The Experts below are selected from a list of 5373 Experts worldwide ranked by ideXlab platform
Gabrielle Potockiveronese - One of the best experts on this subject based on the ideXlab platform.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target β 1 2 mannosidic linkages in candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle PotockiveroneseAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. Beta-mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although a family of Glycoside phosphorylases, GH130, have also been shown to target Beta-1,2 and Beta-1,4 mannosidic linkages. In these phosphorylases bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues are indeed Beta-mannosidases that hydrolyse Beta-1,2-mannosidic linkages through an inverting mechanism. As the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerisation of yeast α-mannans, it is likely that the two enzymes target the Beta-1,2- mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the -1 and +1 subsites showed a pair of glutamates, Glu227 and Glu268 hydrogen bond to O1 of Beta-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and Beta- 1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for Beta-1,2-mannosidic linkages.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target β 1 2 mannosidic linkages in candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle Potockiveronese, Elisabeth C LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. β-Mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although recently, a family of Glycoside phosphorylases, GH130, have also been shown to target β-1,2- and β-1,4-mannosidic linkages. In these phosphorylases, bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues, are indeed β-mannosidases that hydrolyze β-1,2-mannosidic linkages through an inverting mechanism. Because the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerization of yeast α-mannans, it is likely that the two enzymes target the β-1,2-mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the −1 and +1 subsites showed that a pair of glutamates, Glu227 and Glu268, hydrogen bond to O1 of α-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and β-1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for β-1,2-mannosidic linkages.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target 1 2 mannosidic linkages
2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle Potockiveronese, Elisabeth C LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. -Mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although recently, a family of Glycoside phosphorylases, GH130, have also been shown to target -1,2- and -1,4-mannosidic linkages. In these phosphorylases, bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues, are indeed -mannosidases that hydrolyze -1,2-mannosidic linkages through an inverting mechanism. Because the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerization of yeast -mannans, it is likely that the two enzymes target the -1,2mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the 1 and 1 subsites showed that a pair of glutamates, Glu 227 and Glu 268 , hydrogen bond to O1 of -mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and -1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys 199 in BT3780, as a key specificity determinant for -1,2-mannosidic linkages.
Christina M Payne - One of the best experts on this subject based on the ideXlab platform.
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machine learning reveals sequence function relationships in family 7 Glycoside Hydrolases
Journal of Biological Chemistry, 2021Co-Authors: Gregg T Beckham, Jerry Stahlberg, Mats Sandgren, Japheth E Gado, Brent Harrison, Christina M PayneAbstract:Family 7 Glycoside Hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These enzymes are often bimodular, including a catalytic domain and carbohydrate-binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobioHydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able to discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our machine learning results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.
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machine learning reveals sequence function relationships in family 7 Glycoside Hydrolases
bioRxiv, 2020Co-Authors: Gregg T Beckham, Jerry Stahlberg, Mats Sandgren, Japheth E Gado, Brent Harrison, Christina M PayneAbstract:Abstract Family 7 Glycoside Hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, comprised of a catalytic domain attached to a carbohydrate binding module (CBM) via a flexible linker, and exhibit a long active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobioHydrolases (CBH) and endoglucanases (EG). Despite the critical biological and industrial importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, using the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy. The lengths of the A4, B2, B3, and B4 loops were strongly correlated with functional subtype across the GH7 family. Position-specific classification rules were derived such that specific amino acids at 42 different sequence positions predicted the functional subtype with accuracies greater than 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. We propose these positions play vital roles in the functional variation of GH7 cellulases. Taken together, our results complement numerous experimental findings and present functional relationships that can be applied when prospecting GH7 cellulases from nature, for sequence annotation, and to understand or manipulate function.
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towards a molecular level theory of carbohydrate processivity in Glycoside Hydrolases
Current Opinion in Biotechnology, 2014Co-Authors: Gregg T Beckham, Michael E. Himmel, Michael F Crowley, Morten Sorlie, Jerry Stahlberg, Brandon C Knott, Mats Sandgren, Christina M PayneAbstract:Polysaccharide depolymerization in nature is primarily accomplished by processive Glycoside Hydrolases (GHs), which abstract single carbohydrate chains from polymer crystals and cleave glycosidic linkages without dissociating after each catalytic event. Understanding the molecular-level features and structural aspects of processivity is of importance due to the prevalence of processive GHs in biomass-degrading enzyme cocktails. Here, we describe recent advances towards the development of a molecular-level theory of processivity for cellulolytic and chitinolytic enzymes, including the development of novel methods for measuring rates of key steps in processive action and insights gained from structural and computational studies. Overall, we present a framework for developing structure-function relationships in processive GHs and outline additional progress towards developing a fundamental understanding of these industrially important enzymes.
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hallmarks of processivity in Glycoside Hydrolases from crystallographic and computational studies of the serratia marcescens chitinases
Journal of Biological Chemistry, 2012Co-Authors: Christina M Payne, Svein J Horn, Morten Sorlie, Vincent G H Eijsink, Jamil Baban, Paul Hoff Backe, Andrew S Arvai, Bjorn Dalhus, Magnar Bjoras, Gregg T BeckhamAbstract:Abstract Degradation of recalcitrant polysaccharides in nature is typically accomplished by mixtures of processive and non-processive Glycoside Hydrolases (GHs), which exhibit synergistic activity wherein non-processive enzymes provide new sites for productive attachment of processive enzymes. GH processivity is typically attributed to active site geometry, but previous work has demonstrated that processivity can be tuned by point mutations or removal of single loops. To gain additional insights into the differences between processive and non-processive enzymes that give rise to their synergistic activities, this study reports the crystal structure of the catalytic domain of the GH Family 18 non-processive endochitinase, ChiC, from Serratia marcescens. This completes the structural characterization of the co-evolved chitinolytic enzymes from this bacterium and enables structural analysis of their complementary functions. The ChiC catalytic module reveals a shallow substrate binding cleft that lacks aromatic residues vital for processivity, a calcium binding site not previously seen in GH18 chitinases, and, importantly, a displaced catalytic acid (Glu141) suggesting flexibility in the catalytic center. Molecular dynamics simulations of two processive chitinases (ChiA and ChiB), the ChiC catalytic module and an endochitinase from Lactococcus lactis show that the non-processive enzymes have more flexible catalytic machineries and that their bound ligands are more solvated and flexible. These three features, which relate to the more dynamic on-off ligand-binding processes associated with non-processive action, correlate to experimentally measured differences in processivity of the S. marcescens chitinases. These newly defined hallmarks thus appear to be key dynamical metrics in determining processivity in GH enzymes complementing structural insights.
Simon Ladeveze - One of the best experts on this subject based on the ideXlab platform.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target β 1 2 mannosidic linkages in candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle PotockiveroneseAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. Beta-mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although a family of Glycoside phosphorylases, GH130, have also been shown to target Beta-1,2 and Beta-1,4 mannosidic linkages. In these phosphorylases bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues are indeed Beta-mannosidases that hydrolyse Beta-1,2-mannosidic linkages through an inverting mechanism. As the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerisation of yeast α-mannans, it is likely that the two enzymes target the Beta-1,2- mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the -1 and +1 subsites showed a pair of glutamates, Glu227 and Glu268 hydrogen bond to O1 of Beta-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and Beta- 1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for Beta-1,2-mannosidic linkages.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target β 1 2 mannosidic linkages in candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle Potockiveronese, Elisabeth C LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. β-Mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although recently, a family of Glycoside phosphorylases, GH130, have also been shown to target β-1,2- and β-1,4-mannosidic linkages. In these phosphorylases, bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues, are indeed β-mannosidases that hydrolyze β-1,2-mannosidic linkages through an inverting mechanism. Because the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerization of yeast α-mannans, it is likely that the two enzymes target the β-1,2-mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the −1 and +1 subsites showed that a pair of glutamates, Glu227 and Glu268, hydrogen bond to O1 of α-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and β-1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for β-1,2-mannosidic linkages.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target 1 2 mannosidic linkages
2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle Potockiveronese, Elisabeth C LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. -Mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although recently, a family of Glycoside phosphorylases, GH130, have also been shown to target -1,2- and -1,4-mannosidic linkages. In these phosphorylases, bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues, are indeed -mannosidases that hydrolyze -1,2-mannosidic linkages through an inverting mechanism. Because the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerization of yeast -mannans, it is likely that the two enzymes target the -1,2mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the 1 and 1 subsites showed that a pair of glutamates, Glu 227 and Glu 268 , hydrogen bond to O1 of -mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and -1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys 199 in BT3780, as a key specificity determinant for -1,2-mannosidic linkages.
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The GH130 family of mannoside phosphorylases contains Glycoside Hydrolases that target beta-1,2 mannosidic linkages in Candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Arnaud Basle, Simon Ladeveze, Alison Day, Harry Gilbert, Gideon Davies, Gabrielle Veronese, Elisabeth LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. Bêta-mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although a family of Glycoside phosphorylases, GH130, have also been shown to target Bêta-1,2 and Bêta-1,4 mannosidic linkages. In these phosphorylases bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues are indeed Bêta-mannosidases that hydrolyse Bêta-1,2-mannosidic linkages through an inverting mechanism. As the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerisation of yeast α-mannans, it is likely that the two enzymes target the Bêta-1,2- mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the -1 and +1 subsites showed a pair of glutamates, Glu227 and Glu268 hydrogen bond to O1 of Bêta-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and Bêta- 1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for Bêta-1,2-mannosidic linkages.
Fiona Cuskin - One of the best experts on this subject based on the ideXlab platform.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target β 1 2 mannosidic linkages in candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle PotockiveroneseAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. Beta-mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although a family of Glycoside phosphorylases, GH130, have also been shown to target Beta-1,2 and Beta-1,4 mannosidic linkages. In these phosphorylases bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues are indeed Beta-mannosidases that hydrolyse Beta-1,2-mannosidic linkages through an inverting mechanism. As the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerisation of yeast α-mannans, it is likely that the two enzymes target the Beta-1,2- mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the -1 and +1 subsites showed a pair of glutamates, Glu227 and Glu268 hydrogen bond to O1 of Beta-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and Beta- 1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for Beta-1,2-mannosidic linkages.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target β 1 2 mannosidic linkages in candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle Potockiveronese, Elisabeth C LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. β-Mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although recently, a family of Glycoside phosphorylases, GH130, have also been shown to target β-1,2- and β-1,4-mannosidic linkages. In these phosphorylases, bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues, are indeed β-mannosidases that hydrolyze β-1,2-mannosidic linkages through an inverting mechanism. Because the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerization of yeast α-mannans, it is likely that the two enzymes target the β-1,2-mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the −1 and +1 subsites showed that a pair of glutamates, Glu227 and Glu268, hydrogen bond to O1 of α-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and β-1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for β-1,2-mannosidic linkages.
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the gh130 family of mannoside phosphorylases contains Glycoside Hydrolases that target 1 2 mannosidic linkages
2015Co-Authors: Fiona Cuskin, Gideon J. Davies, Harry J Gilbert, Arnaud Basle, Simon Ladeveze, Alison M Day, Gabrielle Potockiveronese, Elisabeth C LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. -Mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although recently, a family of Glycoside phosphorylases, GH130, have also been shown to target -1,2- and -1,4-mannosidic linkages. In these phosphorylases, bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues, are indeed -mannosidases that hydrolyze -1,2-mannosidic linkages through an inverting mechanism. Because the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerization of yeast -mannans, it is likely that the two enzymes target the -1,2mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the 1 and 1 subsites showed that a pair of glutamates, Glu 227 and Glu 268 , hydrogen bond to O1 of -mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and -1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys 199 in BT3780, as a key specificity determinant for -1,2-mannosidic linkages.
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The GH130 family of mannoside phosphorylases contains Glycoside Hydrolases that target beta-1,2 mannosidic linkages in Candida mannan
Journal of Biological Chemistry, 2015Co-Authors: Fiona Cuskin, Arnaud Basle, Simon Ladeveze, Alison Day, Harry Gilbert, Gideon Davies, Gabrielle Veronese, Elisabeth LoweAbstract:The depolymerization of complex glycans is an important biological process that is of considerable interest to environmentally relevant industries. Bêta-mannose is a major component of plant structural polysaccharides and eukaryotic N-glycans. These linkages are primarily cleaved by Glycoside Hydrolases, although a family of Glycoside phosphorylases, GH130, have also been shown to target Bêta-1,2 and Bêta-1,4 mannosidic linkages. In these phosphorylases bond cleavage was mediated by a single displacement reaction in which phosphate functions as the catalytic nucleophile. A cohort of GH130 enzymes, however, lack the conserved basic residues that bind the phosphate nucleophile, and it was proposed that these enzymes function as Glycoside Hydrolases. Here we show that two Bacteroides enzymes, BT3780 and BACOVA_03624, which lack the phosphate binding residues are indeed Bêta-mannosidases that hydrolyse Bêta-1,2-mannosidic linkages through an inverting mechanism. As the genes encoding these enzymes are located in genetic loci that orchestrate the depolymerisation of yeast α-mannans, it is likely that the two enzymes target the Bêta-1,2- mannose residues that cap the glycan produced by Candida albicans. The crystal structure of BT3780 in complex with mannose bound in the -1 and +1 subsites showed a pair of glutamates, Glu227 and Glu268 hydrogen bond to O1 of Bêta-mannose, and either of these residues may function as the catalytic base. The candidate catalytic acid and the other residues that interact with the active site mannose are conserved in both GH130 mannoside phosphorylases and Bêta- 1,2-mannosidases. Functional phylogeny identified a conserved lysine, Lys199 in BT3780, as a key specificity determinant for Bêta-1,2-mannosidic linkages.
Japheth E Gado - One of the best experts on this subject based on the ideXlab platform.
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machine learning reveals sequence function relationships in family 7 Glycoside Hydrolases
Journal of Biological Chemistry, 2021Co-Authors: Gregg T Beckham, Jerry Stahlberg, Mats Sandgren, Japheth E Gado, Brent Harrison, Christina M PayneAbstract:Family 7 Glycoside Hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These enzymes are often bimodular, including a catalytic domain and carbohydrate-binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobioHydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able to discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our machine learning results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.
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machine learning reveals sequence function relationships in family 7 Glycoside Hydrolases
bioRxiv, 2020Co-Authors: Gregg T Beckham, Jerry Stahlberg, Mats Sandgren, Japheth E Gado, Brent Harrison, Christina M PayneAbstract:Abstract Family 7 Glycoside Hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These important enzymes are often bimodular, comprised of a catalytic domain attached to a carbohydrate binding module (CBM) via a flexible linker, and exhibit a long active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobioHydrolases (CBH) and endoglucanases (EG). Despite the critical biological and industrial importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, using the number of residues in the active-site loops as features, were able discriminate GH7 CBHs and EGs with up to 99% accuracy. The lengths of the A4, B2, B3, and B4 loops were strongly correlated with functional subtype across the GH7 family. Position-specific classification rules were derived such that specific amino acids at 42 different sequence positions predicted the functional subtype with accuracies greater than 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. We propose these positions play vital roles in the functional variation of GH7 cellulases. Taken together, our results complement numerous experimental findings and present functional relationships that can be applied when prospecting GH7 cellulases from nature, for sequence annotation, and to understand or manipulate function.