Germany
  
   
  
  Pseudomonas syringae pv. ribicola NVPPB1010
  CSDB ID 9290 (all data & tools)
• Article ID: 1075
  Ovod V, Zdorovenko EL, Shashkov AS, Kocharova NA, Knirel YA "Structure of the O polysaccharide and serological classification of Pseudomonas syringae pv. ribicola NCPPB 1010" - European Journal of Biochemistry 267(8) (2000) 2372-2379
  

  The O polysaccharide (OPS) moiety of the lipopolysaccharide (LPS) of a phytopathogenic bacterium Pseudomonas syringae pv. ribicola NCPPB 1010 was studied by sugar and methylation analyses, Smith degradation, and 1H- and 13C NMR spectroscopy, including 2D COSY, TOCSY, NOESY and H-detected 1H,13C HMQC experiments. The OPS structure was elucidated, and shown to be composed of branched pentasaccharide repeating units (O repeats) of two types, major (1) and minor (2), differing in the position of substitution of one of the rhamnose residues. Both O repeats form structurally homogeneous blocks within the same polysaccharide molecule. Although P. syringae pv. ribicola NCPPB 1010 demonstrates genetic relatedness and similarity in the OPS chemical structure to some other P. syringae pathovars, it did not cross-react with any OPS-specific mAbs produced against heterologous P. syringae strains. Therefore, we propose to classify P. syringae pv. ribicola NCPPB 1010 in a new serogroup, O8.

  structure, structural, polysaccharide, Pseudomonas, O-polysaccharide, O polysaccharide, serological, Pseudomonas syringae, classification, linear, heterogeneity

  NCBI PubMed ID: 10759863
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Medical Technology, University of Tampere, Finland
  Methods: NMR-2D, methylation, NMR, sugar analysis, Smith degradation
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB1010
  CSDB ID 4004 (all data & tools)
• Article ID: 1452
  Corsaro MM, De Castro C, Molinaro A, Parrilli M "Structure of lipopolysaccharides from phytopathogenic Gram-negative bacteria" - Book: Recent Research Developments in Phytochemistry (2001) Vol. 5, 119-138
  

  This review collects the structural data of lipopolysaccharide components arising from all phytopathogenic bacteria so far investigated. The structural approaches and the main biological role of these macromolecules are also reported.

  Lipopolysaccharide, lipopolysaccharides, structure, core, lipid A, O-polysaccharide, gram negative bacteria

  WWW link: https://books.google.ru/books/about/Recent_Research_Developments_in_Phytoche.html?id=5CJacgAACAAJ&redir_esc=y
  Publisher: Research Signpost, Trivandrum, India
  Editors: Pandalai SG
  Institutions: Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte S.Angelo Via Cintia, 4, 80126 Napoli, Italy
  
   
  
  Pseudomonas syringae pv. ribicola VIII NVPPB 1010
  CSDB ID 31737 (all data & tools)
• Article ID: 3968
  Zdorovenko GM, Zdorovenko EL "Pseudomonas syringae lipopolysaccharides: Immunochemical characteristics and structure as a basis for strain classification" - Mikrobiologiia = Microbiology [Russian] 79(1) (2010) 47-57
  

  Lipopolysaccharide (LPS) preparations of 34 Pseudomonas syringae strains of 19 pathovars were prepared by saline extraction from wet cells and purified by repeated ultracentrifugation. The preparations reacted with homologous O-antisera, obtained by rabbit immunization with heat-killed bacterial cells. Through inhibition of homologous reactions between LPS preparations of heterologous strains (enzyme immunoassay, EIA), it was established for the first time that high serological affinity between strains is observed only if their LPS contains O-specific polysaccharide chains (OPS) comprised of completely identical rather than partially similar units. The central linear part of the OPS was found to be serologically inert when shielded with side groups. Data on immunochemical characteristics of the LPS and OPS structure are analyzed in relation to the design of P. syringae classification scheme.

  Lipopolysaccharide, structure, O-specific polysaccharide, Pseudomonas syringae, classification, immunochemistry

  NCBI PubMed ID: 20411661
  Publication DOI: 10.1134/S0026261710010078
  Journal NLM ID: 0376652
  Publisher: Moskva: Izdatelstvo Nauka
  Correspondence: evelina@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Zabolotnyi Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, ul. Zabolotnogo 154, Kyiv, 03143 Ukraine
  Methods: partial acid hydrolysis, EIA, serological methods, de-N-acetylation/deamination
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB 1010
  CSDB ID 25904 (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 anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudomonas syringae pv. ribicola
  CSDB ID 1388 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1075
  Ovod V, Zdorovenko EL, Shashkov AS, Kocharova NA, Knirel YA "Structure of the O polysaccharide and serological classification of Pseudomonas syringae pv. ribicola NCPPB 1010" - European Journal of Biochemistry 267(8) (2000) 2372-2379
  

  The O polysaccharide (OPS) moiety of the lipopolysaccharide (LPS) of a phytopathogenic bacterium Pseudomonas syringae pv. ribicola NCPPB 1010 was studied by sugar and methylation analyses, Smith degradation, and 1H- and 13C NMR spectroscopy, including 2D COSY, TOCSY, NOESY and H-detected 1H,13C HMQC experiments. The OPS structure was elucidated, and shown to be composed of branched pentasaccharide repeating units (O repeats) of two types, major (1) and minor (2), differing in the position of substitution of one of the rhamnose residues. Both O repeats form structurally homogeneous blocks within the same polysaccharide molecule. Although P. syringae pv. ribicola NCPPB 1010 demonstrates genetic relatedness and similarity in the OPS chemical structure to some other P. syringae pathovars, it did not cross-react with any OPS-specific mAbs produced against heterologous P. syringae strains. Therefore, we propose to classify P. syringae pv. ribicola NCPPB 1010 in a new serogroup, O8.

  structure, structural, polysaccharide, Pseudomonas, O-polysaccharide, O polysaccharide, serological, Pseudomonas syringae, classification, linear, heterogeneity

  NCBI PubMed ID: 10759863
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Medical Technology, University of Tampere, Finland
  Methods: NMR-2D, methylation, NMR, sugar analysis, Smith degradation
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB1010
  CSDB ID 4106 (all data & tools)
• Article ID: 1452
  Corsaro MM, De Castro C, Molinaro A, Parrilli M "Structure of lipopolysaccharides from phytopathogenic Gram-negative bacteria" - Book: Recent Research Developments in Phytochemistry (2001) Vol. 5, 119-138
  

  This review collects the structural data of lipopolysaccharide components arising from all phytopathogenic bacteria so far investigated. The structural approaches and the main biological role of these macromolecules are also reported.

  Lipopolysaccharide, lipopolysaccharides, structure, core, lipid A, O-polysaccharide, gram negative bacteria

  WWW link: https://books.google.ru/books/about/Recent_Research_Developments_in_Phytoche.html?id=5CJacgAACAAJ&redir_esc=y
  Publisher: Research Signpost, Trivandrum, India
  Editors: Pandalai SG
  Institutions: Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte S.Angelo Via Cintia, 4, 80126 Napoli, Italy
  
   
  
  Pseudomonas syringae pv. ribicola VIII NVPPB 1010
  CSDB ID 31738 (all data & tools)
• Article ID: 3968
  Zdorovenko GM, Zdorovenko EL "Pseudomonas syringae lipopolysaccharides: Immunochemical characteristics and structure as a basis for strain classification" - Mikrobiologiia = Microbiology [Russian] 79(1) (2010) 47-57
  

  Lipopolysaccharide (LPS) preparations of 34 Pseudomonas syringae strains of 19 pathovars were prepared by saline extraction from wet cells and purified by repeated ultracentrifugation. The preparations reacted with homologous O-antisera, obtained by rabbit immunization with heat-killed bacterial cells. Through inhibition of homologous reactions between LPS preparations of heterologous strains (enzyme immunoassay, EIA), it was established for the first time that high serological affinity between strains is observed only if their LPS contains O-specific polysaccharide chains (OPS) comprised of completely identical rather than partially similar units. The central linear part of the OPS was found to be serologically inert when shielded with side groups. Data on immunochemical characteristics of the LPS and OPS structure are analyzed in relation to the design of P. syringae classification scheme.

  Lipopolysaccharide, structure, O-specific polysaccharide, Pseudomonas syringae, classification, immunochemistry

  NCBI PubMed ID: 20411661
  Publication DOI: 10.1134/S0026261710010078
  Journal NLM ID: 0376652
  Publisher: Moskva: Izdatelstvo Nauka
  Correspondence: evelina@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Zabolotnyi Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, ul. Zabolotnogo 154, Kyiv, 03143 Ukraine
  Methods: partial acid hydrolysis, EIA, serological methods, de-N-acetylation/deamination
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB 1010
  CSDB ID 25905 (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 anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudomonas syringae pv. ribicola
  CSDB ID 1389 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_125613,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1102
  Perry MB, MacLean LL "Structural identification of the lipopolysaccharide O-antigen produced by Yersinia enterocolitica serotype O:28" - European Journal of Biochemistry 267(9) (2000) 2567-2572
  

  The structure of the O-antigenic polysaccharide (O-PS) component of the lipopolysaccharide produced by Yersinia enterocolitica serotype O:28 has been elucidated. From chemical methods involving glycose analysis, periodate oxidation, methylation and the use of one- and two-dimensional NMR spectroscopy, the O-PS was found to be a polymer of repeating branched hexasaccharide units composed of l-rhamnose (four parts), 2-acetamido-2-deoxy-d-glucose (one part), and 2-acetamido-2-deoxy-d-galacturonic acid (one part) having the following structure: [see formula in text].

  Lipopolysaccharide, NMR, O-antigen, polysaccharide structure, Yersinia enterocolitica

  NCBI PubMed ID: 10785376
  Publication DOI: 10.1046/j.1432-1327.2000.01260.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: malcolm.perry@nrc.ca
  Institutions: Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada
  Methods: NMR-2D, methylation, NMR, sugar analysis, periodate oxidation
  
   
  
  Yersinia enterocolitica O28 (NRCC 4120)
  CSDB ID 4044 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4152 (all data & tools)
• Article ID: 2691
  Reimer KB, Pinto BM "Synthesis of oligosaccharides corresponding to the antigenic determinants of the b-haemolytic Streptococci Group A. Part 1. Overall strategy and synthesis of a linear trisaccharide" - Journal of the Chemical Society, Perkin Transactions 1 (1988) 2103-2111
  

  The overall strategy for the synthesis of higher-order oligosaccharides corresponding to the repeating unit of the cell-wall polysaccharide of the β-haemolytic Streptococci Group A is described. The trisaccharide, β-D-GlcpNAc-(1→3)-α-L-Rhap-(1→3)-α-L-Rhap has been synthesized by a series of Königs-Knorr reactions. The selectively protected rhamnose derivative, allyl 2-O-benzoyl-4-O-benzyl-α-L-rhamnopyranoside, reacted with 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-β-D-glucopyranosyl bromide to give the blocked disaccharide. Deallylation, followed by treatment with N,N-dimethyl(chloromethylene)ammonium chloride then gave the corresponding disaccharide chloride. In conjunction with the same rhamnose monosaccharide unit or 8-methoxycarbonyloctyl 2,4-di-O-benzoyl-α-L-rhamnopyranoside, the synthesis of the blocked trisaccharide, as its allyl glycoside or its 8-methoxycarbonyloctyl glycoside, respectively, was accomplished. Transesterification, followed by hydrazinolysis, selective N-acetylation, and hydrogenolysis afforded the pure trisaccharide, as its propyl glycoside or 8-methoxycarbonyloctyl glycoside, for use as a hapten in binding studies and n.m.r. studies or for use in the preparation of glycoconjugates, respectively. Similar treatment of the blocked disaccharide afforded the hapten, β-D-GlcpNAc-(1→3)-α-LRhap, as its propyl glycoside.

  Publication DOI: 10.1039/P19880002103
  Journal NLM ID: 7505598
  Publisher: Chemical Society
  Institutions: Department of Chemistry, Simon Fraser University, Burnab y, British Columbia, Canada V5A IS6
  
   
  
  Streptococcus sp. A
  CSDB ID 138467 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4154 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_131175,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4156 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_131175,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4157 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144825,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1316
  Zdorovenko EL, Zatonsky GV, Kocharova NA, Shashkov AS, Knirel YA, Ovod V "Structures of the O-polysaccharides of two strains of Pseudomonas syringae pv. porri from genomospecies 4" - European Journal of Biochemistry 270(1) (2003) 20-27
  

  Strains of Pseudomonas syringae pv. porri are characterized by a number of pathovar-specific phenotypic and genomic characters and constitute a highly homogeneous group. Using monoclonal antibodies, they all were classified in a novel P. syringae serogroup O9. The O polysaccharides (OPS) isolated from the lipopolysaccharides (LPS) of P. syringae pv. porri NCPPB 3365 and NCPPB 3364T possess multiple oligosaccharide O repeats, some of which are linear and composed of l-rhamnose (l-Rha), whereas the major O repeats are branched with l-rhamnose in the main chain and GlcNAc in side chains (structures 1 and 2). Both branched O repeats, which differ in the position of substitution of one of the Rha residues and in the site of attachment of GlcNAc, were found in the two strains studied, O repeat 1 being major in strain NCPPB 3365 and 2 in strain NCPPB 3364T. [formula: see text]. The relationship between OPS chemotype and serotype on one hand and the genomic characters of P. syringae pv. porri and other pathovars delineated in genomospecies 4 on the other hand is discussed

  Lipopolysaccharide, monoclonal antibody, serological classification, Pseudomonas syringae, O polysaccharide structure

  NCBI PubMed ID: 12492471
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Medical Technology, University of Tampere, Tampere, Finland
  Methods: NMR-2D, methylation, NMR, Smith degradation
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB1010
  CSDB ID 6123 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1316
  Zdorovenko EL, Zatonsky GV, Kocharova NA, Shashkov AS, Knirel YA, Ovod V "Structures of the O-polysaccharides of two strains of Pseudomonas syringae pv. porri from genomospecies 4" - European Journal of Biochemistry 270(1) (2003) 20-27
  

  Strains of Pseudomonas syringae pv. porri are characterized by a number of pathovar-specific phenotypic and genomic characters and constitute a highly homogeneous group. Using monoclonal antibodies, they all were classified in a novel P. syringae serogroup O9. The O polysaccharides (OPS) isolated from the lipopolysaccharides (LPS) of P. syringae pv. porri NCPPB 3365 and NCPPB 3364T possess multiple oligosaccharide O repeats, some of which are linear and composed of l-rhamnose (l-Rha), whereas the major O repeats are branched with l-rhamnose in the main chain and GlcNAc in side chains (structures 1 and 2). Both branched O repeats, which differ in the position of substitution of one of the Rha residues and in the site of attachment of GlcNAc, were found in the two strains studied, O repeat 1 being major in strain NCPPB 3365 and 2 in strain NCPPB 3364T. [formula: see text]. The relationship between OPS chemotype and serotype on one hand and the genomic characters of P. syringae pv. porri and other pathovars delineated in genomospecies 4 on the other hand is discussed

  Lipopolysaccharide, monoclonal antibody, serological classification, Pseudomonas syringae, O polysaccharide structure

  NCBI PubMed ID: 12492471
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Medical Technology, University of Tampere, Tampere, Finland
  Methods: NMR-2D, methylation, NMR, Smith degradation
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB1010
  CSDB ID 6124 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_131175,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1361
  Auzanneau FI, Forooghian F, Pinto BM "Efficient, convergent syntheses of oligosaccharide allyl glycosides corresponding to the Streptococcus group A cell-wall polysaccharide" - Carbohydrate Research 291 (1996) 21-41
  

  oligosaccharide, polysaccharide, Streptococcus, group, Oligosaccharides, cell wall, glycosides, cell wall polysaccharide, glycoside, allyl, chemical glycosylation

  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 6446 (all data & tools)