Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_137473

• Article ID: 251
  Hannesson HH, Hagner-McWhirter A, Tiedemann K, Lindahl U, Malmström A "Biosynthesis of dermatan sulphate. Defructosylated Escherichia coli K4 capsular polysaccharide as a substrate for the D-glucuronyl C-5 epimerase, and an indication of a two-base reaction mechanism" - Biochemical Journal 313(2) (1996) 589-596
  

  The capsular polysaccharide from Escherichia coli K4 consists of a chondroitin ([GlcA(β1→3)GalNAc(β1→4)]n) backbone, to which β-fructofuranose units are linked to C-3 of D-glucuronic acid (GlcA) residues. Removal of the fructose units by mild acid hydrolysis provided a substrate for the GlcA C-5 epimerase, which is involved in the generation of L-iduronic acid (IdoA) units during dermatan sulphate biosynthesis. Incubation of this substrate with solubilized fibroblast microsomal enzyme in the presence of 3H2O resulted in the incorporation of tritium at C-5 of hexuronyl units. A Km of 67 x 10(-6) M hexuronic acid (equivalent to disaccharide units) was determined, which is similar to that (80 x 10(-6) M) obtained for dermatan (desulphated dermatan sulphate). Vmax was about 4 times higher with dermatan than with the K4 substrate. A defructosylated K4 polysaccharide isolated after incubation of bacteria with D-[5-3H]glucose released 3H2O on reaction with the epimerase, and thus could be used to assay the enzyme. Incubation of a K4 substrate with solubilized microsomal epimerase for 6 h in the presence of 3H2O resulted in the formation of about 5% IdoA and approximately equal amounts of 3H in GlcA and IdoA. A corresponding incubation of dermatan yielded approx. 22% GlcA, which contained virtually all the 3H label. These results are tentatively explained in terms of a two-base reaction mechanism, involving a monoprotic L-ido-specific base and a polyprotic D-gluco-specific base. Most of the IdoA residues generated by the enzyme occurred singly, although some formation of two or three consecutive IdoA-containing disaccharide units was observed

  biosynthesis, capsular, polysaccharide, Escherichia, Escherichia coli, capsular polysaccharide, epimerase, mechanism, dermatan sulphate, fructose, reaction, substrate

  NCBI PubMed ID: 8573097
  Journal NLM ID: 2984726R
  Publisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
  Institutions: Department of Medical and Physiological Chemistry, University of Uppsala, Sweden
  
   
  
  Escherichia coli K4
  CSDB ID 6938 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_423153

• Article ID: 675
  Hanniffy O, Shashkov AS, Senchenkova SN, Tomshich SV, Komandrova NA, Romanenko LA, Knirel YA, Savage AV "Structure of a highly acidic O-specific polysaccharide from Pseudoalteromonas haloplanktis KMM 223 (44-1) containing L-iduronic acid and D-QuiNHb4NHb" - Carbohydrate Research 307 (1998) 291-298
  

  An acidic O-specifc polysaccharide was obtained by mild acid degradation of the lipopolysaccharide isolated by phenol±water extraction of Pseudoalteromonas haloplanktis strain KMM 223 (44-1). l-Iduronic acid (IdoA) was found to be a component of the polysaccharide and identifed by NMR spectroscopy and after carboxyl-reduction followed by acid hydrolysis and acetylation, by GLC-MS as 2,3,4-tri-O-acetyl-1,6-anhydroidose. On the basis of 1H and 13C NMR spectroscopic studies, including 1D NOE, 2D NOESY, HSQC and HMBC experiments, the following structure of the branched pentasaccharide repeating unit of the polysaccharide was established:

  structure, strain, polysaccharide, acidic, acid, capsular polysaccharide, NMR spectroscopy, O-specific, O-specific polysaccharide, 2, 4, Pseudoalteromonas haloplanktis, Pseudoalteromonas, iduronic acid, L-iduronic acid, 4-diamino-2, 6-trideoxy-D-glucose, (S)-3-hydroxybutyric acid

  NCBI PubMed ID: 9675369
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Chemistry, University College, Galway, Ireland, Pacifc Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russian Federation
  Methods: NMR-2D, NMR
  
   
  
  Pseudoalteromonas haloplanktis KMM 223 (44-1)
  CSDB ID 475 (all data & tools)
• Article ID: 4100
  Raedts J, Kengen SW, van der OJ "Occurrence of L-iduronic acid and putative D-glucuronyl C5-epimerases in prokaryotes" - Glycoconjugate Journal 28(2) (2011) 57-66
  

  Glycosaminoglycans (GAGs) are polysaccharides that are typically present in a wide diversity of animal tissue. Most common GAGs are well-characterized and pharmaceutical applications exist for many of these compounds, e.g. heparin and hyaluronan. In addition, also bacterial glycosaminoglycan-like structures exist. Some of these bacterial GAGs have been characterized, but until now no bacterial GAG has been found that possesses the modifications that are characteristic for many of the animal GAGs such as sulfation and C5-epimerization. Nevertheless, the latter conversion may also occur in bacterial and archaeal GAGs, as some prokaryotic polysaccharides have been demonstrated to contain L-iduronic acid. However, experimental evidence for the enzymatic synthesis of L-iduronic acid in prokaryotes is as yet lacking. We therefore performed an in silico screen for D-glucuronyl C5-epimerases in prokaryotes. Multiple candidate C5-epimerases were found, suggesting that many more microorganisms are likely to exist possessing an L-iduronic acid residue as constituent of their cell wall polysaccharides.

  Lipopolysaccharide, glycosaminoglycans, capsule polysaccharide, L-iduronic acid, D-glucuronyl C5-epimerase

  NCBI PubMed ID: 21347714
  Journal NLM ID: 8603310
  Publisher: Kluwer Academic Publishers
  Correspondence: John.Raedts@wur.nl
  Institutions: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
  
   
  
  Pseudoalteromonas haloplanktis KMM 223 (44-1)
  CSDB ID 26323 (all data & tools)
• Article ID: 5157
  Goyette-Desjardins G, Vinogradov E, Okura M, Takamatsu D, Gottschalk M, Segura M "Streptococcus suis serotype 3 and serotype 18 capsular polysaccharides contain di-N-acetyl-bacillosamine" - Carbohydrate Research 466 (2018) 18-29
  

  Streptococcus suis serotype 3 is counted among the S. suis serotypes causing clinical disease in pigs. Yet, limited information is available on this serotype. Here we determined for the first time the chemical composition and structure of serotype 3 capsular polysaccharide (CPS), a major bacterial virulence factor and the antigen at the origin of S. suis classification into serotypes. Chemical and spectroscopic data gave the repeating unit sequence for serotype 3: [4)D-GlcA (β1-3)d-QuiNAc4NAc(β1-]n. To the best of our knowledge, this is the first report of di-N-acetyl-d-bacillosamine (QuiNAc4NAc) containing polysaccharides in Streptococci and the second time this rare diamino sugar has been observed in a Gram-positive bacterial species since its initial report. This led to the identification of homologues of UDP-QuiNAc4NAc synthesis genes in S. suis serotype 18. Thus, the repeating unit sequence for serotype 18 is: [3)d-GalNAc(α1-3)[d-Glc (β1-2)]d-GalA4OAc(β1-3)d-GalNAc(α1-3)d-QuiNAc4NAc(α1-]n. A correlation between S. suis serotypes 3 and 18 CPS sequences and genes of these serotypes' cps loci encoding putative glycosyltransferases and polymerase responsible for the biosynthesis of the repeating unit was tentatively established. Knowledge of CPS structure and composition will contribute to better dissect the role of this bacterial component in the pathogenesis of S. suis serotypes 3 and 18.

  polysaccharide, capsular polysaccharide, polysaccharides, carbohydrate structure, Streptococcus suis, Di-N-Acetyl-bacillosamine, Serotype 18, Serotype 3

  NCBI PubMed ID: 30014879
  Publication DOI: 10.1016/j.carres.2018.07.003
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: mariela.segura@umontreal.ca
  Institutions: Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., St-Hyacinthe, Quebec, J2S 2M2, Canada, Canadian Glycomics Network (GlycoNet), University of Alberta, 11227 Saskatchewan Dr., Edmonton, Alberta, T6G 2G2, Canada, National Research Council, 100 Sussex Dr., Ottawa, Ontario, K1A 0R6, Canada, Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan, The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu, 501-1193, Japan
  Methods: 13C NMR, 1H NMR, periodate oxidation, gel filtration, NMR-2D, GC-MS, de-O-acylation, sugar analysis, methanolysis, SEC-MALS, bioinformatic analysis
  
   
  
  Pseudoalteromonas haloplanktis KMM 223 (44-1)
  CSDB ID 12596 (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
  
   
  
  Pseudoalteromonas haloplanktis KMM 223
  CSDB ID 21146 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115013,IEDB_130645,IEDB_130648,IEDB_136044,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_138950,IEDB_141495,IEDB_141794,IEDB_142487,IEDB_142488,IEDB_146664,IEDB_149558,IEDB_151528,IEDB_190606,IEDB_742249,IEDB_918314,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_25,SB_6,SB_7,SB_87,SB_88

• Article ID: 1232
  Sheng S, Cherniak R "Structure of the capsular polysaccharide of Clostridium perfringens Hobbs 10 determined by NMR spectroscopy" - Carbohydrate Research 305(1) (1997) 65-72
  

  The complete primary structure of the type-specific capsular polysaccharide of Clostridium perfringens Hobbs 10 was determined. The polysaccharide was isolated from C. perfringens Hobbs 10 by cold-water extraction of whole, heavily encapsulated cells. The polysaccharide was purified, by ethanol precipitation, deproteination, selective precipitation with hexadecyltrimethylammonium bromide, ion-exchange chromatography and gel-filtration chromatography. The polysaccharide was comprised of D-glucose, D-galactose, N-acetylgalactosamine, and iduronic acid, in molar ratios of 2:2:1:1. Sequence and linkage assignments of the glycosyl residues were obtained by NMR spectroscopy, specifically by the combination of two-dimensional homonuclear DQF-COSY, TQF-COSY and TOCSY, heteronuclear ¿1H, 13C¿ single-quantum coherence (HSQC) and heteronuclear multiple-bond correlation (HMBC) experiments. The capsular polysaccharide of C. perfringens Hobbs 10 is a polymer composed of a hexasaccharide repeating unit with the following structure: [formula: see text] This structure is novel among bacterial cell-surface polysaccharides, and it is only the second of many serotypically distinct capsular polysaccharides of C. perfringens to be described.

  antigen, polysaccharide structure, 2D NMR spectroscopy, HMBC, TOCSY, Clostridium perfringens, DQF-COSY, TQF-COSY, HSQC

  NCBI PubMed ID: 9534227
  Publication DOI: 10.1016/S0008-6215(97)00280-2
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: cherniak@gsu.edu
  Institutions: Department of Chemistry,Georgia State Univetsity, Atlanta,USA
  Methods: NMR
  
   
  
  Clostridium perfringens Hobbs 10
  CSDB ID 4686 (all data & tools)
• Article ID: 5791
  Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" - Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
  

  Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.

  polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component

  Publication DOI: 10.1016/B978-0-12-819475-1.00005-5
  Publisher: Elsevier
  Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
  Editors: Barchi J, Kamerling H
  Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
  
   
  
  Clostridium perfringens Hobbs 10
  CSDB ID 25100 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_115136,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_142354,IEDB_151531,IEDB_241119,IEDB_241120,IEDB_241121,IEDB_423153

• Article ID: 1630
  Lindahl U, Li JP, Kusche-Gullberg M, Salmivirta M, Alaranta S, Veromaa T, Emeis J, Roberts I, Taylor C, Oreste P, Zoppetti G, Naggi A, Torri G, Casu B "Generation of 'neoheparin' from E. coli K5 capsular polysaccharide" - Journal of Medicinal Chemistry 48(2) (2005) 349-352
  

  Heparin remains a major drug in prevention of thromboembolic disease. Concerns related to its animal source have prompted search for heparin analogues. The anticoagulant activity of heparin depends on a specific pentasaccharide sequence that binds antithrombin. We report the generation of a product with antithrombin-binding, anticoagulant, and antithrombotic properties similar to those of heparin, through combined chemical and enzymatic modification of a bacterial (E. coli K5) polysaccharide. The process is readily applicable to large-scale production.

  Escherichia coli, capsular polysaccharide, heparin, chemical synthesis, anticoagulant activity, enzymatic modification

  NCBI PubMed ID: 15658847
  Journal NLM ID: 9716531
  Publisher: Washington, DC: American Chemical Society
  Correspondence: ulf.lindahl@imbim.uu.se
  Institutions: Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
  Methods: biological assays, biosynthetic modifications, chemoenzymatic modifications
  
   
  
  Escherichia coli K5
  CSDB ID 10798 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_130669,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_144987,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983931,SB_192,SB_31,SB_7

• Article ID: 2266
  Andersson M, Ratnayake S, Kenne L, Ericsson L, Stack RJ "Structural studies of the extracellular polysaccharide from Butyrivibrio fibrisolvens strain X6C61" - Carbohydrate Research 246 (1993) 291-301
  

  The capsular polysaccharide from Butyrivibrio fibrisolvens strain X6C61 has been investigated using NMR spectroscopy, mass spectrometry, methylation analysis, and partial acid hydrolysis as the main methods. The polysaccharide is composed of hexasaccharide repeating units having the following structure. [formula: see text] The polysaccharide also contains O-acetyl groups, of which approximately 70% are substituted to O-3 of the β-D-GlcpA residue.

  NCBI PubMed ID: 8370042
  Publication DOI: 10.1016/0008-6215(93)84041-4
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Sweden
  Methods: 13C NMR, 1H NMR
  
   
  
  Butyrivibrio fibrisolvens X6C61
  CSDB ID 117329 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_115136,IEDB_130669,IEDB_136105,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_144987,IEDB_146664,IEDB_151528,IEDB_190606,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983931,SB_192,SB_31,SB_7

• Article ID: 2266
  Andersson M, Ratnayake S, Kenne L, Ericsson L, Stack RJ "Structural studies of the extracellular polysaccharide from Butyrivibrio fibrisolvens strain X6C61" - Carbohydrate Research 246 (1993) 291-301
  

  The capsular polysaccharide from Butyrivibrio fibrisolvens strain X6C61 has been investigated using NMR spectroscopy, mass spectrometry, methylation analysis, and partial acid hydrolysis as the main methods. The polysaccharide is composed of hexasaccharide repeating units having the following structure. [formula: see text] The polysaccharide also contains O-acetyl groups, of which approximately 70% are substituted to O-3 of the β-D-GlcpA residue.

  NCBI PubMed ID: 8370042
  Publication DOI: 10.1016/0008-6215(93)84041-4
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Sweden
  Methods: 13C NMR, 1H NMR
  
   
  
  Butyrivibrio fibrisolvens X6C61
  CSDB ID 117330 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit ; n=3,4
Trivial name: dermatant sulfate
Compound class: mucopolysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_137473

• Article ID: 3317
  Yu H, Chen X "Carbohydrate post-glycosylational modifications" - Organic and Biomolecular Chemistry 5(6) (2007) 865-872
  

  Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological regulation that is achieved by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combined with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented

  synthesis, regulation, glycoconjugates, polysaccharides, enzymatic, modification, structure-activity relationship, methods, epimerization

  Publication DOI: 10.1039/b700034k
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: chen@chem.ucdavis.edu
  Institutions: Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
  
   
  
  Homo sapiens
  CSDB ID 21673 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: dermatant sulfate oligosaccharide
Compound class: mucopolysaccharide
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_885822

• Article ID: 3317
  Yu H, Chen X "Carbohydrate post-glycosylational modifications" - Organic and Biomolecular Chemistry 5(6) (2007) 865-872
  

  Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological regulation that is achieved by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combined with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented

  synthesis, regulation, glycoconjugates, polysaccharides, enzymatic, modification, structure-activity relationship, methods, epimerization

  Publication DOI: 10.1039/b700034k
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: chen@chem.ucdavis.edu
  Institutions: Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
  
   
  
  Homo sapiens
  CSDB ID 21674 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: Heparin sulfate (HS)
Compound class: mucopolysaccharide
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_141807,IEDB_151531,IEDB_241121,IEDB_423153

• Article ID: 3317
  Yu H, Chen X "Carbohydrate post-glycosylational modifications" - Organic and Biomolecular Chemistry 5(6) (2007) 865-872
  

  Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological regulation that is achieved by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combined with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented

  synthesis, regulation, glycoconjugates, polysaccharides, enzymatic, modification, structure-activity relationship, methods, epimerization

  Publication DOI: 10.1039/b700034k
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: chen@chem.ucdavis.edu
  Institutions: Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
  
   
  
  Homo sapiens
  CSDB ID 21676 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: mucopolysaccharide, analog Arixta
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_141807,IEDB_151531,IEDB_241120,IEDB_241121,IEDB_423153

• Article ID: 3317
  Yu H, Chen X "Carbohydrate post-glycosylational modifications" - Organic and Biomolecular Chemistry 5(6) (2007) 865-872
  

  Carbohydrate modification is a common phenomenon in nature. Many carbohydrate modifications such as some epimerization, O-acetylation, O-sulfation, O-methylation, N-deacetylation, and N-sulfation, take place after the formation of oligosaccharide or polysaccharide backbones. These modifications can be categorized as carbohydrate post-glycosylational modifications (PGMs). Carbohydrate PGMs further extend the complexity of the structures and the synthesis of carbohydrates and glycoconjugates. They also increase the capacity of the biological regulation that is achieved by finely tuning the structures of carbohydrates. Developing efficient methods to obtain structurally defined naturally occurring oligosaccharides, polysaccharides, and glycoconjugates with carbohydrate PGMs is essential for understanding the biological significance of carbohydrate PGMs. Combined with high-throughput screening methods, synthetic carbohydrates with PGMs are invaluable probes in structure-activity relationship studies. We illustrate here several classes of carbohydrates with PGMs and their applications. Recent progress in chemical, enzymatic, and chemoenzymatic syntheses of these carbohydrates and their derivatives are also presented

  synthesis, regulation, glycoconjugates, polysaccharides, enzymatic, modification, structure-activity relationship, methods, epimerization

  Publication DOI: 10.1039/b700034k
  Journal NLM ID: 101154995
  Publisher: The Royal Society of Chemistry
  Correspondence: chen@chem.ucdavis.edu
  Institutions: Department of Chemistry, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
  
   
  
  Homo sapiens
  CSDB ID 21677 (all data & tools)

Show legend Show as text

Structure type: polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_135813,IEDB_136021,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_1391965,IEDB_141584,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_423113,IEDB_885822,IEDB_983931,SB_192

• Article ID: 3506
  Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves P, Wang L "Structure and genetics of Shigella O antigens" - FEMS Microbiology Reviews 32(4) (2008) 627-653
  

  This review covers the O antigens of the 46 serotypes of Shigella, but those of most Shigella flexneri are variants of one basic structure, leaving 34 Shigella distinct O antigens to review, together with their gene clusters. Several of the structures and gene clusters are reported for the first time and this is the first such group for which structures and DNA sequences have been determined for all O antigens. Shigella strains are in effect Escherichia coli with a specific mode of pathogenicity, and 18 of the 34 O antigens are also found in traditional E. coli. Three are very similar to E. coli O antigens and 13 are unique to Shigella strains. The O antigen of Shigella sonnei is quite atypical for E. coli and is thought to have transferred from Plesiomonas. The other 12 O antigens unique to Shigella strains have structures that are typical of E. coli, but there are considerably more anomalies in their gene clusters, probably reflecting recent modification of the structures. Having the complete set of structures and genes opens the way for experimental studies on the role of this diversity in pathogenicity.

  structure, O antigen, Shigella, O antigen gene cluster, O antigen diversity

  NCBI PubMed ID: 18422615
  Publication DOI: 10.1111/j.1574-6976.2008.00114.x
  Journal NLM ID: 8902526
  Publisher: Oxford University Press
  Correspondence: wanglei@nankai.edu.cn
  Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China.
  Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, serological methods, genetic methods, biochemical methods
  
   
  
  Shigella boydii B15, Escherichia coli O112ab
  CSDB ID 23057 (all data & tools)

Show legend Show as text

Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_135813,IEDB_136021,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_1391965,IEDB_141584,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_423113,IEDB_885822,IEDB_983931,SB_192

• Article ID: 3532
  Perepelov AV, Liu B, Senchenkova SN, Shashkov AS, Feng L, Knirel YA, Wang L "Structure of the O-polysaccharide of Escherichia coli O112ab containing L-iduronic acid" - Carbohydrate Research 343(3) (2008) 571-575
  

  An acidic O-polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of Escherichia coli O112ab and studied by sugar analysis along with 1H and 13C NMR spectroscopy. The O-polysaccharide was found to contain a rarely occurring sugar component, L-iduronic acid (L-IdoA), and the following structure of the branched pentasaccharide repeating unit was established

  O-antigen, Escherichia coli, NMR spectroscopy, O-polysaccharide, bacterial polysaccharide structure, L-iduronic acid

  NCBI PubMed ID: 18062946
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: perepel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, RussiaTEDA School of Biological Sciences and Biotechnology, Nankai University, 23 HongDa Street, TEDA, Tianjin, ChinaTianjin Key Laboratory for Microbial Functional Genomics, TEDA College, Nankai University, 23 HongDa Street, TEDA, Tianjin, China
  Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, alkaline degradation, NMR-1D
  
   
  
  Escherichia coli O112ab
  CSDB ID 22717 (all data & tools)
• Article ID: 5423
  Dobrochaeva KL, Khasbiulina NR, Shilova NV, Obukhova PS, Knirel YA, Nokel AY, Bovin NV "Human antibodies eluted from ligand-free Sepharose capable of binding bacterial polysaccharides and sulfated glycans" - Molecular Immunology 106 (2019) 63-68
  

  Sepharose matrix without immobilized ligands binds antibodies from human blood serum or immunoglobulin preparations. The eluted antibodies bind bacterial polysaccharides having no structural similarity to agarose (Sepharose is a cross-linked polysaccharide agarose) with a high affinity. It is concluded that the identified antibodies are capable of recognizing spatial rather than linear epitopes of bacterial polysaccharides. This side activity of Sepharose matrix should be taken into account in isolating target antibodies and other proteins from human blood.

  antibodies, bacteria, polysaccharides, printed glycan array, Agarose, Sepharose

  NCBI PubMed ID: 30583222
  Publication DOI: 10.1016/j.molimm.2018.12.011
  Journal NLM ID: 7905289
  Publisher: Elsevier
  Correspondence: N.V. Bovin
  Institutions: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 ul. Miklukho-Maklaya, Moscow, Russian Federation, Semiotik LLC, Moscow, Russian Federation, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky pr., Moscow, Russian Federation, School of Engineering, Computer & Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand
  Methods: serological methods, UV, affinity chromatography, antibody binding, glycan array analysis, microarray binding assays, serum analysis, isolation of antibodies
  
   
  
  Escherichia coli O112ab
  CSDB ID 705 (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 O112ab, Shigella boydii 15
  CSDB ID 1851 (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 O112ab, Shigella boydii 15
  CSDB ID 3390 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-antigen
Contained glycoepitopes: IEDB_130648,IEDB_135813,IEDB_136021,IEDB_137340,IEDB_137473,IEDB_1391961,IEDB_1391965,IEDB_141584,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_423113,IEDB_885822,IEDB_983931,SB_192

• Article ID: 4100
  Raedts J, Kengen SW, van der OJ "Occurrence of L-iduronic acid and putative D-glucuronyl C5-epimerases in prokaryotes" - Glycoconjugate Journal 28(2) (2011) 57-66
  

  Glycosaminoglycans (GAGs) are polysaccharides that are typically present in a wide diversity of animal tissue. Most common GAGs are well-characterized and pharmaceutical applications exist for many of these compounds, e.g. heparin and hyaluronan. In addition, also bacterial glycosaminoglycan-like structures exist. Some of these bacterial GAGs have been characterized, but until now no bacterial GAG has been found that possesses the modifications that are characteristic for many of the animal GAGs such as sulfation and C5-epimerization. Nevertheless, the latter conversion may also occur in bacterial and archaeal GAGs, as some prokaryotic polysaccharides have been demonstrated to contain L-iduronic acid. However, experimental evidence for the enzymatic synthesis of L-iduronic acid in prokaryotes is as yet lacking. We therefore performed an in silico screen for D-glucuronyl C5-epimerases in prokaryotes. Multiple candidate C5-epimerases were found, suggesting that many more microorganisms are likely to exist possessing an L-iduronic acid residue as constituent of their cell wall polysaccharides.

  Lipopolysaccharide, glycosaminoglycans, capsule polysaccharide, L-iduronic acid, D-glucuronyl C5-epimerase

  NCBI PubMed ID: 21347714
  Journal NLM ID: 8603310
  Publisher: Kluwer Academic Publishers
  Correspondence: John.Raedts@wur.nl
  Institutions: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
  
   
  
  Escherichia coli O112ab, Shigella boydii B15
  CSDB ID 26942 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: glycoglycerolipid
Compound class: glycolipid
Contained glycoepitopes: IEDB_141807,IEDB_151531

• Article ID: 4229
  Yagi H, Maruyama A "Novel diglycosyldiacylglycerol from the Gram-negative bacterium Deleya marina" - Biochimica et Biophysica Acta 1393 (1998) 161-165
  

  A glycosyldiacylglycerol was isolated from the marine bacterium Deleya marina (ATCC 25374). The structure was determined, mainly by spectral data, to be 1, 2-diacyl-3-O-[α-2-amino-2-deoxy-glucopyranose-(1→4)-O-α-iduronopyranuronic acid]-glycerol. This is, to our knowledge, the first isolation of diglycosyldiacylglycerol containing both iduronopyranuronic acid and 2-amino-2-deoxy-glucopyranose from Gram-negative bacteria.

  NCBI PubMed ID: 9714788
  Journal NLM ID: 0217513
  Publisher: Elsevier
  Correspondence: hyagi@ccmail.nibh.go
  Institutions: National Institute of Bioscience and Human-Technology, 1-1 Higashi, Tsukuba, Ibaraki 305, Japan
  Methods: 13C NMR, 1H NMR, FAB-MS
  
   
  
  Cobetia marina, Deleya marina
  CSDB ID 109702 (all data & tools)

Show legend Show as text

Structure type: fragment of a bigger structure
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_423153,IEDB_983931,SB_192

• Article ID: 4238
  Paul G, Wieland F "Sequence of the halobacterial glycosaminoglycan" - Journal of Biological Chemistry 262 (1987) 9587-9593
  

  The cell-surface glycoprotein of halobacterium contains a sulfated repeating unit saccharide chain, similar to the mammalian glycosaminoglycans. The composition of a presumptive repeating pentasaccharide unit of this glycosaminoglycan is 1 GlcNAc, 1 GalNAc, 1 Gal, 1 GalA (where GalA represents galacturonic acid), 1 3-O-methyl-GalA, and 2 SO42-. Linkage to protein of this glycoconjugate involves the hitherto unique unit Asn-GalNAc, with the N-linked asparagine residue being the second NH2-terminal amino acid and part of the common N-linked glycosyl acceptor sequence Asn-X-Thr(Ser). Transfer of the completed, sulfated glycosaminoglycan from its lipid precursor to the protein occurs at the cell surface, and the presence of this sulfated saccharide chain in the cell-surface glycoprotein seems to be required to maintain the structural integrity of the rod-shaped halobacteria. In this paper, we report the complete saccharide structure of this N-linked glycosaminoglycan. This structure is deduced from chemical analyses of fragments that were isolated after hydrazinolysis and subsequent nitrous acid deamination or after mild acidic hydrolysis of purified Pronase-derived glycosaminoglycan-peptides. The halobacterial glycosaminoglycan consists, on the average, of 10 repeating pentasaccharide units of the following structure. (formula: see text) The reducing end N-acetylgalactosamine residue is linked directly to the asparagine, without a special saccharide linker region.

  NCBI PubMed ID: 3597425
  Journal NLM ID: 2985121R
  Publisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
  Methods: GLC-MS, gel filtration, partial acid hydrolysis, acid hydrolysis, GLC, deamination, methanolysis, desulfation, hydrazinolysis, reduction, permethylation analysis
  
   
  
  Halobacterium halobium R1M1, Halobacterium halobium
  CSDB ID 234992 (all data & tools)