Found 69 structures.
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1. Compound ID: 722
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Asp-(1-2)-+
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a-L-Rhap2Me-(1-4)-+ |
| |
b-D-GlcpNAcA4Me-(1-4)-b-D-GlcpA-(1-4)-b-D-Xylp2Ac3Ac-(1-4)-a-D-GlcpA2Me-(1-2)-a-D-Manp-(1-3)-Ser-(1-2)-Ala-(1-2)-Ala |
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Structure type: oligomer
Trivial name: glycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_130701,IEDB_136105,IEDB_140630,IEDB_144983,IEDB_150900,IEDB_152206,IEDB_167188,IEDB_174332,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72
The structure is contained in the following publication(s):
- Article ID: 192
Vinogradov E, Perry MB, Kay WW "The structure of the glycopeptides from the fish pathogen Flavobacterium columnare" -
Carbohydrate Research 338(23) (2003) 2653-2658
Proteolytic digestion of the phenol-water extraction product of the fish pathogen Flavobacterium columnare afforded a mixture of glycopeptides in which the oligosaccharide moiety was an unusual hexasaccharide composed of 4-O-methyl-2-acetamido-2-deoxy-D-glucuronic acid (GlcNAcA), D-glucuronic acid (D-GlcA), 2,3-di-O-acetyl-D-xylose (D-Xyl), 2-O-methyl-D-glucuronic acid (D-GlcA), D-mannose (D-Man), and 2-O-methyl-L-rhamnose (L-Rha). By the application of high-resolution 1D and 2D NMR, mass spectrometry, and chemical analysis, the hexasaccharide structure was determined to be: [carbohydrate structure--see text] where all monosaccharides have the D-configuration except for 2-O-methyl-L-rhamnose; and were in the pyranose form. Only one carbohydrate structure was found. The peptide part was represented by tri- to hepta-peptides with a minimal common tripeptide fragment Asp-Ser-Ala, extended with Ala and Val
NMR, MS, Flavobacterium columnare, glycopeptide
NCBI PubMed ID: 14670723Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: evguenii.vinogradov@nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council, 100 Sussex Dr., Ottawa, ON, Canada K1A 0R6, Department of Bacteriology and Biochemistry, University of Victoria, Victoria, BC, Canada V8W 2T2
Methods: NMR-2D, NMR, chemical analysis, MS
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2. Compound ID: 747
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a-Kdop-(2-4)-+
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a-D-GlcpNAc-(1-4)-a-D-GlcpNA-(1-4)-+ | P-4)-+
| | |
?%a-L-Rhap-(1-3)-?%a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-8)-a-Kdop-(2-5)-a-Kdop-(2-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_150908,IEDB_151531,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 198
Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus JO, Brade H, Holst O "Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolyasccharide from Acinetobacter baumannii strain NCTC 10303 (ATCC 17904)" -
Journal of Biological Chemistry 273(43) (1998) 28122-28131
For the first time, the tetrasaccharide Kdo a2→5 Kdo a2→5 (Kdo a2→4)Kdo (Kdo is 3-deoxy-Dmanno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide DGlcpN b1→6 DGlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide DGlcpNAc a1→4 DGlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: [see formula in text] where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.
LPS, structure, core, acid, Acinetobacter, Acinetobacter baumannii, 3-deoxy-D-manno-oct-2-ulopyranosonic
NCBI PubMed ID: 9774431Publication DOI: 10.1074/jbc.273.43.28122Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: oholst@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany, Department of Chemistry, Carlsberg Laboratory, DK-2500 Valby, Denmark, Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University,NL-3584 CA Utrecht, The Netherlands
Methods: NMR-2D, NMR, MS, composition analysis
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3. Compound ID: 748
Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 198
Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus JO, Brade H, Holst O "Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolyasccharide from Acinetobacter baumannii strain NCTC 10303 (ATCC 17904)" -
Journal of Biological Chemistry 273(43) (1998) 28122-28131
For the first time, the tetrasaccharide Kdo a2→5 Kdo a2→5 (Kdo a2→4)Kdo (Kdo is 3-deoxy-Dmanno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide DGlcpN b1→6 DGlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide DGlcpNAc a1→4 DGlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: [see formula in text] where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.
LPS, structure, core, acid, Acinetobacter, Acinetobacter baumannii, 3-deoxy-D-manno-oct-2-ulopyranosonic
NCBI PubMed ID: 9774431Publication DOI: 10.1074/jbc.273.43.28122Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: oholst@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany, Department of Chemistry, Carlsberg Laboratory, DK-2500 Valby, Denmark, Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University,NL-3584 CA Utrecht, The Netherlands
Methods: NMR-2D, NMR, MS, composition analysis
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4. Compound ID: 749
Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 198
Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus JO, Brade H, Holst O "Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolyasccharide from Acinetobacter baumannii strain NCTC 10303 (ATCC 17904)" -
Journal of Biological Chemistry 273(43) (1998) 28122-28131
For the first time, the tetrasaccharide Kdo a2→5 Kdo a2→5 (Kdo a2→4)Kdo (Kdo is 3-deoxy-Dmanno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide DGlcpN b1→6 DGlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide DGlcpNAc a1→4 DGlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: [see formula in text] where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.
LPS, structure, core, acid, Acinetobacter, Acinetobacter baumannii, 3-deoxy-D-manno-oct-2-ulopyranosonic
NCBI PubMed ID: 9774431Publication DOI: 10.1074/jbc.273.43.28122Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: oholst@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany, Department of Chemistry, Carlsberg Laboratory, DK-2500 Valby, Denmark, Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University,NL-3584 CA Utrecht, The Netherlands
Methods: NMR-2D, NMR, MS, composition analysis
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5. Compound ID: 750
Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 198
Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus JO, Brade H, Holst O "Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolyasccharide from Acinetobacter baumannii strain NCTC 10303 (ATCC 17904)" -
Journal of Biological Chemistry 273(43) (1998) 28122-28131
For the first time, the tetrasaccharide Kdo a2→5 Kdo a2→5 (Kdo a2→4)Kdo (Kdo is 3-deoxy-Dmanno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide DGlcpN b1→6 DGlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide DGlcpNAc a1→4 DGlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: [see formula in text] where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.
LPS, structure, core, acid, Acinetobacter, Acinetobacter baumannii, 3-deoxy-D-manno-oct-2-ulopyranosonic
NCBI PubMed ID: 9774431Publication DOI: 10.1074/jbc.273.43.28122Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: oholst@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany, Department of Chemistry, Carlsberg Laboratory, DK-2500 Valby, Denmark, Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University,NL-3584 CA Utrecht, The Netherlands
Methods: NMR-2D, NMR, MS, composition analysis
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6. Compound ID: 754
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a-Kdop-(2-4)-+ P-4)-+
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a-D-GlcpN-(1-4)-a-D-GlcpNA-(1-4)-a-Kdop-(2-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_141807,IEDB_150908,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 198
Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus JO, Brade H, Holst O "Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolyasccharide from Acinetobacter baumannii strain NCTC 10303 (ATCC 17904)" -
Journal of Biological Chemistry 273(43) (1998) 28122-28131
For the first time, the tetrasaccharide Kdo a2→5 Kdo a2→5 (Kdo a2→4)Kdo (Kdo is 3-deoxy-Dmanno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide DGlcpN b1→6 DGlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide DGlcpNAc a1→4 DGlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: [see formula in text] where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.
LPS, structure, core, acid, Acinetobacter, Acinetobacter baumannii, 3-deoxy-D-manno-oct-2-ulopyranosonic
NCBI PubMed ID: 9774431Publication DOI: 10.1074/jbc.273.43.28122Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: oholst@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany, Department of Chemistry, Carlsberg Laboratory, DK-2500 Valby, Denmark, Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University,NL-3584 CA Utrecht, The Netherlands
Methods: NMR-2D, NMR, MS, composition analysis
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7. Compound ID: 755
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R-3HOLau-(1-2)-+
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a-Kdop-(2-4)-+ |
| |
a-D-GlcpN-(1-4)-a-D-GlcpNA-(1-4)-+ | |
| | |
a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-a-L-Rhap-(1-8)-a-Kdop-(2-5)-a-Kdop-(2-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
|
P-4)-+ |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136105,IEDB_141807,IEDB_150908,IEDB_151531,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 198
Vinogradov EV, Petersen BO, Thomas-Oates JE, Duus JO, Brade H, Holst O "Characterization of a novel branched tetrasaccharide of 3-deoxy-D-manno-oct-2-ulopyranosonic acid. The structure of the carbohydrate backbone of the lipopolyasccharide from Acinetobacter baumannii strain NCTC 10303 (ATCC 17904)" -
Journal of Biological Chemistry 273(43) (1998) 28122-28131
For the first time, the tetrasaccharide Kdo a2→5 Kdo a2→5 (Kdo a2→4)Kdo (Kdo is 3-deoxy-Dmanno-oct-2-ulopyranosonic acid) has been identified in a bacterial lipopolysaccharide (LPS), i.e. in the core region of LPS from Acinetobacter baumannii NCTC 10303. The LPS was analyzed using compositional analysis, mass spectrometry, and NMR spectroscopy. The disaccharide DGlcpN b1→6 DGlcpN, phosphorylated at O-1 and O-4', was identified as the carbohydrate backbone of the lipid A. The Kdo tetrasaccharide is attached to O-6' of this disaccharide and is further substituted by short L-rhamnoglycans of varying length and by the disaccharide DGlcpNAc a1→4 DGlcpNA (GlcpNA, 2-amino-2-deoxy-glucopyranosuronic acid). The core region is not substituted by phosphate residues and represents a novel core type of bacterial LPS. The complete carbohydrate backbone of the LPS is shown in Structure I as follows: [see formula in text] where Rha is rhamnose. Except were indicated, monosaccharides possess the D-configuration. Sugars marked with an asterisk are present in non-stoichiometric amounts.
LPS, structure, core, acid, Acinetobacter, Acinetobacter baumannii, 3-deoxy-D-manno-oct-2-ulopyranosonic
NCBI PubMed ID: 9774431Publication DOI: 10.1074/jbc.273.43.28122Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: oholst@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany, Department of Chemistry, Carlsberg Laboratory, DK-2500 Valby, Denmark, Department of Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University,NL-3584 CA Utrecht, The Netherlands
Methods: NMR-2D, NMR, MS, composition analysis
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8. Compound ID: 781
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a-Kdop-(2-4)-+
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b-D-GlcpN-(1-7)-+ |
| |
a-D-GalpN-(1-4)-+ | | P-4)-+
| | | |
a-D-Glcp-(1-2)-b-D-Glcp-(1-4)-b-D-Glcp-(1-4)-b-D-Glcp-(1-3)-a-D-GlcpNAcA-(1-4)-a-Kdop-(2-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137473,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 203
Vinogradov EV, Duus JO, Brade H, Holst O "The structure of the carbohydrate backbone of the lipopolysaccharide from Acinetobacter baumannii strain ATCC 19606" -
European Journal of Biochemistry 269(2) (2002) 422-430
The chemical structure of the phosphorylated carbohydrate backbone of the lipopolysaccharide (LPS) from Acinetobacter baumannii strain ATCC 19606 was investigated by chemical analysis and NMR spectroscopy of oligosaccharides obtained after deacylation or mild acid hydrolysis. From the combined information the following carbohydrate backbones can be deduced: where R1 = H and R2 = α-Glcp-(1→2)-β-Glcp-(1→4)-β-Glcp-(1→4)-β-Glcp-(1 as major and R1 = Ac and R2 = H as minor products. All monosaccharides are d-configured. Also, smaller oligosaccharide phosphates were identified that are thought to represent degradation products of the above structures
Lipopolysaccharide, Acinetobacter baumannii, NMR spectroscopy, structural analysis, core region
NCBI PubMed ID: 11856300Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Department of Chemistry, Carlsberg Laboratory, Valby, Copenhagen, Denmark
Methods: NMR-2D, NMR, chemical methods
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9. Compound ID: 782
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a-Kdop-(2-4)-+
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b-D-GlcpN-(1-7)-+ | P-4)-+
| | |
a-D-GalpNAc-(1-4)-a-D-GlcpNAcA-(1-4)-a-Kdop-(2-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
Show graphically |
Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130648,IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_141807,IEDB_150908,IEDB_151531,IEDB_885822
The structure is contained in the following publication(s):
- Article ID: 203
Vinogradov EV, Duus JO, Brade H, Holst O "The structure of the carbohydrate backbone of the lipopolysaccharide from Acinetobacter baumannii strain ATCC 19606" -
European Journal of Biochemistry 269(2) (2002) 422-430
The chemical structure of the phosphorylated carbohydrate backbone of the lipopolysaccharide (LPS) from Acinetobacter baumannii strain ATCC 19606 was investigated by chemical analysis and NMR spectroscopy of oligosaccharides obtained after deacylation or mild acid hydrolysis. From the combined information the following carbohydrate backbones can be deduced: where R1 = H and R2 = α-Glcp-(1→2)-β-Glcp-(1→4)-β-Glcp-(1→4)-β-Glcp-(1 as major and R1 = Ac and R2 = H as minor products. All monosaccharides are d-configured. Also, smaller oligosaccharide phosphates were identified that are thought to represent degradation products of the above structures
Lipopolysaccharide, Acinetobacter baumannii, NMR spectroscopy, structural analysis, core region
NCBI PubMed ID: 11856300Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Department of Chemistry, Carlsberg Laboratory, Valby, Copenhagen, Denmark
Methods: NMR-2D, NMR, chemical methods
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10. Compound ID: 783
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b-D-GlcpN-(1-7)-+
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a-D-GalpNAc-(1-4)-a-D-GlcpNAcA-(1-4)-Kdo-ol |
Show graphically |
Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_141807,IEDB_151531,IEDB_885822
The structure is contained in the following publication(s):
- Article ID: 203
Vinogradov EV, Duus JO, Brade H, Holst O "The structure of the carbohydrate backbone of the lipopolysaccharide from Acinetobacter baumannii strain ATCC 19606" -
European Journal of Biochemistry 269(2) (2002) 422-430
The chemical structure of the phosphorylated carbohydrate backbone of the lipopolysaccharide (LPS) from Acinetobacter baumannii strain ATCC 19606 was investigated by chemical analysis and NMR spectroscopy of oligosaccharides obtained after deacylation or mild acid hydrolysis. From the combined information the following carbohydrate backbones can be deduced: where R1 = H and R2 = α-Glcp-(1→2)-β-Glcp-(1→4)-β-Glcp-(1→4)-β-Glcp-(1 as major and R1 = Ac and R2 = H as minor products. All monosaccharides are d-configured. Also, smaller oligosaccharide phosphates were identified that are thought to represent degradation products of the above structures
Lipopolysaccharide, Acinetobacter baumannii, NMR spectroscopy, structural analysis, core region
NCBI PubMed ID: 11856300Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Department of Chemistry, Carlsberg Laboratory, Valby, Copenhagen, Denmark
Methods: NMR-2D, NMR, chemical methods
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11. Compound ID: 784
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b-D-GlcpN-(1-7)-+
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a-D-GalpN-(1-4)-+ |
| |
a-D-Glcp-(1-2)-b-D-Glcp-(1-4)-b-D-Glcp-(1-4)-b-D-Glcp-(1-3)-a-D-GlcpNAcA-(1-4)-Kdo-ol |
Show graphically |
Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_137473,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 203
Vinogradov EV, Duus JO, Brade H, Holst O "The structure of the carbohydrate backbone of the lipopolysaccharide from Acinetobacter baumannii strain ATCC 19606" -
European Journal of Biochemistry 269(2) (2002) 422-430
The chemical structure of the phosphorylated carbohydrate backbone of the lipopolysaccharide (LPS) from Acinetobacter baumannii strain ATCC 19606 was investigated by chemical analysis and NMR spectroscopy of oligosaccharides obtained after deacylation or mild acid hydrolysis. From the combined information the following carbohydrate backbones can be deduced: where R1 = H and R2 = α-Glcp-(1→2)-β-Glcp-(1→4)-β-Glcp-(1→4)-β-Glcp-(1 as major and R1 = Ac and R2 = H as minor products. All monosaccharides are d-configured. Also, smaller oligosaccharide phosphates were identified that are thought to represent degradation products of the above structures
Lipopolysaccharide, Acinetobacter baumannii, NMR spectroscopy, structural analysis, core region
NCBI PubMed ID: 11856300Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Department of Chemistry, Carlsberg Laboratory, Valby, Copenhagen, Denmark
Methods: NMR-2D, NMR, chemical methods
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12. Compound ID: 1190
Structure type: polymer chemical repeating unit
Compound class: CPS
The structure is contained in the following publication(s):
- Article ID: 367
Sau S, Lee CY "Cloning of type 8 capsule genes and analysis of gene clusters for the production of different capsular polysaccharides in Staphylococcus aureus" -
Journal of Bacteriology 178(7) (1996) 2118-2126
Eleven serotypes of capsular polysaccharide from Staphylococcus aureus have been reported. We have previously cloned a cluster of type 1 capsule (cap1) genes responsible for type 1 capsular polysaccharide biosynthesis in S. aureus M. To clone the type 8 capsule (cap8) genes, a plasmid library of type 8 strain Becker was screened with a labelled DNA fragment containing the cap1 genes under low-stringency conditions. One recombinant plasmid containing a 14-kb insert was chosen for further study and found to complement 14 of the 18 type 8 capsule-negative (Cap8-) mutants used in the study. Additional library screening, subcloning, and complementation experiments showed that all of the 18 Cap8- mutants were complemented by DNA fragments derived from a 20.5-kb contiguous region of the Becker chromosome. The mutants were mapped into six complementation groups, indicating that the cap8 genes are clustered. By Southern hybridization analyses under high-stringency conditions, we found that DNA fragments containing the cap8 gene cluster show extensive homology with all 17 strains tested, including type 1 strains. By further Southern analyses and cloning of the cap8-related homolog from strain M, we show that strain M carries an additional capsule gene cluster different from the cap1 gene cluster. In addition, by using DNA fragments containing different regions of the cap8 gene cluster as probes to hybridize DNA from different strains, we found that the central region of the cap8 gene cluster hybridizes only to DNAs from certain strains tested whereas the flanking regions hybridize to DNAs of all strains tested. Thus, the cap8 gene clusters and its closely related homologs are likely to have organizations similar to those of the encapsulation genes of other bacterial systems.
capsular polysaccharides, analysis, cloning, type, gene cluster, capsule, Staphylococcus aureus
NCBI PubMed ID: 8606192Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Correspondence: clee@kumc.edu
Institutions: Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160
Methods: genetic methods
- Article ID: 3296
Lee JC, Xu S, Albus A, Livolsi PJ "Genetic analysis of type 5 capsular polysaccharide expression by Staphylococcus aureus" -
Journal of Bacteriology 176(16) (1994) 4883-4889
Capsules are produced by over 90% of Staphylococcus aureus strains, and approximately 25% of clinical isolates express type 5 capsular polysaccharide (CP5). We mutagenized the type 5 strain Reynolds with Tn918 to target genes involved in CP5 expression. From a capsule-deficient mutant, we cloned into a cosmid vector an approximately 26-kb EcoRI fragment containing the transposon insertion. In the absence of tetracycline selection, Tn918 was spontaneously excised, thereby resulting in a plasmid containing 9.4 kb of S. aureus DNA flanking the Tn918 insertion site. The 9.4-kb DNA fragment was used to screen a cosmid library prepared from the wild-type strain. Positive colonies were identified by colony hybridization, and a restriction map of one clone (pJCL19 with an approximately 34-kb insert) carrying the putative capsule gene region was constructed. Fragments of pJCL19 were used to probe genomic DNA digests from S. aureus strains of different capsular serotypes. Fragments on the ends of the cloned DNA hybridized to fragments of similar sizes in most of the strains examined. Blots hybridized to two fragments flanking the central region of the cloned DNA showed restriction fragment length polymorphism. A centrally located DNA fragment hybridized only to DNA from capsular types 2, 4, and 5. DNA from pJCL19 was subcloned to a shuttle vector for complementation studies. A 6.2-kb EcoRI-ClaI fragment complemented CP5 expression in a capsule-negative mutant derived by mutagenesis with ethyl methanesulfonate. These experiments provide the necessary groundwork for identifying genes involved in CP5 expression by S. aureus.
genetic, clinical, expression, gene, genetics, DNA, strain, capsular, polysaccharide, serotype, analysis, capsular polysaccharide, type, mutant, region, insertion, plasmid, capsule, Staphylococcus, Staphylococcus aureus, fragment, Serotypes, site, clone, PDF, capsules, selection, polymorphism
NCBI PubMed ID: 805001Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Institutions: Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.
Methods: serological methods, genetic methods
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13. 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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14. Compound ID: 2746
|
-4)-b-D-GlcpNAcA-(1-4)-a-L-FucpNAm-(1-3)-a-D-6dxylHexpN-4-ulo-(1- |
Show graphically |
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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15. Compound ID: 3018
|
S-3)-+
|
-4)-b-D-GlcpNAcA-(1-6)-a-D-Manp-(1-4)-b-D-GlcpNAcA-(1- |
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Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_130701,IEDB_144983,IEDB_152206,IEDB_983930,SB_44,SB_67,SB_72
The structure is contained in the following publication(s):
- Article ID: 1083
Parolis H, Parolis LAS, Boán IF, Rodríguez-Valera F, Widmalm G, Manca MC, Jansson P, Sutherland IW "The structure of the exopolysaccharide produced by the halophilic Archaeon Haloferax mediterranei strain R4 (ATCC33500)" -
Carbohydrate Research 295 (1996) 147-156
The halophilic Archaeon Haloferax mediterranei exudes into the growth medium a high molecular weight sulfated polysaccharide. The structure of the repeating unit of this polymer was determined by a combination of glycose, methylation, and sulfate analysis, periodate oxidation, and 1D and 2D NMR spectroscopic analysis of the native and periodate-oxidised/reduced polysaccharides. The location of the sulfate group was established from the 1H and 13C NMR data. The structure of the repeating unit of the polysaccharide may be written as [formula: see text]
structure, strain, exopolysaccharide, sulfate, Archaeon, Haloferax, halophilic
NCBI PubMed ID: 9002190Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, School of Pharmaceutical Sciences, Rhodes University, Grahamstown, 6140, South Africa, Departamento de Genetica y Microbiologia, Universidad de Alicante, Campus de San Juan, Apdo. 374, E-03080 Alicante, Spain, Clinical Research centre, Analytical Unit, Karolinska Institute, Huddinge Hospital, Huddinge, Sweden, Institute of Cell and Molecular Biology, Edingurgh University, Mayfield Rd. Edingurgh, EH9 3JH, UK
Methods: methylation, periodate oxidation, NMR-2D, NMR, sugar analysis, sulfate analysis
- Article ID: 5137
Casillo A, Lanzetta R, Parrilli M, Corsaro MM "Exopolysaccharides from Marine and Marine Extremophilic Bacteria: Structures, Properties, Ecological Roles and Applications" -
Marine Drugs 16(2) (2018) pii E69
The marine environment is the largest aquatic ecosystem on Earth and it harbours microorganisms responsible for more than 50% of total biomass of prokaryotes in the world. All these microorganisms produce extracellular polymers that constitute a substantial part of the dissolved organic carbon, often in the form of exopolysaccharides (EPS). In addition, the production of these polymers is often correlated to the establishment of the biofilm growth mode, during which they are important matrix components. Their functions include adhesion and colonization of surfaces, protection of the bacterial cells and support for biochemical interactions between the bacteria and the surrounding environment. The aim of this review is to present a summary of the status of the research about the structures of exopolysaccharides from marine bacteria, including capsular, medium released and biofilm embedded polysaccharides. Moreover, ecological roles of these polymers, especially for those isolated from extreme ecological niches (deep-sea hydrothermal vents, polar regions, hypersaline ponds, etc.), are reported. Finally, relationships between the structure and the function of the exopolysaccharides are discussed.
NMR, capsular polysaccharide, exopolysaccharide, exopolysaccharides, EPS, purification, Extremophile, marine, chemical characterization, GC-MS, structure/activity relationship
NCBI PubMed ID: 29461505Publication DOI: 10.3390/md16020069Journal NLM ID: 101213729Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: corsaro@unina.it; angela.casillo@unina.it
Institutions: Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
- Article ID: 5253
Vijayendra SV, Shamala TR "Film forming microbial biopolymers for commercial applications-A review" -
Critical Reviews in Biotechnology 34(4) (2014) 338-357
Microorganisms synthesize intracellular, structural and extracellular polymers also referred to as biopolymers for their function and survival. These biopolymers play specific roles as energy reserve materials, protective agents, aid in cell functioning, the establishment of symbiosis, osmotic adaptation and support the microbial genera to function, adapt, multiply and survive efficiently under changing environmental conditions. Viscosifying, gelling and film forming properties of these have been exploited for specific significant applications in food and allied industries. Intensive research activities and recent achievements in relevant and important research fields of global interest regarding film forming microbial biopolymers is the subject of this review. Microbial polymers such as pullulan, kefiran, bacterial cellulose (BC), gellan and levan are placed under the category of exopolysaccharides (EPS) and have several other functional properties including film formation, which can be used for various applications in food and allied industries. In addition to EPS, innumerable bacterial genera are found to synthesis carbon energy reserves in their cells known as polyhydroxyalkanoates (PHAs), microbial polyesters, which can be extruded into films with excellent moisture and oxygen barrier properties. Blow moldable biopolymers like PHA along with polylactic acid (PLA) synthesized chemically in vitro using lactic acid (LA), which is produced by LA bacteria through fermentation, are projected as biodegradable polymers of the future for packaging applications. Designing and creating of new property based on requirements through controlled synthesis can lead to improvement in properties of existing polysaccharides and create novel biopolymers of great commercial interest and value for wider applications. Incorporation of antimicrobials such as bacteriocins or silver and copper nanoparticles can enhance the functionality of polymer films especially in food packaging applications either in the form of coatings or wrappings. Use of EPS in combinations to obtain desired properties can be evaluated to increase the application range. Controlled release of active compounds, bioactive protection and resistance to water can be investigated while developing new technologies to improve the film properties of active packaging and coatings. An holistic approach may be adopted in developing an economical and biodegradable packaging material with acceptable properties. An interdisciplinary approach with new innovations can lead to the development of new composites of these biopolymers to enhance the application range. This current review focuses on linking and consolidation of recent research activities on the production and applications of film forming microbial polymers like EPS, PHA and PLA for commercial applications. © 2014 Informa Healthcare USA, Inc.
exopolysaccharides, fermentation, antimicrobial films, biodegradable, polyhydroxyalkanoates, polylactic acid
NCBI PubMed ID: 23919238Publication DOI: 10.3109/07388551.2013.798254Journal NLM ID: 8505177Publisher: CRC Press
Correspondence: Vijayendra SV
; Vijayendra SV
Institutions: Food Microbiology Department, CSIR-Central Food Technological Research Institute (A constituent laboratory of Council of Scientific and Industrial Research, New Delhi), Mysore, Karnataka, India
- Article ID: 5444
Hamidi M, Mirzaei R, Delattre C, Khanaki K, Pierre G, Gardarin C, Petit E, Karimitabar F, Faezi S "Characterization of a new exopolysaccharide produced by Halorubrum sp. TBZ112 and evaluation of its anti-proliferative effect on gastric cancer cells" -
3 Biotech 9(1) (2019) 1
In the present study, we aimed to extract, purify, analyze monosaccharide composition of exopolysaccharide (EPS) produced by Halorubrum sp. TBZ112 (KCTC 4203 and IBRC-M 10773) and also to evaluate its possible antiproliferative activity against human gastric cancer (MKN-45) cell line and its biocompatibility effect on normal cells using human dermal fibroblast (HDF) cell line. Average molecular weight and monosaccharide composition were determined by high-pressure size exclusion chromatography (HPSEC) with multi-angle laser light scattering (MALLS) and high-pressure anion exchange chromatography (HPAEC), respectively. Fourier transform infrared (FTIR) spectroscopy was used for the partial characterization of the EPS. The EPS effect on the cell proliferation and viability of MKN-45 and HDF cells was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and trypan blue dye exclusion, respectively. Strain TBZ112 excreted 480 mg.l-1 of the EPS under optimal growth conditions. The EPS had a molecular weight of 5.052 kDa and was a heteropolysaccharide containing ten moieties mainly composed of mannose (19.95%), glucosamine (15.55%), galacturonic acid (15.43%), arabinose (12.24%), and glucuronic acid (12.05%). No significant difference of the EPS treatments on the proliferation activity of MKN-45 and HDF cells were observed (P > 0.05). For the first time, the EPS from Halorubrum sp. TBZ112, an extremely halophilic archaeon related to Halorubrum genus, was isolated and chemically characterized. The EPS from Halorubrum sp. TBZ112 possesses a relatively low molecular weight and might be applied as a biocompatible compound. More investigations are needed to determine other biological activities of the EPS along with further details of its chemical structure.
exopolysaccharide (EPS), Antiproliferative effect, Halorubrum sp.TBZ112, Monosaccharide composition
NCBI PubMed ID: 30555767Publication DOI: 10.1007/s13205-018-1515-5Journal NLM ID: 101565857Publisher: Berlin: Springer
Correspondence: Korosh Khanaki
;
Institutions: Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran, Institut Pascal UMR CNRS 6602, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France, EA3900 BIOPI, Université de Picardie Jules Verne, Avenue des facultés, Le Bailly, 80025 Amiens cedex, France
Methods: HPAEC, FTIR, composition analysis, HPSEC-MALLS, extraction, statistical analysis
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