Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_136045,IEDB_142489,IEDB_144562,IEDB_152214,IEDB_174333,SB_86

• Article ID: 79
  Forsberg LS, Bhat UR, Carlson RW "Structural characterization of the O-antigenic polysaccharide of the lipopolysaccharide from Rhizobium etli strain CE3. A unique O-acetylated glycan of discrete size, containing 3-O-methyl-6-deoxy-L-talose and 2,3,4-tri-O-methyl-L-fucose" - Journal of Biological Chemistry 275(25) (2000) 18851-18863
  

  The O-antigenic polysaccharide of the Rhizobium etli CE3 lipopolysaccharide (LPS) was structurally characterized using chemical degradations (Smith degradation and beta-elimination of uronosyl residues) in combination with alkylation analysis, electrospray, and matrix-assisted laser desorption ionization-time of flight mass spectrometry, tandem mass spectrometry, and (1)H COSY and TOCSY nuclear magnetic resonance spectroscopy analyses of the native polysaccharide and the derived oligosaccharides. The polysaccharide was found to be a unique, relatively low molecular weight glycan having a fairly discrete size, with surprisingly little variation in the number of repeating units (degree of polymerization = 5). The polysaccharide is O-acetylated and contains a variety of O-methylated glycosyl residues, rendering the native glycan somewhat hydrophobic. The molecular mass of the major de-O-acetylated species, including the reducing end 3-deoxy-d-manno-2-octulosonic acid (Kdo) residue, is 3330 Da. The polysaccharide is comprised of a trisaccharide repeating unit having the structure →4)-α-D-GlcpA-(1→4)-[α-3-O-Me-6-deoxy-Talp-(1→3)]-α-l-Fucp-(1→. The nonreducing end of the glycan is terminated with the capping sequence α-2,3,4-tri-O-Me-Fucp-(1→4)-α-D-GlcpA-(1→, and the reducing end of the molecule consists of the non-repeating sequence →3)-α-L-Fucp-(1→3)-β-D-Manp-(1→3)-β-QuiNA cp-(1→4)-alpha-Kdop-(2→, where QuiNAc is N-acetylquinovosamine (2-N-acetamido-2,6-dideoxyglucose). The reducing end Kdo residue links the O-chain polysaccharide to the core region oligosaccharide, resulting in a unique location for a Kdo residue in LPS, removed four residues distally from the lipid A moiety. Structural heterogeneity in the O-chain arises mainly from the O-acetyl and O-methyl substitution. Methylation analysis using trideuteriomethyl iodide indicates that a portion of the 2,3,4-tri-O-methylfucosyl capping residues, typically 15%, are replaced with 2-O-methyl- and/or 2,3-di-O-methylfucosyl residues. In addition, approximately 25% of the 3,4-linked branching fucosyl residues and 10% of the 3-linked fucosyl residues are 2-O-methylated. A majority of the glucuronosyl residues are methyl-esterified at C-6. These unique structural features may be significant in the infection process

  Lipopolysaccharide, O-antigen, Rhizobium etli, 6-deoxy-L-talose, symbiosis

  NCBI PubMed ID: 10858446
  Publication DOI: 10.1074/jbc.M001090200
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: rcarlson@ccrc.uga.edu
  Institutions: Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, USA
  Methods: methylation, sugar analysis, ESI-MS, ESI-MS/MS
  
   
  
  Rhizobium etli CE3
  CSDB ID 2183 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_136045,IEDB_142489,IEDB_144562,IEDB_152214,IEDB_174333,SB_86

• Article ID: 79
  Forsberg LS, Bhat UR, Carlson RW "Structural characterization of the O-antigenic polysaccharide of the lipopolysaccharide from Rhizobium etli strain CE3. A unique O-acetylated glycan of discrete size, containing 3-O-methyl-6-deoxy-L-talose and 2,3,4-tri-O-methyl-L-fucose" - Journal of Biological Chemistry 275(25) (2000) 18851-18863
  

  The O-antigenic polysaccharide of the Rhizobium etli CE3 lipopolysaccharide (LPS) was structurally characterized using chemical degradations (Smith degradation and beta-elimination of uronosyl residues) in combination with alkylation analysis, electrospray, and matrix-assisted laser desorption ionization-time of flight mass spectrometry, tandem mass spectrometry, and (1)H COSY and TOCSY nuclear magnetic resonance spectroscopy analyses of the native polysaccharide and the derived oligosaccharides. The polysaccharide was found to be a unique, relatively low molecular weight glycan having a fairly discrete size, with surprisingly little variation in the number of repeating units (degree of polymerization = 5). The polysaccharide is O-acetylated and contains a variety of O-methylated glycosyl residues, rendering the native glycan somewhat hydrophobic. The molecular mass of the major de-O-acetylated species, including the reducing end 3-deoxy-d-manno-2-octulosonic acid (Kdo) residue, is 3330 Da. The polysaccharide is comprised of a trisaccharide repeating unit having the structure →4)-α-D-GlcpA-(1→4)-[α-3-O-Me-6-deoxy-Talp-(1→3)]-α-l-Fucp-(1→. The nonreducing end of the glycan is terminated with the capping sequence α-2,3,4-tri-O-Me-Fucp-(1→4)-α-D-GlcpA-(1→, and the reducing end of the molecule consists of the non-repeating sequence →3)-α-L-Fucp-(1→3)-β-D-Manp-(1→3)-β-QuiNA cp-(1→4)-alpha-Kdop-(2→, where QuiNAc is N-acetylquinovosamine (2-N-acetamido-2,6-dideoxyglucose). The reducing end Kdo residue links the O-chain polysaccharide to the core region oligosaccharide, resulting in a unique location for a Kdo residue in LPS, removed four residues distally from the lipid A moiety. Structural heterogeneity in the O-chain arises mainly from the O-acetyl and O-methyl substitution. Methylation analysis using trideuteriomethyl iodide indicates that a portion of the 2,3,4-tri-O-methylfucosyl capping residues, typically 15%, are replaced with 2-O-methyl- and/or 2,3-di-O-methylfucosyl residues. In addition, approximately 25% of the 3,4-linked branching fucosyl residues and 10% of the 3-linked fucosyl residues are 2-O-methylated. A majority of the glucuronosyl residues are methyl-esterified at C-6. These unique structural features may be significant in the infection process

  Lipopolysaccharide, O-antigen, Rhizobium etli, 6-deoxy-L-talose, symbiosis

  NCBI PubMed ID: 10858446
  Publication DOI: 10.1074/jbc.M001090200
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: rcarlson@ccrc.uga.edu
  Institutions: Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, USA
  Methods: methylation, sugar analysis, ESI-MS, ESI-MS/MS
  
   
  
  Rhizobium etli CE3
  CSDB ID 2184 (all data & tools)

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Structure type: oligomer
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531

• Article ID: 1550
  Ovchinnikova OG, Kocharova NA, Torzewska A, Blaszczyk A, Shashkov AS, Knirel YA, Rozalski A "The structure of the O-polysaccharide from the lipopolysaccharide of Providencia stuartii O43 containing an amide of D-galacturonic acid with L-serine" - Carbohydrate Research 340(7) (2005) 1407-1411
  

  The O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Providencia stuartii O43:H28 and studied by sugar and methylation analyses, Smith degradation and 1H and 13C NMR spectroscopy, including 2D ROESY, and H-detected 1H, 13C HSQC and HMBC experiments, as well as a NOESY experiment in a 9:1 H2O/D2O mixture to reveal correlations for NH protons. It was found that the polysaccharide is built up of linear tetrasaccharide repeating units containing an amide of D-galacturonic acid with L-serine [D-GalA6(L-Ser)] and has the following structure:[3)-β-D-GalpA6(L-Ser)-(1→3)-β-D-GlcpNAc-(1→2)-α-D-Rhap4NAc-(1→4)-β-D-GlcpA-(1→]n.

  Lipopolysaccharide, O-antigen, polysaccharide structure, Providencia stuartii, D-galacturonoyl-L-serine

  NCBI PubMed ID: 15854614
  Publication DOI: 10.1016/j.carres.2005.03.011
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology and Immunology, University of Lodz, PL-90237 Lodz, Poland
  Methods: methylation, NMR, sugar analysis, Smith degradation
  
   
  
  Providencia stuartii O43
  CSDB ID 10306 (all data & tools)

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Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_135813,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_141807,IEDB_151531,IEDB_885822

• Article ID: 1820
  L'vov VL, Tokhtamysheva NV, Shaskov AS, Dmitriev BA, Kochetkov NK "Bacterial antigenic polysaccharides. XII. The structure and 13C NMR spectrum of polysaccharide chain of Shigella boydii type 8 lipopolysaccharide" - Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 9 (1983) 60-73
  

  A specific acidic polysaccharide was isolated from Sh. boydii type 8 antigenic lipopolysaccharide after mild hydrolysis followed by chromatography on Sephadex G-50. The polysaccharide consists of D-glucuronic acid, D-galacturonic acid, 2-acetamido-2-deoxy-D-glucose, 2-acetamido-2-deoxy-D-galactose and 2-amino-1,3-propanediol residues in 1:1:1:1:1 ratio. From the results of methylation analysis, partial acid hydrolysis and Smith degradation, the structure of the repeating unit of the specific polysaccharide was deduced as: (Formula: see text). The 13C NMR spectra of native, O-deacetylated and carboxyl-reduced polysaccharides, as well as the spectrum of oligosaccharide produced by Smith degradation were interpreted. The 13C NMR data fully confirmed the structure of the polysaccharide repeating unit.

  NCBI PubMed ID: 6207837
  Journal NLM ID: 7804941
  Publisher: Moskva: Nauka
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Academy of Sciences of the USSR, Moscow, Russia
  Methods: 13C NMR
  
   
  
  Shigella boydii 8
  CSDB ID 2777 (all data & tools)

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Structure type: oligomer
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_136044,IEDB_137472,IEDB_141794,IEDB_190606,SB_165,SB_166,SB_187,SB_195,SB_7,SB_88

• Article ID: 3959
  Varbanets LD, Skoklyuk LB, Zdorovenko EL, Shubchynskyy VV, Pokhil SI "Rahnella aquatilis 95U003 lipopolysaccharide" - Mikrobiologiia = Microbiology [Russian] 79(5) (2010) 602-611
  

  The lipopolysaccharide of a new species of Enterobacteriaceae, Rahnella aquatilis 95U003, was isolated and investigated. The structural components of the lipopolysaccharide molecule, lipid A, core oligosaccharide, and Ospecific polysaccharide, were isolated by mild acidic hydrolysis. In lipid A, 3hydroxytetradecanoic (64.3%) and tetradecanoic (22.3%) acids were found to be predominant fatty acids. In fractions 1 and 2 of the core oligosaccharides, galactose (36.6 and 43.6%), mannose (35.5 and 23.5%), and glucose (42.1 and 25.3%) were shown to be the major monosaccharides. The O-specific polysaccharide consisted of regularly repeating hexasaccharide units of the following structure: (formula, see text).

  Lipopolysaccharide, Rahnella aquatilis, O-specific polysaccharide composition and structure

  Publication DOI: 10.1134/S0026261710050048
  Journal NLM ID: 0376652
  Publisher: Moskva: Izdatelstvo Nauka
  Correspondence: varbanets@serv.imv.kiev.ua
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, str.. Zabolotnogo 154, Kyiv, D 03680 Ukraine, Mechnikov Institute of Microbiology and Immunology, Academy of Medical Sciences, ul. Pushkinskaya 1416, Kharkiv, 61057 Ukraine
  Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, SDS-PAGE, sugar analysis, GLC, mild acid hydrolysis, Smith degradation, serological methods
  
   
  
  Rahnella aquatilis 95U003
  CSDB ID 25874 (all data & tools)

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Structure type: oligomer
Trivial name: heparosan (K5-antigen)
Compound class: CPS
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531

• Article ID: 4882
  Senchenkova SN, Zhang Y, Perepelov AV, Guo X, Shashkov AS, Liu B, Knirel YA "Structure and biosynthesis gene cluster of the O-antigen of Escherichia coli O12" - Biochemistry (Moscow) 81(4) (2016) 401-406
  

  Two polysaccharides were isolated from Escherichia coli O12, the major being identified as the O12-antigen and the minor as the K5-antigen. The polysaccharides were studied by sugar analysis, Smith degradation, and one- and two-dimensional (1)H and (13)C NMR spectroscopy. As a result, the following structure of the O12-polysaccharide was elucidated, which, to our knowledge, has not been hitherto found in bacterial carbohydrates: →2)-β-d-Glcp-(1→6)-α-d-GlcpNAc-(1→3)-α-l-FucpNAc-(1→3)-β-d-GlcpNAc-(1→. The →4)-β-d-GlcpA-(1→4)-α-d-GlcpNAc-(1→ structure established for the K5-polysaccharide (heparosan) is previously known. Functions of genes in the O-antigen biosynthesis gene cluster of E. coli O12 were assigned by comparison with sequences in the available databases and found to be consistent with the O12-polysaccharide structure.

  Escherichia coli, glycosyltransferase, O-antigen gene cluster, O-Polysaccharide structure

  NCBI PubMed ID: 27293097
  Publication DOI: 10.1134/S0006297916040106
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Correspondence: yknirel@gmail.com
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Nankai University, TEDA Institute of Biological Sciences and Biotechnology,300457 Tianjin, P. R. China
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, GLC, Smith degradation, NMR-1D, GPC, mild acid degradation, function analysis of gene clusters
  
   
  
  Escherichia coli O12 (G1280)
  CSDB ID 11554 (all data & tools)

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Structure type: oligomer
Trivial name: type K20 CPS
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_1391962,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_143794,IEDB_150899,IEDB_151531,IEDB_151771,IEDB_190606,SB_137,SB_165,SB_166,SB_187,SB_195,SB_29,SB_7,SB_88

• Article ID: 5166
  Kasimova AA, Kenyon JJ, Arbatsky NP, Shashkov AS, Popova AV, Shneider MM, Knirel YA, Hall RM "Acinetobacter baumannii K20 and K21 capsular polysaccharide structures establish roles for UDP-glucose dehydrogenase Ugd2, pyruvyl transferase Ptr2 and two glycosyltransferases" - Glycobiology 28(11) (2018) 876-884
  

  Infections caused by Acinetobacter baumannii isolates from the major global clones, GC1 and GC2, are difficult to treat with antibiotics, and phage therapy, which requires extensive knowledge of the variation in the surface polysaccharides, is an option under consideration. The gene clusters directing the synthesis of capsular polysaccharide (CPS) in A. baumannii GC1 isolate A388 and GC2 isolate G21 differ by a single glycosyltransferase (gtr) gene. They include genes encoding a novel UDP-glucose dehydrogenase (Ugd2) and a putative pyruvyl transferase (Ptr2). The composition and structures of the linear K20 and K21 tetrasaccharide repeats (K units) of the CPSs isolated from A338 and G21, respectively, were established by sugar analyses and Smith degradation along with 1D and 2D 1H and 13C NMR spectroscopy. The K20 and K21 CPSs are the first known to include GlcpA produced by Ugd2 and d-galactose with an (R)-configured 4,6-pyruvic acid acetal added by Prt2. The first sugar in the tetrasaccharide K units is 2-acetamido-4-amino-2,4,6-trideoxy-d-glucose (d-QuipNAc4N) that carries a 4-N-[(S)-3-hydroxybutanoyl] group in some K units and a 4-N-acetyl group in the others. Accordingly, K unit polymerases WzyK20 and WzyK21 form a β-d-QuipNAc4NR-(1→2)-d-Galp bond. The K20 and K21 units differ only in the configuration of the glycosidic linkages of d-GlcpNAc allowing the unique inverting glycosyltransferases Gtr43 and the retaining glycosyltransferase Gtr45 to be assigned to the formation of the β-d-GlcpNAc-(1→4)-d-GlcpA and α-d-GlcpNAc-(1→4)-d-GlcpA linkages, respectively.

  Acinetobacter baumannii, capsular polysaccharide, glucuronic acid, Pyruvic acid acetal, K locus

  NCBI PubMed ID: 30107435
  Publication DOI: 10.1093/glycob/cwy074
  Journal NLM ID: 9104124
  Publisher: IRL Press at Oxford University Press
  Correspondence: johanna.kenyon@qut.edu.au
  Institutions: M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninskii prosp., Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, 9 Miusskaya pl., Moscow, Russia, School of Molecular Bioscience, The University of Sydney, Cnr of Maze Cres and Butlin Ave, Darlington Campus, Sydney, Australia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, Brisbane, Australia, Moscow Institute of Physics and Technology, 9 Institutskii per., Dolgoprudny, Moscow Region, Russia, School of Life and Environmental Sciences, The University of Sydney, Cnr of Maze Cres and Butlin Ave, Darlington Campus, Sydney, Australia
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, GLC, Smith degradation, GPC, bioinformatic analysis (BLASTp)
  
   
  
  Acinetobacter baumannii A388
  CSDB ID 12622 (all data & tools)