Found 36 structures.
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1. 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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2. 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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3. 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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4. 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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5. Compound ID: 755
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R-3HOLau-(1-2)-+
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a-Kdop-(2-4)-+ |
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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
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P-4)-+ |
Show graphically |
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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6. Compound ID: 781
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a-Kdop-(2-4)-+
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b-D-GlcpN-(1-7)-+ |
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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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7. Compound ID: 782
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a-Kdop-(2-4)-+
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b-D-GlcpN-(1-7)-+ | P-4)-+
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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 |
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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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8. 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 |
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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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9. 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 |
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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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10. Compound ID: 3119
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a-D-GlcpNAcA6NH2-(1-4)-+
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-4)-a-D-GalpNAc-(1-3)-a-D-GalpNAcA-(1-3)-a-D-QuipNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_130648,IEDB_137473,IEDB_1391961,IEDB_141584,IEDB_885822
The structure is contained in the following publication(s):
- Article ID: 1136
Reddy GP, Hayat U, Xu QW, Reddy KV, Wang YH, Chiu KW, Morris JG, Bush CA "Structure determination of the capsular polysaccharide from Vibrio vulnificus strain 6353" -
European Journal of Biochemistry 255(1) (1998) 279-288
Vibrio vulnificus is a pathogenic gram-negative bacterium, endemic to brackish waters, which is often isolated from sediments, from the water column or from shellfish. It is associated with wound infections and septicemia in humans and the virulence of V. vulnificus has been strongly associated with encapsulation. The capsular polysaccharide purified from a virulent strain of V. vulnificus 6353 did not show cross reactivity with antibodies to the capsular polysaccharide of a related pathogenic strain of V. vulnificus (MO6-24) the structure of which was recently reported. NMR spectroscopic analysis of the purified polysaccharide from strain 6353 showed that the polymer is composed of four sugar residues per repeating subunit including 2,6-dideoxy-2-N-acetylamino-α-D-glucose (QuiNAc), 2-deoxy-2-N-acetylamino-α-D-galactose (α-D-GalNAc), 2-deoxy-2-N-acetylamino-α-D-galcturonic acid (α-D-GalNAcA) and 2-N-acetylamino-α-D-glucuronamide (α-D-GlcNAcANH2). The 1H- and 13C NMR spectra were completely assigned by homonuclear and heteronuclear NMR spectroscopy. Sugar types and anomeric configurations were determined from proton homonuclear coupling constants and glycosidic linkages were determined from 1H-13C heteronuclear multiple bond correlation spectra. Sugar identities were confirmed by high performance anion-exchange chromatography and absolute configurations were determined by gas chromatography in combination with molecular modeling and NMR spectroscopy. The structure of the polysaccharide repeating unit is: [→4)-α-D-GalpNAc-(1→3)-α-D-GalpNAcA-(1→3)-α-D-QuipNAc-(1→]n α-D-GlcpNAcANH2(1→4)-→. While there are some common features shared among the structures of the capsular polysaccharides of pathogenic strains of V. vulnificus, there are distinct differences in the detailed structures.
NMR, structure, polysaccharide, bacteria, Vibrio, Vibrio vulnificus
NCBI PubMed ID: 9692929Publication DOI: 10.1046/j.1432-1327.1998.2550279.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: bush@umbc.edu
Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore MD, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore MD, USA
Methods: 13C NMR, 1H NMR, NMR-2D, HPLC
- 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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11. Compound ID: 6022
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D-Rhap2Me-(1-2)-+
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D-Manp2Me-(1-4)-D-GlcpNAcA-(1-4)-D-GlcpA-(1-4)-D-Glcp-(1-4)-D-GlcpA2Me-(1-4)-D-Manp-(1-3)-Ser |
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Structure type: oligomer
Compound class: O-glycoprotein
Contained glycoepitopes: IEDB_115136,IEDB_130701,IEDB_137485,IEDB_1394181,IEDB_140630,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_150900,IEDB_152206,IEDB_423153,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_72
The structure is contained in the following publication(s):
- Article ID: 2679
Reinhold BB, Hauer CR, Plummer TH, Reinhold VN "Detailed structural analysis of a novel, specific O-linked glycan from the prokaryote Flavobacterium meningosepticum" -
Journal of Biological Chemistry 270 (1995) 13197-13203
Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
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12. Compound ID: 6942
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a-Kdop-(2-4)-+
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b-D-GlcpN-(1-7)-+ |
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a-D-GalpN-(1-4)-+ | | P-4)-+
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a-D-Glcp-(1-6)-a-D-Glcp-(1-6)-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: LPS
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: 3166
Leone S, Molinaro A, Pessione E, Mazzoli R, Giunta C, Sturiale L, Garozzo D, Lanzetta R, Parrilli M "Structural elucidation of the core-lipid A backbone from the lipopolysaccharide of Acinetobacter radioresistens S13, an organic solvent tolerant Gram-negative bacterium" -
Carbohydrate Research 341(5) (2006) 582-590
The structure of the core oligosaccharide of the lipopolysaccharide from an organic solvent tolerant Gram-negative bacterium, Acinetobacter radioresistens S13, was investigated by chemical analysis, NMR spectroscopy and MALDI-TOF mass spectrometry. All the experiments were performed on the oligosaccharides obtained either by alkaline degradation or mild acid hydrolysis. The data showed the presence of two novel oligosaccharide molecules containing a trisaccharide of 3-deoxy-D-manno-octulopyranosonic acid in the inner core region and a glucose rich outer core whose structure is the following: [structure: see text] R=H in the main oligosaccharide and β-Glc in the minor product. The bacterium was grown on aromatic (phenol and benzoic acid) and nonaromatic carbon sources and the core oligosaccharide resulted to occur always with this novel structure.
Lipopolysaccharide, carbohydrate, NMR spectroscopy, Acinetobacter radioresistens
NCBI PubMed ID: 16445894Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: molinaro@unina.it
Institutions: Dipartimento di Chimica Organica e Biochimica, Universita degli Studi di Napoli Federico II, Via Cintia, 4, I-80126 Napoli, Italy
Methods: methylation, NMR, SDS-PAGE, mild acid hydrolysis, MALDI-TOF MS, composition analysis
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13. Compound ID: 6944
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b-D-GlcpN-(1-7)-+
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a-D-GalpN-(1-4)-+ |
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a-D-Glcp-(1-6)-a-D-Glcp-(1-6)-b-D-Glcp-(1-4)-b-D-Glcp-(1-3)-a-D-GlcpNAcA-(1-4)-a-Kdo |
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Structure type: oligomer
Compound class: LPS
Contained glycoepitopes: IEDB_130650,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: 3166
Leone S, Molinaro A, Pessione E, Mazzoli R, Giunta C, Sturiale L, Garozzo D, Lanzetta R, Parrilli M "Structural elucidation of the core-lipid A backbone from the lipopolysaccharide of Acinetobacter radioresistens S13, an organic solvent tolerant Gram-negative bacterium" -
Carbohydrate Research 341(5) (2006) 582-590
The structure of the core oligosaccharide of the lipopolysaccharide from an organic solvent tolerant Gram-negative bacterium, Acinetobacter radioresistens S13, was investigated by chemical analysis, NMR spectroscopy and MALDI-TOF mass spectrometry. All the experiments were performed on the oligosaccharides obtained either by alkaline degradation or mild acid hydrolysis. The data showed the presence of two novel oligosaccharide molecules containing a trisaccharide of 3-deoxy-D-manno-octulopyranosonic acid in the inner core region and a glucose rich outer core whose structure is the following: [structure: see text] R=H in the main oligosaccharide and β-Glc in the minor product. The bacterium was grown on aromatic (phenol and benzoic acid) and nonaromatic carbon sources and the core oligosaccharide resulted to occur always with this novel structure.
Lipopolysaccharide, carbohydrate, NMR spectroscopy, Acinetobacter radioresistens
NCBI PubMed ID: 16445894Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: molinaro@unina.it
Institutions: Dipartimento di Chimica Organica e Biochimica, Universita degli Studi di Napoli Federico II, Via Cintia, 4, I-80126 Napoli, Italy
Methods: methylation, NMR, SDS-PAGE, mild acid hydrolysis, MALDI-TOF MS, composition analysis
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14. Compound ID: 7329
Structure type: monomer
Trivial name: UDP-2-acetamido-2,3-dideoxy-α-D-glucuronic acid, UDP-N-acetyl-D-glucuronic acid, UDP-N-acetyl-α-D-glucosaminuronic acid, UDP-GlcNAcA, UDP-D-GlcNAcA, UDP-D-GlcNAc
Compound class: nucleoside diphosphate sugar
The structure is contained in the following publication(s):
- Article ID: 3320
Westman EL, McNally DJ, Rejzek M, Miller WL, Kannathasan VS, Preston A, Maskell DJ, Field RA, Brisson JR, Lam JS "Identification and biochemical characterization of two novel UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerases from respiratory pathogens" -
Biochemical Journal 405(1) (2007) 123-130
The heteropolymeric O-antigen of the lipopolysaccharide from Pseudomonas aeruginosa serogroup O5 as well as the band-A trisaccharide from Bordetella pertussis contain the di-N-acetylated mannosaminuronic acid derivative, β-D-ManNAc3NAcA (2,3-diacetamido-2,3-dideoxy-β-D-mannuronic acid). The biosynthesis of the precursor for this sugar is proposed to require five steps, through which UDP-α-D-GlcNAc (UDP-N-acetyl-α-D-glucosamine) is converted via four steps into UDP-α-D-GlcNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid), and this intermediate compound is then epimerized by WbpI (P. aeruginosa), or by its orthologue, WlbD (B. pertussis), to form UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid). UDP-α-D-GlcNAc3NAcA, the proposed substrate for WbpI and WlbD, was obtained through chemical synthesis. His6-WbpI and His6-WlbD were overexpressed and then purified by affinity chromatography using FPLC. Capillary electrophoresis was used to analyse reactions with each enzyme, and revealed that both enzymes used UDP-α-D-GlcNAc3NAcA as a substrate, and reacted optimally in sodium phosphate buffer (pH 6.0). Neither enzyme utilized UDP-α-D-GlcNAc, UDP-α-D-GlcNAcA (UDP-2-acetamido-2,3-dideoxy-α-D-glucuronic acid) or UDP-α-D-GlcNAc3NAc (UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucose) as substrates. His6-WbpI or His6-WlbD reactions with UDP-α-D-GlcNAc3NAcA produce a novel peak with an identical retention time, as shown by capillary electrophoresis. To unambiguously characterize the reaction product, enzyme-substrate reactions were allowed to proceed directly in the NMR tube and conversion of substrate into product was monitored over time through the acquisition of a proton spectrum at regular intervals. Data collected from one- and two-dimensional NMR experiments showed that His6-WbpI catalysed the 2-epimerization of UDP-α-D-GlcNAc3NAcA, converting it into UDP-α-D-ManNAc3NAcA. Collectively, these results provide evidence that WbpI and WlbD are UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerases
Lipopolysaccharide, O-antigen, Pseudomonas aeruginosa, 3-diacetamido-2, 2-epimerase, mannosaminuronic acid biosynthesis, sugar-nucleotide metabolism, UDP-2, 3-dideoxy-α-D-glucuronic acid
NCBI PubMed ID: 17346239Publication DOI: 10.1042/BJ20070017Journal NLM ID: 2984726RPublisher: London, UK : Published by Portland Press on behalf of the Biochemical Society
Correspondence: jlam@uoguelph.ca
Institutions: Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
Methods: 13C NMR, 1H NMR, 31P NMR, NMR-1D, genetic methods, biochemical methods, HPLC, capillary electrophoresis (CE), IR-MALDI-TOF MS
- Article ID: 3518
Miller WL, Matewish MJ, McNally DJ, Ishiyama N, Anderson EM, Brewer D, Brisson JR, Berghuis AM, Lam JS "Flagellin glycosylation in Pseudomonas aeruginosa PAK requires the O-antigen biosynthesis enzyme WbpO" -
Journal of Biological Chemistry 283(6) (2008) 3507-3518
Pseudomonas aeruginosa PAK (serotype O6) produces a single, polar, glycosylated flagellum composed of a-type flagellin. To determine whether or not flagellin glycosylation in this serotype requires O-antigen genes, flagellin was isolated from the wild type, three O-antigen deficient mutants wbpL, wbpO and wbpP, and a wbpO mutant complemented with a plasmid containing a wild-type copy of wbpO. Flagellin from the wbpO mutant was smaller (42 kDa) than that of the wild-type (45 kDa), or other mutants strains, and exhibited an altered isoelectric point (pI 4.8) when compared to PAK flagellin (pI 4.6). These differences were due to the truncation of the glycan moiety in the wbpO-flagellin. Thus, flagellin glycosylation in P. aeruginosa PAK apparently requires a functional WbpO but not WbpP. Since WbpP was previously proposed to catalyze a metabolic step in the biosynthesis of B-band O antigen that precedes the action of WbpO, these results prompted us to reevaluate the two-step pathway catalyzed by WbpO and WbpP. Results from WbpO-WbpP coupled-enzymatic assays showed that either WbpO or WbpP is capable of initiating the two-step pathway; however, the kinetic parameters favored the WbpO reaction to occur first, converting UDP-N-acetyl-D-glucosamine to UDP-N-acetyl-D-glucuronic acid prior to the conversion to UDP-N-acetyl-D-galacturonic acid by WbpP. This is the first report to show that a C4 epimerase could utilize UDP-N-acetyl-hexuronic acid as a substrate.
biosynthesis, O-antigen, Pseudomonas aeruginosa, glycosylation, Flagellin
NCBI PubMed ID: 18065759Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: jlam@uoguelph.ca
Institutions: Department of Microbiology, University of Guelph, Guelph, ON N1G 2W1
Methods: SDS-PAGE, MALDI-TOF MS, serological methods, genetic methods, biochemical methods, capillary electrophoresis (CE)
- Article ID: 3569
Westman EL, Preston A, Field RA, Lam JS "Biosynthesis of a rare di-N-acetylated sugar in the lipopolysaccharide of both Pseudomonas aeruginosa and Bordetella pertussis occurs via an identical scheme despite different gene clusters" -
Journal of Bacteriology 190(18) (2008) 6060-6069
Pseudomonas aeruginosa and Bordetella pertussis produce lipopolysaccharide (LPS) that contains 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid (D-ManNAc3NAcA). A five-enzyme biosynthetic pathway that requires WbpA, WbpB, WbpE, WbpD and WbpI has been proposed for the production of this sugar in P. aeruginosa, based on analysis of genes present in the B-band LPS biosynthesis cluster. In the analogous B. pertussis cluster, homologs of wbpB-I are present but a putative dehydrogenase was missing; therefore, the biosynthetic mechanism for UDP-D-ManNAc3NAcA was unclear. Non-polar knockout mutants of each P. aeruginosa gene were constructed. Complementation analysis of the mutants demonstrated that B-band LPS production was restored to P. aeruginosa knockout mutants when the relevant B. pertussis genes were supplied in trans. Thus, the genes that encode the putative oxidase, transaminase, N-acetyltransferase, and epimerase enzymes in B. pertussis are functional homologs of those in P. aeruginosa. Two candidate dehydrogenase genes were located by searching the B. pertussis genome; these have 80% identity to P. aeruginosa wbpO (serotype O6) and 32% identity to wbpA (serotype O5). These genes, wbpO1629 and wbpO3150, were shown to complement a wbpA knockout in P. aeruginosa. Capillary electrophoresis was used to characterize the enzymatic activities of purified WbpO1629 and WbpO3150, and mass spectrometry analysis confirmed that the two enzymes are dehydrogenases capable of converting UDP-D-GlcNAc, to a lesser extent UDP-D-GalNAc, and to a much lesser extent, UDP-D-Glc. Together, these results suggest that B. pertussis produces UDP-D-ManNAc3NAcA through the same pathway proposed in P. aeruginosa, despite differences in the genomic context of the genes involved
Lipopolysaccharide, biosynthesis, Pseudomonas aeruginosa, gene cluster, Bordetella pertussis, WbpA, WbpI
NCBI PubMed ID: 18621892Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Correspondence: jlam@uoguelph.ca
Institutions: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada, School of Clinical Veterinary Science, University of Bristol, Langford, Bristol, UK, Department of Biological Chemistry, John Innes Centre, Norwich, UK
Methods: MALDI-MS, Western blotting, genetic methods, biochemical methods, capillary electrophoresis (CE)
- Article ID: 3726
Larkin A, Imperiali B "Biosynthesis of UDP-GlcNAc(3NAc)A by WbpB, WbpE, and WbpD: enzymes in the Wbp pathway responsible for O-antigen assembly in Pseudomonas aeruginosa PAO1" -
Biochemistry 48(23) (2009) 5446-5455
The B-band O-antigen of the lipopolysaccharide found in the opportunistic pathogen Pseudomonas aeruginosa PAO1 (serotype O5) comprises a repeating trisaccharide unit that is critical for virulence and protection from host defense systems. One of the carbohydrates in this repeating unit, the rare diacetylated aminuronic acid derivative 2,3-diacetamido-2,3-dideoxy-β-D-mannuronic acid (ManNAc(3NAc)A), is thought to be produced by five enzymes (WbpA, WbpB, WbpE, WbpD, and WbpI) in a stepwise manner starting from UDP-GlcNAc. Although the genes responsible for the biosynthesis of this sugar are known, only two of the five encoded proteins (WbpA and WbpI) have been thoroughly investigated. In this report, we describe the cloning, overexpression, purification, and biochemical characterization of the three central enzymes in this pathway, WbpB, WbpE, and WbpD. Using a combination of capillary electrophoresis, RP-HPLC, and NMR spectroscopy, we show that WbpB and WbpE are a dehydrogenase/aminotransferase pair that converts UDP-GlcNAcA to UDP-GlcNAc(3NH(2))A in a coupled reaction via a unique NAD(+) recycling pathway. In addition, we confirm that WbpD catalyzes the acetylation of UDP-GlcNAc(3NH(2))A to give UDP-GlcNAc(3NAc)A. Notably, WbpA, WbpB, WbpE, WbpD, and WbpI can be combined in vitro to generate UDP-ManNAc(3NAc)A in a single reaction vessel, thereby providing supplies of this complex glycosyl donor for future studies of lipopolysaccharide assembly. This work completes the biochemical characterization of the enzymes in this pathway and provides novel targets for potential therapeutics to combat infections with drug resistant P. aeruginosa strains.
biosynthesis, lipopolysaccharides, O-antigen, B-band, Pseudomonas aeruginosa, Enzymes, acetylation, Uridine Diphosphate Sugars, WbpA, WbpI, WbpB, WbpE, WbpD
NCBI PubMed ID: 19348502Journal 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: 13C NMR, 1H NMR, NMR-2D, SDS-PAGE, ESI-MS, Western blotting, genetic methods, biochemical methods, capillary electrophoresis (CE), RP-HPLC
- Article ID: 3803
Westman EL, McNally DJ, Charchoglyan A, Brewer D, Field RA, Lam JS "Characterization of WbpB, WbpE, and WbpD, and reconstitution of a pathway for the biosynthesis of UDP-2,3-diacetamido-2,3-dideoxy-D-mannuronic acid in Pseudomonas aeruginosa" -
Journal of Biological Chemistry 284(18) (2009) 11854-11862
The lipopolysaccharide of Pseudomonas aeruginosa PAO1 contains an unusual sugar, 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid (D-ManNAc3NAcA). wbpB, wbpE, and wbpD are thought to encode oxidase, transaminase, and N-acetyltransferase enzymes. To characterize their functions, recombinant proteins were overexpressed and purified from heterologous hosts. Activities of His6-WbpB and His6-WbpE were detected only when both proteins were combined in the same reaction. Using a direct MALDI-TOF mass spectrometry approach, we identified ions that corresponded to the predicted products of WbpB (UDP-3-keto-D-GlcNAcA) and WbpE (UDP-D-GlcNAc3NA) in the coupled enzyme-substrate reaction. Additionally, in reactions involving WbpB, WbpE and WbpD, an ion consistent with the expected product of WbpD (UDP-D-GlcNAc3NAcA) was identified. Preparative quantities of UDP-D-GlcNAc3NA and UDP-D-GlcNAc3NAcA were enzymatically synthesized. These compounds were purified by HPLC and their structures were elucidated by NMR spectroscopy. This is the first report of the functional characterization of these proteins, and the enzymatic synthesis of UDP-D-GlcNAc3NA and UDP-D-GlcNAc3NAcA.
biosynthesis, Pseudomonas aeruginosa, MALDI-TOF mass spectrometry, enzymatic synthesis, Recombinant Proteins
NCBI PubMed ID: 19282284Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: jlam@uoguelph.ca
Institutions: Microbiology, University of Guelph, Guelph, ON N1G 2W1
Methods: 13C NMR, 1H NMR, SDS-PAGE, 31P NMR, MALDI-TOF MS, NMR-1D, genetic methods, biochemical methods, capillary electrophoresis (CE)
- Article ID: 3853
Gu X, Glushka J, Lee SG, Bar-Peled M "Biosynthesis of a new UDP-sugar, UDP-2-acetamido-2-deoxyxylose, in the human pathogen Bacillus cereus subspecies cytotoxis NVH 391-98" -
Journal of Biological Chemistry 285(32) (2010) 24825-24833
We have identified an operon and characterized the functions of two genes from the severe food-poisoning bacterium, Bacillus cereus subsp. cytotoxis NVH 391-98, that are involved in the synthesis of a unique UDP-sugar, UDP-2-acetamido-2-deoxyxylose (UDP-N-acetyl-xylosamine, UDP-XylNAc). UGlcNAcDH encodes a UDP-N-acetyl-glucosamine 6-dehydrogenase, converting UDP-N-acetylglucosamine (UDP-GlcNAc) to UDP-N-acetyl-glucosaminuronic acid (UDP-GlcNAcA). The second gene in the operon, UXNAcS, encodes a distinct decarboxylase not previously described in the literature, which catalyzes the formation of UDP-XylNAc from UDP-GlcNAcA in the presence of exogenous NAD(+). UXNAcS is specific and cannot utilize UDP-glucuronic acid and UDP-galacturonic acid as substrates. UXNAcS is active as a dimer with catalytic efficiency of 7 mM(-1) s(-1). The activity of UXNAcS is completely abolished by NADH but unaffected by UDP-xylose. A real-time NMR-based assay showed unambiguously the dual enzymatic conversions of UDP-GlcNAc to UDP-GlcNAcA and subsequently to UDP-XylNAc. From the analyses of all publicly available sequenced genomes, it appears that UXNAcS is restricted to pathogenic Bacillus species, including Bacillus anthracis and Bacillus thuringiensis. The identification of UXNAcS provides insight into the formation of UDP-XylNAc. Understanding the metabolic pathways involved in the utilization of this amino-sugar may allow the development of drugs to combat and eradicate the disease.
biosynthesis, gene, Gene Expression Regulation, Uridine Diphosphate Sugars, Bacillus cereus, Uridine diphosphate Xylose
NCBI PubMed ID: 20529859Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: peled@ccrc.uga.edu
Institutions: Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, USA
Methods: 1H NMR, NMR-2D, MALDI-TOF MS, NMR-1D, genetic methods, biochemical methods, HPLC
- Article ID: 3872
King JD, Vinogradov E, Tran V, Lam JS "Biosynthesis of uronamide sugars in Pseudomonas aeruginosa O6 and Escherichia coli O121 O antigens" -
Environmental Microbiology 12(6) (2010) 1531-1544
Summary The major component of the outer leaflet of the outer membrane of Gram-negative bacteria is lipopolysaccharide (LPS). The outermost domain of LPS is a polysaccharide called O antigen. Pseudomonas aeruginosa establishes biofilms on wet surfaces in a wide range of habitats and mutations in O-antigen biosynthesis genes affect bacterial adhesion and the structure of these biofilms. The P. aeruginosa O6 O antigen contains a 2-acetamido-2-deoxy-d-galacturonamide (d-GalNAcAN) residue. O-antigen biosynthesis in this serotype requires the wbpS gene, which encodes a protein with conserved domains of the glutamine-dependent amidotransferase family. Replacement of conserved amino acids in the N-terminal glutaminase conserved domain of WbpS inhibited O-antigen biosynthesis under restricted-ammonia conditions, but not in rich media; suggesting that this domain functions to provide ammonia for O-antigen biosynthesis under restricted-ammonia conditions, by hydrolysis of glutamine. Escherichia coli O121 also produces a d-GalNAcAN-containing O antigen, and possesses a homologue of wbpS called wbqG. An E. coli O121 wbqG mutant was cross-complemented by providing wbpS in trans, and vice versa, showing that these two genes are functionally interchangeable. The E. coli O121 wbqG mutant O antigen contains 2-acetamido-2-deoxy-d-galacturonate (d-GalNAcA), instead of d-GalNAcAN, demonstrating that wbqG is specifically required for biosynthesis of the carboxamide in this sugar.
biosynthesis, O-antigen, Pseudomonas aeruginosa, Biofilm
NCBI PubMed ID: 20192967Publication DOI: 10.1111/j.1462-2920.2010.02182.xJournal NLM ID: 100883692Publisher: Blackwell Publishing
Correspondence: jlam@uoguelph.ca
Institutions: Department of Molecular and Cellular Biology, University of Guelph, Ontario N1G 2W1, Canada
Methods: 13C NMR, 1H NMR, NMR-2D, X-ray, SDS-PAGE, DNA techniques, Western blotting, genetic methods, microscopy, CE-MS
- Article ID: 3885
Larkin A, Olivier NB, Imperiali B "Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-antigen Assembly" -
Biochemistry 49(33) (2010) 7227-7237
In recent years, the opportunistic pathogen Pseudomonas aeruginosa has emerged as a major source of hospital-acquired infections. Effective treatment has proven increasingly difficult due to the spread of multidrug resistant strains and thus requires a deeper understanding of the biochemical mechanisms of pathogenicity. The central carbohydrate of the P. aeruginosa PAO1 (O5) B-band O-antigen, ManNAc(3NAc)A, has been shown to be critical for virulence and is produced in a stepwise manner by five enzymes in the Wbp pathway (WbpA, WbpB, WbpE, WbpD and WbpI). Herein, we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5'-phosphate (PLP) and product UDP-GlcNAc(3NH2)A as the external aldimine at 1.9 A resolution. We also report the structures of WbpE in complex with PMP alone as well as the PLP internal aldimine, and show that the dimeric structure of WbpE observed in the crystal structure is confirmed by analytical ultracentrifugation. Analysis of these structures reveals that the active site of the enzyme is composed of residues from both subunits. In particular, we show that a key residue (Arg229), which has previously been implicated in direct interactions with the carboxylate moiety of α-ketoglutarate, is also uniquely positioned to bestow specificity for the 6' carboxyl group of GlcNAc(3NH2)A through a salt bridge. This finding is intriguing, because while an analogous basic residue is present in WbpE homologs that do not process C6'-carboxyl-modified saccharides, recent structural studies reveal that this side chain is retracted to accommodate a neutral C-6' carbon. This work represents the first structural analysis of a nucleotide sugar aminotransferase with a bound product modified at the C2', C3', and C6' positions and provides insight into a novel target for treatment of P. aeruginosa infection.
O-antigen, Pseudomonas aeruginosa, crystal structure, WbpA, WbpI, aminotransferase WbpE
NCBI PubMed ID: 20604544Journal 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: SDS-PAGE, MALDI-MS, Western blotting, genetic methods, biochemical methods, crystallization
- Article ID: 3954
Thoden JB, Holden HM "Structural and functional studies of WlbA: A dehydrogenase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid" -
Biochemistry 49(36) (2010) 7939-7948
2,3-Diacetamido-2,3-dideoxy-d-mannuronic acid (ManNAc3NAcA) is an unusual dideoxy sugar first identified nearly 30 years ago in the lipopolysaccharide of Pseudomonas aeruginosa O:3a,d. It has since been observed in other organisms, including Bordetella pertussis, the causative agent of whooping cough. Five enzymes are required for the biosynthesis of UDP-ManNAc3NAcA starting from UDP-N-acetyl-d-glucosamine. Here we describe a structural study of WlbA, the NAD-dependent dehydrogenase that catalyzes the second step in the pathway, namely, the oxidation of the C-3' hydroxyl group on the UDP-linked sugar to a keto moiety and the reduction of NAD(+) to NADH. This enzyme has been shown to use α-ketoglutarate as an oxidant to regenerate the oxidized dinucleotide. For this investigation, three different crystal structures were determined: the enzyme with bound NAD(H), the enzyme in a complex with NAD(H) and α-ketoglutarate, and the enzyme in a complex with NAD(H) and its substrate (UDP-N-acetyl-d-glucosaminuronic acid). The tetrameric enzyme assumes an unusual quaternary structure with the dinucleotides positioned quite closely to one another. Both α-ketoglutarate and the UDP-linked sugar bind in the WlbA active site with their carbon atoms (C-2 and C-3', respectively) abutting the re face of the cofactor. They are positioned approximately 3 A from the nicotinamide C-4. The UDP-linked sugar substrate adopts a highly unusual curved conformation when bound in the WlbA active site cleft. Lys 101 and His 185 most likely play key roles in catalysis.
biosynthesis, Pseudomonas, Bordetella, Bordetella pertussis, crystal structure, Enzymes, dehydrogenase, WlbA
NCBI PubMed ID: 20690587Journal NLM ID: 0370623Publisher: American Chemical Society
Correspondence: Hazel_Holden@biochem.wisc.edu
Institutions: Department of Biochemistry, University of Wisconsin, Madison, WI, USA
Methods: X-ray, genetic methods, biochemical methods, crystallization
- Article ID: 4417
Wang Q, Perepelov AV, Beutin L, Senchenkova SN, Xu Y, Shashkov AS, Ding P, Knirel YA, Feng L "Structural and genetic characterization of the Escherichia coli O180 O antigen and identification of a UDP-GlcNAc 6-dehydrogenase" -
Glycobiology 22(10) (2012) 1321-1331
The O antigen is an essential component of the lipopolysaccharides on the surface of Gram-negative bacteria and its variation provides a major basis for serotyping schemes. The Escherichia coli O-antigen form O180 was first designated in 2004, and O180 strains were found to contain virulence factors and cause diarrhea. Different O-antigen forms are almost entirely due to genetic variations in the O-antigen gene clusters. In this study, the chemical structure and gene cluster of E. coli O180 O antigen were investigated. A tetrasaccharide repeating unit with the following structure: -4)-b-D-ManpNAc3NAcA-(1-2)-a-L-Rhap(I)-(1-3)-b-L-Rhap(II)-(1-4)-a-D-GlcpNAc-(1- was identified in the E. coli O180 O antigen, including the residue D-ManpNAc3NAcA (2,3-diacetamido-2,3-dideoxy-D-mannopyranuronic acid) that had not been hitherto identified in E. coli. Genes in the O-antigen gene cluster were assigned functions based on their similarities with those from available databases, and five genes involved in the synthesis of UDP-D-ManpNAc3NAcA (the nucleotide-activated form of D-ManpNAc3NAcA) were identified. The gnaA gene, encoding the enzyme involved in the initial step of the UDP-D-ManpNAc3NAcA biosynthetic pathway, was cloned and the enzyme product was expressed, purified and assayed for its activity. GnaA was characterized using capillary electrophoresis and electrospray ionization mass spectrometry and identified as a UDP-GlcNAc 6-dehydrogenase. The kinetic and physicochemical parameters of GnaA also were determined.
biosynthesis, O-antigen, Escherichia coli O180, UDP-D-ManNAc3NAcA
NCBI PubMed ID: 22730467Publication DOI: 10.1093/glycob/cws098Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: fenglu63@nankai.edu.cn
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, People's Republic of China
Methods: 13C NMR, 1H NMR, NMR-2D, DNA sequencing, chemical analysis, ESI-MS, GLC, genetic methods, enzymatic analysis, RP-HPLC, CE
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15. Compound ID: 9235
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a-Kdo-(2-4)-+
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b-D-GlcpN-(1-7)-+ |
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a-D-GalpN-(1-4)-+ | |
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a-D-Glcp-(1-2)-b-D-Galp-(1-4)-b-D-Glcp-(1-4)-b-D-Glcp-(1-3)-a-D-GlcpNAcA-(1-4)-a-Kdo-(2-5)-a-Kdo |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_136044,IEDB_137472,IEDB_137473,IEDB_141794,IEDB_141807,IEDB_142487,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_153217,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_6,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 3946
Silipo A, Molinaro A "The Diversity of the Core Oligosaccharide in Lipopolysaccharides" -
Book: Endotoxins: Structure, Function and Recognition (series: Subcellular Biochemistry, Part 1) (2010) Vol. 53, Chapter 4, 69-99
Bacterial lipopolysaccharides (LPSs) are the major component of the outer membrane of Gram-negative bacteria. They have a structural role since they contribute to the cellular rigidity by increasing the strength of cell wall and mediating contacts with the external environment that can induce structural changes to allow life in different conditions. Furthermore, the low permeability of the outer membrane acts as a barrier to protect bacteria from host-derived antimicrobial compounds. Lipopolysaccharides are amphiphilic macromolecules generally comprising three defined regions distinguished by their genetics, structures and function: the lipid A, the core oligosaccharide and a polysaccharide portion, the O-chain. In some Gram-negative bacteria LPS can terminate with the core portion to form rough type LPS (R-LPS, LOS). The core oligosaccharide is an often branched and phosphorylated heterooligosaccharide with less than fifteen sugars, more conserved in the inner region, proximal to the lipid A, and often carrying non-stoichiometric substitutions leading to variation and micro-heterogeneity. The core oligosaccharide contributes to the bacterial viability and stability of the outer membrane, can assure the serological specificity and possesses antigenic properties.
core oligosaccharide, endotoxin, Gram-negative bacteria, innate immunity, glyco-conjugates
NCBI PubMed ID: 20593263Publication DOI: 10.1007/978-90-481-9078-2_4Publisher: Springer Science+Business Media B.V.
Correspondence: molinaro@unina.it
Editors: Wang X, Quinn PJ
Institutions: Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Santangelo, Via Cintia 4, Napoli, I-80126, Italy
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