Found 48 structures.
Displayed structures from 1 to 15
Next 15 structure(s)
Expand all compounds
Collapse all compounds
Show all as text (SweetDB notation)
Show all graphically (SNFG notation)
1. Compound ID: 4799
Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136906,IEDB_137472,IEDB_141794,IEDB_149136,IEDB_151528,IEDB_190606,IEDB_581504,SB_7
The structure is contained in the following publication(s):
- Article ID: 1800
Vasil'ev VN, Zakharova IY "Structure of the determinant group in O-specific polysaccharide of E. coli O20:K84:H34 (145)" -
Bioorganicheskaya Khimia = Bioorganic Chemistry [Russian] 2 (1976) 199-206
Journal NLM ID: 7804941Publisher: Moskva: Nauka
Expand this compound
Collapse this compound
2. Compound ID: 6169
|
a-D-Galp-(1-3)-+
|
a-D-Galp-(1-2)-b-D-Ribf-(1-4)-a-D-Galp-(1-2)-D-Rib |
Show graphically |
Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_115013,IEDB_130645,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_149136,IEDB_151528,IEDB_190606,IEDB_581504,IEDB_742246,IEDB_918313,SB_7,SB_87
The structure is contained in the following publication(s):
- Article ID: 2757
Vasil'ev VN, Zakharova IY, Kovalenko EA "Structure of the side chains of serogroup O20 Escherichia coli O-antigens" -
Mikrobiologichnyi Zhurnal = Microbiological Journal [Ukrainian] 42 (1980) 456-461
no abstract
NCBI PubMed ID: 6997698Journal NLM ID: 7910045Publisher: Kyiv: Naukova Dumka
Expand this compound
Collapse this compound
3. Compound ID: 7232
Structure type: monomer
Contained glycoepitopes: IEDB_149136,IEDB_581504,IEDB_581505
The structure is contained in the following publication(s):
- Article ID: 3271
De Leon GP, Elowe NH, Koteva KP, Valvano MA, Wright GD "An In Vitro Screen of Bacterial Lipopolysaccharide Biosynthetic Enzymes Identifies an Inhibitor of ADP-Heptose Biosynthesis" -
Chemistry and Biology 13(4) (2006) 437-441
The lipopolysaccharide (LPS)-rich outer membrane of gram-negative bacteria provides a protective barrier that insulates these organisms from the action of numerous antibiotics. Breach of the LPS layer can therefore provide access to the cell interior to otherwise impermeant toxic molecules and can expose vulnerable binding sites for immune system components such as complement. Inhibition of LPS biosynthesis, leading to a truncated LPS molecule, is an alternative strategy for antibacterial drug development in which this vital cellular structure is weakened. A significant challenge for in vitro screens of small molecules for inhibition of LPS biosynthesis is the difficulty in accessing the complex carbohydrate substrates. We have optimized an assay of the enzymes required for LPS heptose biosynthesis that simultaneously surveys five enzyme activities by using commercially available substrates and report its use in a small-molecule screen that identifies an inhibitor of heptose synthesis
Lipopolysaccharide, biosynthesis, synthesis, LPS, structure, heptose, alternative, biosynthetic, Bacterial, carbohydrate, cell, molecule, Research, complex, bacteria, activity, biochemistry, Gram-negative bacteria, enzyme, gram negative bacteria, Gram-negative, cellular, inhibition, component, binding, binding site, site, Enzymes, action, membrane, substrate, heptose biosynthesis, protective, outer membrane, PDF, assay, immune, immune system, in vitro, use, challenge, development, drug, layer, complement, inhibitor, antibiotic, antimicrobial, antibacterial, toxic, Binding Sites, antibiotics, barrier
NCBI PubMed ID: 16632256Journal NLM ID: 9500160Publisher: Maryland Heights, MO: Elsevier
Correspondence: wrightge@mcmaster.ca
Institutions: Antimicrobial Research Centre Department of Biochemistry and Biomedical Sciences McMaster University Hamilton, Hamilton, ON, Canada, Infectious Diseases Research Group Siebens-Drake Research Institute Department of Microbiology and Immunology The University of Western Ontario London, Ontario N6A 5C1 Canada
Methods: biochemical methods
Expand this compound
Collapse this compound
4. Compound ID: 7250
|
L-Ala-(1-6)-+
|
D-Ala2Ac-(1-3)-b-D-Quip3N-(1-4)-a-D-GalpA-(1-2)-D-Rib |
Show graphically |
Structure type: oligomer
Contained glycoepitopes: IEDB_149136,IEDB_581504
The structure is contained in the following publication(s):
- Article ID: 3274
Sidorczyk Z, Swierzko A, Vinogradov EV, Knirel YA, Shashkov AS "Structural and immunochemical studies of the O-specific polysaccharide of Proteus penneri strain 14" -
Archivum Immunologiae et Therapiae Experimentalis 42(3) (1994) 209-215
The complete structure of the O-antigen of Proteus penneri strain 14, containing D-alanine and L-alanine was established using methylation, solvolysis with anhydrous hydrogen fluoride, partial acid hydrolysis, 1H- and 13C-NMR spectroscopy. The role of partial structures of the pentasaccharide repeating unit in manifesting serological specificity and cross-reactivity of this strain with some other bacteria is discussed.
Lipopolysaccharide, structure, role, strain, structural, polysaccharide, O-antigen, repeating unit, O antigen, hydrogen, acid, immunology, O-polysaccharide, bacteria, O-specific, O-specific polysaccharide, Proteus, serological, specificity, Proteus penneri, methylation, spectroscopy, immunochemical, partial structure, pentasaccharide, cross-reactivity, crossreactivity, PDF, solvolysis, hydrogen fluoride, D-alanine, lysis
NCBI PubMed ID: 7487355Journal NLM ID: 0114365Publisher: Basel, Boston: Birkhaüser
Correspondence: zsidor@biol.uni.lodz.pl
Institutions: Institute of Microbiology and Immunology, University of Lodz, Poland.
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, chemical analysis, mild acid hydrolysis, NMR-1D, serological methods
Expand this compound
Collapse this compound
5. Compound ID: 8596
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_581504,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 3744
Molinaro A, Newman M, Lanzetta R, Parrilli M "The structures of lipopolysaccharides from plant-associated Gram-negative bacteria" -
European Journal of Organic Chemistry 2009(34) (2009) 5887-5896
Gram-negative bacterial lipopolysaccharides (LPSs) have multiple roles in plant-microbe interactions. LPSs contribute to the low permeabilities of bacterial outer membranes, which act as barriers to protect bacteria from plant-derived antimicrobial substances. Conversely, perception of LPSs by plant cells can lead to the triggering of defence responses or to the priming of the plant to respond more rapidly and/or to a greater degree to subsequent pathogen challenge. LPSs are thus key molecules in the interactions between bacteria and plants, either in symbiosis or pathogenesis. Since LPSs are glycoconjugates genetically and chemically consisting of three different molecular regions, their detailed structure elucidation is a very topical and major scientific task for chemists, and is achieved by a combination of state-of-art chemical and spectroscopic techniques. Knowledge of LPSs' chemical structures is an important prerequisite for any further understanding of the biological processes in plant-microbe interactions. Moreover, the LPSs from Gram-negative bacteria - especially those originating from plant-associated bacteria - are a great source of novel monosaccharides with unusual and occasionally astounding chemical structures, never found in the eukaryotic world. This review presents the structures of LPSs from plant-associated bacteria isolated and identified from 2001 onwards.
lipopolysaccharides, structure elucidation, glycolipids, innate immunity, immunochemistry, plant-associated bacteria
Publication DOI: 10.1002/ejoc.200900682Journal NLM ID: 9805750Publisher: Wiley-VCH
Correspondence: molinaro@unina.it
Institutions: Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli “Federico II”, via Cinthia 4, 80126 Napoli, Italy, Fax: +39-081-674393, Faculty of Life Sciences, Department of Plant Biology & Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
Expand this compound
Collapse this compound
6. Compound ID: 10497
|
-2)-b-D-Quip4NFo-(1-2)-b-D-Ribp-(1-4)-b-D-GlcpA-(1-4)-b-D-GlcpA-(1-3)-a-D-FucpNAc4N-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_115136,IEDB_140630,IEDB_142345,IEDB_423153,IEDB_581504
The structure is contained in the following publication(s):
- Article ID: 4329
Knirel YA "Structure of O-antigens" -
Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.
Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis
Publication DOI: 10.1007/978-3-7091-0733-1_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Expand this compound
Collapse this compound
7. Compound ID: 12014
|
R-3HOBut-(1-7)-a-Psep5Ac-(2-4)-+
|
-3)-b-D-Ribp-(1-3)-b-D-GalpNAc-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_581504
The structure is contained in the following publication(s):
- Article ID: 4796
Senchenkova SN, Popova AV, Shashkov AS, Shneider MM, Mei Z, Arbatsky NP, Liu B, Miroshnikov KA, Volozhantsev NV, Knirel YA "Structure of a new pseudaminic acid-containing capsular polysaccharide of Acinetobacter baumannii LUH5550 having the KL42 capsule biosynthesis locus" -
Carbohydrate Research 407 (2015) 154-157
The capsular polysaccharide from Acinetobacter baumannii LUH5550 was studied by 1D and 2D (1)H and (13)C NMR spectroscopy. The following structure of the branched trisaccharide repeating unit was established: [structure: see text] where Pse5Ac7RHb indicates 5-acetamido-3,5,7,9-tetradeoxy-7-[(R)-3-hydroxybutanoylamino]-L-glycero-L-manno-non-2-ulosonic acid. The genes in the capsule biosynthesis locus designated KL42 are consistent with the structure established.
Acinetobacter baumannii, pseudaminic acid, capsular polysaccharide structure, polysaccharide gene locus
NCBI PubMed ID: 25776191Publication DOI: 10.1016/j.carres.2015.02.006Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: yknirel@gmail.com
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, mild acid hydrolysis, NMR-1D, GPC, bioinformatic analysis
- Article ID: 4819
Giguere D "Surface polysaccharides from Acinetobacter baumannii: Structures and syntheses" -
Carbohydrate Research 418 (2015) 29-43
The emergence of multidrug-resistance Acinetobacter baumannii requires novel approaches for prevention, treatment and diagnosis. The structures of surface polysaccharides from A. baumannii are valuable tools to understand pathogenesis, virulence and immunogenicity. The synthesis of bacterial mono- or polysaccharides may result in novel probes to become important therapeutic options in the fight against A. baumannii. This report exemplifies the relevance of glycochemistry for the development of new antibiotics.
lipopolysaccharides, capsular polysaccharides, Acinetobacter, Acinetobacter baumannii, polysaccharide synthesis, surface polysaccharides
NCBI PubMed ID: 26531136Publication DOI: 10.1016/j.carres.2015.10.001Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: denis.giguere@chm.ulaval.ca
Institutions: Département de Chimie, Université Laval, Québec City, Québec, Canada G1V 0A6
- Article ID: 5458
Kenyon JJ, Arbatsky NP, Shashkov AS, Shneider MM, Popova AV, Hall RM, Knirel YA "Production of the K16 capsular polysaccharide by Acinetobacter baumannii ST25 isolate D4 involves a novel glycosyltransferase encoded in the KL16 gene cluster" -
International Journal of Biological Macromolecules 128 (2019) 101-106
A new capsular polysaccharide (CPS) biosynthesis gene cluster, KL16, was found in the genome sequence of a clinical Acinetobacter baumannii ST25 isolate, D4. The variable part of KL16 contains a module of genes for synthesis of 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetylpseudaminic acid, Pse5Ac7Ac), a gene encoding ItrA3 that initiates the CPS synthesis with d-GlcpNAc, and two glycosyltransferase (Gtr) genes. The K16 CPS was studied by sugar analysis and Smith degradation along with 1D and 2D 1H and 13C NMR spectroscopy, and shown to be built up of linear trisaccharide repeats containing d-galactose (d-Gal), N-acetyl-d-glucosamine (d-GlcNAc), and Pse5Ac7Ac. The d-Galp residue is linked to the d-GlcpNAc initiating sugar via a β-(1→3) linkage evidently formed by a Gtr5 variant, Gtr5K16, encoded in KL16. This reveals an altered or relaxed substrate specificity of this variant as the majority of Gtr5-type glycosyltransferases have previously been shown to form a β-d-Galp-(1→3)-d-GalpNAc linkage. The β-Psep5Ac7Ac-(2→4)-d-Galp linkage is predicted to be formed by the other glycosyltransferase, Gtr37, which does not match members of any known glycosyltransferase family.
Acinetobacter baumannii, capsular polysaccharide, 5, glycosyltransferase, 7-Di-N-acetylpseudaminic acid, KL16 K locus
NCBI PubMed ID: 30664967Publication DOI: 10.1016/j.ijbiomac.2019.01.080Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: J.J. Kenyon
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, M. M. Shemyakin & Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia, Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, GLC, Smith degradation, function analysis of gene clusters
- 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: 6411
Kasimova AA, Sharar NS, Ambrose SJ, Knirel YA, Shneider MM, Timoshina OY, Popova AV, Perepelov AV, Dmitrenok AS, Hsu LY, Hall RM, Kenyon JJ "The Acinetobacter baumannii K70 and K9 capsular polysaccharides consist of related K-units linked by the same Wzy polymerase and cleaved by the same phage depolymerases" -
Microbiology Spectrum 11(6) (2023) e0302523
Bacteriophage show promise for the treatment of Acinetobacter baumannii infections that resist all therapeutically suitable antibiotics. Many tail-spike depolymerases encoded by phage that are able to degrade A. baumannii capsular polysaccharide (CPS) exhibit specificity for the linkage present between K-units that make up CPS polymers. This linkage is formed by a specific Wzy polymerase, and the ability to predict this linkage using sequence-based methods that identify the Wzy at the K locus could assist with the selection of phage for therapy. However, little is known about the specificity of Wzy polymerase enzymes. Here, we describe a Wzy polymerase that can accommodate two different but similar sugars as one of the residues it links and phage depolymerases that can cleave both types of bond that Wzy forms.
Acinetobacter baumannii, capsular polysaccharide, Wzy polymerase, phage depolymerase, K70
NCBI PubMed ID: 37975684Publication DOI: 10.1128/spectrum.03025-23Journal NLM ID: 101634614Publisher: Washington, DC: ASM Press
Correspondence: J.J. Kenyon
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, Russia, M. M. Shemyakin and Y. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia, School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, Australia, Saw Swee Hock School of Public Health, National University of Singapore, Queenstown, Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Queenstown, Singapore
Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, sugar analysis, DNA techniques, GLC, Smith degradation, HPLC, GPC, bioinformatic analysis, phage depolymerisation, HR-ESI-MS
- Article ID: 6413
Knirel YA, Kasimova AA, Arbatsky NP, Shneider MM, Popova AV, Brovko FA, Shashkov AS, Senchenkova SN, Perepelov AV, Shpirt AM "5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic Acids in the Capsular Polysaccharides of Acinetobacter baumannii" -
Biochemistry (Moscow) 88(2) (2023) 202-210
The polysaccharide capsule surrounding bacterial cell plays an important role in pathogenesis of infections caused by the opportunistic pathogen Acinetobacter baumannii by providing protection from external factors. The structures of the capsular polysaccharide (CPS) produced by A. baumannii isolates and the corresponding CPS biosynthesis gene clusters are highly diverse, although many of them are related. Many types of A. baumannii CPSs contain isomers of 5,7-diamino-3,5,7,9-tetradeoxynon-2-ulosonic acid (DTNA). Three of these isomers, namely acinetaminic acid (l-glycero-l-altro isomer), 8-epiacinetaminic acid (d-glycero-l-altro isomer), and 8-epipseudaminic acid (d-glycero-l-manno isomer), have not been found so far in naturally occurring carbohydrates from other species. In A. baumannii CPSs, DTNAs carry N-acyl substituents at positions 5 and 7; in some CPSs, both N-acetyl and N-(3-hydroxybutanoyl) groups are present. Remarkably, pseudaminic acid carries the (R)-isomer and legionaminic acid carries the (S)-isomer of the 3-hydroxybutanoyl group. The review addresses the structure and genetics of biosynthesis of A. baumannii CPSs containing di-N-acyl derivatives of DTNA.
Acinetobacter baumannii, capsular polysaccharide, nonulosonic acid, Bacterial polysaccharide, capsule, higher monosaccharide, acyl group
NCBI PubMed ID: 37072328Publication DOI: 10.1134/S0006297923020049Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Correspondence: Y.A. Knirel
Institutions: State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, 117913, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia, Branch of the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry in Pushchino, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
Expand this compound
Collapse this compound
8. Compound ID: 12869
|
b-D-Galp-(1-3)-b-D-GlcpNAc-(1-4)-a-D-GalpA-(1-2)-a-L-Rhap-(1-2)-b-D-Ribp |
Show graphically |
Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_136044,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_1391962,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_143794,IEDB_150899,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_581504,IEDB_885823,SB_137,SB_165,SB_166,SB_187,SB_195,SB_29,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 5119
Naumenko OI, Guo X, Senchenkova SN, Geng P, Perepelov AV, Shashkov AS, Liu B, Knirel YA "Structure and gene cluster of the O-antigen of Escherichia coli O54" -
Carbohydrate Research 462 (2018) 34-38
Mild acid hydrolysis of the lipopolysaccharide of Escherichia coli O54 afforded an O-polysaccharide, which was studied by sugar analysis, solvolysis with anhydrous trifluoroacetic acid, and 1H and 13C NMR spectroscopy. Solvolysis cleaved predominantly the linkage of β-d-Ribf and, to a lesser extent, that of β-d-GlcpNAc, whereas the other linkages, including the linkage of α-l-Rhap, were stable under selected conditions (40 °C, 5 h). The following structure of the O-polysaccharide was established: →4)-α-d-GalpA-(1 → 2)-α-l-Rhap-(1 → 2)-β-d-Ribf-(1 → 4)-β-d-Galp-(1 → 3)-β-d-GlcpNAc-(1→ The O-antigen gene cluster of E. coli O54 was analyzed and found to be consistent in general with the O-polysaccharide structure established but there were two exceptions: i) in the cluster, there were genes for phosphoserine phosphatase and serine transferase, which have no apparent role in the O-polysaccharide synthesis, and ii) no ribofuranosyltransferase gene was present in the cluster. Both uncommon features are shared by some other enteric bacteria.
O-antigen, Escherichia coli, O-polysaccharide, bacterial polysaccharide structure, O-antigen gene cluster
NCBI PubMed ID: 29660546Publication DOI: 10.1016/j.carres.2018.04.001Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: A.V. Perepelov
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China, Russian Federation, School of Basic Medical Sciences, Tianjin Medical University, Heping District, Tianjin, 300070, PR China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, GLC, GPC, acetylation, delipidation, function analysis of gene clusters, solvolysis with trifluoroacetic acid
Expand this compound
Collapse this compound
9. Compound ID: 12870
Structure type: oligomer
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136105,IEDB_149136,IEDB_225177,IEDB_581504,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 5119
Naumenko OI, Guo X, Senchenkova SN, Geng P, Perepelov AV, Shashkov AS, Liu B, Knirel YA "Structure and gene cluster of the O-antigen of Escherichia coli O54" -
Carbohydrate Research 462 (2018) 34-38
Mild acid hydrolysis of the lipopolysaccharide of Escherichia coli O54 afforded an O-polysaccharide, which was studied by sugar analysis, solvolysis with anhydrous trifluoroacetic acid, and 1H and 13C NMR spectroscopy. Solvolysis cleaved predominantly the linkage of β-d-Ribf and, to a lesser extent, that of β-d-GlcpNAc, whereas the other linkages, including the linkage of α-l-Rhap, were stable under selected conditions (40 °C, 5 h). The following structure of the O-polysaccharide was established: →4)-α-d-GalpA-(1 → 2)-α-l-Rhap-(1 → 2)-β-d-Ribf-(1 → 4)-β-d-Galp-(1 → 3)-β-d-GlcpNAc-(1→ The O-antigen gene cluster of E. coli O54 was analyzed and found to be consistent in general with the O-polysaccharide structure established but there were two exceptions: i) in the cluster, there were genes for phosphoserine phosphatase and serine transferase, which have no apparent role in the O-polysaccharide synthesis, and ii) no ribofuranosyltransferase gene was present in the cluster. Both uncommon features are shared by some other enteric bacteria.
O-antigen, Escherichia coli, O-polysaccharide, bacterial polysaccharide structure, O-antigen gene cluster
NCBI PubMed ID: 29660546Publication DOI: 10.1016/j.carres.2018.04.001Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: A.V. Perepelov
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Higher Chemical College of the Russian Academy of Sciences, D. I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China, Russian Federation, School of Basic Medical Sciences, Tianjin Medical University, Heping District, Tianjin, 300070, PR China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, ESI-MS, GLC, GPC, acetylation, delipidation, function analysis of gene clusters, solvolysis with trifluoroacetic acid
Expand this compound
Collapse this compound
10. Compound ID: 13063
|
a-L-Fucp-(1-3)-+ a-L-Fucp-(1-3)-+ a-L-Fucp-(1-3)-+ a-D-Glcp-(1-4)-b-D-Galp-(1-7)-+ EtN-(1--P--7)--+
| | | | |
a-L-Fucp-(1-2)-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-{{{-b-D-Galp-(1-4)-b-D-GlcpNAc-(1-3)-}}}b-D-Galp-(1-4)-D-GlcpNAc-(1-?)-{{{-b-D-Ribp-(1-2)-}}}b-D-Ribp-(1-4)-b-D-Galp-(1-3)-a-D-Glcp-(1-6)-D-gro-a-D-manHepp-(1-3)-a-L-Fucp-(1-3)-b-D-GlcpNAc-(1-2)-D-gro-a-D-manHepp-(1-2)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2--/(2->6)lipid A/ |
Show graphically |
Structure type: oligomer
Aglycon: (2->6)lipid A
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130644,IEDB_130646,IEDB_130650,IEDB_130654,IEDB_130655,IEDB_130697,IEDB_135813,IEDB_136044,IEDB_136045,IEDB_137340,IEDB_137472,IEDB_137776,IEDB_140088,IEDB_140108,IEDB_140122,IEDB_141500,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_143250,IEDB_144556,IEDB_144562,IEDB_144998,IEDB_145669,IEDB_146664,IEDB_147455,IEDB_149555,IEDB_149557,IEDB_149561,IEDB_150092,IEDB_150939,IEDB_150948,IEDB_151531,IEDB_152214,IEDB_153553,IEDB_158550,IEDB_174333,IEDB_190606,IEDB_2151203,IEDB_2189046,IEDB_2189047,IEDB_461719,IEDB_461720,IEDB_461721,IEDB_581504,IEDB_952752,IEDB_983931,SB_147,SB_154,SB_157,SB_165,SB_166,SB_173,SB_187,SB_192,SB_195,SB_30,SB_34,SB_7,SB_86,SB_88
The structure is contained in the following publication(s):
- Article ID: 5179
Li H, Tang H, Debowski AW, Stubbs KA, Marshall BJ, Benghezal M "Lipopolysaccharide Structural Differences between Western and Asian Helicobacter pylori Strains" -
Toxins 10(9) (2018) 364
Recent structural analysis of the lipopolysaccharide (LPS) isolated from Helicobacter pylori G27 wild-type and O-antigen ligase mutant resulted in the redefinition of the core-oligosaccharide and O-antigen domains. The short core-oligosaccharide (Glc-Gal-Hep-III-Hep-II-Hep-I-KDO) and its attached trisaccharide (Trio, GlcNAc-Fuc-Hep) appear to be highly conserved structures among H. pylori strains. The G27 LPS contains a linear glucan?heptan linker between the core-Trio and distal Lewis antigens. This linker domain was commonly identified in Western strains. In contrast, out of 12 partial LPS structures of Asian strains, none displayed the heptan moiety, despite the presence of Lewis antigens. This raises the question of how Lewis antigens are attached to the Trio, and whether the LPS structure of Asian strains contain another linker. Of note, a riban was identified as a linker in LPS of the mouse-adapted SS1 strain, suggesting that alternative linker structures can occur. In summary, additional full structural analyses of LPS in Asian strains are required to assess the presence or absence of an alternative linker in these strains. It will also be interesting to study the glucan-heptan linker moieties in pathogenesis as H. pylori infections in Asia are usually more symptomatic than the ones presented in the Western world.
Lipopolysaccharide, structure, Helicobacter pylori
NCBI PubMed ID: 30205541Publication DOI: 10.3390/toxins10090364Journal NLM ID: 101530765Publisher: Basel: MDPI
Correspondence: H.T.
; M.B.
Institutions: West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu 610041, China, Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, WA 6009, Australia, School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia
Expand this compound
Collapse this compound
11. Compound ID: 13899
|
b-D-Ribp-(1-4)-a-L-Rhap-(1-3)-+
|
-4)-b-D-ManpNAc-(1-4)-a-L-Rhap-(1--P--4)--b-D-ManpNAc-(1-4)-b-D-Glcp-(1- |
Show graphically |
Structure type: polymer biological repeating unit
Contained glycoepitopes: IEDB_136105,IEDB_142488,IEDB_146664,IEDB_1625474,IEDB_225177,IEDB_581504,IEDB_885813,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5486
Paton JC, Trappetti C "Streptococcus pneumoniae Capsular Polysaccharide" -
Microbiology Spectrum 7(2) (2019) ID GPP3-0019-2018
The polysaccharide capsule of Streptococcus pneumoniae is the dominant surface structure of the organism and plays a critical role in virulence, principally by interfering with host opsonophagocytic clearance mechanisms. The capsule is the target of current pneumococcal vaccines, but there are 98 currently recognised polysaccharide serotypes and protection is strictly serotype-specific. Widespread use of these vaccines is driving changes in serotype prevalence in both carriage and disease. This chapter summarises current knowledge on the role of the capsule and its regulation in pathogenesis, the mechanisms of capsule synthesis, the genetic basis for serotype differences, and provides insights into how so many structurally distinct capsular serotypes have evolved. Such knowledge will inform ongoing refinement of pneumococcal vaccination strategies.
Streptococcus pneumoniae, capsular polysaccharide, gene cluster, function analysis, pneumococcal vaccines
NCBI PubMed ID: 30977464Publication DOI: 10.1128/microbiolspec.GPP3-0019-2018Journal NLM ID: 101634614Publisher: Washington, DC: ASM Press
Correspondence: James Patton
Institutions: Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, 5005, Australia
Expand this compound
Collapse this compound
12. Compound ID: 13901
|
b-D-Ribp-(1-4)-a-L-Rhap-(1-3)-+
|
-4)-b-D-ManpNAc-(1-4)-a-L-Rhap-(1--P--4)--b-D-ManpNAc-(1-4)-b-D-Glcp-(1-
|
b-D-Glcp-(1-6)-+ |
Show graphically |
Structure type: polymer biological repeating unit
Contained glycoepitopes: IEDB_136105,IEDB_142488,IEDB_146664,IEDB_1625474,IEDB_225177,IEDB_581504,IEDB_885813,IEDB_885823,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5486
Paton JC, Trappetti C "Streptococcus pneumoniae Capsular Polysaccharide" -
Microbiology Spectrum 7(2) (2019) ID GPP3-0019-2018
The polysaccharide capsule of Streptococcus pneumoniae is the dominant surface structure of the organism and plays a critical role in virulence, principally by interfering with host opsonophagocytic clearance mechanisms. The capsule is the target of current pneumococcal vaccines, but there are 98 currently recognised polysaccharide serotypes and protection is strictly serotype-specific. Widespread use of these vaccines is driving changes in serotype prevalence in both carriage and disease. This chapter summarises current knowledge on the role of the capsule and its regulation in pathogenesis, the mechanisms of capsule synthesis, the genetic basis for serotype differences, and provides insights into how so many structurally distinct capsular serotypes have evolved. Such knowledge will inform ongoing refinement of pneumococcal vaccination strategies.
Streptococcus pneumoniae, capsular polysaccharide, gene cluster, function analysis, pneumococcal vaccines
NCBI PubMed ID: 30977464Publication DOI: 10.1128/microbiolspec.GPP3-0019-2018Journal NLM ID: 101634614Publisher: Washington, DC: ASM Press
Correspondence: James Patton
Institutions: Research Centre for Infectious Diseases, Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, 5005, Australia
Expand this compound
Collapse this compound
13. Compound ID: 14755
|
R-Lac-(1-5)-b-Psep7Ac-(2-2)-a-D-Glcp-(1-3)-b-D-GalpNAcA-(1-2)-b-D-Ribp |
Show graphically |
Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_581504,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5796
Kokoulin MS, Kuzmich AS, Romanenko LA, Chikalovets IV, Chernikov OV "Structure and in vitro Bioactivity against Cancer Cells of the Capsular Polysaccharide from the Marine Bacterium Psychrobacter marincola" -
Marine Drugs 18(5) (2020) 268
Psychrobacter marincola KMM 277T is a psychrophilic Gram-negative bacterium that has been isolated from the internal tissues of an ascidian Polysyncraton sp. Here, we report the structure of the capsular polysaccharide from P. marincola KMM 277T and its effect on the viability and colony formation of human acute promyelocytic leukemia HL-60 cells. The polymer was purified by several separation methods, including ultracentrifugation and chromatographic procedures, and the structure was elucidated by means of chemical analysis, 1-D, and 2-D NMR spectroscopy techniques. It was found that the polysaccharide consists of branched hexasaccharide repeating units containing two 2-N-acetyl-2-deoxy-d-galacturonic acids, and one of each of 2-N-acetyl-2-deoxy-d-glucose, d-glucose, d-ribose, and 7-N-acetylamino-3,5,7,9-tetradeoxy-5-N-[(R)-2-hydroxypropanoylamino]- l-glycero-l-manno-non-2-ulosonic acid. To our knowledge, this is the first finding a pseudaminic acid decorated with lactic acid residue in polysaccharides. The biological analysis showed that the capsular polysaccharide significantly reduced the viability and colony formation of HL-60 cells. Taken together, our data indicate that the capsular polysaccharide from P. marincola KMM 277T is a promising substance for the study of its antitumor properties and the mechanism of action in the future.
capsular polysaccharide, pseudaminic acid, Marine bacteria, lactic acid, Psychrobacter, Antiproliferative activity, HL-60
NCBI PubMed ID: 32438723Publication DOI: 10.3390/md18050268Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: maxchem@mail.ru
Institutions: G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159/2, Prospect 100 let Vladivostoku, 690022 Vladivostok, Russia, Far Eastern Federal University, 8, Sukhanova str., 690950 Vladivostok, Russia
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, partial acid hydrolysis, GC-MS, GC, Smith degradation, composition analysis, HPLC, GPC, PAGE, cell viability assay, soft agar assay
Expand this compound
Collapse this compound
14. Compound ID: 14756
Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_581504,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5796
Kokoulin MS, Kuzmich AS, Romanenko LA, Chikalovets IV, Chernikov OV "Structure and in vitro Bioactivity against Cancer Cells of the Capsular Polysaccharide from the Marine Bacterium Psychrobacter marincola" -
Marine Drugs 18(5) (2020) 268
Psychrobacter marincola KMM 277T is a psychrophilic Gram-negative bacterium that has been isolated from the internal tissues of an ascidian Polysyncraton sp. Here, we report the structure of the capsular polysaccharide from P. marincola KMM 277T and its effect on the viability and colony formation of human acute promyelocytic leukemia HL-60 cells. The polymer was purified by several separation methods, including ultracentrifugation and chromatographic procedures, and the structure was elucidated by means of chemical analysis, 1-D, and 2-D NMR spectroscopy techniques. It was found that the polysaccharide consists of branched hexasaccharide repeating units containing two 2-N-acetyl-2-deoxy-d-galacturonic acids, and one of each of 2-N-acetyl-2-deoxy-d-glucose, d-glucose, d-ribose, and 7-N-acetylamino-3,5,7,9-tetradeoxy-5-N-[(R)-2-hydroxypropanoylamino]- l-glycero-l-manno-non-2-ulosonic acid. To our knowledge, this is the first finding a pseudaminic acid decorated with lactic acid residue in polysaccharides. The biological analysis showed that the capsular polysaccharide significantly reduced the viability and colony formation of HL-60 cells. Taken together, our data indicate that the capsular polysaccharide from P. marincola KMM 277T is a promising substance for the study of its antitumor properties and the mechanism of action in the future.
capsular polysaccharide, pseudaminic acid, Marine bacteria, lactic acid, Psychrobacter, Antiproliferative activity, HL-60
NCBI PubMed ID: 32438723Publication DOI: 10.3390/md18050268Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: maxchem@mail.ru
Institutions: G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159/2, Prospect 100 let Vladivostoku, 690022 Vladivostok, Russia, Far Eastern Federal University, 8, Sukhanova str., 690950 Vladivostok, Russia
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, partial acid hydrolysis, GC-MS, GC, Smith degradation, composition analysis, HPLC, GPC, PAGE, cell viability assay, soft agar assay
Expand this compound
Collapse this compound
15. Compound ID: 14757
|
R-Lac-(1-5)-b-Psep7Ac-(2-2)-a-D-Glcp-(1-3)-b-D-GalpNAcA-(1-2)-b-D-Ribp-(1-4)-+
|
-3)-b-D-GlcpNAc-(1-3)-a-D-GalpNAcA-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_581504,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5796
Kokoulin MS, Kuzmich AS, Romanenko LA, Chikalovets IV, Chernikov OV "Structure and in vitro Bioactivity against Cancer Cells of the Capsular Polysaccharide from the Marine Bacterium Psychrobacter marincola" -
Marine Drugs 18(5) (2020) 268
Psychrobacter marincola KMM 277T is a psychrophilic Gram-negative bacterium that has been isolated from the internal tissues of an ascidian Polysyncraton sp. Here, we report the structure of the capsular polysaccharide from P. marincola KMM 277T and its effect on the viability and colony formation of human acute promyelocytic leukemia HL-60 cells. The polymer was purified by several separation methods, including ultracentrifugation and chromatographic procedures, and the structure was elucidated by means of chemical analysis, 1-D, and 2-D NMR spectroscopy techniques. It was found that the polysaccharide consists of branched hexasaccharide repeating units containing two 2-N-acetyl-2-deoxy-d-galacturonic acids, and one of each of 2-N-acetyl-2-deoxy-d-glucose, d-glucose, d-ribose, and 7-N-acetylamino-3,5,7,9-tetradeoxy-5-N-[(R)-2-hydroxypropanoylamino]- l-glycero-l-manno-non-2-ulosonic acid. To our knowledge, this is the first finding a pseudaminic acid decorated with lactic acid residue in polysaccharides. The biological analysis showed that the capsular polysaccharide significantly reduced the viability and colony formation of HL-60 cells. Taken together, our data indicate that the capsular polysaccharide from P. marincola KMM 277T is a promising substance for the study of its antitumor properties and the mechanism of action in the future.
capsular polysaccharide, pseudaminic acid, Marine bacteria, lactic acid, Psychrobacter, Antiproliferative activity, HL-60
NCBI PubMed ID: 32438723Publication DOI: 10.3390/md18050268Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: maxchem@mail.ru
Institutions: G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159/2, Prospect 100 let Vladivostoku, 690022 Vladivostok, Russia, Far Eastern Federal University, 8, Sukhanova str., 690950 Vladivostok, Russia
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, partial acid hydrolysis, GC-MS, GC, Smith degradation, composition analysis, HPLC, GPC, PAGE, cell viability assay, soft agar assay
Expand this compound
Collapse this compound
Next 15 structure(s)
Total list of structure IDs on all result pages of the current query:
Total list of corresponding CSDB IDs (permanent record IDs):
Execution: 1 sec