Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115009,IEDB_116046,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_1391962,IEDB_140624,IEDB_140629,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142488,IEDB_143794,IEDB_144998,IEDB_146664,IEDB_150077,IEDB_150899,IEDB_151531,IEDB_190606,IEDB_241118,IEDB_423115,IEDB_983931,SB_137,SB_165,SB_166,SB_187,SB_192,SB_195,SB_29,SB_7,SB_88

• Article ID: 82
  Fudala R, Kondakova AN, Bednarska K, Senchenkova SN, Shashkov AS, Knirel YA, Zähringer U, Kaca W "Structure and serological characterization of the O-antigen of Proteus mirabilis O18 with a phosphocholine-containing oligosaccharide phosphate repeating unit" - Carbohydrate Research 338(18) (2003) 1835-1842
  

  A phosphorylated, choline-containing polysaccharide was obtained by O-deacylation of the lipopolysaccharide (LPS) of Proteus mirabilis O18 by treatment with aqueous 12% ammonia, whereas hydrolysis with dilute acetic acid resulted in depolymerisation of the polysaccharide chain by the glycosyl phosphate linkage. Treatment of the O-deacylated LPS with aqueous 48% hydrofluoric acid cleaved the glycosyl phosphate group but, unexpectedly, did not affect the choline phosphate group. The polysaccharide and the derived oligosaccharides were studied by NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, ROESY, 1H,13C HMQC and HMQC-TOSCY experiments, along with chemical methods, and the following structure of the pentasaccharide phosphate repeating unit was established: [carbohydrate structure in text] Where ChoP=Phosphocoline Immunochemical studies of the LPS, O-deacylated LPS and partially dephosphorylated pentasaccharide using rabbit polyclonal anti-P. mirabilis O18 serum showed the importance of the glycosyl phosphate group in manifesting the serological specificity of the O18-antigen

  Lipopolysaccharide, O-polysaccharide, Proteus mirabilis, Glycosyl phosphate, Phosphocholine

  NCBI PubMed ID: 12932366
  Publication DOI: 10.1016/S0008-6215(03)00274-X
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: wkaca@cmiwpan.lodz.pl
  Institutions: Institute of Microbiology and Immunology, University of Lodz, 90-237 Lodz, Poland
  Methods: NMR-2D, methylation, NMR, sugar analysis, MS
  
   
  
  Proteus mirabilis O18
  CSDB ID 2081 (all data & tools)
• Article ID: 540
  Kondakova AN, Fudala R, Bednarska K, Senchenkova SN, Knirel YA, Kaca W "Structure of the neutral O-polysaccharide and biological activities of the lipopolysaccharide of Proteus mirabilis O20" - Carbohydrate Research 339(3) (2004) 623-628
  

  Mild acid degradation of the lipopolysaccharide (LPS) of Proteus mirabilis O20 resulted in depolymerisation of the O-polysaccharide to give a repeating-unit pentasaccharide. A polysaccharide was obtained by O-deacylation of the LPS followed by nitrous acid deamination. The derived pentasaccharide and polysaccharide were studied by NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, ROESY, 1H,13C HMQC and HMQC-TOSCY experiments, along with chemical methods, and the following structure of the repeating unit of the O-polysaccharide was established: [Carbohydrate structure: see text]. As opposite to most other P. mirabilis O-polysaccharides studied, that of P. mirabilis O20 is neutral. A week serological cross-reactivity was observed between anti-P. mirabilis O20 serum and LPS of a number of Proteus serogroups with known O-polysaccharide structure. The ability of LPS of P. mirabilis O20 to activate the serine protease cascade was tested in Limulus amoebocyte lysate and in human blood plasma and compared with that of P. mirabilis O14a,14c having an acidic O-polysaccharide. The LPS of P. mirabilis O20 was found to be less active in both assays than the LPS of P. mirabilis O14a,14c and, therefore, the structurally variable O-polysaccharide may influenced the biological activity of the conserved lipid A moiety of the LPS.

  Lipopolysaccharide, Proteus mirabilis, O-Polysaccharide structure, Serological cross-reactivity, Blood serum

  NCBI PubMed ID: 15013399
  Publication DOI: 10.1016/j.carres.2003.11.016
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: rafalfu@wp.pl
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology and Immunology, University of Lodz,90-237 Lodz, Poland, Center for Medical Biology and Microbiology, Polish Academy of Sciences,93-232 Lodz, Poland, Institute of Microbiology, Swietokrzyska Academy, Kielce 25-406, Poland
  Methods: NMR-2D, methylation, NMR, sugar analysis
  
   
  
  Proteus mirabilis O18
  CSDB ID 9429 (all data & tools)
• Article ID: 3364
  Nikolaev AV, Botvinko IV, Ross AJ "Natural phosphoglycans containing glycosyl phosphate units: structural diversity and chemical synthesis" - Carbohydrate Research 342(3-4) (2007) 297-344
  

  An anomeric phosphodiester linkage formed by a glycosyl phosphate unit and a hydroxyl group of another monosaccharide is found in many glycopolymers of the outer membrane in bacteria (e.g., capsular polysaccharides and lipopolysaccharides), yeasts and protozoa. The polymers (phosphoglycans) composed of glycosyl phosphate (or oligoglycosyl phosphate) repeating units could be chemically classified as poly(glycosyl phosphates). Their importance as immunologically active components of the cell wall and/or capsule of numerous microorganisms upholds the need to develop routes for the chemical preparation of these biopolymers. In this paper, we (1) present a review of the primary structures (known to date) of natural phosphoglycans from various sources, which contain glycosyl phosphate units, and (2) discuss different approaches and recent achievements in the synthesis of glycosyl phosphosaccharides and poly(glycosyl phosphates).

  synthesis, structure, polysaccharides, Phosphoglycans, Anomeric phosphodiesters

  NCBI PubMed ID: 17092493
  Publication DOI: 10.1016/j.carres.2006.10.006
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: a.v.nikolaev@dundee.ac.uk
  Institutions: College of Life Sciences, Division of Biological Chemistry and Molecular Microbiology, University of Dundee, Dundee DD1 5EH, UK.
  
   
  
  Proteus mirabilis O18
  CSDB ID 21777 (all data & tools)
• Article ID: 4042
  Kaca W, Glenska J, Lechowicz L, Grabowski S, Brauner A, Kwinkowski M "Serotyping of Proteus mirabilis clinical strains based on lipopolysaccharide O-polysaccharide and core oligosaccharide structures" - Biochemistry (Moscow) 76(7) (2011) 851-861
  

  The aim of this work was to serotype Proteus mirabilis urinary tract infection (UTI) strains based on chemically defined O-antigens with the use of two clinical collections from Sweden and Poland consisting of 99 and 24 UTI strains, respectively. A simple two-step serotyping scheme was proposed using enzyme immunoassay with heat-stable surface antigens of Proteus cells and immunoblotting with isolated lipopolysaccharides (LPSs). Using polyclonal anti-P. mirabilis rabbit antisera, 50 Swedish and 8 Polish strains were classified into serogroups O10, O38, O36, O30, O17, O23, O9, O40, O49, O27, O5, O13, O24, O14, and O33. From the Swedish strains, 10 belonged to serogroup O10 and five to each of serogroups O38, O36, and O9. Therefore, none of the O-serogroups was predominant. The majority of the serotyped clinical strains possess acidic O-antigens containing uronic acids and various acidic non-carbohydrate substituents. In immunoblotting, antisera cross-reacted with both O-antigen and core of LPSs. The core region of 19 LPSs bound a single serum, and that of 12 LPSs bound more than two sera. Following bioinformatic analysis of the available sequences, a molecular approach to the prediction of Proteus core oligosaccharide structures was proposed. The identification of the core type of P. mirabilis R110, derived from a serogroup O3 wild strain, using restriction fragments length polymorphism analysis of galacturonic acid transferase is shown as an example. In summary, the most frequent O-serogroups among P. mirabilis UTI stains were identified. The diversity of serological reactions of LPSs is useful for serotyping of P. mirabilis clinical isolates. A possible role of the acidic components of O-antigens in UTI is discussed.

  Lipopolysaccharide, O-antigen, Proteus mirabilis, serology, serotyping, glycosyl transferas

  NCBI PubMed ID: 21999547
  Publication DOI: 10.1134/S0006297911070169
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: wieslaw.kaca@ujk.edu.pl
  Institutions: Department of Microbiology, Institute of Biology, Jan Kochanowski University, Kielce, Poland
  Methods: PCR, SDS-PAGE, EIA, serological methods, immunoblotting, bioinformatic analysis
  
   
  
  Proteus mirabilis O18
  CSDB ID 26661 (all data & tools)
• Article ID: 4829
  Young NM, Foote SJ, Wakarchuk WW "Review of phosphocholine substituents on bacterial pathogen glycans: synthesis, structures and interactions with host proteins" - Molecular Immunology 56(4) (2013) 563-573
  

  Among the non-carbohydrate components of glycans, the addition of phosphocholine (ChoP) to the glycans of pathogens occurs more rarely than acetylation or methylation, but it has far more potent biological consequences. These arise from ChoP's multiple interactions with host proteins, which are important at all stages of the infection process. These stages include initial adherence to cells, encountering the host's innate immune system and then the adaptive immune system. Thus, in the initial stages of an infection, ChoP groups are an asset to the pathogen, but they can turn into a disadvantage subsequently. In this review, we have focussed on structural aspects of these phenomena. We describe the biosynthesis of the ChoP modification, the structures of the pathogen glycans known to carry ChoP groups and the host proteins that recognize ChoP.

  Haemophilus influenzae, Streptococcus pneumoniae, Phosphocholine, 4, 2-acetamido-4-amino-2, 6-trideoxyhexose, C-reactive protein, choline phosphate, ChoP, lipotechoic acid, LTA

  NCBI PubMed ID: 23911414
  Publication DOI: 10.1016/j.molimm.2013.05.237
  Journal NLM ID: 7905289
  Publisher: Elsevier
  Correspondence: martin.young@nrc-cnrc.gc.ca; wwakarchuk@ryerson.ca
  Institutions: Human Health Therapeutics, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6, Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
  
   
  
  Proteus mirabilis O18
  CSDB ID 30996 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115009,IEDB_116046,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_1391962,IEDB_140624,IEDB_140629,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142488,IEDB_143794,IEDB_144998,IEDB_146664,IEDB_150899,IEDB_151531,IEDB_190606,IEDB_423115,IEDB_983931,SB_137,SB_165,SB_166,SB_187,SB_192,SB_195,SB_29,SB_7,SB_88

• Article ID: 82
  Fudala R, Kondakova AN, Bednarska K, Senchenkova SN, Shashkov AS, Knirel YA, Zähringer U, Kaca W "Structure and serological characterization of the O-antigen of Proteus mirabilis O18 with a phosphocholine-containing oligosaccharide phosphate repeating unit" - Carbohydrate Research 338(18) (2003) 1835-1842
  

  A phosphorylated, choline-containing polysaccharide was obtained by O-deacylation of the lipopolysaccharide (LPS) of Proteus mirabilis O18 by treatment with aqueous 12% ammonia, whereas hydrolysis with dilute acetic acid resulted in depolymerisation of the polysaccharide chain by the glycosyl phosphate linkage. Treatment of the O-deacylated LPS with aqueous 48% hydrofluoric acid cleaved the glycosyl phosphate group but, unexpectedly, did not affect the choline phosphate group. The polysaccharide and the derived oligosaccharides were studied by NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, ROESY, 1H,13C HMQC and HMQC-TOSCY experiments, along with chemical methods, and the following structure of the pentasaccharide phosphate repeating unit was established: [carbohydrate structure in text] Where ChoP=Phosphocoline Immunochemical studies of the LPS, O-deacylated LPS and partially dephosphorylated pentasaccharide using rabbit polyclonal anti-P. mirabilis O18 serum showed the importance of the glycosyl phosphate group in manifesting the serological specificity of the O18-antigen

  Lipopolysaccharide, O-polysaccharide, Proteus mirabilis, Glycosyl phosphate, Phosphocholine

  NCBI PubMed ID: 12932366
  Publication DOI: 10.1016/S0008-6215(03)00274-X
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: wkaca@cmiwpan.lodz.pl
  Institutions: Institute of Microbiology and Immunology, University of Lodz, 90-237 Lodz, Poland
  Methods: NMR-2D, methylation, NMR, sugar analysis, MS
  
   
  
  Proteus mirabilis O18
  CSDB ID 2191 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115009,IEDB_116046,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_1391962,IEDB_140624,IEDB_140629,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_142488,IEDB_143794,IEDB_144998,IEDB_146664,IEDB_150899,IEDB_151531,IEDB_190606,IEDB_241118,IEDB_423115,IEDB_983931,SB_137,SB_165,SB_166,SB_187,SB_192,SB_195,SB_29,SB_7,SB_88

• Article ID: 82
  Fudala R, Kondakova AN, Bednarska K, Senchenkova SN, Shashkov AS, Knirel YA, Zähringer U, Kaca W "Structure and serological characterization of the O-antigen of Proteus mirabilis O18 with a phosphocholine-containing oligosaccharide phosphate repeating unit" - Carbohydrate Research 338(18) (2003) 1835-1842
  

  A phosphorylated, choline-containing polysaccharide was obtained by O-deacylation of the lipopolysaccharide (LPS) of Proteus mirabilis O18 by treatment with aqueous 12% ammonia, whereas hydrolysis with dilute acetic acid resulted in depolymerisation of the polysaccharide chain by the glycosyl phosphate linkage. Treatment of the O-deacylated LPS with aqueous 48% hydrofluoric acid cleaved the glycosyl phosphate group but, unexpectedly, did not affect the choline phosphate group. The polysaccharide and the derived oligosaccharides were studied by NMR spectroscopy, including 2D 1H,1H COSY, TOCSY, ROESY, 1H,13C HMQC and HMQC-TOSCY experiments, along with chemical methods, and the following structure of the pentasaccharide phosphate repeating unit was established: [carbohydrate structure in text] Where ChoP=Phosphocoline Immunochemical studies of the LPS, O-deacylated LPS and partially dephosphorylated pentasaccharide using rabbit polyclonal anti-P. mirabilis O18 serum showed the importance of the glycosyl phosphate group in manifesting the serological specificity of the O18-antigen

  Lipopolysaccharide, O-polysaccharide, Proteus mirabilis, Glycosyl phosphate, Phosphocholine

  NCBI PubMed ID: 12932366
  Publication DOI: 10.1016/S0008-6215(03)00274-X
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: wkaca@cmiwpan.lodz.pl
  Institutions: Institute of Microbiology and Immunology, University of Lodz, 90-237 Lodz, Poland
  Methods: NMR-2D, methylation, NMR, sugar analysis, MS
  
   
  
  Proteus mirabilis O18
  CSDB ID 2192 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136105,IEDB_140629,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_225177,IEDB_423115,IEDB_885813,IEDB_885823,IEDB_983931,SB_192

• 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.
  
   
  
  Aeromonas salmonicida
  CSDB ID 7221 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: inner core
Trivial name: outer core regions of 2-Hex glycoform
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_140087,IEDB_140629,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_2189047,IEDB_423115,IEDB_983931,SB_192

• Article ID: 423
  Wu YP, McQuiston JH, Cox A, Pack TD, Inzana TJ "Molecular cloning and mutagenesis of a DNA locus involved in lipooligosaccharide biosynthesis in Haemophilus somnus" - Infection and Immunity 68(1) (2000) 310-319
  

  Haemophilus somnus undergoes antigenic and structural phase variation in its lipooligosaccharide (LOS). A gene (lob-1) containing repetitive 5'-CAAT-3' sequences that may, in part, contribute to phase variation was cloned and sequenced (T. J. Inzana et al., Infect. Immun. 65:4675-4681, 1997). We have now identified another putative gene (lob-2A) immediately upstream from lob-1. Lob-2A contained homology to several LOS biosynthesis proteins of the family Pasteurellaceae and the LgtB and LgtE galactosyltransferases of Neisseria meningitidis and N. gonorrhoeae. Unlike lob-1, lob-2A contained 18 to 20 5'-GA-3' repeats 141 bp upstream of the termination codon as determined by PCR amplification of DNA from individual colonies. Twenty repeats were most common, but when 19 5'-GA-3' repeats were present a stop codon would occur 1 bp after the last 5'-GA-3' repeat. A 630-bp SalI-BsgI fragment within lob-2A was deleted, and a kanamycin resistance (Km(r)) gene was inserted into this site to create pCAAT∆lob2A. Following electroporation of pCAAT∆lob2A into H. somnus 738, several allelic exchange mutants were isolated. The LOS electrophoretic profile of one mutant, strain 738-lob2A1::Km, was altered, and the phase variation rate was reduced but phase variation was not eliminated. A variant with 19 5'-GA-3' repeats in lob-2A had an LOS profile similar to that of 738-lob2A1::Km, suggesting that lob-2A was turned off in this phase. Nanoelectrospray mass spectrometry (nES-MS) and nuclear magnetic resonance spectroscopy showed that 738-lob2A1::Km was deficient in the terminal βGal(1-3)βGlcNAc residue present in parent strain 738. Mutant 738-lob2A1::Km was significantly more sensitive to the bactericidal action of normal bovine serum and was less virulent in mice than was parent strain 738. When H. somnus 129Pt was electrotransformed with shuttle vector pLS88 containing lob-2A, its LOS electrophoretic profile was modified and additional N-acetylhexosamine residues were present, as determined by nES-MS analysis. These results indicated that lob-2A may be an N-acetylglucosamine transferase involved in LOS biosynthesis and phase variation and that LOS structure is important to H. somnus virulence

  biosynthesis, Haemophilus, Lipooligosaccharide, DNA, molecular, locus, cloning, mutagenesis, Haemophilus somnus

  NCBI PubMed ID: 10603403
  Journal NLM ID: 0246127
  Publisher: American Society for Microbiology
  Correspondence: tinzana@vt.edu
  Institutions: Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, and Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A 0R6
  Methods: 1H NMR, virulence assays, PCR, DNA sequencing, DNA techniques, MS, immunoblotting, electrotransformation, RT-PCR, serum bactericidal assays
  
   
  
  Haemophilus somnus 738-lob2A1::K
  CSDB ID 8716 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_115136,IEDB_136045,IEDB_140629,IEDB_140630,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144998,IEDB_146664,IEDB_152214,IEDB_174333,IEDB_423115,IEDB_983931,SB_192,SB_86

• Article ID: 758
  Cescutti P, Toffanin R, Fett WF, Osman SF, Pollesello P, Paoletti S "Structural investigation of the exopolysaccharide produced by Pseudomonas flavescens strain B62 - Degradation by a fungal cellulase and isolation of the oligosaccharide repeating unit" - European Journal of Biochemistry 251(3) (1998) 971-979
  

  Pseudomonas flavescens strain B62 (NCPPB 3063) is a recently described bacterium isolated from walnut blight cankers. This strain has been designated as the type strain of a Pseudomonas rRNA group-I species. Strain B62 produced a mixture of two exopolysaccharides, differing in weight average relative molecular mass and composition. Only the most abundant exopolysaccharide (90% by mass), corresponding to the one with the lower molecular mass, was investigated by use of methylation analysis, partial acid hydrolysis, and NMR spectroscopy. The polysaccharide was depolymerised by the action of the cellulase produced by Penicillum funiculosum and the oligosaccharide obtained, corresponding to the repeating unit, was characterised by NMR spectroscopy and ion-spray mass spectrometry. The repeating unit of the B62 exopolysaccharide is (See structure in text) where X is glucose (75%) or mannose (25 %), and Lac is lactate. The O-acetyl groups are present only on 75% of the repeating units, and they are linked to the C6 of the hexose residues in non-stoichiometric amounts.

  NMR, oligosaccharide, structure, exopolysaccharide, degradation, isolation, cellulase, fungal, Pseudomonas flavescens

  NCBI PubMed ID: 9490074
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: cescutti@bbcm.univ.trieste.it
  Institutions: Dipartimento di Biochimica, Biofisica e Chimica delle Macromolecole, Universita` di Trieste, Trieste, Italy, POLY-tech Scarl, Area di Ricerca, Trieste, Italy, US Department of Agriculture, ARS, Eastern Regional Research Center, Wyndmoor, USA, Orion Pharma, R&D, Drug Design Unit, NMR-lab, Espoo, Finland
  Methods: NMR-2D, methylation, partial acid hydrolysis, NMR, ESI-MS
  
   
  
  Pseudomonas flavescens B62
  CSDB ID 1308 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_140629,IEDB_140630,IEDB_141584,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_232584,IEDB_423115,IEDB_423153,IEDB_885822,IEDB_983931,SB_192

• Article ID: 1525
  Katzenellenbogen E, Kocharova NA, Zatonsky GV, Shashkov AS, Knirel YA, Gamian A, Bogulska M "Structure of the O-polysaccharide of Hafnia alvei strain PCM 1189 that has hexa- to octa-saccharide repeating units owing to incomplete glucosylation" - Carbohydrate Research 340(2) (2005) 263-270
  

  The O-polysaccharide of Hafnia alvei PCM 1189 consists of D-glucose, D-galactose, D-GalNAc and D-GlcA and lacks the strict regularity. The intact and carboxyl-reduced polysaccharides as well as oligosaccharides obtained by partial acid hydrolysis were studied by chemical and enzymatic analyses, methylation and NMR spectroscopy. The following structure was established for the O-polysaccharide, which is built up of branched hexa- to octasaccharide repeating units differing in the number of lateral glucose residues: [structure: see text] where the glucose residues shown in italics are nonstoichiometric substituents. The repeating units include also a minor O-acetyl group, whose position was not determined.

  Lipopolysaccharide, O-antigen, Hafnia alvei, enterobacteria, bacterial polysaccharide structure

  NCBI PubMed ID: 15639246
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Immunochemistry Department, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
  Methods: methylation, NMR, sugar analysis, enzymatic analysis
  
   
  
  Hafnia alvei PCM 1189
  CSDB ID 10269 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: O-deacylated lipid A
Trivial name: glycolipid
Compound class: LOS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_137777,IEDB_137779,IEDB_138949,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_140629,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_2189047,IEDB_423115,IEDB_983931,SB_192

• Article ID: 1771
  Phillips NJ, Apicella MA, Griffiss JM, Gibson BW "Structural studies of the lipooligosaccharides from Haemophilus influenzae type b strain A2" - Biochemistry 32 (1993) 2003-2012
  

  The outer membrane lipooligosaccharides (LOS) from Haemophilus influenzae type b strain A2 are a heterogeneous mixture of glycolipids containing a conserved Lipid A structure and a variable oligosaccharide moiety. After O-deacylation by treatment with anhydrous hydrazine, the O-deacylated LOS mixture was analyzed by electrospray mass spectrometry and shown to contain 11 components, ranging in M(r) from 2277.8 to 3416.4. The majority of these structures contained a variable number of hexoses, three L-glycero-D-manno-heptoses, and one 3-deoxy-D-manno-octulosonic acid (KDO) residue attached to a diphosphorylated O-deacylated Lipid A moiety. Additional phosphate and phosphoethanolamine (PEA) groups were also present on the oligosaccharide structures. Two minor high molecular weight components were also observed that contained N-acetylhexosamine and sialic acid. Neuraminidase treatment of the O-deacylated LOS mixture resulted in the loss of sialic acid from these latter two species. After mild acid hydrolysis and separation by size-exclusion chromatography, liquid secondary ion mass spectrometry identified six major and four minor oligosaccharides, ranging in M(r) from 1243.4 to 2215.8. These released oligosaccharides contained a common heptose trisaccharide core structure with anhydro-KDO at the reducing terminus, which arises as an artifact of the hydrolysis procedure by beta-elimination of a phosphate group from the 4-position of KDO. Selected oligosaccharide fractions were subjected to composition and methylation analyses and sequenced by tandem mass spectrometry. Taken together, these data defined the major O-deacylated LOS as follows: [formula: see text] Higher molecular weight structures in the mixture contained galactose, N-acetylglucosamine, and sialic acid as additional branch sugars, suggesting that H. influenzae A2 is capable of forming a sialylated lactosamine structure.

  NCBI PubMed ID: 8448159
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Institutions: Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
  Methods: EI-MS
  
   
  
  Haemophilus influenzae b (A2)
  CSDB ID 107893 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_136906,IEDB_137472,IEDB_140629,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_423115,IEDB_885813,IEDB_983931,SB_192,SB_7

• Article ID: 1908
  Rosell KG, Jennings HJ "Structural elucidation of the capsular polysaccharide of Streptococcus pneumonia type 9N" - Canadian Journal of Biochemistry and Cell Biology = Revue canadienne de biochimie et biologie cellulaire 61 (1983) 1102-1107
  

  The specific capsular polysaccharide of Streptococcus pneumoniae type 9N (American type 9) contains D-glucose, D-glucuronic acid, 2-acetamido-2-deoxy-D-glucose, and 2-acetamido-2-deoxy-D-mannose in the molar ratio of 2:1:1:1. Accumulated data from spectroscopic (13C and 1H nuclear magnetic resonance) and methylation analyses of the native and specifically degraded polysaccharide indicated that it was linear and composed of the following pentasaccharide repeating unit; -4)-α-D-GlcpA-(1→3)-α-D-Glcp-(1→3)-β-D-ManpNAc-(1→4)-α-D-Glcp-(1→4)-β-D-GlcpNAc(1→. Structural regions in the type 9N polysaccharide common to those of types 9A, 9L, and 9V have been identified which account for the cross-reactivity of this groups of polysaccharides.

  NCBI PubMed ID: 6652561
  Publication DOI: 10.1139/o83-140
  Journal NLM ID: 8302763
  Publisher: Ottawa: National Research Council Of Canada
  Institutions: Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario K1A OR6 Canada
  Methods: 13C NMR, 1H NMR, methylation, GLC-MS, partial acid hydrolysis, sugar analysis, GLC, Smith degradation, GPC, optical rotation measurement, oxidation with chromium trioxide
  
   
  
  Streptococcus pneumoniae 9A
  CSDB ID 112112 (all data & tools)
• Article ID: 1911
  Richards JC, Perry MB "Structural analysis of the specific polysaccharide of Streptococcus pneumoniae type 9L (American type 49)" - Canadian Journal of Biochemistry and Cell Biology = Revue canadienne de biochimie et biologie cellulaire 62 (1984) 1309-1320
  

  The specific capsular polysaccharide produced by Streptococcus pneumoniae type 9L (American type 49) is composed of D-galactose (one part), D-glucose (one part), D-glucuronic acid (one part), 2-acetamido-2-deoxy-D-mannose (one part), and 2-acetamido-2-deoxy-D-glucose (one part). Partial acid hydrolysis, periodate oxidation, nitrous acid deamination, optical rotation, methylation, and 13C and 1H nuclear magnetic resonance studies showed that the polysaccharide is an unbranched high molecular weight linear polymer of a repeating pentasaccharide unit having the structure: (formula; see text).

  NCBI PubMed ID: 6529704
  Publication DOI: 10.1139/o84-167
  Journal NLM ID: 8302763
  Publisher: Ottawa: National Research Council Of Canada
  Institutions: Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario K1A OR6 Canada
  Methods: gel filtration, 13C NMR, 1H NMR, methylation, GLC-MS, partial acid hydrolysis, sugar analysis, TLC, GLC, carboxyl reduction, paper chromatography, de-N-acetylation, ion-exchange chromatography, immunodiffusion assays, periodate oxidation, optical rotation measurement, nitrous deamination
  
   
  
  Streptococcus pneumoniae 9A
  CSDB ID 622 (all data & tools)
• Article ID: 1920
  Bennett LG, Bishop CT "Structure of the type XXXIII Streptococcus pneumoniae (pneumococcal) capsular polysaccharide" - Canadian Journal of Chemistry 58 (1980) 2724-2727
  

  The type XXXIII Streptococcus pneumoniae (pneumococcal) capsular polysaccharide contains D-glucose (2 mol), D-galactose (1 mol), D-glucuronic acid (1 mol), and 2-acetamido-2-deoxy-D-mannose (1 mol). Structural investigations by methylation analysis, specific degradations, and nmr spectroscopy showed that the repeating unit was a linear pentasaccharide of the following structure: → 3)-α-D-Galp-(1 → 3)-β-D-ManpNAc-(1 → 4)-α-D-Glcp-(1 → 4)-β-D-Glcp(1-4)-α-D-GlcpA-(1 →.

  Publication DOI: 10.1139/v80-434
  Journal NLM ID: 0372705
  Publisher: National Research Council of Canada Canada
  Institutions: Division of Biological Sciences, National Research Council of Canada, Ottawa, Ont., Canad
  Methods: gel filtration, 1H NMR, methylation, partial acid hydrolysis, GC-MS, sugar analysis, GLC, carboxyl reduction, b-elimination, GPC, ion-exchange chromatography, periodate oxidation, optical rotation measurement
  
   
  
  Streptococcus pneumoniae 9A
  CSDB ID 112187 (all data & tools)
• Article ID: 4430
  Ovodov YS "Bacterial capsular antigens. Structural patterns of capsular antigens" - Biochemistry (Moscow) 71(9) (2006) 937-954
  

  Structural patterns of bacterial capsular antigens including capsular polysaccharides and exoglycans are given in this review. In addition, the immunological activity of capsular antigens and their role in type specificity of bacteria are discussed.

  structure, capsular polysaccharides, bacterial capsular antigens, bacterial exoglycans, immunological activity, type specificity

  NCBI PubMed ID: 17009947
  Publication DOI: 10.1134/S000629790609001X
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: ovoys@physiol.komisc.ru
  Institutions: Institute of Physiology, Komi Science Center, Urals Branch of the Russian Academy of Sciences, Syktyvkar 167982, Russia
  
   
  
  Streptococcus pneumoniae type 9A
  CSDB ID 28711 (all data & tools)
  Streptococcus pneumoniae type 9N
  CSDB ID 28713 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: EPS
Contained glycoepitopes: IEDB_135614,IEDB_136044,IEDB_137472,IEDB_140629,IEDB_141794,IEDB_141806,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149136,IEDB_190606,IEDB_241101,IEDB_423115,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88

• Article ID: 1934
  Morris VJ, Brownsey GJ, Gunning AP, Harris JE "Gelation of the extracellular polysaccharide produced by Agrobacterium rhizogenes" - Carbohydrate Polymers 13 (1990) 221-225
  

  It has been shown that the extracellular polysaccharide (EPS) produced by Agrobacterium rhizogenes will form thermoreversible gels. This EPS belongs to a family of polysaccharide structures all of which have the same backbone structure substituted with different side chains. The EPS produced by Rhizobium meliloti IFO 13336 also belongs to this family of structures and T. Harada (Biochem. Soc. Symp., 48 (1983) 97) has reported gelation of this polysaccharide. Thus it is possible that gelation is a common feature of this family of structures. Possible biological and ecological consequences of gelation are discussed.

  structure, Rhizobium, Rhizobium leguminosarum, Agrobacterium, extracellular polysaccharides, ecological, gelation

  Publication DOI: 10.1016/0144-8617(90)90085-7
  Journal NLM ID: 8307156
  Publisher: Elsevier
  Institutions: AFRC Institute of Food Research, Norwich Laboratory, Norwich, UK
  Methods: gelation, rheological study
  
   
  
  Agrobacterium rhizogenes
  CSDB ID 112936 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: EPS
Contained glycoepitopes: IEDB_136044,IEDB_136906,IEDB_137472,IEDB_140629,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_420421,IEDB_423115,IEDB_857742,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88

• Article ID: 1985
  Amemura A, Hisamatsu M, Ghai SK, Harada T "Structural studies on a new polysaccharide, containing D-riburonic acid, from Rhizobium meliloti IFO 13336" - Carbohydrate Research 91 (1981) 59-65
  

  The structure of an extracellular, acidic polysaccharide from Rhizobium meliloti IFO 13336 was studied by a method involving successive fragmentation with specific β-D-glycanases of Flavobacterium M64. The polysaccharide is composed of repeating units of the octasaccharide shown. An acidic component was identified as D-riburonic acid.

  Publication DOI: 10.1016/S0008-6215(00)80991-X
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
  Methods: 1H NMR, methylation, enzymatic hydrolysis, GLC, paper chromatography, Heynz and Lenz method
  
   
  
  Rhizobium meliloti IFO 13336
  CSDB ID 213544 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_140629,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_420421,IEDB_423115,IEDB_857742,IEDB_983931,SB_192

• Article ID: 2058
  Saadat S, Kamisango K, Ballou CE, Dell A "Enzymic degradation of the mycobacterial O-methyl-D-glucose polysaccharide by a Rhizopus-mold alpha amylase, an enzyme active on 6-O-methyl-amylo-oligosaccharides" - Carbohydrate Research 148(2) (1986) 309-319
  

  : An enzyme activity that catalyzes hydrolysis of an α-(1→4)-linked 6-O-methyl-D-glucan was detected in, and purified from, Rhizopus oryzae mold. The enzyme acts like an alpha amylase and digests unmodified amylo-oligosaccharides 10 to 15 times as fast as it does the 6-O-methyl and 6-deoxy derivatives. When the limit product obtained by digesting the mycobacterial O-methyl-D-glucose polysaccharide with pancreatic alpha amylase and Aspergillus glucoamylase was further digested with the Rhizopus alpha amylase, di-, tri-, and tetra-saccharide fragments composed of α-(1→4)-linked 6-O-methyl-D-glucose were released. The rest of the molecule was recovered as oligosaccharides terminated by two, or three, α-(1→4)-linked 6-O-methyl-D-glucose residues.

  NCBI PubMed ID: 3486714
  Publication DOI: 10.1016/s0008-6215(00)90398-7
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Biochemistry, University of California, Berkeley, California 94720 U.S.A., Department of Biochemistry, Imperial College, London SW7 Great Britain
  
   
  
  Mycobacterium
  CSDB ID 114623 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_140629,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_420417,IEDB_420421,IEDB_423115,IEDB_857742,IEDB_983931,SB_192

• Article ID: 2058
  Saadat S, Kamisango K, Ballou CE, Dell A "Enzymic degradation of the mycobacterial O-methyl-D-glucose polysaccharide by a Rhizopus-mold alpha amylase, an enzyme active on 6-O-methyl-amylo-oligosaccharides" - Carbohydrate Research 148(2) (1986) 309-319
  

  : An enzyme activity that catalyzes hydrolysis of an α-(1→4)-linked 6-O-methyl-D-glucan was detected in, and purified from, Rhizopus oryzae mold. The enzyme acts like an alpha amylase and digests unmodified amylo-oligosaccharides 10 to 15 times as fast as it does the 6-O-methyl and 6-deoxy derivatives. When the limit product obtained by digesting the mycobacterial O-methyl-D-glucose polysaccharide with pancreatic alpha amylase and Aspergillus glucoamylase was further digested with the Rhizopus alpha amylase, di-, tri-, and tetra-saccharide fragments composed of α-(1→4)-linked 6-O-methyl-D-glucose were released. The rest of the molecule was recovered as oligosaccharides terminated by two, or three, α-(1→4)-linked 6-O-methyl-D-glucose residues.

  NCBI PubMed ID: 3486714
  Publication DOI: 10.1016/s0008-6215(00)90398-7
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Biochemistry, University of California, Berkeley, California 94720 U.S.A., Department of Biochemistry, Imperial College, London SW7 Great Britain
  
   
  
  Mycobacterium
  CSDB ID 114624 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_140629,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_420417,IEDB_420421,IEDB_423115,IEDB_857742,IEDB_983931,SB_192

• Article ID: 2058
  Saadat S, Kamisango K, Ballou CE, Dell A "Enzymic degradation of the mycobacterial O-methyl-D-glucose polysaccharide by a Rhizopus-mold alpha amylase, an enzyme active on 6-O-methyl-amylo-oligosaccharides" - Carbohydrate Research 148(2) (1986) 309-319
  

  : An enzyme activity that catalyzes hydrolysis of an α-(1→4)-linked 6-O-methyl-D-glucan was detected in, and purified from, Rhizopus oryzae mold. The enzyme acts like an alpha amylase and digests unmodified amylo-oligosaccharides 10 to 15 times as fast as it does the 6-O-methyl and 6-deoxy derivatives. When the limit product obtained by digesting the mycobacterial O-methyl-D-glucose polysaccharide with pancreatic alpha amylase and Aspergillus glucoamylase was further digested with the Rhizopus alpha amylase, di-, tri-, and tetra-saccharide fragments composed of α-(1→4)-linked 6-O-methyl-D-glucose were released. The rest of the molecule was recovered as oligosaccharides terminated by two, or three, α-(1→4)-linked 6-O-methyl-D-glucose residues.

  NCBI PubMed ID: 3486714
  Publication DOI: 10.1016/s0008-6215(00)90398-7
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Biochemistry, University of California, Berkeley, California 94720 U.S.A., Department of Biochemistry, Imperial College, London SW7 Great Britain
  
   
  
  Mycobacterium
  CSDB ID 114625 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_130701,IEDB_137473,IEDB_137485,IEDB_140629,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_152206,IEDB_423115,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_72

• Article ID: 2367
  Neal DJ, Wilkinson SG "Lipopolysaccharides from Pseudomonas maltophilia. Structural studies of the side-chain, core, and lipid-A regions of the lipopolysaccharide from strain NCTC 10257" - European Journal of Biochemistry 128 (1982) 143-149
  

  Structural studies have been carried out on the O-specific polysaccharide, the core oligosaccharide, and the lipid A from the lipopolysaccharide of Pseudomonas maltophilia NCTC 10257. By means of 13C nuclear magnetic resonance spectroscopy, a tetrasaccharide repeating-unit for the O-specific polymer has been confirmed. However, the data suggest that the L-rhamnopyranosyl residue at the branching point has the alpha configuration rather than beta as proposed previously [Neal, D.J. and Wilkinson, S.G. (1979) Carbohydr. Res. 69, 191-201]. The core oligosaccharide contains residues of D-glucose, D-mannose phosphate, D-galactosamine (not N-acetylated), D-galacturonic acid, and a 3-deoxyoctulosonic acid (but no aldoheptose). A partial structure for the oligosaccharide is proposed. Lipid A is based on phosphorylated glucosamine residues, with N-fatty acyl and O-fatty acyl substituents. The major fatty acids are 9-methyldecanoic acid, 2-hydroxy-9-methyldecanoic acid, 3-hydroxy-9-methyldecanoic acid (each ester-linked), 3-hydroxydodecanoic acid, and 3-hydroxy-11-methyldodecanoic acid (both mainly amide-linked). The results of this study provide further evidence for a relationship between P. maltophilia and some Xanthomonas species.

  NCBI PubMed ID: 71732011
  Publication DOI: 10.1111/j.1432-1033.1982.tb06944.x
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Institutions: Department of Chemistry, University of Hull
  Methods: 13C NMR, 1H NMR, GC-MS
  
   
  
  Pseudomonas maltophilia NCTC 10257
  CSDB ID 122685 (all data & tools)