Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 114
  Toukach FV, Shashkov AS "Computer-assisted structural analysis of regular glycopolymers on the basis of 13C NMR data" - Carbohydrate Research 335(2) (2001) 101-104
  

  A computer-assisted approach to the prediction of the primary structures of regular glycopolymers is described. The analysis is based on comparing the calculated 13C NMR spectra of all the possible structures of the repeating unit (for the given monomeric composition) to an experimental 13C NMR spectrum. The spectra generation is based on the spectral database containing information on the 13C chemical shifts of monomers, di- and trimeric fragments. If the required data are missing from this database, the special database for average glycosylation effects is used. The analysis reveals those structures with the calculated 13C NMR spectrum most close to observed. The structures of repeating units of any topology containing up to six residues linked by glycosidic, amidic or phospho-diester bridges can be predicted. Unambiguous selection of the proper structure from the output list of possible structures may require additional experimental data. Testing the created program and databases on bacterial polysaccharides and their derivatives containing up to three non-sugar residues (alditols, amino acids, phosphate groups etc.) per repeating unit revealed the good convergence of prediction with independently obtained structural data.

  NMR, structural, analysis, structural analysis, 13C NMR, calculation, computer, glycopolymer, regular

  NCBI PubMed ID: 11567641
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: tou@cacr.ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 117913 Moscow, Russian Federation.
  Methods: NMR simulation
  
   
  
  Proteus penneri 2
  CSDB ID 5427 (all data & tools)
• Article ID: 1222
  Shashkov AS, Arbatsky NP, Toukach FV, Knirel YA, Moll H, Zähringer U, Zych K, Sidorczyk Z "Structure of the O-specific polysaccharide of a serologically separate strain of Proteus penneri 2 from a new proposed serogroup O66" - European Journal of Biochemistry 261(2) (1999) 392-397
  

  structure, strain, polysaccharide, neutral, O-specific, O-specific polysaccharide, Proteus, serogroup, Proteus penneri, 6-deoxy-L-talose, 2, 3, 3-diamino-2, serologically, 3-diacetamido-2, 6-trideoxy-L-mannose

  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
  Methods: NMR
  
   
  
  Proteus penneri 2
  CSDB ID 4757 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 1097
  Perepelov AV, Senchenkova SN, Shashkov AS, Rozalski A, Knirel YA "Structure of the O-specific polysaccharide of the bacterium Proteus vulgaris O15 containing a novel regioisomer of N-acetylmuramic acid" - Carbohydrate Research 337(24) (2002) 2463-2468
  

  An acidic O-specific polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Proteus vulgaris O15 and studied by sugar and methylation analyses along with 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, ROESY, and H-detected 1H,(13)C HMQC experiments. The polysaccharide was found to contain an ether of GlcNAc with lactic acid, and the following structure of the repeating unit was established: →3)-α-D-GlcpNAc4(R-Lac)6Ac-(1→2)-β-D-GlcpA-(1→3)-α-L6dTalp2Ac-(1→3)-β-D-GlcpNAc-(1→ where L6dTal and D-GlcNAc4(R-Lac) are 6-deoxy-L-talose and 2-acetamido-4-O-[(R)-1-carboxyethyl]-2-deoxy-D-glucose, respectively. The latter sugar, which to our knowledge has not been hitherto found in nature, was isolated from the polysaccharide by solvolysis with anhydrous triflic acid and identified by comparison with the authentic synthetic compound. Serological studies with the Smith-degraded polysaccharide showed an importance of 2-substituted GlcA for manifesting of the immunospecificity of P. vulgaris O15.

  Lipopolysaccharide, NMR, LPS, structure, polysaccharide, O-antigen, acid, phosphate, bacteria, O-specific, O-specific polysaccharide, Proteus, Proteus vulgaris, teichoic acid-like, glycerol

  NCBI PubMed ID: 12493231
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: perepel@ioc.ac.ru
  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, 90- 237 Lodz, Poland, Centre of Microbiology and Virology, Polish Academy of Sciences, Lodowa 106, 93- 232 Lodz, Poland
  Methods: methylation, NMR-2D, NMR, sugar analysis
  
   
  
  Proteus penneri 2 (O66)
  CSDB ID 4165 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 1222
  Shashkov AS, Arbatsky NP, Toukach FV, Knirel YA, Moll H, Zähringer U, Zych K, Sidorczyk Z "Structure of the O-specific polysaccharide of a serologically separate strain of Proteus penneri 2 from a new proposed serogroup O66" - European Journal of Biochemistry 261(2) (1999) 392-397
  

  structure, strain, polysaccharide, neutral, O-specific, O-specific polysaccharide, Proteus, serogroup, Proteus penneri, 6-deoxy-L-talose, 2, 3, 3-diamino-2, serologically, 3-diacetamido-2, 6-trideoxy-L-mannose

  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
  Methods: NMR
  
   
  
  Proteus penneri 2
  CSDB ID 4674 (all data & tools)
• Article ID: 3463
  Drzewiecka D, Arbatsky NP, Shashkov AS, Staczek P, Knirel YA, Sidorczyk Z "Structure and serological properties of the O-antigen of two clinical Proteus mirabilis strains classified into a new Proteus O77 serogroup" - FEMS Immunology and Medical Microbiology 54(2) (2008) 185-194
  

  Two Proteus mirabilis strains, 3 B-m and 3 B-k, were isolated from urine and faeces of a hospitalized patient from Lodz, Poland. It was suggested that one strain originated from the other, and the presence of the bacilli in the patient’s urinary tract was most probably a consequence of autoinfection. The O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of P. mirabilis 3 B-m and studied by sugar analysis and nuclear magnetic resonance spectroscopy, including two-dimensional rotating frame Overhause effect spectroscopy (ROESY) and 1H,13C heteronuclear single quantum coherence (HSQC) experiments. The following structure of the linear trisaccharide-repeating unit of the O-polysaccharide was established: ! 2)-b-D-Glcp-(1 ! 3)-a-L-6dTalp2Ac-(1 ! 3)-b-D-GlcpNAc-(1 ! where 6dTal2Ac stands for 2-O-acetyl-6-deoxy-L-talose. It resembles the structure of the O-polysaccharide of Proteus penneri O66, which includes additional lateral residues of 2,3-diacetamido-2,3,6-trideoxy-L-mannose. The lipopolysaccharides from two P. mirabilis strains studied were serologically identical to each other but not to that from any of the existing 76 Proteus O-serogroups. Therefore, the strains were classified into a new O77 serogroup specially created in the genus Proteus. Serological studies using Western blot and enzyme-linked immunosorbent assay with intact and adsorbed O-antisera showed that the P. mirabilis O77 antigen is related to Proteus vulgaris O2 and P. penneri O68 antigens, and a putative disaccharide epitope responsible for the cross-reactivity was revealed.

  Lipopolysaccharide, O-specific polysaccharide, Proteus mirabilis, 6-deoxy-L-talose, autoinfection

  NCBI PubMed ID: 18665848
  Journal NLM ID: 9315554
  Publisher: Elsevier
  Correspondence: domkam@biol.uni.lodz.pl
  Institutions: Department of General Microbiology,Institute of Microbiology and Immunology,University of Lodz, Banacha 12/16, 90-237
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, mild acid hydrolysis, serological methods, genetic methods
  
   
  
  Proteus penneri O66
  CSDB ID 22935 (all data & tools)

Show legend Show as text

Structure type: oligomer

• Article ID: 1222
  Shashkov AS, Arbatsky NP, Toukach FV, Knirel YA, Moll H, Zähringer U, Zych K, Sidorczyk Z "Structure of the O-specific polysaccharide of a serologically separate strain of Proteus penneri 2 from a new proposed serogroup O66" - European Journal of Biochemistry 261(2) (1999) 392-397
  

  structure, strain, polysaccharide, neutral, O-specific, O-specific polysaccharide, Proteus, serogroup, Proteus penneri, 6-deoxy-L-talose, 2, 3, 3-diamino-2, serologically, 3-diacetamido-2, 6-trideoxy-L-mannose

  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
  Methods: NMR
  
   
  
  Proteus penneri 2
  CSDB ID 4758 (all data & tools)

Show legend Show as text

Structure type: monomer

• Article ID: 1222
  Shashkov AS, Arbatsky NP, Toukach FV, Knirel YA, Moll H, Zähringer U, Zych K, Sidorczyk Z "Structure of the O-specific polysaccharide of a serologically separate strain of Proteus penneri 2 from a new proposed serogroup O66" - European Journal of Biochemistry 261(2) (1999) 392-397
  

  structure, strain, polysaccharide, neutral, O-specific, O-specific polysaccharide, Proteus, serogroup, Proteus penneri, 6-deoxy-L-talose, 2, 3, 3-diamino-2, serologically, 3-diacetamido-2, 6-trideoxy-L-mannose

  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
  Methods: NMR
  
   
  
  Proteus penneri 2
  CSDB ID 4759 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 1467
  Knirel YA, Kaca W, Rozalski A, Sidorczyk Z "Structure of the O-antigenic polysaccharides of Proteus bacteria" - Polish Journal of Chemistry 73 (1999) 895-907
  

  Data on the composition and structure of the O-specific polysaccharides (O-antigens) of the lipopolysaccharides of the genus Proteus are summarized and discussed as the molecular basis for serotyping of these medically important bacteria.

  structure, O-antigen, Proteus, Bacterial polysaccharide, epitope specificity

  Journal NLM ID: 7901356
  WWW link: http://www.ichf.edu.pl/pjch/pj-1999/pj0699.htm#0895
  Publisher: Państwowe Wydawnictwo Naukowe
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences,Leninsky Prospekt 47, Moscow, Russia, Institute of Microbiology and Immunology, University of ŁódźŸ, Banacha 12/16, 90-237 ŁódŸź, Poland, Center of Microbiology and Virology, Polish Academy of Sciences, Lodowa 106, 93-232 ŁódźŸ, Poland
  
   
  
  Proteus penneri O66 (2)
  CSDB ID 31878 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136105,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_141807,IEDB_144983,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983930,SB_44,SB_7,SB_72

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

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

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

  NCBI PubMed ID: 7533007
  Journal NLM ID: 0376536
  Publisher: Nauka/Interperiodica
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Escherichia coli O119
  CSDB ID 108674 (all data & tools)
• Article ID: 2237
  Anderson AN, Richards JC, Perry MB "Structure of the O-antigen of Escherichia coli 0119 lipopolysaccharide" - Carbohydrate Research 237 (1992) 249-262
  

  The structure of the O-polysaccharide component of the lipopolysaccharide produced by Escherichia coli 0119 was determined by the use of methylation analysis, periodate oxidation, 1D and 2D nuclear magnetic resonance spectroscopy, and mass spectrometric methods. The O-polysaccharide was found to be a high molecular weight polymer of a repeating pentasaccharide unit composed of D-mannose, D-galactose, L-rhamnose, 2-acetamido-2-deoxy-D-glucose, and 2-acetamido-2,3-dideoxy-3-formamido-D-rhamnose residues (1:1:1:1:1) and had the structure: [formula: see text].

  NMR, Escherichia coli, O-polysaccharide

  NCBI PubMed ID: 1284112
  Publication DOI: 10.1016/S0008-6215(92)84247-P
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Institute of Biological Sciences, National Research Council of Canada, Ottawa, Ontario
  Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, FAB-MS, Smith degradation
  
   
  
  Escherichia coli O119, Escherichia coli NRCC 4326, Escherichia coli NRCC 4325
  CSDB ID 117023 (all data & tools)
• Article ID: 3197
  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 O119
  CSDB ID 20675 (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 O119
  CSDB ID 1859 (all data & tools)
• Article ID: 5760
  Dobrochaeva K, Khasbiulina N, Shilova N, Antipova N, Obukhova P, Galanina O, Blixt O, Kunz H, Filatov A, Knirel Y, Le Pendu J, Khaidukov S, Bovin N "Specificity of human natural antibodies referred to as anti-Tn" - Molecular Immunology 120 (2020) 74-82
  

  To understand the role of human natural IgM known as antibodies against the carbohydrate epitope Tn, the antibodies were isolated using GalNAcα-Sepharose affinity chromatography, and their specificity was profiled using microarrays (a glycan array printed with oligosaccharides and bacterial polysaccharides, as well as a glycopeptide array), flow cytometry, and inhibition ELISA. The antibodies bound a restricted number of GalNAcα-terminated oligosaccharides better than the parent monosaccharide, e.g., 6-O-Su-GalNAcα and GalNAcα1-3Galβ1-3(4)GlcNAcβ. The binding with several bacterial polysaccharides that have no structural resemblance to the affinity ligand GalNAcα was quite unexpected. Given that GalNAcα is considered the key fragment of the Tn antigen, it is surprising that these antibodies bind weakly GalNAcα-OSer and do not bind a wide variety of GalNAcα-OSer/Thr-containing mucin glycopeptides. At the same time, we have observed specific binding to cells having Tn-positive glycoproteins containing similar glycopeptide motifs in a conformationally rigid macromolecule. Thus, specific recognition of the Tn antigen apparently requires that the naturally occurring "anti-Tn" IgM recognize a complex epitope comprising the GalNAcα as an essential component and a fairly long amino acid sequence where the amino acids adjacent to GalNAcα do not contact the antibody paratope; i.e., the antibodies recognize a spatial epitope or a molecular pattern rather than a classical continuous sequence. In addition, we have not found any increase in the binding of natural antibodies when GalNAcα residues were clustered. These results may help in further development of anticancer vaccines based on synthetic Tn constructs.

  cancer, glycans, natural antibodies, anti-glycan antibodies, Tn antigen

  NCBI PubMed ID: 32087569
  Publication DOI: 10.1016/j.molimm.2020.02.005
  Journal NLM ID: 7905289
  Publisher: Elsevier
  Correspondence: professorbovin@yandex.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, Semiotik LLC, 16/10 Miklukho-Maklaya, Moscow, Russian Federation, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of the Ministry of Healthcare of Russian Federation, Moscow, Russian Federation, National Research University Higher School of Economics, Moscow, Russian Federation, Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark, Institut Fur Organische Chemie, Johannes Gutenberg-Universitat Mainz, Duesbergweg 10-14, D-55128, Mainz, Germany, Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, Russian Federation, University of Nantes, Inserm, U892 IRT UN, 8 Quai MonCousu, BP70721 Nantes, FR 44007, France
  Methods: ELISA, affinity chromatography, flow cytometry analysis, printed glycan array (PGA) analysis, FACS assay
  
   
  
  Escherichia coli O119
  CSDB ID 3392 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_141807,IEDB_144983,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_983930,SB_44,SB_7,SB_72

• Article ID: 2237
  Anderson AN, Richards JC, Perry MB "Structure of the O-antigen of Escherichia coli 0119 lipopolysaccharide" - Carbohydrate Research 237 (1992) 249-262
  

  The structure of the O-polysaccharide component of the lipopolysaccharide produced by Escherichia coli 0119 was determined by the use of methylation analysis, periodate oxidation, 1D and 2D nuclear magnetic resonance spectroscopy, and mass spectrometric methods. The O-polysaccharide was found to be a high molecular weight polymer of a repeating pentasaccharide unit composed of D-mannose, D-galactose, L-rhamnose, 2-acetamido-2-deoxy-D-glucose, and 2-acetamido-2,3-dideoxy-3-formamido-D-rhamnose residues (1:1:1:1:1) and had the structure: [formula: see text].

  NMR, Escherichia coli, O-polysaccharide

  NCBI PubMed ID: 1284112
  Publication DOI: 10.1016/S0008-6215(92)84247-P
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Institute of Biological Sciences, National Research Council of Canada, Ottawa, Ontario
  Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, FAB-MS, Smith degradation
  
   
  
  Escherichia coli O119, Escherichia coli NRCC 4326, Escherichia coli NRCC 4325
  CSDB ID 2728 (all data & tools)

Show legend Show as text

Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_144983,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_983930,SB_44,SB_7,SB_72

• Article ID: 2237
  Anderson AN, Richards JC, Perry MB "Structure of the O-antigen of Escherichia coli 0119 lipopolysaccharide" - Carbohydrate Research 237 (1992) 249-262
  

  The structure of the O-polysaccharide component of the lipopolysaccharide produced by Escherichia coli 0119 was determined by the use of methylation analysis, periodate oxidation, 1D and 2D nuclear magnetic resonance spectroscopy, and mass spectrometric methods. The O-polysaccharide was found to be a high molecular weight polymer of a repeating pentasaccharide unit composed of D-mannose, D-galactose, L-rhamnose, 2-acetamido-2-deoxy-D-glucose, and 2-acetamido-2,3-dideoxy-3-formamido-D-rhamnose residues (1:1:1:1:1) and had the structure: [formula: see text].

  NMR, Escherichia coli, O-polysaccharide

  NCBI PubMed ID: 1284112
  Publication DOI: 10.1016/S0008-6215(92)84247-P
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Institute of Biological Sciences, National Research Council of Canada, Ottawa, Ontario
  Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, FAB-MS, Smith degradation
  
   
  
  Escherichia coli O119, Escherichia coli NRCC 4326, Escherichia coli NRCC 4325
  CSDB ID 2729 (all data & tools)

Show legend Show as text

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

• Article ID: 2298
  Whittaker DV, Parolis LAS, Parolis H "Escherichia coli K48 capsular polysaccharide: a glycan containing a novel diacetamido sugar" - Carbohydrate Research 256 (1994) 289-301
  

  The structure of the exocellular capsular polysaccharide expressed by Escherichia coli O8:K48:H9 has been investigated by hydrolysis and methylation analysis, and by NMR spectroscopic studies of the polysaccharide and of the oligosaccharides generated by solvolysis with anhydrous HF. The capsular polysaccharide was shown to have the repeating unit: [formula: see text] where β-L-Sugp represents 2,3-diacetamido-2,3,6-trideoxy-β-L-mannopyranose.

  NCBI PubMed ID: 8187104
  Publication DOI: 10.1016/0008-6215(94)84214-0
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: School of Pharmaceutical Sciences, Rhodes University, Grahamstown, South Africa
  
   
  
  Escherichia coli K48
  CSDB ID 117876 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, K-antigen, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_135813,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_151527,IEDB_151531,IEDB_153212,IEDB_423153,SB_74,SB_85

• Article ID: 2298
  Whittaker DV, Parolis LAS, Parolis H "Escherichia coli K48 capsular polysaccharide: a glycan containing a novel diacetamido sugar" - Carbohydrate Research 256 (1994) 289-301
  

  The structure of the exocellular capsular polysaccharide expressed by Escherichia coli O8:K48:H9 has been investigated by hydrolysis and methylation analysis, and by NMR spectroscopic studies of the polysaccharide and of the oligosaccharides generated by solvolysis with anhydrous HF. The capsular polysaccharide was shown to have the repeating unit: [formula: see text] where β-L-Sugp represents 2,3-diacetamido-2,3,6-trideoxy-β-L-mannopyranose.

  NCBI PubMed ID: 8187104
  Publication DOI: 10.1016/0008-6215(94)84214-0
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: School of Pharmaceutical Sciences, Rhodes University, Grahamstown, South Africa
  
   
  
  Escherichia coli K48
  CSDB ID 117877 (all data & tools)
• Article ID: 4925
  Senchenkova SN, Guo X, Naumenko OI, Shashkov AS, Perepelov AV, Liu B, Knirel YA "Structure and genetics of the O-antigens of Escherichia coli O182-O187" - Carbohydrate Research 435 (2016) 58-67
  

  O-polysaccharides (OPSs) were obtained by mild acid degradation of the lipopolysaccharides of Escherichia coli O182-O187, and their structures were established by sugar analysis, Smith degradation, and 1H and 13C NMR spectroscopy. In addition to the monosaccharides that occur often in E. coli OPSs (d-Glc, d-Gal, d-Man, d-GlcNAc, d-GalNAc, d-GlcA, l-Fuc, d-Rib), a number of less common components were identified as the OPS constituents, including 2-acetamido-2-deoxy-l-quinovose and 4-deoxy-4-[(S)-3-hydroxybutanoyl-l-alanyl]-d-quinovose (O186), 3-acetamido-3-deoxy-d-fucose (O187), 3-deoxy-3-[(R)-3-hydroxybutanoyl]-d-fucose (O184), and 2,3-diacetamido-2,3-dideoxy-l-rhamnose (O182). The OPS structures of E. coli O183 and O182 are identical to those of the OPS of Shigella boydii type 10 and the capsular polysaccharide of E. coli K48, respectively. The OPSs of E. coli O186 and O123 are closely related differing in the presence of a Glc residue in the former in place of a GlcNAc residue in the latter. The O-antigen gene clusters of the bacteria studied were analyzed and their contents were found to be consistent with the OPS structures. Predicted glycosyltransferases encoded in the gene clusters were tentatively assigned to glycosidic linkages based on similarities to sequences of other E. coli O-serogroups available from GenBank and taking into account the OPS structures established.

  Lipopolysaccharide, O-antigen, Escherichia coli, bacterial polysaccharide structure, O-antigen gene cluster

  Publication DOI: 10.1016/j.carres.2016.09.014
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: yknirel@gmail.com
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, Smith degradation, GPC, mild acid degradation, function analysis of gene clusters
  
   
  
  Escherichia coli O182, Escherichia coli K48
  CSDB ID 11311 (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 O182
  CSDB ID 1924 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_153212,SB_74,SB_85

• Article ID: 2298
  Whittaker DV, Parolis LAS, Parolis H "Escherichia coli K48 capsular polysaccharide: a glycan containing a novel diacetamido sugar" - Carbohydrate Research 256 (1994) 289-301
  

  The structure of the exocellular capsular polysaccharide expressed by Escherichia coli O8:K48:H9 has been investigated by hydrolysis and methylation analysis, and by NMR spectroscopic studies of the polysaccharide and of the oligosaccharides generated by solvolysis with anhydrous HF. The capsular polysaccharide was shown to have the repeating unit: [formula: see text] where β-L-Sugp represents 2,3-diacetamido-2,3,6-trideoxy-β-L-mannopyranose.

  NCBI PubMed ID: 8187104
  Publication DOI: 10.1016/0008-6215(94)84214-0
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: School of Pharmaceutical Sciences, Rhodes University, Grahamstown, South Africa
  
   
  
  Escherichia coli K48
  CSDB ID 117878 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_135849,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823,SB_74,SB_85

• Article ID: 3714
  Knirel YA, Senchenkova SN, Shashkov AS, Esteve C, Alcaide E, Merino S, Tomas JM "Structure of a polysaccharide from the lipopolysaccharide of Vibrio vulnificus CECT4602 containing 2-acetamido-2,3,6-trideoxy-3-[(S)- and (R)-3-hydroxybutanoylamino]-L-mannose" - Carbohydrate Research 344(4) (2009) 479-483
  

  A polysaccharide was isolated by GPC after mild acid treatment of the lipopolysaccharide of Vibrio vulnificus CECT4602 and found to contain L-Rha, D-GlcpNAc and 2-acetamido-2,3,6-trideoxy-3-(3-hydroxybutanoylamino)-L-mannose (L-RhaNAc3NHb). GLC analysis of the trifluoroacetylated (S)-2-octyl esters derived by full acid hydrolysis of the polysaccharide showed that approximately 80% of the 3-hydroxybutanoic acid has the S configuration and approximately 20% the R configuration. The following structure of the polysaccharide was established by (1)H and (13)C NMR spectroscopies, including 2D ROESY and (1)H/(13)C HMBC experiments: [carbohydrate sequence see in text].

  Lipopolysaccharide, bacterial polysaccharide structure, 2, 3, 3-diamino-2, 6-trideoxy-L-mannose, 3-hydroxybutanoyl group; Vibrio vulnificus

  NCBI PubMed ID: 19128797
  Publication DOI: 10.1016/j.carres.2008.12.012
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Departamento de Microbiología y Ecología, Universidad de València, E-46100 Burjassot, Valencia, Spain, Departamento Microbiología, Facultad Biología, Universidad de Barcelona, E-08071 Barcelona, Spain
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis
  
   
  
  Vibrio vulnificus CECT4602
  CSDB ID 23742 (all data & tools)
• Article ID: 6301
  Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" - Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
  

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

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

  NCBI PubMed ID: 35750381
  Publication DOI: 10.1016/S1875-5364(22)60177-8
  Journal NLM ID: 101504416
  Publisher: Beijing: Science Press; Elsevier
  Correspondence: J. Yin
  Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
  
   
  
  Vibrio vulnificus CECT4602
  CSDB ID 21158 (all data & tools)

Show legend Show as text

Structure type: polymer biological repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 4049
  Knirel YA, Perepelov AV, Kondakova AN, Senchenkova SN, Sidorczyk Z, Rozalski A, Kaca W "Structure and serology of O-antigens as the basis for classification of Proteus strains" - Innate Immunity 17(1) (2011) 70-96
  

  This review is devoted to structural and serological characteristics of the O-antigens (O-polysaccharides) of the lipopolysaccharides of various Proteus species, which provide the basis for classifying Proteus strains to O-serogroups. The antigenic relationships of Proteus strains within and beyond the genus as well as their O-antigen-related bioactivities are also discussed.

  Lipopolysaccharide, O-antigen, Proteus, polysaccharide structure, classification, Serological cross-reactivity, immunospecificity

  NCBI PubMed ID: 20305038
  Publication DOI: 10.1177/1753425909360668
  Journal NLM ID: 101469670
  Publisher: Sage Publications
  Correspondence: yknirel@gmail.com
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology, Biotechnology and Immunology, University of Lodz, Lodz, Poland, Department of Microbiology, Jan Kochanowski University, Kielce, Poland
  
   
  
  Proteus penneri O66 2
  CSDB ID 26767 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192

• Article ID: 4092
  Perepelov AV, Ni Z, Wang Q, Shevelev SD, Senchenkova SN, Shashkov AS, Wang L, Knirel YA "Structure and gene cluster of the O-antigen of Escherichia coli O109; chemical and genetic evidences of the presence of L-RhaN3N derivatives in the O-antigens of E. coli O109 and O119" - FEMS Immunology and Medical Microbiology 61(1) (2011) 47-53
  

  O-antigen representing the O-polysaccharide chain of the lipopolysaccharide is the most variable constituent on the cell surface of Gram-negative bacteria and a player in their pathogenicity. The O-polysaccharide of Escherichia coli O109 was studied by sugar analysis and nuclear magnetic resonance spectroscopy and found to contain a rarely occurring monosaccharide, 2,3-diacetamido-2,3,6-trideoxy-l-mannose (l-RhaNAc3NAc). The following structure of the tetrasaccharide repeating unit of the O-polysaccharide was established, which is closely related to that of Proteus penneri O66: Ac--4-β-L-RhapNAc3NAc→4)-α-D-Glcp-(1→3)-α-L-6dTalp-(1→3)-β-D-GlcpNAc-(1→. The O-antigen gene cluster of E. coli O109 was sequenced and all 14 genes found were assigned functions based on their similarity to genes from the available databases. Putative genes for synthesis of l-RhaN3N were found in E. coli O109 and their homologues in E. coli O119, whose O-antigen has been reported earlier to contain 2-acetamido-2,3,6-trideoxy-3-formamido-d-mannose (d-RhaNAc3NFo). Analysis by GLC of the (S)-2-octyl glycosides confirmed that the absolute configuration of RhaN3N in E. coli O119 should be revised from D TO L.

  O-antigen, Escherichia coli, 2, 3, 3-diamino-2, O-antigen gene cluster, 6-trideoxy-L-mannose

  NCBI PubMed ID: 20964722
  Publication DOI: 10.1111/j.1574-695X.2010.00745.x
  Journal NLM ID: 9315554
  Publisher: Elsevier
  Correspondence: perepel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, sugar analysis, acid hydrolysis, GLC, function analysis of gene clusters
  
   
  
  Escherichia coli O109, Proteus penneri O66
  CSDB ID 26313 (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 O109
  CSDB ID 1848 (all data & tools)