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Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_130689,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_1391963,IEDB_141584,IEDB_141794,IEDB_143260,IEDB_149136,IEDB_190606,IEDB_885822,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_88

• Article ID: 1573
  Urbina F, Nordmark EL, Yang Z, Weintraub A, Scheutz F, Widmalm G "Structural elucidation of the O-antigenic polysaccharide from the enteroaggregative Escherichia coli strain 180/C3 and its immunochemical relationship with E. coli O5 and O65" - Carbohydrate Research 340(4) (2005) 645-650
  

  The structure of the O-antigen polysaccharide (PS) from the enteroaggregative Escherichia coli strain 180/C3 has been determined. Sugar and methylation analysis together with (1)H and (13)C NMR spectroscopy were the main methods used. The PS is composed of tetrasaccharide repeating units with the following structure:Analysis of NMR data indicates that the presented sequence of sugar residues also represents the biological repeating unit of the O-chain. The structure is closely related to that of O-antigen polysaccharide from E. coli O5 and partially to that of E. coli O65. The difference between the O-antigen from the 180/C3 strain and that of E. coli O5 is the linkage to the d-Quip3NAc residue, which in the latter strain is 4-O-substituted. The E. coli O65 O-antigen contains as part of its linear pentasaccharide repeating unit a similar structural element, namely →4)-β-D-GalpA-(1→3)-α-D-GlcpNAc-(1→2)-β-D-Quip3NAc-(1→, thereby indicating that a common epitope could be present for the two polysaccharides. Monospecific anti-E. coli O5 rabbit serum did not distinguish between the two positional isomeric structures neither in slide agglutination nor in an indirect enzyme immunoassay. The anti-O65 serum did react with both the 180/C3 and O5 LPS showing a partial cross-reactivity

  Lipopolysaccharide, NMR, LPS, structure, common, tetrasaccharide, chemistry, clinical, strain, structural, polysaccharide, methylation analysis, O-antigen, repeating unit, analysis, polysaccharides, O antigen, Escherichia, Escherichia coli, O-antigenic, O-antigenic polysaccharide, epitope, NMR spectroscopy, serology, biological, linkage, sugar, methylation, medicine, spectroscopy, method, elucidation, immunochemical, sequence, enzyme, O-chain, difference, pentasaccharide, methods, linear, relationship, serum, cross-reactivity, crossreactivity, bacteriology, enzyme immunoassay, immunoassay, indirect enzyme immunoassay, biological repeating unit, Enteroaggregative, rabbit, physiological, agglutination

  NCBI PubMed ID: 15721335
  Publication DOI: 10.1016/j.carres.2005.01.001
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: G. Widmalm
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, Department of Chemistry and Physiological Sciences, Universidad Nacional Autonoma de Nicaragua, UNAN-Leon, Nicaragua, Department of Laboratory Medicine, Division of Clinical Bacteriology, Karolinska Institutet, Karolinska University Hospita, Huddinge, Stockholm, Sweden, The International Escherichia and Klebsiella Centre (WHO), Artillerivej 5, DK-2300 Copenhagen S, Denmark
  Methods: methylation, NMR, sugar analysis
  
   
  
  Escherichia coli 180/C3
  CSDB ID 10174 (all data & tools)
• Article ID: 4611
  Sarkar A, Fontana C, Imberty A, Perez S, Widmalm G "Conformational Preferences of the O-Antigen Polysaccharides of Escherichia coli O5ac and O5ab Using NMR Spectroscopy and Molecular Modeling" - Biomacromolecules 14(7) (2013) 2215-2224
  

  Escherichia coli serogroup O5 comprises two different subgroups (O5ab and O5ac), which are indiscernible from the point of view of standard immunological serotyping. The structural similarities between the O-antigen polysaccharides (PSs) of these two strains are remarkable, with the only difference being the glycosidic linkage connecting the biological tetrasaccharide repeating units. In the present study, a combination of NMR spectroscopy and molecular modeling methods were used to elucidate the conformational preferences of these two PSs. The NMR study was based on the analysis of intra- and inter-residue proton-proton distances using NOE build-up curves. Molecular models of the repeating units and their extension to polysaccharides were obtained, taking into account the conformational flexibility as assessed by the force field applied and a genetic algorithm. The agreements between experimentally measured and calculated distances could only be obtained by considering an averaging of several low energy conformations observed in the molecular models.

  NMR, conformation, O-antigen, Escherichia coli, molecular modeling

  NCBI PubMed ID: 23721050
  Publication DOI: 10.1021/bm400354y
  Journal NLM ID: 100892849
  Publisher: Washington, DC: American Chemical Society
  Correspondence: serge.perez@cermav.cnrs.fr; gw@organ.su.se
  Institutions: Centre de Recherches sur les Macromolecules Vegetales - CNRS, affiliated with Universite Grenoble and ICMG, BP 53 X, 38041 Grenoble Cedex, France
  Methods: 13C NMR, 1H NMR, NMR-2D, conformation analysis, molecular modeling
  
   
  
  Escherichia coli O5ac
  CSDB ID 29338 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_130689,IEDB_134627,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_1391963,IEDB_141584,IEDB_141794,IEDB_143260,IEDB_149136,IEDB_190606,IEDB_885822,SB_165,SB_166,SB_187,SB_195,SB_23,SB_24,SB_7,SB_8,SB_88

• 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 O5ac strain 180/C3
  CSDB ID 20638 (all data & tools)
• Article ID: 4012
  Duda KA, Lindner B, Brade H, Leimbach A, Brzuszkiewicz E, Dobrindt U, Holst O "The lipopolysaccharide of the mastitis isolate Escherichia coli strain 1303 comprises a novel O-antigen and the rare K-12 core type" - Microbiology 157(Pt6) (2011) 1750-1760
  

  Mastitis represents one of the most significant health problems of dairy herds. The two major causative agents of this disease are Escherichia coli and Staphylococcus aureus. Of the first, its lipopolysaccharide (LPS) is thought to play a prominent role during infection. Here, we report the O-antigen (OPS, O-specific polysaccharide) structure of the LPS from bovine mastitis isolate E. coli 1303. The structure was determined utilizing chemical analyzes, mass spectrometry as well as 1D and 2D NMR spectroscopy methods. The O-repeating unit was characterized as -[→4)-β-D-Quip3NAc-(1→3)-α-L-Fucp2OAc-(1→4)-β-D-Galp-(1→3)-α-D-GalpNAc-(1→]- in which the O-acetyl substitution was non-stoichiometric. The nucleotide sequence of the O-antigen gene cluster of E. coli strain 1303 was also determined. In large parts, this determinant located between the gnd and galF genes comprises a presently unknown DNA sequence with 13 putative open reading frames. The O-antigen of E. coli 1303 was shown to substitute O-7 of the terminal L,D-heptose of the K-12 core oligosaccharide. Interestingly, the non-OPS-substituted core oligosaccharide represented a truncated version of the K-12 outer core, namely terminal L,D-heptose and glucose were missing, however, it possessed a third Kdo residue in the inner core. On the base of structural and genetic data we show that the mastitis isolate E. coli strain 1303 represents a new subtype of serotype O5 and possesses the K-12 core type which is rather uncommon among human and bovine isolates.

  Lipopolysaccharide, structure, O-antigen, Escherichia coli, NMR spectroscopy, gene cluster, Staphylococcus aureus, mastitis

  NCBI PubMed ID: 21372091
  Publication DOI: 10.1099/mic.0.046912-0
  Journal NLM ID: 0376646
  Publisher: Washington, DC: Kluwer Academic/Plenum Publishers
  Correspondence: Katarzyna Duda
  Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, D-23845 Borstel, Germany, Division of Immunochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, D-23845 Borstel, Germany, Division of Medical and Biochemical Microbiology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, D-23845 Borstel, Germany, Institute for Molecular Infection Biology, Julius-Maximilians-University of Würzburg, D-97070 Würzburg, Germany, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, D-37077 Göttingen, Germany, Institute for Hygiene, University of Münster, D-48149 Münster, Germany
  Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, SDS-PAGE, sugar analysis, GLC, ESI-FTICR-MS, Western blotting, de-O-acylation with hydrazine, NMR-1D, methanolysis
  
   
  
  Escherichia coli O5ac
  CSDB ID 26610 (all data & tools)
• Article ID: 4016
  Feinberg H, Taylor ME, Razi N, McBride R, Knirel YA, Graham SA, Drickamer K, Weis WI "Structural basis for langerin recognition of diverse pathogen and mammalian glycans through a single binding site" - Journal of Molecular Biology 405(4) (2011) 1027-1039
  

  Langerin mediates the carbohydrate-dependent uptake of pathogens by Langerhans cells in the first step of antigen presentation to the adaptive immune system. Langerin binds to an unusually diverse number of endogenous and pathogenic cell surface carbohydrates, including mannose-containing O-specific polysaccharides derived from bacterial lipopolysaccharides identified here by probing a microarray of bacterial polysaccharides. Crystal structures of the carbohydrate-recognition domain from human langerin bound to a series of oligomannose compounds, the blood group B antigen, and a fragment of ?-glucan reveal binding to mannose, fucose, and glucose residues by Ca(2+) coordination of vicinal hydroxyl groups with similar stereochemistry. Oligomannose compounds bind through a single mannose residue, with no other mannose residues contacting the protein directly. There is no evidence for a second Ca(2+)-independent binding site. Likewise, a ?-glucan fragment, Glc?1-3Glc?1-3Glc, binds to langerin through the interaction of a single glucose residue with the Ca(2+) site. The fucose moiety of the blood group B trisaccharide Gal?1-3(Fuc?1-2)Gal also binds to the Ca(2+) site, and selective binding to this glycan compared to other fucose-containing oligosaccharides results from additional favorable interactions of the nonreducing terminal galactose, as well as of the fucose residue. Surprisingly, the equatorial 3-OH group and the axial 4-OH group of the galactose residue in 6SO(4)-Gal?1-4GlcNAc also coordinate Ca(2+), a heretofore unobserved mode of galactose binding in a C-type carbohydrate-recognition domain bearing the Glu-Pro-Asn signature motif characteristic of mannose binding sites. Salt bridges between the sulfate group and two lysine residues appear to compensate for the nonoptimal binding of galactose at this site.

  carbohydrate recognition, langerin, C-type lectin

  NCBI PubMed ID: 21112338
  Publication DOI: 10.1016/j.jmb.2010.11.039
  Journal NLM ID: 2985088R
  Publisher: Elsevier
  Correspondence: bill.weis@stanford.edu
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA, Division of Molecular Biosciences, Department of Life Sciences, Imperial College, London SW7 2AZ, UK, Glycan Array Synthesis Core-D, Consortium for Functional Glycomics, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
  Methods: crystallization
  
   
  
  Escherichia coli 180/C3
  CSDB ID 26620 (all data & tools)
• Article ID: 4291
  Dziadziuszko H, Kumirska J, Muza S, Czerwicka M, Lubecka EA, Stepnowski P, Kunikowska D "Immunochemical studies of Salmonella Dakar and Salmonella Telaviv O-antigens (serogroup O:28)" - FEMS Microbiology Letters 326(1) (2012) 55-61
  

  Salmonella Dakar and Salmonella Telaviv bacteria belong to serogroup O:28, which represents 107 serovars and possesses only the epitope O28. Salmonella Telaviv has the subfactors O28(1) and O28(2) , whereas S. Dakar has O28(1) and O28(3) . So far, only limited serological and immunological information for this serogroup is available in the literature. Knowledge of the structures of their O-polysaccharides and the immunochemical investigations performed in this work allowed to reveal the nature of subfactor O28(1) as attributed to the presence of 3-linked (or 3,4-disubstituted) α-D-GalpNAc in the main chains of S. Dakar and S. Telaviv O-polysaccharides. An explanation for the cross-reactions between Salmonella enterica O28 O-antigens and other Salmonella O-polysaccharides and their structural similarity to Escherichia coli O-serogroups is also given.

  monoclonal antibody, Serogroup O:28, Salmonella bacterial strains, immunochemical study, O-antigen (OPS), epitope O28

  NCBI PubMed ID: 22092663
  Publication DOI: 10.1111/j.1574-6968.2011.02431.x
  Journal NLM ID: 7705721
  Publisher: Blackwell Publishing
  Correspondence: kumirska@ chem.univ.gda.pl
  Institutions: Department of Molecular Microbiology and Serology, National Salmonella Centre, Medical University of Gdansk, Gdansk, Poland
  Methods: SDS-PAGE, ELISA, serological methods, periodate oxidation
  
   
  
  Escherichia coli C3
  CSDB ID 28335 (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 O5ac
  CSDB ID 1505 (all data & tools)