Show legend Show as text

Structure type: oligomer
Trivial name: pilin glycan
Contained glycoepitopes: IEDB_114701,IEDB_150900,IEDB_167188,IEDB_174332,IEDB_838988

• Article ID: 37
  Castric P, Cassels FJ, Carlson RW "Structural characterization of the Pseudomonas aeruginosa 1244 pilin glycan" - Journal of Biological Chemistry 276(28) (2001) 26479-26485
  

  An antigenic similarity between lipopolysaccharide (LPS) and glycosylated pilin of Pseudomonas aeruginosa 1244 was noted. We purified a glycan-containing molecule from proteolytically digested pili and showed it to be composed of three sugars and serine. This glycan competed with pure pili and LPS for reaction with an LPS-specific monoclonal antibody, which also inhibited twitching motility by P. aeruginosa bearing glycosylated pili. One-dimensional NMR analysis of the glycan indicated the sugars to be 5N β OHC(4)7NfmPse, Xyl, and FucNAc. The complete proton assignments of these sugars as well as the serine residue were determined by COSY and TOCSY. Electrospray ionization mass spectrometry (MS) determined the mass of this molecule to be 771.5. The ROESY NMR spectrum, tandem MS/MS analysis, and methylation analysis provided information on linkage and the sequence of oligosaccharide components. These data indicated that the molecule had the following structure: α-5N β OHC(4)7NFmPse-(2→4)β-Xyl-(1→3)-β-FucNAc-(1→3)-β-Ser

  structural, characterization, Pseudomonas, Pseudomonas aeruginosa, glycan, pilin, pseudaminic acid

  NCBI PubMed ID: 11342554
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Correspondence: castric@duq.edu
  Institutions: Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
  Methods: 1H NMR, NMR-2D, GLC-MS, sugar analysis, ESI-MS, Western blotting, amino acid analysis, MS/MS
  
   
  
  Pseudomonas aeruginosa 1244
  CSDB ID 1697 (all data & tools)

Show legend Show as text

Structure type: monomer
Contained glycoepitopes: IEDB_838988

• Article ID: 125
  Tsvetkov YE, Shashkov AS, Knirel YA, Zähringer U "Synthesis and NMR spectroscopy of nine stereoisomeric 5,7-diacetamido-3,5,7,9-tetradeoxynon-2-ulosonic acids" - Carbohydrate Research 335(4) (2001) 221-243
  

  Derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids are essential constituents of some bacterial polysaccharides and glycoproteins. In order to establish reliably the configuration of the natural sugars, nine stereoisomeric 5,7-diacetamido-3,5,7,9-tetradeoxynon-2-ulosonic acids were synthesized, including di-N-acetyl-legionaminic and -pseudaminic acids (the D-glycero-D-galacto and L-glycero-L-manno isomers, respectively) and their isomers at C-4, C-5, C-7, and C-8 having the L-glycero-D-galacto, D-glycero-D-talo, L-glycero-D-talo, D-glycero-L-altro, L-glycero-L-altro, D-glycero-L-manno, and L-glycero-L-gluco configurations. Synthesis was performed by condensation of 2,4-diacetamido-2,4,6-trideoxy-L-gulose, -D-mannose, -D-talose, and -L-allose with oxalacetic acid under basic conditions, the reaction of the last two precursors being accompanied by epimerisation at C-2. The 1H and 13C NMR data of the synthetic compounds are discussed. Acetylated methyl esters of the C-7 and C-8 isomeric nonulosonic acids were prepared and used for analysis of the side-chain conformation by NMR spectroscopy.

  NMR, synthesis, LPS, Bacterial, identification, acid, NMR spectroscopy, pseudaminic acid, putative, spectroscopy, 5, 7-diamino-3, 7, 9-tetradeoxynon-2-ulosonic acid, lipopolysaccharide components, 7-diacetamido-3, 9-tetradeoxynon-2-ulosonic acids, 2, 4-diacetamido-2, 4, 6-trideoxyhexoses, legionaminic acid, 9-teradeoxynonulosonic acid, component, isomer

  NCBI PubMed ID: 11595217
  Publication DOI: 10.1016/S0008-6215(01)00235-X
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: tsvetkov@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospeckt 47, Moscow, Russian Federation, Forschungszentrum Borstel, Zentrum fur Medizin und Biowissenschaften, Borstel, Germany.
  Methods: 13C NMR, 1H NMR
  
   
  
  (bacteria)
  CSDB ID 5349 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: K-antigen, CPS
Contained glycoepitopes: IEDB_838988

• Article ID: 363
  Rodríguez-Carvajal MA, Bernabé M, Espartero JL, Tejero-Mateo P, Gil-Serrano A, Jiménez-Barbero J "Studies on the solution conformation and dynamics of a polysaccharide from Sinorhizobium fredii HH103 and its monosaccharide repeating unit" - Journal of Molecular Graphics and Modelling 18(2) (2000) 135-142
  

  The conformational behavior of the homopolysaccharide isolated from Sinorhizobium fredii HH103 and its monosaccharide repeating unit (5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulosonic acid) was analyzed by nuclear magnetic resonance (NMR) spectroscopy and extensive molecular dynamics simulations (MD). The results indicate that the glycosidic linkages and lateral cheins may adopy a variety of conformations. MD simulations using the generalized Born solvent-accessible surface area (GB/SA) continuum solvent model for water and the MM3* force field provide a population distribution of conformers that satisfactorily agrees with the experimental NMR data for the torsional degrees of freedom of the molecule.

  NMR, K-antigen, polysaccharide, molecular dynamics, pseudaminic acid

  NCBI PubMed ID: 10994517
  Journal NLM ID: 9716237
  Publisher: New York, NY: Elsevier
  Correspondence: iqoj101@iqoug.csic.es
  Institutions: Departamento Quimica Organica, Facultad Quimica, University of Sevilla, Sevilla, Spain, Instituto Quimica Organica, CSIC, Madrid, Spain, Dpto. Quimica Organica y Farmaceutica, Facultad Farmacia, University of Sevilla, Sevilla, Spain
  Methods: NMR, MD simulations
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 8063 (all data & tools)
• Article ID: 5748
  Chidwick HS, Fascione MA "Mechanistic and structural studies into the biosynthesis of the bacterial sugar pseudaminic acid (Pse5Ac7Ac)" - Organic and Biomolecular Chemistry 18(5) (2020) 799-809
  

  The non-mammalian nonulosonic acid sugar pseudaminic acid (Pse) is present on the surface of a number of human pathogens including Campylobacter jejuni and Helicobacter pylori and other bacteria such as multidrug resistant Acinetobacter baumannii. It is likely important for evasion of the host immune sysyem, and also plays a role in bacterial motility through flagellin glycosylation. Herein we review the mechanistic and structural characterisation of the enzymes responsible for the biosynthesis of the Pse parent structure, Pse5Ac7Ac in bacteria.

  biosynthesis, structure, Acinetobacter baumannii, Campylobacter jejuni, pseudaminic acid, nonulosonic acid, Helicobacter pylori, structural studies, Enzymes, glycosylation, immune, Flagellin

  NCBI PubMed ID: 31913385
  Publication DOI: 10.1039/c9ob02433f
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: martin.fascione@york.ac.uk
  Institutions: Department of Chemistry, University of York, York, YO10 5DD, UK
  
   
  
  Sinorhizobium fredii
  CSDB ID 3327 (all data & tools)

Show legend Show as text

Structure type: monomer
Contained glycoepitopes: IEDB_838988

• Article ID: 363
  Rodríguez-Carvajal MA, Bernabé M, Espartero JL, Tejero-Mateo P, Gil-Serrano A, Jiménez-Barbero J "Studies on the solution conformation and dynamics of a polysaccharide from Sinorhizobium fredii HH103 and its monosaccharide repeating unit" - Journal of Molecular Graphics and Modelling 18(2) (2000) 135-142
  

  The conformational behavior of the homopolysaccharide isolated from Sinorhizobium fredii HH103 and its monosaccharide repeating unit (5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulosonic acid) was analyzed by nuclear magnetic resonance (NMR) spectroscopy and extensive molecular dynamics simulations (MD). The results indicate that the glycosidic linkages and lateral cheins may adopy a variety of conformations. MD simulations using the generalized Born solvent-accessible surface area (GB/SA) continuum solvent model for water and the MM3* force field provide a population distribution of conformers that satisfactorily agrees with the experimental NMR data for the torsional degrees of freedom of the molecule.

  NMR, K-antigen, polysaccharide, molecular dynamics, pseudaminic acid

  NCBI PubMed ID: 10994517
  Journal NLM ID: 9716237
  Publisher: New York, NY: Elsevier
  Correspondence: iqoj101@iqoug.csic.es
  Institutions: Departamento Quimica Organica, Facultad Quimica, University of Sevilla, Sevilla, Spain, Instituto Quimica Organica, CSIC, Madrid, Spain, Dpto. Quimica Organica y Farmaceutica, Facultad Farmacia, University of Sevilla, Sevilla, Spain
  Methods: NMR, MD simulations
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 8135 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: K-antigen
Contained glycoepitopes: IEDB_838988

• Article ID: 645
  Gil-Serrano AM, Rodríguez-Carvajal MA, Tejero-Mateo P, Espartero JL, Menendez M, Corzo J, Ruiz-Sainz JE, Buendía-Clavería AM "Structural determination of a 5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulosonic acid-containing homopolysaccharide isolated from Sinorhizobium fredii HH103" - Biochemical Journal 342(3) (1999) 527-535
  

  The structure of a polysaccharide from Sinorhizobium fredii HH103 has been determined. This polysaccharide was isolated by following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, matrix-assisted laser desorption ionization MS, electron-impact high-resolution MS, one-dimensional (1)H-NMR and (13)C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a homopolymer of a 3:1 mixture of 5-acetamido-3,5,7, 9-tetradeoxy-7-[(R)- and (S)-3-hydroxybutyramido]-l-glycero-l-manno-nonulosonic acid. The sugar residues are attached via a glycosidic linkage to the OH group of the 3-hydroxybutyramido substituent and thus the monomers are linked via both glycosidic and amidic linkages. In contrast with the Sinorhizobium K-antigens previously reported, which are composed of a disaccharide repeating unit, the K-antigen polysacharide of S. fredii HH103 is a homopolysaccharide.

  structural, K-antigen, capsular polysaccharide, determination, structural determination, acid, pseudaminic acid, 5, 7-diamino-3, 7, Sinorhizobium, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 10477263
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Correspondence: agil@cica.es
  Institutions: Departamento de Quimica Organica, Facultad de Quimica, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Quimica Organica y Farmaceutica, Facultad de Farmacia, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Bioquimica y Biologia Molecular, Facultad de Biologia, Universidad de La Laguna, 38206 Tenerife, Spain, Departamento de Microbiologia, Facultad de Biologia, Universidad de Sevilla, 41080 Sevilla, Spain.
  Methods: NMR-2D, methylation, FAB-MS, NMR, MALDI-MS
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 420 (all data & tools)

Show legend Show as text

Structure type: homopolymer
Compound class: K-antigen
Contained glycoepitopes: IEDB_838988

• Article ID: 645
  Gil-Serrano AM, Rodríguez-Carvajal MA, Tejero-Mateo P, Espartero JL, Menendez M, Corzo J, Ruiz-Sainz JE, Buendía-Clavería AM "Structural determination of a 5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero-L-manno-nonulosonic acid-containing homopolysaccharide isolated from Sinorhizobium fredii HH103" - Biochemical Journal 342(3) (1999) 527-535
  

  The structure of a polysaccharide from Sinorhizobium fredii HH103 has been determined. This polysaccharide was isolated by following the protocol for lipopolysaccharide extraction. On the basis of monosaccharide analysis, methylation analysis, fast atom bombardment MS, matrix-assisted laser desorption ionization MS, electron-impact high-resolution MS, one-dimensional (1)H-NMR and (13)C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a homopolymer of a 3:1 mixture of 5-acetamido-3,5,7, 9-tetradeoxy-7-[(R)- and (S)-3-hydroxybutyramido]-l-glycero-l-manno-nonulosonic acid. The sugar residues are attached via a glycosidic linkage to the OH group of the 3-hydroxybutyramido substituent and thus the monomers are linked via both glycosidic and amidic linkages. In contrast with the Sinorhizobium K-antigens previously reported, which are composed of a disaccharide repeating unit, the K-antigen polysacharide of S. fredii HH103 is a homopolysaccharide.

  structural, K-antigen, capsular polysaccharide, determination, structural determination, acid, pseudaminic acid, 5, 7-diamino-3, 7, Sinorhizobium, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 10477263
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Correspondence: agil@cica.es
  Institutions: Departamento de Quimica Organica, Facultad de Quimica, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Quimica Organica y Farmaceutica, Facultad de Farmacia, Universidad de Sevilla, 41071 Sevilla, Spain, Departamento de Bioquimica y Biologia Molecular, Facultad de Biologia, Universidad de La Laguna, 38206 Tenerife, Spain, Departamento de Microbiologia, Facultad de Biologia, Universidad de Sevilla, 41080 Sevilla, Spain.
  Methods: NMR-2D, methylation, FAB-MS, NMR, MALDI-MS
  
   
  
  Sinorhizobium fredii HH103
  CSDB ID 554 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_141807,IEDB_151531,IEDB_838988

• Article ID: 888
  Kondakova AN, Perepelov AV, Bartodziejska B, Shashkov AS, Senchenkova SN, Wykrota M, Knirel YA, Rozalski A "Structure of the acidic O-specific polysaccharide from Proteus vulgaris O39 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-non-2-ulosonic acid" - Carbohydrate Research 333(3) (2001) 241-249
  

  Lipopolysaccharide, NMR, LPS, structure, polysaccharide, O-antigen, acidic, acidic polysaccharide, acid, phosphate, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, Proteus, serogroup, Proteus penneri, 2-aminoethyl phosphate, Proteus vulgaris, 5, 7, solvolysis, 7diacetamido-3, 9-tetradeoxy-L-glycero-L-manno-nonulosonic acid, triflic acid, selective cleavage

  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D.Zelinsky Institute of Ogranic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR, ESI-MS, triflic acid solvolysis, borohydride reduction
  
   
  
  Proteus vulgaris O39
  CSDB ID 2855 (all data & tools)
• Article ID: 1468
  Knirel YA, Perepelov AV "Trifluoromethanesulfonic acid: a useful reagent for the solvolytic cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Australian Journal of Chemistry 55(1-2) (2002) 69-72
  

  The initial data on the application of triflic acid was summarized for the isolation of complex monosachharide derivatives and oligosachharides in the structural analysis of various bacterial polysachharides. Solvolysis proceeded selectively and without destruction of the sugars. Varying the temperature and duration of the reaction enabled preparation of oligosaccharides of different sizes.

  polysaccharide, structural analysis, bacterial polysaccharides, solvolysis, trifluoromethanesulfonic acid, triflic acid

  Publication DOI: 10.1071/CH01181
  Journal NLM ID: 0370614
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: 13C NMR, 1H NMR, GLC, MS, triflic acid solvolysis
  
   
  
  Proteus vulgaris O39
  CSDB ID 31915 (all data & tools)
• Article ID: 1469
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Proteus vulgaris O39
  CSDB ID 31927 (all data & tools)
• Article ID: 3355
  Perepelov AV, Bartodziejska B, Shashkov AS, Wykrota M, Knirel YA, Rozalski A "Structure of a glucosyl phosphate-containing O-polysaccharide of Proteus vulgaris O42" - Carbohydrate Research 342(18) (2007) 2826-2831
  

  An O-polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of Proteus vulgaris O42 and studied by sugar and methylation analyses along with 1H, 13C and 31P NMR spectroscopy. The following structure of the polysaccharide having a linear pentasaccharide phosphate repeating unit was established:

  Lipopolysaccharide, O-antigen, NMR spectroscopy, Proteus vulgaris, bacterial polysaccharide structure, Glucosyl phosphate

  NCBI PubMed ID: 17936254
  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, Lodz, Poland
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, chemical analysis, 31P NMR, GLC, mild acid hydrolysis, NMR-1D, serological methods, alkaline hydrolysis
  
   
  
  Proteus vulgaris O39
  CSDB ID 21748 (all data & tools)
• Article ID: 3425
  Bushmarinov IS, Ovchinnikova OG, Kocharova NA, Toukach FV, Torzewska A, Shashkov AS, Knirel YA, Rozalski A "Structure of the O-polysaccharide and serological cross-reactivity of the lipopolysaccharide of Providencia alcalifaciens O32 containing N-acetylisomuramic acid" - Carbohydrate Research 342(2) (2007) 268-273
  

  The O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Providencia alcalifaciens O32 and studied by sugar and methylation analyses, solvolysis with triflic acid, 1H and 13C NMR spectroscopy, including two-dimensional 1H,1H COSY, TOCSY, ROESY, H-detected 1H,13C HSQC and HMBC experiments. It was found that the polysaccharide has a branched tetrasaccharide repeating unit containing 2-acetamido-3-O-[(S)-1-carboxyethyl]-2-deoxy-D-glucose (D-GlcNAc3Slac, N-acetylisomuramic acid) with the following structure: [STRUCTURE: SEE TEXT]. Serological studies with O-antisera showed antigenic relationships between P. alcalifaciens O32 and O29 as well as several other Providencia and Proteus strains sharing putative epitopes on the O-polysaccharides.

  Lipopolysaccharide, O-antigen, Providencia alcalifaciens, polysaccharide structure, isomuramic acid

  NCBI PubMed ID: 17182016
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: olga.ovchinnikova@gmail.com
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, sugar analysis, mild acid hydrolysis, serological methods, triflic acid solvolysis
  
   
  
  Proteus vulgaris O39
  CSDB ID 22021 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Proteus vulgaris O39
  CSDB ID 1458 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_838988,IEDB_885822

• Article ID: 888
  Kondakova AN, Perepelov AV, Bartodziejska B, Shashkov AS, Senchenkova SN, Wykrota M, Knirel YA, Rozalski A "Structure of the acidic O-specific polysaccharide from Proteus vulgaris O39 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-non-2-ulosonic acid" - Carbohydrate Research 333(3) (2001) 241-249
  

  Lipopolysaccharide, NMR, LPS, structure, polysaccharide, O-antigen, acidic, acidic polysaccharide, acid, phosphate, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, Proteus, serogroup, Proteus penneri, 2-aminoethyl phosphate, Proteus vulgaris, 5, 7, solvolysis, 7diacetamido-3, 9-tetradeoxy-L-glycero-L-manno-nonulosonic acid, triflic acid, selective cleavage

  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D.Zelinsky Institute of Ogranic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR, ESI-MS, triflic acid solvolysis, borohydride reduction
  
   
  
  Proteus vulgaris O39
  CSDB ID 3000 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_136045,IEDB_142489,IEDB_144562,IEDB_152214,IEDB_174333,IEDB_838988,SB_86

• Article ID: 888
  Kondakova AN, Perepelov AV, Bartodziejska B, Shashkov AS, Senchenkova SN, Wykrota M, Knirel YA, Rozalski A "Structure of the acidic O-specific polysaccharide from Proteus vulgaris O39 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-non-2-ulosonic acid" - Carbohydrate Research 333(3) (2001) 241-249
  

  Lipopolysaccharide, NMR, LPS, structure, polysaccharide, O-antigen, acidic, acidic polysaccharide, acid, phosphate, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, Proteus, serogroup, Proteus penneri, 2-aminoethyl phosphate, Proteus vulgaris, 5, 7, solvolysis, 7diacetamido-3, 9-tetradeoxy-L-glycero-L-manno-nonulosonic acid, triflic acid, selective cleavage

  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D.Zelinsky Institute of Ogranic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR, ESI-MS, triflic acid solvolysis, borohydride reduction
  
   
  
  Proteus vulgaris O39
  CSDB ID 3001 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_838988,IEDB_885822

• Article ID: 888
  Kondakova AN, Perepelov AV, Bartodziejska B, Shashkov AS, Senchenkova SN, Wykrota M, Knirel YA, Rozalski A "Structure of the acidic O-specific polysaccharide from Proteus vulgaris O39 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-non-2-ulosonic acid" - Carbohydrate Research 333(3) (2001) 241-249
  

  Lipopolysaccharide, NMR, LPS, structure, polysaccharide, O-antigen, acidic, acidic polysaccharide, acid, phosphate, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, Proteus, serogroup, Proteus penneri, 2-aminoethyl phosphate, Proteus vulgaris, 5, 7, solvolysis, 7diacetamido-3, 9-tetradeoxy-L-glycero-L-manno-nonulosonic acid, triflic acid, selective cleavage

  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D.Zelinsky Institute of Ogranic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR, ESI-MS, triflic acid solvolysis, borohydride reduction
  
   
  
  Proteus vulgaris O39
  CSDB ID 3078 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_838988

• Article ID: 888
  Kondakova AN, Perepelov AV, Bartodziejska B, Shashkov AS, Senchenkova SN, Wykrota M, Knirel YA, Rozalski A "Structure of the acidic O-specific polysaccharide from Proteus vulgaris O39 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-non-2-ulosonic acid" - Carbohydrate Research 333(3) (2001) 241-249
  

  Lipopolysaccharide, NMR, LPS, structure, polysaccharide, O-antigen, acidic, acidic polysaccharide, acid, phosphate, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, Proteus, serogroup, Proteus penneri, 2-aminoethyl phosphate, Proteus vulgaris, 5, 7, solvolysis, 7diacetamido-3, 9-tetradeoxy-L-glycero-L-manno-nonulosonic acid, triflic acid, selective cleavage

  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D.Zelinsky Institute of Ogranic Chemistry, Russian Academy of Sciences, Moscow, Russia
  Methods: NMR, ESI-MS, triflic acid solvolysis, borohydride reduction
  
   
  
  Proteus vulgaris O39
  CSDB ID 3079 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_140630,IEDB_838988

• Article ID: 1024
  Muldoon J, Shashkov AS, Senchenkova SN, Tomshich SV, Komandrova NA, Romanenko LA, Knirel YA, Savage AV "Structure of an acidic polysaccharide from a marine bacterium Pseudoalteromonas distincta KMM 638 containing 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid" - Carbohydrate Research 330 (2001) 231-239
  

  An acidic polysaccharide was obtained from the lipopolysaccharide of Pseudoalteromonas distincta strain KMM 638, isolated from a marine sponge, and found to contain D-GlcA, D-GalNAc, 2-acetamido-2,6-dideoxy-D-glucose (D-QuiNAc) and two unusual acidic amino sugars: 2-acetamido-2-deoxy-D-galacturonic acid (D-GalNAcA) and 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid (Pse5Ac7Fo, a derivative of pseudaminic acid). Oligosaccharides were derived from the polysaccharide by partial acid hydrolysis and mild alkaline degradation and characterised by electrospray ionisation (ESI) MS and 1H and 13C NMR spectroscopy. Based on these data and NMR spectroscopic studies of the initial and O-deacetylated polysaccharides, including quaternary carbon detection, 2D COSY, TOCSY, ROESY, H-detected 1H,13C HMQC and HMBC experiments, the following structure of the branched pentasaccharide repeating unit was established: [structure: see text].

  structure, strain, polysaccharide, acidic, acidic polysaccharide, acid, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, 5, 7-diamino-3, 7, marine, Pseudoalteromonas, 2-amino-2-deoxygalacturonic acid, 9-teradeoxy-L-glycero-L-manno-nonulosonic acid

  NCBI PubMed ID: 11217976
  Publication DOI: 10.1016/S0008-6215(00)00280-9
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: angela.savage@nuigalway.ie
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Chemistry, National University of Ireland, Galway, Ireland, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladi6ostok 690022, Russia
  Methods: NMR-2D, partial acid hydrolysis, NMR, ESI-MS, de-O-acetylation
  
   
  
  Pseudoalteromonas distincta KMM 638
  CSDB ID 3719 (all data & tools)
• Article ID: 4434
  Nazarenko EL, Komandrova NA, Gorshkova RP, Tomshich SV, Zubkov VA, Kilcoyne M, Savage AV "Structures of polysaccharides and oligosaccharides of some Gram-negative marine Proteobacteria" - Carbohydrate Research 338(23) (2003) 2449-2457
  

  The chemical structures of polysaccharides and LPS core oligosaccharides, isolated from various Gram-negative marine bacteria from the genera Pseudoalteromonas and Shewanella belonging to the Alteromonadaceae family and gamma-subclass of Proteobacteria, are reviewed. The polysaccharides are distinguished by the acidic character (e.g., due to the presence of hexuronic and aldulosonic acids and their derivatives) and the occurrence of unusual sugars, including N-acyl derivatives of 6-deoxyamino sugars, such as N-acetyl-D-quinovosamine, N-acetyl-L-fucosamine and N-acetyl-6-deoxy-L-talosamine, and higher sugars like 2,6-dideoxy-2-acetamido-4-C-(3'-carboxamide-2',2'-dihydroxypropyl)-D-galac topyranose (shewanellose). Many constituent sugars have various uncommon non-sugar substituents, such as alanine, formic, lactic and hydroxybutyric acids, sulfate, phosphate, and 2-aminopropane-1,3-diol.

  Lipopolysaccharide, oligosaccharide structure, O-antigen, polysaccharide structure, Shewanella, Pseudoalteromonas, Proteobacteria

  NCBI PubMed ID: 14670708
  Publication DOI: 10.1016/j.carres.2003.06.004
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: A.V. Savage
  Institutions: Department of Chemistry, National University of Ireland, Galway, Ireland, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russian Federation
  
   
  
  Pseudoalteromonas distincta KMM 638
  CSDB ID 28824 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_115136,IEDB_130648,IEDB_137473,IEDB_140630,IEDB_838988

• Article ID: 1024
  Muldoon J, Shashkov AS, Senchenkova SN, Tomshich SV, Komandrova NA, Romanenko LA, Knirel YA, Savage AV "Structure of an acidic polysaccharide from a marine bacterium Pseudoalteromonas distincta KMM 638 containing 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid" - Carbohydrate Research 330 (2001) 231-239
  

  An acidic polysaccharide was obtained from the lipopolysaccharide of Pseudoalteromonas distincta strain KMM 638, isolated from a marine sponge, and found to contain D-GlcA, D-GalNAc, 2-acetamido-2,6-dideoxy-D-glucose (D-QuiNAc) and two unusual acidic amino sugars: 2-acetamido-2-deoxy-D-galacturonic acid (D-GalNAcA) and 5-acetamido-3,5,7,9-tetradeoxy-7-formamido-L-glycero-L-manno-nonulosonic acid (Pse5Ac7Fo, a derivative of pseudaminic acid). Oligosaccharides were derived from the polysaccharide by partial acid hydrolysis and mild alkaline degradation and characterised by electrospray ionisation (ESI) MS and 1H and 13C NMR spectroscopy. Based on these data and NMR spectroscopic studies of the initial and O-deacetylated polysaccharides, including quaternary carbon detection, 2D COSY, TOCSY, ROESY, H-detected 1H,13C HMQC and HMBC experiments, the following structure of the branched pentasaccharide repeating unit was established: [structure: see text].

  structure, strain, polysaccharide, acidic, acidic polysaccharide, acid, bacteria, O-specific, O-specific polysaccharide, pseudaminic acid, 5, 7-diamino-3, 7, marine, Pseudoalteromonas, 2-amino-2-deoxygalacturonic acid, 9-teradeoxy-L-glycero-L-manno-nonulosonic acid

  NCBI PubMed ID: 11217976
  Publication DOI: 10.1016/S0008-6215(00)00280-9
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: angela.savage@nuigalway.ie
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Chemistry, National University of Ireland, Galway, Ireland, Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladi6ostok 690022, Russia
  Methods: NMR-2D, partial acid hydrolysis, NMR, ESI-MS, de-O-acetylation
  
   
  
  Pseudoalteromonas distincta KMM 638
  CSDB ID 3893 (all data & tools)

Show legend Show as text

Structure type: monomer
Aglycon: FLaA and FLaB proteins
Contained glycoepitopes: IEDB_838988

• Article ID: 1177
  Schirm M, Soo EC, Aubry AJ, Austin J, Thibault P, Logan SM "Structural, genetic and functional characterization of the flagellin glycosylation process in Helicobacter pylori" - Molecular Microbiology 48(6) (2003) 1579-1592
  

  Mass spectrometry analyses of the complex polar flagella from Helicobacter pylori demonstrated that both FlaA and FlaB proteins are post-translationally modified with pseudaminic acid (Pse5Ac7Ac, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno -n o n-ulosonic acid). Unlike Campylobacter, flagellar glycosylation in Helicobacter displays little heterogeneity in isoform or glycoform distribution, although all glycosylation sites are located in the central core region of the protein monomer in a manner similar to that found in Campylobacter. Bioinformatic analysis revealed five genes (HP0840, HP0178, HP0326A, HP0326B, HP0114) homologous to other prokaryote genes previously reported to be involved in motility, flagellar glycosylation or polysaccharide biosynthesis. Insertional mutagenesis of four of these homologues in Helicobacter (HP0178, HP0326A, HP0326B, HP0114) resulted in a non-motile phenotype, no structural flagella filament and only minor amounts of flagellin protein detectable by Western immunoblot. However, mRNA levels for the flagellin structural genes remained unaffected by each mutation. In view of the combined bioinformatic and structural evidence indicating a role for these gene products in glycan biosynthesis, subsequent investigations focused on the functional characterization of the respective gene products. A novel approach was devised to identify biosynthetic sugar nucleotide precursors from intracellular metabolic pools of parent and isogenic mutants using capillary electrophoresis-electrospray mass spectrometry (CE-ESMS) and precursor ion scanning. HP0326A, HP0326B and the HP0178 gene products are directly involved in the biosynthesis of the nucleotide-activated form of Pse, CMP-Pse. Mass spectral analyses of the cytosolic extract from the HP0326A and HP0326B isogenic mutants revealed the accumulation of a mono- and a diacetamido trideoxyhexose UDP sugar nucleotide precursor

  biosynthesis, genetic, core, Bacterial Proteins, biosynthetic, chemistry, functional, gene, genetics, growth & development, human, metabolism, microbiology, phenotype, role, Sequence Analysis, DNA, structural, characterization, polysaccharide, analysis, ion, form, acid, animal, Campylobacter, complex, Female, level, mice, Molecular Sequence Data, protein, spectrometry, mutant, mutants, glycan, pseudaminic acid, sugar, core region, region, mass spectrometry, precursor, modified, Helicobacter pylori, mutation, intracellular, polar, site, glycosylation, Helicobacter, proteins, mutagenesis, isogenic, distribution, amino acid sequence, electrophoresis, heterogeneity, Mass, Electrospray Ionization, physiology, approach, accumulation, polysaccharide biosynthesis, homologous, extract, Capillary, flagella, Flagellin, mRNA, Stomach, sugar nucleotide

  NCBI PubMed ID: 12791140
  Journal NLM ID: 8712028
  Publisher: Blackwell Publishing
  Correspondence: susan.logan@nrc.ca
  Institutions: University of Montreal, Department of Chemistry, Canada
  
   
  
  Helicobacter pylori
  CSDB ID 4618 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130646,IEDB_135813,IEDB_136044,IEDB_137340,IEDB_137472,IEDB_140108,IEDB_140122,IEDB_141794,IEDB_141807,IEDB_151531,IEDB_190606,IEDB_838988,SB_165,SB_166,SB_187,SB_195,SB_30,SB_7,SB_88

• Article ID: 1254
  Staaf M, Weintraub A, Widmalm G "Structure determination of the O-antigenic polysaccharide from the enteroinvasive Escherichia coli O136" - European Journal of Biochemistry 263(3) (1999) 656-661
  

  The structure of the O-antigen polysaccharide of the lipopolysaccharide from the enteroinvasive Escherichia coli O136 has been elucidated. The composition of the repeating unit was established by sugar and methylation analysis together with 1H and 13C NMR spectroscopy. Two-dimensional nuclear Overhauser effect spectroscopy (NOESY) and heteronuclear multiple-bond correlation experiments were used to deduce the sequence. The absolute configuration for the nonulosonic acid (NonA) could be determined using spin-spin coupling constants, 13C chemical shifts and NOESY. The anomeric configuration of the NonA was determined via vicinal and geminal 13C,1H coupling constants. The structure of the repeating unit of the polysaccharide from E. coli O136 is as follows, in which β-NonpA is 5,7-diacetamido-3,5,7, 9-tetradeoxy-Lglycero-β-Lmanno-nonulosonic acid: -4)-β-NonpA-(2-4)-β-D-Galp-(1-4)-β-D-GlcpNAc-(1-

  Lipopolysaccharide, NMR, LPS, structure, strain, structural, polysaccharide, O-antigen, Escherichia, Escherichia coli, determination, O-antigenic, O-antigenic polysaccharide, nonulosonic acid, elucidation, Structure determination, Enteroaggregative, Enteroinvasive

  NCBI PubMed ID: 10469128
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: gw+AEA-oragan.su.se
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Sweden, Karolinska Institute, Department of Immunology, Microbiology, Pathology and Infectious Diseases, Division of Clinical and Oral Bacteriology, Huddinge University Hospital, Sweden
  Methods: 13C NMR, 1H NMR, NMR-2D, methylation, NMR
  
   
  
  Escherichia coli O136
  CSDB ID 4938 (all data & tools)
• Article ID: 1469
  Knirel YA, Shashkov AS, Tsvetkov YE, Jansson P, Zähringer U "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers: chemistry and biochemistry" - Book: Advances in Carbohydrate Chemistry and Biochemistry (2003) Vol. 58, 371-417
  

  This chapter provides an overview of the chemistry of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids in bacterial glycopolymers. Ald-2-ulosonic acids are the important components of natural glycoconjugates. Sialic acids—namely, N- and O-acyl derivatives of 5-amino-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid (neuraminic acid, Neu), generally occur in glycoconjugates of vertebrates and play a significant role in their recognition, regulation, and protection. A deamino analogue of neuraminic acid—3-deoxy-D-glycero-D-galacto-non-2-ulosonic acid (Kdn)—has also been found in a variety of animal tissues. 3-Deoxy-D-manno-oct-2-ulosonic acid (Kdo) is an essential component of lipopolysaccharides (LPSs) of Gram-negative bacteria that functions to link the carbohydrate portion to the lipid moiety. In rare cases, Kdo in LPS is replaced with a 3-hydroxylated analogue—D-glycero-D-talo-oct-2-ulosonic acid. The chapter focuses on the occurrence and characterization of derivatives of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acids and presents experimental approaches that are used to identify them and to elucidate the structures of the bacterial polysaccharides that contain the nonulosonic acids. It also presents the recent data on the biosynthesis of these sugars and discusses their role in immune recognition.

  Lipopolysaccharide, LPS, structure, polysaccharide, Bacterial polysaccharide, 5, 7-diamino-3, 7, higher sugar, 9-tetradeoxynonulosonic acid

  NCBI PubMed ID: 14719362
  Publication DOI: 10.1016/S0065-2318(03)58007-6
  Publisher: Elsevier Inc.
  Correspondence: knirel@ioc.ac.ru
  Editors: Horton D
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Karolinska Institute, Clinical Research Center, Huddinge University Hospital, Huddinge, Sweden
  
   
  
  Escherichia coli O136
  CSDB ID 31926 (all data & tools)
• Article ID: 3196
  Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" - FEMS Microbiology Reviews 30(3) (2006) 382-403
  

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

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

  NCBI PubMed ID: 16594963
  Publication DOI: 10.1111/j.1574-6976.2006.00016.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: andrej.weintraub@ki.se
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
  
   
  
  Escherichia coli O136
  CSDB ID 20682 (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 O136
  CSDB ID 1878 (all data & tools)
• Article ID: 5748
  Chidwick HS, Fascione MA "Mechanistic and structural studies into the biosynthesis of the bacterial sugar pseudaminic acid (Pse5Ac7Ac)" - Organic and Biomolecular Chemistry 18(5) (2020) 799-809
  

  The non-mammalian nonulosonic acid sugar pseudaminic acid (Pse) is present on the surface of a number of human pathogens including Campylobacter jejuni and Helicobacter pylori and other bacteria such as multidrug resistant Acinetobacter baumannii. It is likely important for evasion of the host immune sysyem, and also plays a role in bacterial motility through flagellin glycosylation. Herein we review the mechanistic and structural characterisation of the enzymes responsible for the biosynthesis of the Pse parent structure, Pse5Ac7Ac in bacteria.

  biosynthesis, structure, Acinetobacter baumannii, Campylobacter jejuni, pseudaminic acid, nonulosonic acid, Helicobacter pylori, structural studies, Enzymes, glycosylation, immune, Flagellin

  NCBI PubMed ID: 31913385
  Publication DOI: 10.1039/c9ob02433f
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: martin.fascione@york.ac.uk
  Institutions: Department of Chemistry, University of York, York, YO10 5DD, UK
  
   
  
  Escherichia coli O136
  CSDB ID 32080 (all data & tools)