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1. Compound ID: 305
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Subst-(1-3)-a-L-Fucp-(1-3)-b-D-Manp-(1-3)-b-D-6dxylHexpN-4-ulo-(1-4)-a-Kdop-(2--/core-lipid A/
Subst = O-antigen |
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Structure type: oligomer
Aglycon: core-lipid A
Trivial name: core oligosaccharide with o-antigen
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_136045,IEDB_137485,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_152206,IEDB_152214,IEDB_174333,IEDB_983930,SB_44,SB_72,SB_86
The structure is contained in the following publication(s):
- Article ID: 80
Forsberg LS, Noel KD, Box J, Carlson RW "Genetic locus and structural characterization of the biochemical defect in the O-antigenic polysaccharide of the symbiotically deficient Rhizobium etli mutant, CE166: Replacement of N-acetylquinovosamine with its hexosyl-4-ulose precursor" -
Journal of Biological Chemistry 278(51) (2003) 51347-51359
The O-antigen polysaccharide (OPS) of Rhizobium etli CE3 lipopolysaccharide (LPS) is linked to the core oligosaccharide via an N-acetylquinovosaminosyl (QuiNAc) residue. A mutant of CE3, CE166, produces LPS with reduced amounts of OPS, and a suppressed mutant, CE166α, produces LPS with nearly normal OPS levels. Both mutants are deficient in QuiNAc production. Characterization of OPS from CE166 and CE166α showed that QuiNAc was replaced by its 4-keto derivative, 2-acetamido-2,6-dideoxyhexosyl-4-ulose. The identity of this residue was determined by NMR and mass spectrometry, and by gas chromatography-mass spectrometry analysis of its 2-acetamido-4-deutero-2,6-dideoxyhexosyl derivatives produced by reduction of the 4-keto group using borodeuteride. Mass spectrometric and methylation analyses showed that the 2-acetamido-2,6-dideoxyhexosyl-4-ulosyl residue was 3-linked and attached to the core-region external Kdo III residue of the LPS, the same position as that of QuiNAc in the CE3 LPS. DNA sequencing revealed that the transposon insertion in strain CE166 was located in an open reading frame whose predicted translation product, LpsQ, falls within a large family of predicted open reading frames, which includes biochemically characterized members that are sugar epimerases and/or reductases. A hypothesis to be tested in future work is that lpsQ encodes UDP-2-acetamido-2,6-dideoxyhexosyl-4-ulose reductase, the second step in the synthesis of UDP-QuiNAc from UDP-GlcNAc
Lipopolysaccharide, NMR, genetic, synthesis, LPS, oligosaccharide, core, DNA, strain, structural, characterization, polysaccharide, O-antigen, analysis, O antigen, group, linked, locus, O-antigenic, O-antigenic polysaccharide, Kdo, core oligosaccharide, level, spectrometry, mutant, mutants, Rhizobia, Rhizobium, Rhizobium etli, sugar, core region, biochemical, derivative, DNA sequencing, epimerase, external, families, gas chromatography-mass spectrometry, insertion, mass spectrometry, methylation, Open Reading Frames, position, precursor, production, reduced, reduction, sequencing, translation, transposon
NCBI PubMed ID: 14551189Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: rcarlson@ccrc.uga.edu
Institutions: Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, USA
Methods: methylation, NMR-2D, NMR, sugar analysis, MS
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2. Compound ID: 2745
|
-4)-b-D-GlcpNAcA3Ac-(1-4)-a-L-FucpNAm3Ac-(1-3)-a-D-6dxylHexpN-4-ulo-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
The structure is contained in the following publication(s):
- Article ID: 961
MacLean LL, Perry MB, Crump EM, Kay WW "Structural characterization of the lipopolysaccharide O-polysaccharide antigen produced by Flavobacterium columnare ATCC43622 Leann L. MacLean, Malcolm B. Perry, Elizabeth M. Crump, William W. Kay" -
European Journal of Biochemistry 270(16) (2003) 3440-3446
The structure of the antigenic O-chain polysaccharide of Flavobacterium columnare ATCC43622, a Gram-negative bacterium that causes columnaris disease in warm water fish, was determined by high-field 1D and 2D NMR techniques, MS, and chemical analyses. The O-chain was shown to be an unbranched linear polymer of a trisaccharide repeating unit composed of 2-acetamido-2-deoxy-d-glucuronic acid (d-GlcNAcA), 2-acetamidino-2,6-dideoxy-l-galactose (l-FucNAm) and 2-acetamido-2,6-dideoxy-d-xylo-hexos-4-ulose (d-Sug) (1 : 1 : 1), having the structure: [structure: see text].
Lipopolysaccharide, antigen, structural, characterization, O-polysaccharide, O polysaccharide, Flavobacterium
NCBI PubMed ID: 12899701Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: malcolm.perry@nrc.ca
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada, Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
Methods: NMR-2D, NMR, chemical analysis, MS
- 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: 35750381Publication DOI: 10.1016/S1875-5364(22)60177-8Journal NLM ID: 101504416Publisher: 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
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3. Compound ID: 2746
|
-4)-b-D-GlcpNAcA-(1-4)-a-L-FucpNAm-(1-3)-a-D-6dxylHexpN-4-ulo-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
The structure is contained in the following publication(s):
- Article ID: 961
MacLean LL, Perry MB, Crump EM, Kay WW "Structural characterization of the lipopolysaccharide O-polysaccharide antigen produced by Flavobacterium columnare ATCC43622 Leann L. MacLean, Malcolm B. Perry, Elizabeth M. Crump, William W. Kay" -
European Journal of Biochemistry 270(16) (2003) 3440-3446
The structure of the antigenic O-chain polysaccharide of Flavobacterium columnare ATCC43622, a Gram-negative bacterium that causes columnaris disease in warm water fish, was determined by high-field 1D and 2D NMR techniques, MS, and chemical analyses. The O-chain was shown to be an unbranched linear polymer of a trisaccharide repeating unit composed of 2-acetamido-2-deoxy-d-glucuronic acid (d-GlcNAcA), 2-acetamidino-2,6-dideoxy-l-galactose (l-FucNAm) and 2-acetamido-2,6-dideoxy-d-xylo-hexos-4-ulose (d-Sug) (1 : 1 : 1), having the structure: [structure: see text].
Lipopolysaccharide, antigen, structural, characterization, O-polysaccharide, O polysaccharide, Flavobacterium
NCBI PubMed ID: 12899701Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: malcolm.perry@nrc.ca
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, Ontario, Canada, Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
Methods: NMR-2D, NMR, chemical analysis, MS
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4. Compound ID: 3188
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L-Ala2Fo-(1-3)-+
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-4)-b-D-GlcpNAc3NA6NH2-(1-4)-b-D-GlcpNAc3NAmA-(1-4)-a-L-GalpNAc3NAcA-(1-3)-b-D-6dxylHexpNAc-4-ulo-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS, O-polysaccharide, O-antigen
The structure is contained in the following publication(s):
- Article ID: 1166
Sadovskaya I, Brisson JR, Khieu NH, Mutharia LM, Altman E "Structural characterization of the lipopolysaccharide O-antigen and capsular polysaccharide of Vibrio ordalii serotype O:2" -
European Journal of Biochemistry 253(1) (1998) 319-327
Structures of the capsular and O-chain polysaccharides of Vibrio ordalii serotype O:2, the causative agent of vibriosis in salmonid fish, were determined by high-field NMR techniques, mass spectrometric methods and partial hydrolysis. Both polymers were shown to be composed of linear tetrasaccharide repeating units, having the structure: carbohydrate sequence [see text]
Lipopolysaccharide, NMR, capsular polysaccharide, Vibrio ordalii
NCBI PubMed ID: 9578491Publication DOI: 10.1046/j.1432-1327.1998.2530319.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: eleonora.altman@nrc.ca
Institutions: Institute for Biological Sciences, National Research Council of Canada, Ottawa, Canada, Department of Microbiology, College of Biological Sciences, University of Guelph, Canada
Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, composition analysis
- 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/B978-0-12-819475-1.00005-5Publisher: 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
- 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: 35750381Publication DOI: 10.1016/S1875-5364(22)60177-8Journal NLM ID: 101504416Publisher: 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
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5. Compound ID: 3589
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a-L-6dTalpNAc-(1-2)-b-D-GlcpA-(1-3)-+
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-4)-b-D-Glcp-(1-4)-a-L-FucpNAc-(1-3)-b-D-6dxylHexpNAc-4-ulo-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 1347
Abeygunawardana C, Williams TC, Sumner JS, Hennessey JP "Development and validation of an NMR-based identity assay for bacterial polysaccharides" -
Analytical Biochemistry 279(2) (2000) 226-240
A method utilizing NMR spectroscopy has been developed to confirm the identity of bacterial polysaccharides used to formulate a polyvalent pneumococcal polysaccharide vaccine. The method is based on 600 MHz proton NMR spectra of individual serotype-specific polysaccharides. A portion of the anomeric region of each spectrum (5.89 to 4.64 ppm) is compared to spectra generated for designated reference samples for each polysaccharide of interest. The selected region offers a spectral window that is unique to a given polysaccharide and is sensitive to any structural alteration of the repeating units. The similarity of any two spectral profiles is evaluated using a correlation coefficient (rho), where rho >/= 0.95 between a sample and reference profile indicates a positive identification of the sample polysaccharide. This method has been shown to be extremely selective in its ability to discriminate between serotype-specific polysaccharides, some of which differ by no more than a single glycosidic linkage. Furthermore, the method is rapid and does not require extensive sample manipulations or pretreatments. The method was validated as a qualitative identity assay and will be incorporated into routine quality control testing of polysaccharide powders to be used in preparation of the polyvalent pneumococcal vaccine PNEUMOVAX 23. The specificity and reproducibility of the NMR-based identity assay is superior to the currently used colorimetric assays and can be readily adapted for use with other bacterial polysaccharide preparations as well.
NMR, Bacterial, polysaccharide, Bacterial polysaccharide, polysaccharides, bacterial polysaccharides, assay, development, identity assay, method development, validation
NCBI PubMed ID: 10706792Publication DOI: 10.1006/abio.1999.447Journal NLM ID: 0370535Publisher: Academic Press
Correspondence: abey@merck.com
Institutions: Bioprocess and Bioanalytical Research, Merck Research Laboratories, West Point, Pensylvania, USA
Methods: NMR
- Article ID: 4554
Kokoulin MS, Kalinovsky AI, Komandrova NA, Tovarchi VE, Tomshich SV, Nedashkovskaya OI, Vaskovsky VE "The structure of the O-specific polysaccharide from marine bacterium Litorimonas taeanensis G5 containing 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-D-quinovose and 2-acetamido-2,6-dideoxy-L-xylo-hexos-4-ulose" -
Carbohydrate Research 375 (2013) 105-111
The O-polysaccharide was isolated from the lipopolysaccharide of Litorimonas taeanensis G5T and studied by chemical methods along with 1H and 13C NMR spectroscopy, including 1H, 1H COSY, 1D and 2D TOCSY, NOESY, 1H, 13C HSQC, HMBC, and H2BC experiments. The following new structure of the O-polysaccharide of L. taeanensis G5T containing 2-acetamido-2-deoxy-d-galacturonic acid (d-GalNAcA), 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-d-quinovose (d-QuiNAc4NR), and 2-acetamido-2,6-dideoxy-l-xylo-hexos-4-ulose (l-Sug) was established: where R is (3S,5S)-3,5-dihydroxyhexanoic acid.
O-specific polysaccharide, 2-acetamido-2, 6-dideoxy-L-xylo-hexos-4-ulose, 2-Acetamido-4-((3S, 5S)-3, 5-dihydroxyhexanamido)-2, 4-dideoxy-D-quinovose, Litorimonas taeanensis
NCBI PubMed ID: 23694711Publication DOI: 10.1016/j.carres.2013.04.004Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: maxchem@mail.ru
Institutions: G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, NMR-1D, triflic acid solvolysis, borohydride reduction
- Article ID: 4828
Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH "Pneumococcal Capsules and Their Types: Past, Present, and Future" -
Clinical Microbiology Reviews 28(3) (2015) 871-899
Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.
serotype, Streptococcus pneumoniae, vaccines, Pneumococcal Capsules
NCBI PubMed ID: 26085553Publication DOI: 10.1128/CMR.00024-15Journal NLM ID: 8807282Publisher: Washington, DC: American Society for Microbiology
Correspondence: Moon H. Nahm
Institutions: Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA, Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Wentworthville, New South Wales, Australia, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia, Division of Infectious Disease, Department of Internal Medicine, Korea University Guro Hospital, Seoul, South Korea, SSI Diagnostica, Division of Microbiology and Diagnostics, Statens Serum Institut, Copenhagen, Denmark, Pneumonia Program Strategy Team, Bill & Melinda Gates Foundation, Seattle, Washington, USA, Laboratory for Molecular Structure, NIBSC, South Mimms, Herts, United Kingdom, Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Article ID: 4836
Berti F, Ravenscroft N "Characterization of Carbohydrate Vaccines by NMR Spectroscopy" -
Methods in Molecular Biology 1331 (2015) 189-209
Physicochemical techniques are a powerful tool for the structural characterization of carbohydrate-based vaccines. High-field Nuclear Magnetic Resonance (NMR) spectroscopy has been established as an extremely useful and robust method for tracking the industrial manufacturing process of these vaccines from polysaccharide bulk antigen through to the final formulation. Here, we describe the use of proton NMR for structural identity and conformity testing of carbohydrate-based vaccines.
carbohydrates, capsular polysaccharide, antigens, nuclear magnetic resonance spectroscopy, vaccines
NCBI PubMed ID: 26169742Publication DOI: 10.1007/978-1-4939-2874-3_12Journal NLM ID: 9214969Publisher: Springer
Correspondence: francesco.x.berti@gsk.com
Institutions: Research, GSK Vaccines, Via Fiorentina 1, 53100, Siena, Italy
- Article ID: 5093
Lisboa MP, Khan N, Martin C, Xu FF, Reppe K, Geissner A, Govindan S, Witzenrath M, Pereira CL, Seeberger PH "Semisynthetic glycoconjugate vaccine candidate against Streptococcus pneumoniae serotype 5" -
Proceedings of the National Academy of Sciences of the USA 114(42) (2017) 11063-11068
Glycoconjugate vaccines based on isolated capsular polysaccharide (CPS) save millions of lives annually by preventing invasive pneumococcal disease caused by Streptococcus pneumoniae Some components of the S. pneumoniae glycoconjugate vaccine Prevnar13 that contains CPS antigens from 13 serotypes undergo modifications or degradation during isolation and conjugation, resulting in production problems and lower efficacy. We illustrate how stable, synthetic oligosaccharide analogs of labile CPS induce a specific protective immune response against native CPS using S. pneumoniae serotype 5 (ST-5), a problematic CPS component of Prevnar13. The rare aminosugar l-PneuNAc and a branched l-FucNAc present in the natural repeating unit (RU) are essential for antibody recognition and avidity. The epitope responsible for specificity differs from the part of the antigen that is stabilized by chemical modification. Glycoconjugates containing stable, monovalent synthetic oligosaccharide analogs of ST-5 CPS RU induced long-term memory and protective immune responses in rabbits superior to those elicited by the ST-5 CPS component in multivalent Prevnar13.
vaccine, glycoconjugate, S. pneumoniae, carbohydrate chemistry, serotype 5
NCBI PubMed ID: 28973947Publication DOI: 10.1073/pnas.1706875114Journal NLM ID: 7505876Publisher: National Academy of Sciences
Correspondence: claney.pereira@vaxxilon.com; peter.seeberger@mpikg.mpg.de
Institutions: Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, D-14424 Potsdam, Germany, Department of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany, Department of Infectious Diseases and Pulmonary Medicine, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
Methods: 13C NMR, 1H NMR, NMR-2D, IR, SDS-PAGE, TLC, ELISA, chemical synthesis, biological assays, glycosylation, optical rotation measurement, statistical analysis, immunization, conjugation, HR-ESI-MS, microarray analysis, flow cytometry, microarray binding assays
- Article ID: 5473
Zou W, Li J, Vinogradov E, Cox A "Removal of cell wall polysaccharide in pneumococcal capsular polysaccharides by selective degradation via deamination" -
Carbohydrate Polymers 218 (2019) 199-207
Pneumococcal cell wall polysaccharide (C-PS), a contaminant in pneumococcal capsular polysaccharide (Pn-PS) vaccines is degraded by mild deamination of the 4-amino-2-acetamido-2,4,6-tri-deoxy-galactose (AAT) in C-PS, which was carried out by addition of 5% aqueous sodium nitrite to a solution of polysaccharide in 5% aqueous acetic acid. Glycosidic linkage and functional groups such as O-acetates, phosphodiesters, and pyruvates were preserved under the conditions. The small fragments from degraded C-PS were removed by ultrafiltration or dialysis to provide essentially C-PS free Pn-PS. Because of the presence of AAT in its structure the deamination is not suitable for the purification of type 1 Pn-PS. Meanwhile, the mass and NMR spectroscopic analysis on the deamination products suggests that both type 1 Pn-PS and C-PS degraded following a major pathway of 5,4-hydride shift, cleavage of AAT O5-C1 bond, C1 hemiacetal formation, and its hydrolysis to release neighboring GalA- in type 1 Pn-PS and GalNAc(6-O-PCho)- in C-PS
mechanism, degradation, deamination, cell wall polysaccharide, pneumococcal capsular polysaccharide
NCBI PubMed ID: 31221321Publication DOI: 10.1016/j.carbpol.2019.03.070Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: W. Zou
Institutions: Human Health Therapeutic Research Center, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, K1A 0R6, Canada
Methods: 13C NMR, 1H NMR, gel filtration, sugar analysis, MS/MS, MS, dialysis, SEC-HPLC, ultrafiltration, mild deamination
- 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/B978-0-12-819475-1.00005-5Publisher: 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
- Article ID: 6058
Genning M, Kurbatova EA, Nifantiev NE "Synthetic Analogs of Streptococcus pneumoniae Capsular Polysaccharides and Immunogenic Activities of Glycoconjugates" -
Russian Journal of Bioorganic Chemistry 47(1) (2021) 1-25
treptococcus pneumoniae is a Gram-positive bacterium (pneumococcus) that causes severe diseases in adults and children. It was established that some capsular polysaccharides of the clinically significant serotypes of S. pneumoniae in the composition of commercial pneumococcal polysaccharide or conjugate vaccines exhibit low immunogenicity. The review considers production methods and structural features of the synthetic oligosaccharides from the problematic pneumococcal serotypes that are characterized with low immunogenicity due to destruction or detrimental modification occurring in the process of their preparation and purification. Bacterial serotypes that cause severe pneumococcal diseases as well as serotypes not included in the composition of the pneumococcal conjugate vaccines are also discussed. It is demonstrated that the synthetic oligosaccharides corresponding to protective glycotopes of the capsular polysaccharides of various pneumococcal serotypes are capable of inducing formation of the protective opsonizing antibodies and immunological memory. Optimal constructs of oligosaccharides from the epidemiologically significant pneumococcal serotypes are presented that can be used for designing synthetic pneumococcal vaccines, as well as test systems for diagnosis of S. pneumoniae infections and monitoring of vaccination efficiency.
oligosaccharide, antibodies, ligand, vaccine, immunogen, Opsonophagocytosis, protective activity, pneumococci
NCBI PubMed ID: 33776393Publication DOI: 10.1134/S1068162021010076Journal NLM ID: 9420101Publisher: Springer Science and Business Media
Correspondence: nen@ioc.ac.ru
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Mechnikov Research Institute for Vaccines and Sera, 105064 Moscow, Russia
- Article ID: 6073
Javed J, Mandal PK "Bacterial surface capsular polysaccharides from Streptococcus pneumoniae: A systematic review on structures, syntheses, and glycoconjugate vaccines" -
Carbohydrate Research 502 (2021) 108277
The polysaccharide capsule of Streptococcus pneumoniae constitutes the outermost surface structure of the organism and plays a critical role in virulence. The capsule is the target of current pneumococcal vaccines and glycoconjugates and has important medical and industrial applications. Widespread use of these vaccines is driving changes in serotype prevalence in disease. A massive array of sugars and glycosidic linkages experienced with complete diversity of potential polysaccharide structures. However, it is impossible to collect a sufficient quantity of glycan antigens for the preparation of CPS-based glycoconjugate vaccines from natural sources with high purity and for thorough biological evaluation. So nowadays, the development of a chemical synthetic strategy and their conjugation with a carrier protein to form synthetic glycoconjugate vaccines has been used to gain access on a large scale. This review provides a comprehensive summary of structures, synthesis as well as recent development of synthetic glycoconjugate vaccines, which will support research and may benefit the glycochemical and medical sciences.
synthesis, Streptococcus pneumoniae, glycoconjugate vaccines, polysaccharides, Pneumococcal Infections
NCBI PubMed ID: 33743443Publication DOI: 10.1016/j.carres.2021.108277Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: P.K. Mandal
Institutions: Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow, 226 031, India, Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
- Article ID: 6461
Shende N, Karale A, Bore P, Bhagade S, Gulhane A, Mallya AD, Dhere RM "Evaluation of structural modification induced activation of pneumococcal polysaccharide by GC-MS for the conjugate vaccine" -
Carbohydrate Research 531 (2023) 108878
Polysaccharide (Ps) activation evaluation is an imperative quality attribute in a conjugate vaccine. Pneumococcal polysaccharide (PnPs) serotypes 5, 6B, 14, 19A and 23F were cyanylated for 3 and 8 min. The cyanylated and non-cyanylated polysaccharides were methanolysed and derivatized to assess the activation of each sugar by GC-MS. The activation of 22 and 27% serotype 6B and 11 and 36% in serotype 23 F Ps at 3 and 8 min respectively showed controlled conjugation kinetics with CRM197 carrier protein estimated by SEC-HPLC and optimal absolute molar mass by SEC-MALS. The Glc and Gal are the most commonly activated sugars of all PnPs serotypes while N-acetyl sugars PneuNAc, GalNAc and Rha in serotypes 5, 14 and 19A respectively showed >50% activation which contributes to conjugate aggregate formation at 8 min compared to 3 min cyanylation. The GC-MS analysis of structural modifications at functional groups entails important information to characterize the activated polysaccharide for consistent conjugate vaccine manufacturing.
activation, conjugate vaccine, pneumococcal polysaccharide, GC-MS, cyanylation, SEC-HPLC, SEC-MALS
NCBI PubMed ID: 37390792Publication DOI: 10.1016/j.carres.2023.108878Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: A.D. Mallya
Institutions: Research and Development Department, Serum Institute of India Pvt. Ltd, Hadapsar, Pune, Maharashtra, 411028, India
Methods: GC-MS, methanolysis, SEC-MALS, conjugation, SEC-HPLC, CDAP-cyanylation, quantification
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6. Compound ID: 4107
|
a-L-6dTalpNAc-(1-2)-b-D-GlcpA-(1-3)-+
|
-4)-b-D-Glcp-(1-4)-a-L-FucpNAc-(1-3)-b-D-6dxylHexpN-4-ulo-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 1520
Jones C "NMR assays for carbohydrate-based vaccines" -
Journal of Pharmaceutical and Biomedical Analysis 38(5) (2005) 840-850
Antibodies against the cell surface carbohydrates of many microbial pathogens protect against infection. This was initially exploited by the development of purified polysaccharide vaccines, but glycoconjugate vaccines, in which the cell surface carbohydrate of a microbial pathogen is covalently attached to an appropriate carrier protein, are proving the most effective means to generate this protective immunity. Carbohydrate-based vaccines against Haemophilus influenzae Type b, Neisseria meningitidis, Streptococcus pneumoniae and Salmonella enterica serotype Typhi (S. Typhi) are already licensed, and many similar products are in various stages of development. For many of these vaccines, biological assays are not available or are inappropriate and NMR spectroscopy is proving a valuable tool for the characterisation and quality control of existing and novel products. This review highlights some of the areas in which NMR spectroscopy is currently used, and where further developments may be expected.
capsular polysaccharide, O-acetylation, pneumonia, glycoconjugate, meningitis, carbohydrate-based vaccines, identity, typhoid
NCBI PubMed ID: 16087046Publication DOI: 10.1016/j.jpba.2005.01.044Journal NLM ID: 8309336Publisher: London: Elsevier
Institutions: Laboratory for Molecular Structure, National Institute for Biological Standards and Control, South Mimms, UK
Methods: NMR
- Article ID: 6386
Gaikwad WK, Dhere RM, Jana SK, Mallya AD, Soni DJ, Gholap M, Ravenscroft N, Kodam KM "Effect of trifluoroacetic acid on the antigenicity of capsular polysaccharides obtained from various Streptococcus pneumoniae serotypes" -
Carbohydrate Polymers 320 (2023) 121204
Determining the safety, antigenicity, and immunogenicity by in vitro and in vivo studies is a prerequisite for the development of new vaccines. And this study investigated it for a vaccine made from Streptococcus pneumoniae serotypes 2, 5, 12F, 18C, and 22F. The crude CPS was purified and partially depolymerized by conventional and trifluoroacetic acid methods. 1H NMR analysis confirmed the identity of the depolymerized CPS which gave similar profiles to reference polysaccharides, except for serotype 18C which was de-O-acetylated during TFA treatment. The antigenicity of the depolymerized CPS prepared by either method was comparable to that of the native CPS for serotypes 2, 5, 18C, and 22F based on multiplex bead based competitive inhibition assay. This study demonstrated a relationship between antigenicity and immunogenicity, which offers more suitable candidates for conjugation. It was found that after partial depolymerization process, the CPS with optimal molecular size resulted in higher antigenicity. The immunogenicity of S. pneumoniae serotype 2 conjugates in mice was evaluated by opsonophagocytic assay and a multiplex bead-based assay, wherein on day 42 after immunization, the total and functional IgG titer was found to be increased by 32-fold.
Streptococcus pneumoniae, immunogenicity, antigenicity, CRM197, pneumococcal conjugate vaccine, trifluoroacetic acid
NCBI PubMed ID: 37659807Publication DOI: 10.1016/j.carbpol.2023.121204Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: R.M. Dhere
; K.M. Kodam
Institutions: Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa, Department of Technology, Savitribai Phule Pune University, Pune 411007, India, Division of Biochemistry, Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India, Research and Development Department, Serum Institute of India Pvt. Ltd, Hadapsar, Pune 411028, India
Methods: 1H NMR, chemical analysis, inhibition studies, partial depolymerization, immunization, conjugation, fermentation, SEC-HPLC, opsonophagocytic assay
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7. Compound ID: 4336
|
2HOSuc2(70%)Ac-(4-3)-+
|
-4)-a-L-GalpNAmA3Ac-(1-3)-a-D-6dxylHexpN-4-ulo-(1-4)-b-D-GlcpNAc3NA-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
The structure is contained in the following publication(s):
- Article ID: 1627
Kilcoyne M, Shashkov AS, Knirel YA, Gorshkova RP, Nazarenko EL, Ivanova EP, Gorshkova NM, Senchenkova SN, Savage AV "The structure of the O-polysaccharide of the Pseudoalteromonas rubra ATCC 29570T lipopolysaccharide containing a keto sugar" -
Carbohydrate Research 340(15) (2005) 2369-2375
The structure of the phenol-soluble polysaccharide from Pseudoalteromonas rubra type strain ATCC 29570T has been elucidated using 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, gNOESY, ROESY, 1H,13C gHMQC and gHMBC experiments. It is concluded that the trisaccharide repeating unit of the polysaccharide has the following structure: [carbohydrate structure: see text] where Sug is 2-acetamido-2,6-dideoxy-D-xylo-hexos-4-ulose, Am is acetimidoyl and Acyl is a malic acid residue, which is O-acetylated in approximately 70% of the units.
Lipopolysaccharide, structure, strain, polysaccharide, type, O-polysaccharide, O polysaccharide, O-specific, O-specific polysaccharide, sugar, sugars, Shewanella, amino, keto sugar, amino sugar, Pseudoalteromonas, amino sugars
NCBI PubMed ID: 16126182Journal NLM ID: 0043535Publisher: 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 Science, Vladivostok 690022, Russian Federation
Methods: NMR, composition analysis
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8. Compound ID: 4337
|
2HOSuc-(4-3)-+
|
-4)-a-L-GalpNAmA-(1-3)-a-D-6dxylHexpN-4-ulo-(1-4)-b-D-GlcpNAc3NA-(1- |
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Structure type: polymer chemical repeating unit
The structure is contained in the following publication(s):
- Article ID: 1627
Kilcoyne M, Shashkov AS, Knirel YA, Gorshkova RP, Nazarenko EL, Ivanova EP, Gorshkova NM, Senchenkova SN, Savage AV "The structure of the O-polysaccharide of the Pseudoalteromonas rubra ATCC 29570T lipopolysaccharide containing a keto sugar" -
Carbohydrate Research 340(15) (2005) 2369-2375
The structure of the phenol-soluble polysaccharide from Pseudoalteromonas rubra type strain ATCC 29570T has been elucidated using 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, gNOESY, ROESY, 1H,13C gHMQC and gHMBC experiments. It is concluded that the trisaccharide repeating unit of the polysaccharide has the following structure: [carbohydrate structure: see text] where Sug is 2-acetamido-2,6-dideoxy-D-xylo-hexos-4-ulose, Am is acetimidoyl and Acyl is a malic acid residue, which is O-acetylated in approximately 70% of the units.
Lipopolysaccharide, structure, strain, polysaccharide, type, O-polysaccharide, O polysaccharide, O-specific, O-specific polysaccharide, sugar, sugars, Shewanella, amino, keto sugar, amino sugar, Pseudoalteromonas, amino sugars
NCBI PubMed ID: 16126182Journal NLM ID: 0043535Publisher: 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 Science, Vladivostok 690022, Russian Federation
Methods: NMR, composition analysis
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9. Compound ID: 4340
|
L-Ala2Fo-(1-3)-+
|
-4)-a-L-GulpNAc3NAcA-(1-3)-b-D-6dxylHexpN-4-ulo-(1-4)-b-D-GlcpNAc3NA6NH2-(1-4)-b-D-GlcpNAc3NAmA-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS, O-polysaccharide
The structure is contained in the following publication(s):
- Article ID: 1627
Kilcoyne M, Shashkov AS, Knirel YA, Gorshkova RP, Nazarenko EL, Ivanova EP, Gorshkova NM, Senchenkova SN, Savage AV "The structure of the O-polysaccharide of the Pseudoalteromonas rubra ATCC 29570T lipopolysaccharide containing a keto sugar" -
Carbohydrate Research 340(15) (2005) 2369-2375
The structure of the phenol-soluble polysaccharide from Pseudoalteromonas rubra type strain ATCC 29570T has been elucidated using 1H and 13C NMR spectroscopy, including 2D COSY, TOCSY, gNOESY, ROESY, 1H,13C gHMQC and gHMBC experiments. It is concluded that the trisaccharide repeating unit of the polysaccharide has the following structure: [carbohydrate structure: see text] where Sug is 2-acetamido-2,6-dideoxy-D-xylo-hexos-4-ulose, Am is acetimidoyl and Acyl is a malic acid residue, which is O-acetylated in approximately 70% of the units.
Lipopolysaccharide, structure, strain, polysaccharide, type, O-polysaccharide, O polysaccharide, O-specific, O-specific polysaccharide, sugar, sugars, Shewanella, amino, keto sugar, amino sugar, Pseudoalteromonas, amino sugars
NCBI PubMed ID: 16126182Journal NLM ID: 0043535Publisher: 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 Science, Vladivostok 690022, Russian Federation
Methods: NMR, composition analysis
- Article ID: 4554
Kokoulin MS, Kalinovsky AI, Komandrova NA, Tovarchi VE, Tomshich SV, Nedashkovskaya OI, Vaskovsky VE "The structure of the O-specific polysaccharide from marine bacterium Litorimonas taeanensis G5 containing 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-D-quinovose and 2-acetamido-2,6-dideoxy-L-xylo-hexos-4-ulose" -
Carbohydrate Research 375 (2013) 105-111
The O-polysaccharide was isolated from the lipopolysaccharide of Litorimonas taeanensis G5T and studied by chemical methods along with 1H and 13C NMR spectroscopy, including 1H, 1H COSY, 1D and 2D TOCSY, NOESY, 1H, 13C HSQC, HMBC, and H2BC experiments. The following new structure of the O-polysaccharide of L. taeanensis G5T containing 2-acetamido-2-deoxy-d-galacturonic acid (d-GalNAcA), 2-acetamido-4-((3S,5S)-3,5-dihydroxyhexanamido)-2,4-dideoxy-d-quinovose (d-QuiNAc4NR), and 2-acetamido-2,6-dideoxy-l-xylo-hexos-4-ulose (l-Sug) was established: where R is (3S,5S)-3,5-dihydroxyhexanoic acid.
O-specific polysaccharide, 2-acetamido-2, 6-dideoxy-L-xylo-hexos-4-ulose, 2-Acetamido-4-((3S, 5S)-3, 5-dihydroxyhexanamido)-2, 4-dideoxy-D-quinovose, Litorimonas taeanensis
NCBI PubMed ID: 23694711Publication DOI: 10.1016/j.carres.2013.04.004Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: maxchem@mail.ru
Institutions: G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, NMR-1D, triflic acid solvolysis, borohydride reduction
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10. Compound ID: 6531
|
a-L-6dTalpNAc-(1-2)-b-D-GlcpA-(1-3)-+
|
-4)-b-D-Glcp-(1-4)-a-L-FucpNAc-(1-3)-b-D-6dxylHexpNAc-4-ulo-(1-
6dxylHexpN-4-ulo = 2-amino-2,6-dideoxy-xylo-hexos-4-ulose |
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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_423153,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 2950
Jansson PE, Lindberg B, Lindquist U "Structural studies of the capsular polysaccharide from Streptococcus pneumoniae type 5" -
Carbohydrate Research 140 (1985) 101-110
The structure of the capsular polysaccharide (S5) elaborated by Streptococcus pneumoniae type 5 has been investigated by using n.m.r. spectroscopy, methylation analysis, and various specific degradations. It is concluded that the polysaccharide is composed of pentasaccharide repeating-units having the following structure: (Formula: see text) In this structure, L-PneNAc stands for 2-acetamido-2,6-dideoxy-L-talose (pneumosamine) and D-Sug for 2-acetamido-2,6-dideoxy-D-xylo-hexos-4-ulose. The latter sugar accounts for the lability of S5 towards alkali. N.m.r. spectra indicate heterogeneity in S5, most probably associated with the hexosyl-4-ulose residue.
NCBI PubMed ID: 4053092Journal NLM ID: 0043535Publisher: Elsevier
Methods: 13C NMR, 1H NMR, methylation, acid hydrolysis, GLC, Smith degradation, borohydride reduction
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11. Compound ID: 6857
Structure type: monomer
Trivial name: UDP-hexos-4-ulose sugar, UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hexos-4-ulose, UPD-2-acetamido-2,6-dideoxy-α-D-xylo-4-hexulose
Compound class: nucleoside diphosphate sugar
The structure is contained in the following publication(s):
- Article ID: 3141
McNally DJ, Schoenhofen IC, Mulrooney EF, Whitfield DM, Vinogradov E, Lam JS, Logan SM, Brisson JR "Identification of Labile UDP-Ketosugars in Helicobacter pylori, Campylobacter jejuni and Pseudomonas aeruginosa: Key Metabolites used to make Glycan Virulence Factors" -
Chembiochem: a European Journal of Chemical Biology 7(12) (2006) 1865-1868
biosynthesis, carbohydrates, Pseudomonas, Campylobacter jejuni, bacteria, Helicobacter pylori, metabolite, hexos-4-ulose
NCBI PubMed ID: 17031886Publication DOI: 10.1002/cbic.200600298Journal NLM ID: 100937360Publisher: Weinheim, Germany: Wiley Interscience
Correspondence: david.mcnally@nrc-cnrc.gc.ca
Institutions: National Research Council of Canada-Institute for Biological Sciences, Ottawa ON, K1A 0R6, Canada, Fax: (+1) 613-952-9092
Methods: NMR, genetic methods
- Article ID: 3196
Schoenhofen IC, Lunin VV, Julien JP, Li Y, Ajamian E, Matte A, Cygler M, Brisson JR, Aubry A, Logan SM, Bhatia S, Wakarchuk WW, Young NM "Structural and functional characterization of PseC, an aminotransferase involved in the biosynthesis of pseudaminic acid, an essential flagellar modification in Helicobacter pylori" -
Journal of Biological Chemistry 281(13) (2006) 8907-8916
Helicobacter pylori flagellin is heavily glycosylated with the novel sialic acid-like nonulosonate, pseudaminic acid (Pse). The glycosylation process is essential for assembly of functional flagellar filaments and consequent bacterial motility. Because motility is a key virulence factor for this and other important pathogens, the Pse biosynthetic pathway offers potential for novel therapeutic targets. From recent NMR analyses, we determined that the conversion of UDP-α-D-Glc-NAc to the central intermediate in the pathway, UDP-4-amino-4,6-dideoxy-β-L-AltNAc, proceeds by formation of UDP-2-acetamido-2,6-dideoxy-β-L-arabino-4-hexulose by the dehydratase/epimerase PseB (HP0840) followed with amino transfer by the aminotransferase, PseC (HP0366). The central role of PseC in the H. pylori Pse biosynthetic pathway prompted us to determine crystal structures of the native protein, its complexes with pyridoxal phosphate alone and in combination with the UDP-4-amino-4,6-dideoxy-β-L-AltNAc product, the latter being converted to the external aldimine form in the active site of the enzyme. In the binding site, the AltNAc sugar ring adopts a (4)C(1) chair conformation, which is different from the predominant (1)C(4) form found in solution. The enzyme forms a homodimer where each monomer contributes to the active site, and these structures have permitted the identification of key residues involved in stabilization, and possibly catalysis, of the β-L-arabino intermediate during the amino transfer reaction. The essential role of Lys(183) in the catalytic event was confirmed by site-directed mutagenesis. This work presents for the first time a nucleotide-sugar aminotransferase co-crystallized with its natural ligand, and, in conjunction with the recent functional characterization of this enzyme, these results will assist in elucidating the aminotransferase reaction mechanism within the Pse biosynthetic pathway.
biosynthesis, pseudaminic acid, Helicobacter pylori, Flagellin, aminotransferase, PseC
NCBI PubMed ID: 16421095Publication DOI: 10.1074/jbc.M512987200Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: Martin.Young@nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council, Ottawa, Ontario K1A 0R6, Biotechnology Research, Institute, National Research Council, Montreal, Quebec H4P 2R2, Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
Methods: NMR-2D, NMR, SDS-PAGE, genetic methods, biochemical methods, capillary electrophoresis (CE), crystallization
- Article ID: 3404
Guerry P, Ewing CP, Schoenhofen IC, Logan SM "Protein glycosylation in Campylobacter jejuni: partial suppression of pglF by mutation of pseC" -
Journal of Bacteriology 189(18) (2007) 6731-6733
Campylobacter jejuni has systems for N- and O-linked protein glycosylation. Although biochemical evidence demonstrated that a pseC mutant in the O-linked pathway accumulated the product of pglF in the N-linked pathway, analyses of transformation frequencies and glycosylation statuses of N-glycosylated proteins indicated a partial suppression of pglF by pseC
biosynthesis, Bacterial Proteins, Campylobacter jejuni, glycosylation
NCBI PubMed ID: 17631632Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Correspondence: guerryp@nmrc.navy.mil
Institutions: Enteric Diseases Department, Naval Medical Research Center, 503 Robert Grant Ave., Silver Spring, MD 20910, USA
Methods: PCR, serological methods, genetic methods
- Article ID: 3475
Glaze PA, Watson DC, Young NM, Tanner ME "Biosynthesis of CMP-N,N'-diacetyllegionaminic acid from UDP-N,N'-diacetylbacillosamine in Legionella pneumophila" -
Biochemistry 47(10) (2008) 3272-3282
Legionaminic acid is a nine-carbon α-keto acid that is similar in structure to other members of the sialic acid family that includes neuraminic acid and pseudaminic acid. It is found as a component of the lipopolysaccharide in several bacterial species and is perhaps best known for its presence in the O-antigen of the causative agent of Legionnaires' disease, Legionella pneumophila. In this work, the enzymes responsible for the biosynthesis and activation of N, N'-diacetyllegionaminic acid are identified for the first time. A cluster of three L. pneumophila genes bearing homology to known sialic acid biosynthetic genes (neuA,B,C) were cloned and overexpressed in Escherichia coli. The NeuC homologue was found to be a hydrolyzing UDP- N, N'-diacetylbacillosamine 2-epimerase that converts UDP- N, N'-diacetylbacillosamine into 2,4-diacetamido-2,4,6-trideoxymannose and UDP. Stereochemical and isotopic labeling studies showed that the enzyme utilizes a mechanism involving an initial anti elimination of UDP to form a glycal intermediate and a subsequent syn addition of water to generate product. This is similar to the hydrolyzing UDP- N-acetylglucosamine 2-epimerase (NeuC) of sialic acid biosynthesis, but the L. pneumophila enzyme would not accept UDP-GlcNAc as an alternate substrate. The NeuB homologue was found to be a N, N'-diacetyllegionaminic acid synthase that condenses 2,4-diacetamido-2,4,6-trideoxymannose with phosphoenolpyruvate (PEP), although the in vitro activity of the recombinant enzyme (isolated as a MalE fusion protein) was very low. The synthase activity was dependent on the presence of a divalent metal ion, and the reaction proceeded via a C-O bond cleavage process, similar to the reactions catalyzed by the sialic acid and pseudaminic acid synthases. Finally, the NeuA homologue was shown to possess the CMP- N, N'-diacetyllegionaminic acid synthetase activity that generates the activated form of legionaminic acid used in lipopolysaccharide biosynthesis. Together, the three enzymes constitute a pathway that converts a UDP-linked bacillosamine derivative into a CMP-linked legionaminic acid derivative
O-antigen, lipopolysaccharide biosynthesis, pseudaminic acid, neuraminic acid, Legionella pneumophila, legionaminic acid, Legionella, bacillosamine
NCBI PubMed ID: 18275154Journal NLM ID: 0370623Publisher: American Chemical Society
Correspondence: mtanner@chem.ubc.ca
Institutions: Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
Methods: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, 31P NMR, genetic methods, biochemical methods
- Article ID: 3476
Gonzalez D, Grillo MJ, De Miguel MJ, Ali T, Arce-Gorvel V, Delrue RM, Conde-Alvarez R, Munoz P, Lopez-Goni I, Iriarte M, Marin CM, Weintraub A, Widmalm G, Zygmunt M, Letesson JJ, Gorvel JP, Blasco JM, Moriyón I "Brucellosis vaccines: assessment of Brucella melitensis lipopolysaccharide rough mutants defective in core and O-polysaccharide synthesis and export" -
PLoS One 3(7) (2008) e2760
BACKGROUND: The brucellae are facultative intracellular bacteria that cause brucellosis, one of the major neglected zoonoses. In endemic areas, vaccination is the only effective way to control this disease. Brucella melitensis Rev 1 is a vaccine effective against the brucellosis of sheep and goat caused by B. melitensis, the commonest source of human infection. However, Rev 1 carries a smooth lipopolysaccharide with an O-polysaccharide that elicits antibodies interfering in serodiagnosis, a major problem in eradication campaigns. Because of this, rough Brucella mutants lacking the O-polysaccharide have been proposed as vaccines. METHODOLOGY/PRINCIPAL FINDINGS: To examine the possibilities of rough vaccines, we screened B. melitensis for lipopolysaccharide genes and obtained mutants representing all main rough phenotypes with regard to core oligosaccharide and O-polysaccharide synthesis and export. Using the mouse model, mutants were classified into four attenuation patterns according to their multiplication and persistence in spleens at different doses. In macrophages, mutants belonging to three of these attenuation patterns reached the Brucella characteristic intracellular niche and multiplied intracellularly, suggesting that they could be suitable vaccine candidates. Virulence patterns, intracellular behavior and lipopolysaccharide defects roughly correlated with the degree of protection afforded by the mutants upon intraperitoneal vaccination of mice. However, when vaccination was applied by the subcutaneous route, only two mutants matched the protection obtained with Rev 1 albeit at doses one thousand fold higher than this reference vaccine. These mutants, which were blocked in O-polysaccharide export and accumulated internal O-polysaccharides, stimulated weak anti-smooth lipopolysaccharide antibodies. CONCLUSIONS/SIGNIFICANCE: The results demonstrate that no rough mutant is equal to Rev 1 in laboratory models and question the notion that rough vaccines are suitable for the control of brucellosis in endemic areas
virulence, O-polysaccharide, vaccine, Brucella melitensis, brucellosis
NCBI PubMed ID: 18648644Journal NLM ID: 101285081Publisher: San Francisco, CA: Public Library of Science
Correspondence: Imoriyon@unav.es
Institutions: Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain
Methods: 1H NMR, SDS-PAGE, serological methods, genetic methods
- Article ID: 3516
McNally DJ, Schoenhofen IC, Houliston RS, Khieu NH, Whitfield DM, Logan SM, Jarrell HC, Brisson JR "CMP-Pseudaminic Acid is a Natural Potent Inhibitor of PseB, the First Enzyme of the Pseudaminic Acid Pathway in Campylobacter jejuni and Helicobacter pylori" -
ChemMedChem 3(1) (2008) 55-59
No abstract available
Research, acid, Campylobacter, Campylobacter jejuni, NMR spectroscopy, pseudaminic acid, biological, Helicobacter pylori, enzyme, natural, pathway, Helicobacter, inhibitors, STD, STD NMR spectroscopy, potent
NCBI PubMed ID: 17893902Journal NLM ID: 101259013Publisher: Wiley-VCH
Correspondence: david.mcnally@nrc-cnrc.gc.ca
Institutions: National Research Council of Canada-Institute for Biological Sciences, Ottawa ON, K1A 0R6, Canada, Fax: (+1) 613-952-9092
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, NMR-1D, genetic methods, biochemical methods, STD NMR
- Article ID: 3649
Olivier NB, Chen MM, Behr JR, Imperiali B "In vitro biosynthesis of UDP-N,N'-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system" -
Biochemistry 45(45) (2006) 13659-13669
In Campylobacter jejuni 2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose, termed N,N'-diacetylbacillosamine (Bac2,4diNAc), is the first carbohydrate in the glycoprotein N-linked heptasaccharide. With uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) as a starting point, two enzymes of the general protein glycosylation (Pgl) pathway in C. jejuni (PglF and PglE) have recently been shown to modify this sugar nucleotide to form UDP-2-acetamido-4-amino-2,4,6-trideoxy-α-D-glycopyranose (UDP-4-amino-sugar) [Schoenhofen, I. C., et al. (2006) J. Biol. Chem. 281, 723-732]. PglD has been proposed to catalyze the final step in N,N'-diacetylbacillosamine synthesis by N-acetylation of the UDP-4-amino-sugar at the C4 position. We have cloned, overexpressed, and purified PglD from the pgl locus of C. jejuni NCTC 11168 and identified it as the acetyltransferase that modifies the UDP-4-amino-sugar to form UDP-N,N'-diacetylbacillosamine, utilizing acetyl-coenzyme A as the acetyl group donor. The UDP-N,N'-diacetylbacillosamine product was purified from the reaction by reverse phase C18 HPLC and the structure determined by NMR analysis. Additionally, the full-length PglF was overexpressed and purified in the presence of detergent as a GST fusion protein, allowing for derivation of kinetic parameters. We found that the UDP-4-amino-sugar was readily synthesized from UDP-GlcNAc in a coupled reaction using PglF and PglE. We also demonstrate the in vitro biosynthesis of the complete heptasaccharide lipid-linked donor by coupling the action of eight enzymes (PglF, PglE, PglD, PglC, PglA, PglJ, PglH, and PglI) in the Pgl pathway in a single reaction vessel.
biosynthesis, Campylobacter jejuni, glycosylation, acetyltransferase
NCBI PubMed ID: 17087520Journal NLM ID: 0370623Publisher: American Chemical Society
Correspondence: imper@mit.edu
Institutions: Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
Methods: 1H NMR, 31P NMR, ESI-MS, MALDI-MS, genetic methods, biochemical methods, HPLC, capillary electrophoresis (CE)
- Article ID: 3824
Brisson JR, Vinogradov E, McNally DJ, Khieu NH, Schoenhofen IC, Logan SM, Jarrell H "The application of NMR spectroscopy to functional glycomics" -
Book: Methods in Molecular Biology (2010) Vol. 600, 155-173
Glycomics which is the study of saccharides and genes responsible for their formation requires the continuous development of rapid and sensitive methods for the identification of glycan structures. It involves glycoanalysis which relies upon the development of methods for determining the structure and interactions of carbohydrates. For the application of functional glycomics to microbial virulence, carbohydrates and their associated metabolic and carbohydrate processing enzymes and respective genes can be identified and exploited as targets for drug discovery, glyco-engineering, vaccine design, and detection and diagnosis of diseases. Glycomics also encompasses the detailed understanding of carbohydrate-protein interactions and this knowledge can be applied to research efforts focused toward the development of vaccines and immunological therapies to alleviate infectious diseases.
NMR, structural analysis, molecular modeling, polysaccharides, HR-MAS, Glycomics, glycans, glycoanalysis, protein–carbohydrate interactions
NCBI PubMed ID: 19882127Publisher: Totowa, NJ: Humana Press
Editors: Holst O, Walker JM, Beck A
Institutions: Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
Methods: NMR
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12. Compound ID: 7524
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2HOSuc2(70%)Ac-(4-3)-+
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-4)-a-L-GalpNAmA3Ac-(1-3)-a-D-6dxylHexpNAc-4-ulo-(1-4)-b-D-GlcpNAc3NA-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
The structure is contained in the following publication(s):
- Article ID: 3380
Leone S, Silipo A, Nazarenko EL, Lanzetta R, Parrilli E, Molinaro A "Molecular structure of endotoxins from Gram-negative marine bacteria: An update" -
Marine Drugs 5(3) (2007) 85-112
Marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. The main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. Nonetheless, lipopolysaccharides (LPSs), or their portions, from Gram-negative marine bacteria, have often shown low virulence, and represent potential candidates in the development of drugs to prevent septic shock. Besides, the molecular architecture of such molecules is related to the possibility of thriving in marine habitats, shielding the cell from the disrupting action of natural stress factors. Over the last few years, the depiction of a variety of structures of lipids A, core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been given. In particular, here we will examine the most recently encountered structures for bacteria belonging to the genera Shewanella, Pseudoalteromonas and Alteromonas, of gamma-Proteobacteria phylum, and to the genera Flavobacterium, Cellulophaga, Arenibacter and Chryseobacterium, of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention will be paid to the chemical features expressed by these structures (characteristic monosaccharides, non-glycidic appendages, phosphate groups), to the typifying traits of LPSs from marine bacteria and to the possible correlation existing between such features and the adaptation, over years, of bacteria to marine environments.
Lipopolysaccharide, lipid A, O-polysaccharide, endotoxin, Marine bacteria, marine bacteriae
Publication DOI: 10.1002/ejoc.200400882Journal NLM ID: 101213729WWW link: http://www.mdpi.org/marinedrugs/papers/md503085.pdfPublisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: molinaro@unina.it
Institutions: Dipartimento di Chimica Organica e Biochimica, Università degli studi di Napoli “Federico II”, via Cintia 4, I-80126 Napoli, Italy, Pacific Institute of Bioorganic Chemistry, Far-East Branch of the Russian Academy of Sciences, 690022 Vladivostok-22, Russian Federation
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, 31P NMR, mild acid hydrolysis, alkaline degradation, MALDI-TOF MS, methanolysis
- Article ID: 4359
Nazarenko EL, Crawford RJ, Ivanova EP "The structural diversity of carbohydrate antigens of selected Gram-negative marine bacteria" -
Marine Drugs 9(10) (2011) 1914-1954
Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens) found in cell walls of gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobacteria phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.
O-specific polysaccharides, carbohydrate antigens, marine microorganisms
NCBI PubMed ID: 22073003Publication DOI: 10.3390/md9101914Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: elnaz@piboc.dvo.ru
Institutions: Pacific Institute of Bioorganic Chemistry, Far East Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia, Faculty of Life and Social Sciences, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
Methods: 13C NMR, 1H NMR, methylation, periodate oxidation, NMR-2D, FAB-MS, partial acid hydrolysis, NMR, HF solvolysis, sugar analysis, 31P NMR, ESI-MS, acid hydrolysis, mild acid hydrolysis, HPAEC, ESI-ICR-MS, Smith degradation, chemical methods, MALDI-TOF MS, MS, de-O-acetylation, NMR-1D, GPC, alkaline hydrolysis, CE-ESI-MS, CE-MS, hydrazinolysis
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13. Compound ID: 7709
Structure type: monomer
Trivial name: methyl 2-acetamido-2,6-dideoxy-α-D-xylo-hexopyranosid-4-ulose
The structure is contained in the following publication(s):
- Article ID: 3443
Borowski S, Michalik D, Reinke H, Vogel C, Hanuszkiewicz A, Duda KA, Holst O "Synthesis of methyl 2-acetamido-2,6-dideoxy-a- and b-D-xylo-hexopyranosid-4-ulose, a keto sugar which misled the analytical chemists" -
Carbohydrate Research 343(6) (2008) 1004-1011
To understand the contradictory results on the structure of the lipopolysaccharide isolated from a Yersinia enterocolitica O:3, both anomers of methyl 2-acetamido-2,6-dideoxy-d-xylo-hexopyranosid-4-ulose were prepared. The key steps of the synthetic pathway were the selective acetylation of the methyl 2-acetamido-2,6-dideoxy-α,β-D-glucopyranosides, the oxidation of the 4-position to form the keto-sugars, and deacetylation to provide the target compound. Surprisingly, the last step was accompanied by a disproportionation to give methyl 2-acetamido-2,6-dideoxy-α- and β-D-glucopyranosides and N-(5-hydroxy-6-methyl-4-oxo-4H-pyran-3-yl)acetamide as side-products.
reduction, oxidation, D-Glucosamine, Anomerization, Keto-sugar, Selective acetylation
NCBI PubMed ID: 18314095Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: christian.vogel@uni-rostock.de
Institutions: University of Rostock, Institute of Chemistry, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, chemical synthesis, MS, NMR-1D
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14. Compound ID: 7710
Structure type: monomer
Trivial name: methyl 2-acetamido-2,6-dideoxy-α-D-xylo-hexopyranosid-4-ulose
The structure is contained in the following publication(s):
- Article ID: 3443
Borowski S, Michalik D, Reinke H, Vogel C, Hanuszkiewicz A, Duda KA, Holst O "Synthesis of methyl 2-acetamido-2,6-dideoxy-a- and b-D-xylo-hexopyranosid-4-ulose, a keto sugar which misled the analytical chemists" -
Carbohydrate Research 343(6) (2008) 1004-1011
To understand the contradictory results on the structure of the lipopolysaccharide isolated from a Yersinia enterocolitica O:3, both anomers of methyl 2-acetamido-2,6-dideoxy-d-xylo-hexopyranosid-4-ulose were prepared. The key steps of the synthetic pathway were the selective acetylation of the methyl 2-acetamido-2,6-dideoxy-α,β-D-glucopyranosides, the oxidation of the 4-position to form the keto-sugars, and deacetylation to provide the target compound. Surprisingly, the last step was accompanied by a disproportionation to give methyl 2-acetamido-2,6-dideoxy-α- and β-D-glucopyranosides and N-(5-hydroxy-6-methyl-4-oxo-4H-pyran-3-yl)acetamide as side-products.
reduction, oxidation, D-Glucosamine, Anomerization, Keto-sugar, Selective acetylation
NCBI PubMed ID: 18314095Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: christian.vogel@uni-rostock.de
Institutions: University of Rostock, Institute of Chemistry, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, chemical synthesis, MS, NMR-1D
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15. Compound ID: 8655
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D-gro-a-D-manHepp-(1-7)-L-gro-a-D-manHepp-(1-7)-+
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b-D-Glcp-(1-3)-+ | b-D-Glcp-(1-4)-+ a-Kdop-(2-4)-+ P-4)-+
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b-D-Glcp-(1-6)-a-D-GalpNAc-(1-6)-a-D-Galp-(1-4)-a-D-GalpNAc-(1-3)-b-D-6dxylHexpNAc-4-ulo-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
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b-D-Glcp-(1-2)-+ |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130648,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_135394,IEDB_136906,IEDB_137472,IEDB_137473,IEDB_1391961,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_141584,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144989,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189046,IEDB_2189047,IEDB_226811,IEDB_885822,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 3765
Pinta E, Duda KA, Hanuszkiewicz A, Kaczyński Z, Lindner B, Miller WL, Hyytiainen H, Vogel C, Borowski S, Kasperkiewicz K, Lam JS, Radziejewska-Lebrecht J, Skurnik M, Holst O "Identification and Role of a 6-Deoxy-4-Keto-Hexosamine in the Lipopolysaccharide Outer Core of Yersinia enterocolitica Serotype O:3" -
Chemistry 15(38) (2009) 9747-9754
The outer core (OC) region of Yersinia enterocolitica serotype O:3 lipopolysaccharide is a hexasaccharide essential for the integrity of the outer membrane. It is involved in resistance against cationic antimicrobial peptides and plays a role in virulence during early phases of infection. We show here that the proximal residue of the OC hexasaccharide is a rarely encountered 4-keto-hexosamine, 2-acetamido-2,6-dideoxy-D-xylo-hex-4-ulopyranose (Sugp) and that WbcP is a UDP-GlcNAc-4,6-dehydratase enzyme responsible for the biosynthesis of the nucleotide-activated form of this rare sugar converting UDP-2-acetamido-2-deoxy-D-glucopyranose (UDP-D-GlcpNAc) to UDP-2-acetamido-2,6-dideoxy-D-xylo-hex-4-ulopyranose (UDP-Sugp). In an aqueous environment, the 4-keto group of this sugar was present in the 4-dihydroxy form, due to hydration. Furthermore, evidence is provided that the axial 4-hydroxy group of this dihydroxy function was crucial for the biological role of the OC, that is, in the bacteriophage and enterocoliticin receptor structure and in the epitope of a monoclonal antibody.
biosynthesis, lipopolysaccharides, receptors, Hexosamines, structural biology
NCBI PubMed ID: 19697383Publication DOI: 10.1002/chem.200901255Publisher: Vch Verlagsgesellschaft
Correspondence: mikael.skurnik@helsenki.fi
Institutions: Infection Biology Research Program, Haartman Institute, Department of Bacteriology and Immunology, P.O.Box 21 (Haartmaninkatu 3), 00014 University of Helsinki (Finland), Fax: (+358) 9-191 26382
Methods: 13C NMR, 1H NMR, NMR-2D, de-O-acylation, SDS-PAGE, 31P NMR, ESI-ICR-MS, DOC-PAGE, composition analysis, NMR-1D, genetic methods, biochemical methods
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