Found 5 structures.
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1. Compound ID: 8018
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b-D-Galp1S-(1-4)-b-D-Sugp2Ac-(1-1)-PhNO2-(?--/p-nitrophenyl/
Sug = 4-thiogalactosamine = SMILES N{2}[C@H]1{1}[C@H](O)O[C@H](CO)[C@H]({4}S)[C@@H]1O |
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Structure type: oligomer
Aglycon: p-nitrophenyl
Trivial name: 4-nitrophenyl (b-d-galactopyranosyl)-(1-4)-S-2-acetamido-2,4-deoxy-4-thio-b-d-glucopyranoside
The structure is contained in the following publication(s):
- Article ID: 3525
Namdjou DJ, Chen HM, Vinogradov E, Brochu D, Withers SG, Wakarchuk WW "A b-1,4-galactosyltransferase from Helicobacter pylori is an efficient and versatile biocatalyst displaying a novel activity for thioglycoside synthesis" -
Chembiochem: a European Journal of Chemical Biology 9(10) (2008) 1632-1640
Helicobacter pylori is a highly persistent and common pathogen in humans. It is the causative agent of chronic gastritis and its further stages. HP0826 is the β-1,4-galactosyltransferase involved in the biosynthesis of the LPS O-chain backbone of H. pylori. Though it was first cloned nearly a decade ago, there are surprisingly limited data about the characteristics of HP0826, especially given its prominent role in H. pylori pathogenicity. We here demonstrate that HP0826 is a highly efficient and promiscuous biocatalyst. We have exploited two novel enzymatic activities for the quantitative synthesis of the thiodisaccharide Gal-β-S-1,4-GlcNAc-pNP as well as Gal-β-1,4-Man-pNP. We further show that Neisseria meningitidis β-1,4-galactosyltransferases LgtB can be used as an equally efficient catalyst in the latter reaction. Thiodisaccharides have been extensively used in structural biology but can also have therapeutic uses. The Gal-β-1,4-Man linkage is found in the Leishmania species LPG backbone disaccharide repeats and cap, which have been associated with vector binding in Leishmaniasis
specificity, glycosyltransferases, acceptor, kinetics, saccharides, biocatalysis
NCBI PubMed ID: 18491328Publication DOI: 10.1002/cbic.200700775Journal NLM ID: 100937360Publisher: Weinheim, Germany: Wiley Interscience
Correspondence: warren.wakarchuk@nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A0R6, Canada
Methods: 13C NMR, 1H NMR, NMR-2D, ESI-MS, genetic methods, biochemical methods, capillary electrophoresis (CE)
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2. Compound ID: 8019
Structure type: oligomer
Trivial name: 4-nitrophenyl (b-d-galactopyranosyl)-(1-4)-b-d-mannopyranoside
Contained glycoepitopes: IEDB_134623,IEDB_136044,IEDB_137472,IEDB_137485,IEDB_141794,IEDB_144983,IEDB_152206,IEDB_190606,IEDB_983930,SB_165,SB_166,SB_187,SB_195,SB_44,SB_7,SB_72,SB_88
The structure is contained in the following publication(s):
- Article ID: 3525
Namdjou DJ, Chen HM, Vinogradov E, Brochu D, Withers SG, Wakarchuk WW "A b-1,4-galactosyltransferase from Helicobacter pylori is an efficient and versatile biocatalyst displaying a novel activity for thioglycoside synthesis" -
Chembiochem: a European Journal of Chemical Biology 9(10) (2008) 1632-1640
Helicobacter pylori is a highly persistent and common pathogen in humans. It is the causative agent of chronic gastritis and its further stages. HP0826 is the β-1,4-galactosyltransferase involved in the biosynthesis of the LPS O-chain backbone of H. pylori. Though it was first cloned nearly a decade ago, there are surprisingly limited data about the characteristics of HP0826, especially given its prominent role in H. pylori pathogenicity. We here demonstrate that HP0826 is a highly efficient and promiscuous biocatalyst. We have exploited two novel enzymatic activities for the quantitative synthesis of the thiodisaccharide Gal-β-S-1,4-GlcNAc-pNP as well as Gal-β-1,4-Man-pNP. We further show that Neisseria meningitidis β-1,4-galactosyltransferases LgtB can be used as an equally efficient catalyst in the latter reaction. Thiodisaccharides have been extensively used in structural biology but can also have therapeutic uses. The Gal-β-1,4-Man linkage is found in the Leishmania species LPG backbone disaccharide repeats and cap, which have been associated with vector binding in Leishmaniasis
specificity, glycosyltransferases, acceptor, kinetics, saccharides, biocatalysis
NCBI PubMed ID: 18491328Publication DOI: 10.1002/cbic.200700775Journal NLM ID: 100937360Publisher: Weinheim, Germany: Wiley Interscience
Correspondence: warren.wakarchuk@nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A0R6, Canada
Methods: 13C NMR, 1H NMR, NMR-2D, ESI-MS, genetic methods, biochemical methods, capillary electrophoresis (CE)
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3. Compound ID: 20700
Structure type: oligomer
Trivial name: pNP-laminaribiose
Contained glycoepitopes: IEDB_142488,IEDB_146664,IEDB_153543,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 8252
Nakatani Y, Larsen DS, Cutfield SM, Cutfield JF "Major change in regiospecificity for the exo-1,3-β-glucanase from Candida albicans following its conversion to a glycosynthase" -
Biochemistry 53(20) (2014) 3318-3326
The exo-1,3-β-glucanase (Exg) from Candida albicans is involved in cell wall β-D-glucan metabolism and morphogenesis through its hydrolase and transglycosidase activities. Previous work has shown that both these activities strongly favor β-1,3-linkages. The E292S Exg variant displayed modest glycosynthase activity using α-D-glucopyranosyl fluoride (α-GlcF) as the donor and pNP-β-D-glucopyranoside (pNPGlc) as the acceptor but surprisingly showed a marked preference for synthesizing β-1,6-linked over β-1,3- and β-1,4-linked disaccharide products. With pNPXyl as the acceptor, the preference became β-1,4 over β-1,3. The crystal structure of the glycosynthase bound to both of its substrates, α-GlcF and pNPGlc, is the first such ternary complex structure to be determined. The results revealed that the donor bound in the -1 subsite, as expected, while the acceptor was oriented in the +1 subsite to facilitate β-1,6-linkage, thereby supporting the results from solution studies. A second crystal structure containing the major product of glycosynthesis, pNP-gentiobiose, showed that the -1 subsite allows another docking position for the terminal sugar; i.e., one position is set up for catalysis, whereas the other is an intermediate stage prior to the displacement of water from the active site by the incoming sugar hydroxyls. The +1 subsite, an aromatic "clamp", permits several different sugar positions and orientations, including a 180°flip that explains the observed variable regiospecificity. The p-nitrophenyl group on the acceptor most likely influences the unexpectedly observed β-1,6-specificity through its interaction with F229. These results demonstrate that tailoring the specificity of a particular glycosynthase depends not only on the chemical structure of the acceptor but also on understanding the structural basis of the promiscuity of the native enzyme.
regiospecificity, glucanase
NCBI PubMed ID: 24804868Publication DOI: 10.1021/bi500239mJournal NLM ID: 0370623Publisher: American Chemical Society
Correspondence: Cutfield JF
Institutions: Biochemistry Department, University of Otago, Dunedin, New Zealand, Chemistry Department, University of Otago, Dunedin, New Zealand
Methods: 13C NMR, 1H NMR, NMR-2D, TLC, MS, enzymatic synthesis
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4. Compound ID: 20701
Structure type: oligomer
Contained glycoepitopes: IEDB_141806,IEDB_142488,IEDB_146664,IEDB_241101,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 8252
Nakatani Y, Larsen DS, Cutfield SM, Cutfield JF "Major change in regiospecificity for the exo-1,3-β-glucanase from Candida albicans following its conversion to a glycosynthase" -
Biochemistry 53(20) (2014) 3318-3326
The exo-1,3-β-glucanase (Exg) from Candida albicans is involved in cell wall β-D-glucan metabolism and morphogenesis through its hydrolase and transglycosidase activities. Previous work has shown that both these activities strongly favor β-1,3-linkages. The E292S Exg variant displayed modest glycosynthase activity using α-D-glucopyranosyl fluoride (α-GlcF) as the donor and pNP-β-D-glucopyranoside (pNPGlc) as the acceptor but surprisingly showed a marked preference for synthesizing β-1,6-linked over β-1,3- and β-1,4-linked disaccharide products. With pNPXyl as the acceptor, the preference became β-1,4 over β-1,3. The crystal structure of the glycosynthase bound to both of its substrates, α-GlcF and pNPGlc, is the first such ternary complex structure to be determined. The results revealed that the donor bound in the -1 subsite, as expected, while the acceptor was oriented in the +1 subsite to facilitate β-1,6-linkage, thereby supporting the results from solution studies. A second crystal structure containing the major product of glycosynthesis, pNP-gentiobiose, showed that the -1 subsite allows another docking position for the terminal sugar; i.e., one position is set up for catalysis, whereas the other is an intermediate stage prior to the displacement of water from the active site by the incoming sugar hydroxyls. The +1 subsite, an aromatic "clamp", permits several different sugar positions and orientations, including a 180°flip that explains the observed variable regiospecificity. The p-nitrophenyl group on the acceptor most likely influences the unexpectedly observed β-1,6-specificity through its interaction with F229. These results demonstrate that tailoring the specificity of a particular glycosynthase depends not only on the chemical structure of the acceptor but also on understanding the structural basis of the promiscuity of the native enzyme.
regiospecificity, glucanase
NCBI PubMed ID: 24804868Publication DOI: 10.1021/bi500239mJournal NLM ID: 0370623Publisher: American Chemical Society
Correspondence: Cutfield JF
Institutions: Biochemistry Department, University of Otago, Dunedin, New Zealand, Chemistry Department, University of Otago, Dunedin, New Zealand
Methods: 13C NMR, 1H NMR, NMR-2D, TLC, MS, enzymatic synthesis
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5. Compound ID: 21589
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b-D-GlcpNAc-(1-2)-a-D-Manp-(1-3)-+
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a-D-Manp-(1-6)-+ |
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a-D-Manp-(1-3)-a-D-Manp-(1-6)-b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-1)-PhNO2
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b-D-GlcpNAc-(1-4)-+ |
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Structure type: oligomer
Compound class: mannan
Contained glycoepitopes: IEDB_123886,IEDB_130701,IEDB_135813,IEDB_137340,IEDB_137485,IEDB_140116,IEDB_141793,IEDB_141807,IEDB_141828,IEDB_144983,IEDB_151079,IEDB_151531,IEDB_152206,IEDB_153212,IEDB_153220,IEDB_164174,IEDB_187201,IEDB_429156,IEDB_548907,IEDB_857734,IEDB_983930,SB_197,SB_198,SB_33,SB_44,SB_67,SB_72,SB_73,SB_74,SB_77,SB_85
The structure is contained in the following publication(s):
- Article ID: 8715
Yamanoi T, Oda Y, Katsuraya K, Inazu T, Yamamoto K "Complete NMR assignment of a bisecting hybrid-type oligosaccharide transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase" -
Carbohydrate Research 427 (2016) 60-65
This study describes the complete nuclear magnetic resonance (NMR) spectral assignment of a bisecting hybrid-type oligosaccharide 1, transferred by Mucor hiemalis endo-β-N-acetylglucosaminidase (Endo-M). Through 1H- and 13C-NMR, DQF-COSY, HSQC, HMBC, TOCSY, and NOESY experiments, we determine the structure of the glycoside linkage formed by the Endo-M transglycosylation, i.e., the connection between GlcNAc and GlcNAc in oligosaccharide 1.
bisecting hybrid-type oligosaccharide, endo-M, endo-β-N-acetylglucosaminidase, NMR spectral assignment, transglycosylation product
NCBI PubMed ID: 27131291Publication DOI: 10.1016/j.carres.2016.03.013Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: Yamanoi T
Institutions: Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan, Technology Joint Management Office, Tokai University, Hiratsuka, Kanagawa, Japan, Department of Human Ecology, Wayo Women’s University, Chiba, Japan, Department of Applied Chemistry, School of Engineering, Institute of Glycoscience, Tokai University, Hiratsuka, Kanagawa, Japan, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
Methods: 13C NMR, 1H NMR, TOCSY, DQF-COSY, HMBC, COSY, NOESY, HSQC
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