| anno_start anno_end anno_text entity_type sentence section | |
| 32 60 family 5 glycoside hydrolase protein_type Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism TITLE | |
| 0 20 Glycoside hydrolases protein_type Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. ABSTRACT | |
| 22 25 GHs protein_type Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. ABSTRACT | |
| 20 31 full-length protein_state Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 32 41 structure evidence Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 47 56 cellulase protein_type Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 62 84 Bacillus licheniformis species Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 86 93 BlCel5B protein Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 112 127 GH5 subfamily 4 protein_type Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 166 183 ancillary modules structure_element Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 185 199 Ig-like module structure_element Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 204 209 CBM46 structure_element Here, we report the full-length structure of a cellulase from Bacillus licheniformis (BlCel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. ABSTRACT | |
| 6 27 X-ray crystallography experimental_method Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 29 57 small-angle X-ray scattering experimental_method Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 62 92 molecular dynamics simulations experimental_method Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 125 130 CBM46 structure_element Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 158 174 catalytic domain structure_element Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 176 178 CD structure_element Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 195 211 fully functional protein_state Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 212 223 active site site Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. ABSTRACT | |
| 4 18 Ig-like module structure_element The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. ABSTRACT | |
| 68 73 CBM46 structure_element The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. ABSTRACT | |
| 86 88 CD structure_element The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. ABSTRACT | |
| 112 127 binding subsite site The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. ABSTRACT | |
| 43 45 GH protein_type This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme. ABSTRACT | |
| 88 93 CBM46 structure_element This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme. ABSTRACT | |
| 114 137 catalytically competent protein_state This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme. ABSTRACT | |
| 0 5 Plant taxonomy_domain Plant biomass-the most abundant source of carbohydrates on Earth-is primarily composed of cellulose microfibrils surrounded by a hydrated heteropolymeric matrix of hemicellulose and lignin. INTRO | |
| 42 55 carbohydrates chemical Plant biomass-the most abundant source of carbohydrates on Earth-is primarily composed of cellulose microfibrils surrounded by a hydrated heteropolymeric matrix of hemicellulose and lignin. INTRO | |
| 90 99 cellulose chemical Plant biomass-the most abundant source of carbohydrates on Earth-is primarily composed of cellulose microfibrils surrounded by a hydrated heteropolymeric matrix of hemicellulose and lignin. INTRO | |
| 164 177 hemicellulose chemical Plant biomass-the most abundant source of carbohydrates on Earth-is primarily composed of cellulose microfibrils surrounded by a hydrated heteropolymeric matrix of hemicellulose and lignin. INTRO | |
| 182 188 lignin chemical Plant biomass-the most abundant source of carbohydrates on Earth-is primarily composed of cellulose microfibrils surrounded by a hydrated heteropolymeric matrix of hemicellulose and lignin. INTRO | |
| 0 5 Plant taxonomy_domain Plant biomass may be subjected to thermo-chemical pretreatments and enzymatic reactions to produce soluble fermentable sugars. INTRO | |
| 119 125 sugars chemical Plant biomass may be subjected to thermo-chemical pretreatments and enzymatic reactions to produce soluble fermentable sugars. INTRO | |
| 49 58 cellulose chemical The canonical model of hydrolytic degradation of cellulose requires at least three classes of enzymes. INTRO | |
| 0 18 Cellobiohydrolases protein_type Cellobiohydrolases (CBHs) processively cleave the glycosidic bonds at the reducing and non-reducing ends of cellulose chains in crystalline regions to produce cellobiose. INTRO | |
| 20 24 CBHs protein_type Cellobiohydrolases (CBHs) processively cleave the glycosidic bonds at the reducing and non-reducing ends of cellulose chains in crystalline regions to produce cellobiose. INTRO | |
| 108 117 cellulose chemical Cellobiohydrolases (CBHs) processively cleave the glycosidic bonds at the reducing and non-reducing ends of cellulose chains in crystalline regions to produce cellobiose. INTRO | |
| 159 169 cellobiose chemical Cellobiohydrolases (CBHs) processively cleave the glycosidic bonds at the reducing and non-reducing ends of cellulose chains in crystalline regions to produce cellobiose. INTRO | |
| 0 14 Endoglucanases protein_type Endoglucanases (EGs) introduce random cuts in the amorphous regions of cellulose and create new chain extremities for CBH attack; thus, these enzymes act synergistically. INTRO | |
| 16 19 EGs protein_type Endoglucanases (EGs) introduce random cuts in the amorphous regions of cellulose and create new chain extremities for CBH attack; thus, these enzymes act synergistically. INTRO | |
| 71 80 cellulose chemical Endoglucanases (EGs) introduce random cuts in the amorphous regions of cellulose and create new chain extremities for CBH attack; thus, these enzymes act synergistically. INTRO | |
| 118 121 CBH protein_type Endoglucanases (EGs) introduce random cuts in the amorphous regions of cellulose and create new chain extremities for CBH attack; thus, these enzymes act synergistically. INTRO | |
| 13 23 cellobiose chemical The released cellobiose molecules are then enzymatically converted into glucose by β-glucosidases. INTRO | |
| 72 79 glucose chemical The released cellobiose molecules are then enzymatically converted into glucose by β-glucosidases. INTRO | |
| 83 97 β-glucosidases protein_type The released cellobiose molecules are then enzymatically converted into glucose by β-glucosidases. INTRO | |
| 30 50 glycoside hydrolases protein_type The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 52 55 GHs protein_type The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 82 98 catalytic domain structure_element The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 100 102 CD structure_element The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 146 163 ancillary modules structure_element The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 165 168 AMs structure_element The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 202 217 less structured protein_state The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 218 225 linkers structure_element The molecular architecture of glycoside hydrolases (GHs) frequently consists of a catalytic domain (CD), where hydrolysis occurs, and one or more ancillary modules (AMs), which are usually connected by less structured linkers. INTRO | |
| 24 27 AMs structure_element The most common type of AMs are carbohydrate-binding modules (CBMs), which are able to recognize and bind specific carbohydrate chains. INTRO | |
| 32 60 carbohydrate-binding modules structure_element The most common type of AMs are carbohydrate-binding modules (CBMs), which are able to recognize and bind specific carbohydrate chains. INTRO | |
| 62 66 CBMs structure_element The most common type of AMs are carbohydrate-binding modules (CBMs), which are able to recognize and bind specific carbohydrate chains. INTRO | |
| 115 127 carbohydrate chemical The most common type of AMs are carbohydrate-binding modules (CBMs), which are able to recognize and bind specific carbohydrate chains. INTRO | |
| 59 63 CBMs structure_element Generally distinct and independent structural domains, the CBMs facilitate carbohydrate hydrolysis by increasing the local concentration of enzymes at the surface of insoluble substrates, thereby targeting the CD component to its cognate ligands. INTRO | |
| 75 87 carbohydrate chemical Generally distinct and independent structural domains, the CBMs facilitate carbohydrate hydrolysis by increasing the local concentration of enzymes at the surface of insoluble substrates, thereby targeting the CD component to its cognate ligands. INTRO | |
| 210 212 CD structure_element Generally distinct and independent structural domains, the CBMs facilitate carbohydrate hydrolysis by increasing the local concentration of enzymes at the surface of insoluble substrates, thereby targeting the CD component to its cognate ligands. INTRO | |
| 0 4 CBMs structure_element CBMs might also disrupt the crystalline structure of cellulose microfibrils, although the underlying mechanism remains poorly understood. INTRO | |
| 53 62 cellulose chemical CBMs might also disrupt the crystalline structure of cellulose microfibrils, although the underlying mechanism remains poorly understood. INTRO | |
| 6 10 CBMs structure_element Thus, CBMs enhance the accessibility of CDs to carbohydrate chains to improve enzymatic activity, making them important candidates for the development of effective biomass-degrading enzymes in industrial settings. INTRO | |
| 40 43 CDs structure_element Thus, CBMs enhance the accessibility of CDs to carbohydrate chains to improve enzymatic activity, making them important candidates for the development of effective biomass-degrading enzymes in industrial settings. INTRO | |
| 47 59 carbohydrate chemical Thus, CBMs enhance the accessibility of CDs to carbohydrate chains to improve enzymatic activity, making them important candidates for the development of effective biomass-degrading enzymes in industrial settings. INTRO | |
| 31 37 active protein_state Although there are examples of active GHs that lack AMs, the majority of the enzymes depend on AMs for activity. INTRO | |
| 38 41 GHs protein_type Although there are examples of active GHs that lack AMs, the majority of the enzymes depend on AMs for activity. INTRO | |
| 47 51 lack protein_state Although there are examples of active GHs that lack AMs, the majority of the enzymes depend on AMs for activity. INTRO | |
| 52 55 AMs structure_element Although there are examples of active GHs that lack AMs, the majority of the enzymes depend on AMs for activity. INTRO | |
| 95 98 AMs structure_element Although there are examples of active GHs that lack AMs, the majority of the enzymes depend on AMs for activity. INTRO | |
| 18 22 CBMs structure_element In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 63 65 CD structure_element In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 66 88 substrate-binding site site In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 105 132 carbohydrate-active enzymes protein_type In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 142 159 endo/exocellulase protein_type In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 160 162 E4 protein In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 168 186 Thermobifida fusca species In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 188 199 chitinase B protein In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 205 224 Serratia marcescens species In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 228 246 starch phosphatase protein_type In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 252 272 Arabidopsis thaliana species In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 279 294 GH5 subfamily 4 protein_type In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 296 301 GH5_4 protein_type In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 303 316 endoglucanase protein_type In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 322 341 Bacillus halodurans species In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 343 350 BhCel5B protein In several cases, CBMs were shown to extend and complement the CD substrate-binding site in multimodular carbohydrate-active enzymes, such as endo/exocellulase E4 from Thermobifida fusca, chitinase B from Serratia marcescens, a starch phosphatase from Arabidopsis thaliana and a GH5 subfamily 4 (GH5_4) endoglucanase from Bacillus halodurans (BhCel5B). INTRO | |
| 79 82 GH9 protein_type A pioneer work of Sakon et al. revealed that rigid structural extension of the GH9 CD by a type C CBM3 imprints a processive mode of action to this endoglucanase. INTRO | |
| 83 85 CD structure_element A pioneer work of Sakon et al. revealed that rigid structural extension of the GH9 CD by a type C CBM3 imprints a processive mode of action to this endoglucanase. INTRO | |
| 91 102 type C CBM3 structure_element A pioneer work of Sakon et al. revealed that rigid structural extension of the GH9 CD by a type C CBM3 imprints a processive mode of action to this endoglucanase. INTRO | |
| 148 161 endoglucanase protein_type A pioneer work of Sakon et al. revealed that rigid structural extension of the GH9 CD by a type C CBM3 imprints a processive mode of action to this endoglucanase. INTRO | |
| 33 36 CBM structure_element Further publications showed that CBM-based structural extensions of the active site are important for substrate engagement and recognition. INTRO | |
| 72 83 active site site Further publications showed that CBM-based structural extensions of the active site are important for substrate engagement and recognition. INTRO | |
| 39 54 X-ray structure evidence Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 62 73 tri-modular structure_element Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 74 79 GH5_4 protein_type Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 80 93 endoglucanase protein_type Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 99 118 Bacillus halodurans species Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 145 152 BlCel5B protein Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 164 169 CBM46 structure_element Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 187 198 active site site Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 215 217 CD structure_element Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 225 256 immunoglobulin (Ig)-like module structure_element Recently, Venditto et al. reported the X-ray structure of the tri-modular GH5_4 endoglucanase from Bacillus halodurans (31% sequence identity to BlCel5B), with the CBM46 extension of the active site appended to the CD via an immunoglobulin (Ig)-like module. INTRO | |
| 0 10 Removal of experimental_method Removal of the CBM46 caused a ~60-fold reduction of the activity of the enzyme against β-glucans, but showed little or no effect against xyloglucan hydrolysis. INTRO | |
| 15 20 CBM46 structure_element Removal of the CBM46 caused a ~60-fold reduction of the activity of the enzyme against β-glucans, but showed little or no effect against xyloglucan hydrolysis. INTRO | |
| 87 96 β-glucans chemical Removal of the CBM46 caused a ~60-fold reduction of the activity of the enzyme against β-glucans, but showed little or no effect against xyloglucan hydrolysis. INTRO | |
| 137 147 xyloglucan chemical Removal of the CBM46 caused a ~60-fold reduction of the activity of the enzyme against β-glucans, but showed little or no effect against xyloglucan hydrolysis. INTRO | |
| 14 19 CBM46 structure_element Moreover, the CBM46 mediated a significant increase in the BhCel5B activity in plant cell wall settings. INTRO | |
| 59 66 BhCel5B protein Moreover, the CBM46 mediated a significant increase in the BhCel5B activity in plant cell wall settings. INTRO | |
| 79 84 plant taxonomy_domain Moreover, the CBM46 mediated a significant increase in the BhCel5B activity in plant cell wall settings. INTRO | |
| 0 8 Modeling experimental_method Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 12 23 cellotriose chemical Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 31 48 negative subsites site Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 56 67 active site site Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 71 78 BhCel5B protein Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 96 119 structural conservation protein_state Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 127 129 -1 residue_number Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 206 211 CBM46 structure_element Modeling of cellotriose in the negative subsites of the active site of BhCel5B demonstrated the structural conservation of the -1 position, but provided little information about direct interactions between CBM46 and the substrate. INTRO | |
| 41 49 β-glucan chemical It was speculated that β-1,3 kink of the β-glucan might allow the ligand to reach for the CBM46, whereas pure β-1,4 linkages in the backbone of xyloglucan chains would restrict binding to the CD, thus explaining the lack of influence of the CBM46 on the enzymatic activity of BhCel5B against xyloglucans in solution. INTRO | |
| 90 95 CBM46 structure_element It was speculated that β-1,3 kink of the β-glucan might allow the ligand to reach for the CBM46, whereas pure β-1,4 linkages in the backbone of xyloglucan chains would restrict binding to the CD, thus explaining the lack of influence of the CBM46 on the enzymatic activity of BhCel5B against xyloglucans in solution. INTRO | |
| 144 154 xyloglucan chemical It was speculated that β-1,3 kink of the β-glucan might allow the ligand to reach for the CBM46, whereas pure β-1,4 linkages in the backbone of xyloglucan chains would restrict binding to the CD, thus explaining the lack of influence of the CBM46 on the enzymatic activity of BhCel5B against xyloglucans in solution. INTRO | |
| 192 194 CD structure_element It was speculated that β-1,3 kink of the β-glucan might allow the ligand to reach for the CBM46, whereas pure β-1,4 linkages in the backbone of xyloglucan chains would restrict binding to the CD, thus explaining the lack of influence of the CBM46 on the enzymatic activity of BhCel5B against xyloglucans in solution. INTRO | |
| 241 246 CBM46 structure_element It was speculated that β-1,3 kink of the β-glucan might allow the ligand to reach for the CBM46, whereas pure β-1,4 linkages in the backbone of xyloglucan chains would restrict binding to the CD, thus explaining the lack of influence of the CBM46 on the enzymatic activity of BhCel5B against xyloglucans in solution. INTRO | |
| 276 283 BhCel5B protein It was speculated that β-1,3 kink of the β-glucan might allow the ligand to reach for the CBM46, whereas pure β-1,4 linkages in the backbone of xyloglucan chains would restrict binding to the CD, thus explaining the lack of influence of the CBM46 on the enzymatic activity of BhCel5B against xyloglucans in solution. INTRO | |
| 292 303 xyloglucans chemical It was speculated that β-1,3 kink of the β-glucan might allow the ligand to reach for the CBM46, whereas pure β-1,4 linkages in the backbone of xyloglucan chains would restrict binding to the CD, thus explaining the lack of influence of the CBM46 on the enzymatic activity of BhCel5B against xyloglucans in solution. INTRO | |
| 28 33 CBM46 structure_element It was also argued that the CBM46 could potentialize the activity by driving BhCel5B towards xyloglucan-rich regions in the context of the plant cell walls, but no large-scale conformational adjustments of the AMs have been shown to occur or suggested to take part in the enzymatic activity. INTRO | |
| 77 84 BhCel5B protein It was also argued that the CBM46 could potentialize the activity by driving BhCel5B towards xyloglucan-rich regions in the context of the plant cell walls, but no large-scale conformational adjustments of the AMs have been shown to occur or suggested to take part in the enzymatic activity. INTRO | |
| 93 116 xyloglucan-rich regions structure_element It was also argued that the CBM46 could potentialize the activity by driving BhCel5B towards xyloglucan-rich regions in the context of the plant cell walls, but no large-scale conformational adjustments of the AMs have been shown to occur or suggested to take part in the enzymatic activity. INTRO | |
| 139 144 plant taxonomy_domain It was also argued that the CBM46 could potentialize the activity by driving BhCel5B towards xyloglucan-rich regions in the context of the plant cell walls, but no large-scale conformational adjustments of the AMs have been shown to occur or suggested to take part in the enzymatic activity. INTRO | |
| 210 213 AMs structure_element It was also argued that the CBM46 could potentialize the activity by driving BhCel5B towards xyloglucan-rich regions in the context of the plant cell walls, but no large-scale conformational adjustments of the AMs have been shown to occur or suggested to take part in the enzymatic activity. INTRO | |
| 145 153 extended protein_state Although initially introduced as contradictory theories, these two limiting cases can be unified considering the flux description concept or the extended conformational selection model. INTRO | |
| 77 104 carbohydrate-active enzymes protein_type While local ligand-induced conformational adjustments have been reported for carbohydrate-active enzymes, cognate ligands recognition and hydrolysis mediated by a large-scale conformational mobility of distinct domains in multidomain settings is uncommon for endoglucanases. INTRO | |
| 259 273 endoglucanases protein_type While local ligand-induced conformational adjustments have been reported for carbohydrate-active enzymes, cognate ligands recognition and hydrolysis mediated by a large-scale conformational mobility of distinct domains in multidomain settings is uncommon for endoglucanases. INTRO | |
| 20 37 crystal structure evidence Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 43 54 full-length protein_state Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 55 60 GH5_4 protein_type Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 73 95 Bacillus licheniformis species Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 97 104 BlCel5B protein Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 124 127 AMs structure_element Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 129 143 Ig-like module structure_element Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 148 153 CBM46 structure_element Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 171 173 CD structure_element Here, we report the crystal structure of a full-length GH5_4 enzyme from Bacillus licheniformis (BlCel5B) that exhibits two AMs (Ig-like module and CBM46) appended to the CD. INTRO | |
| 3 45 structurally and functionally characterize experimental_method We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 80 103 protein crystallography experimental_method We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 105 133 small-angle X-ray scattering experimental_method We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 135 139 SAXS experimental_method We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 142 181 molecular dynamics computer simulations experimental_method We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 186 211 site-directed mutagenesis experimental_method We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 231 234 AMs structure_element We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 313 320 BlCel5B protein We structurally and functionally characterize the enzyme using a combination of protein crystallography, small-angle X-ray scattering (SAXS), molecular dynamics computer simulations and site-directed mutagenesis, and show that the AMs and their conformational mobility are essential for the enzymatic activity of BlCel5B. INTRO | |
| 70 75 CBM46 structure_element We find that the large-scale conformational adjustments of the distal CBM46 mediated by the Ig-like hinge domain are crucial in active-site assembly for optimal substrate binding and hydrolysis. INTRO | |
| 92 112 Ig-like hinge domain structure_element We find that the large-scale conformational adjustments of the distal CBM46 mediated by the Ig-like hinge domain are crucial in active-site assembly for optimal substrate binding and hydrolysis. INTRO | |
| 128 139 active-site site We find that the large-scale conformational adjustments of the distal CBM46 mediated by the Ig-like hinge domain are crucial in active-site assembly for optimal substrate binding and hydrolysis. INTRO | |
| 20 27 BlCel5B protein We propose that the BlCel5B conformational selection/induced-fit mechanism of hydrolysis represents a novel paradigm that applies to several GH5_4 members and, possibly, to a number of other multidomain GHs. INTRO | |
| 141 146 GH5_4 protein_type We propose that the BlCel5B conformational selection/induced-fit mechanism of hydrolysis represents a novel paradigm that applies to several GH5_4 members and, possibly, to a number of other multidomain GHs. INTRO | |
| 203 206 GHs protein_type We propose that the BlCel5B conformational selection/induced-fit mechanism of hydrolysis represents a novel paradigm that applies to several GH5_4 members and, possibly, to a number of other multidomain GHs. INTRO | |
| 0 7 BlCel5B protein BlCel5B Crystal Structure RESULTS | |
| 8 25 Crystal Structure evidence BlCel5B Crystal Structure RESULTS | |
| 0 7 BlCel5B protein BlCel5B crystals in the substrate-free form and complexed with cellopentaose (C5) were obtained and diffracted to 1.7 Å and 1.75 Å resolutions, respectively (Supplementary Table 1). RESULTS | |
| 8 16 crystals evidence BlCel5B crystals in the substrate-free form and complexed with cellopentaose (C5) were obtained and diffracted to 1.7 Å and 1.75 Å resolutions, respectively (Supplementary Table 1). RESULTS | |
| 24 38 substrate-free protein_state BlCel5B crystals in the substrate-free form and complexed with cellopentaose (C5) were obtained and diffracted to 1.7 Å and 1.75 Å resolutions, respectively (Supplementary Table 1). RESULTS | |
| 48 62 complexed with protein_state BlCel5B crystals in the substrate-free form and complexed with cellopentaose (C5) were obtained and diffracted to 1.7 Å and 1.75 Å resolutions, respectively (Supplementary Table 1). RESULTS | |
| 63 76 cellopentaose chemical BlCel5B crystals in the substrate-free form and complexed with cellopentaose (C5) were obtained and diffracted to 1.7 Å and 1.75 Å resolutions, respectively (Supplementary Table 1). RESULTS | |
| 78 80 C5 chemical BlCel5B crystals in the substrate-free form and complexed with cellopentaose (C5) were obtained and diffracted to 1.7 Å and 1.75 Å resolutions, respectively (Supplementary Table 1). RESULTS | |
| 4 18 substrate-free protein_state The substrate-free and complexed structures exhibited no substantial conformational differences (with the exception of the substrate). RESULTS | |
| 23 32 complexed protein_state The substrate-free and complexed structures exhibited no substantial conformational differences (with the exception of the substrate). RESULTS | |
| 33 43 structures evidence The substrate-free and complexed structures exhibited no substantial conformational differences (with the exception of the substrate). RESULTS | |
| 35 40 loops structure_element Because of minor variations in the loops located distal to the substrate-binding site, a root mean squared deviation (rmsd) of 0.33 Å between the complexed and substrate-free structures was observed. RESULTS | |
| 63 85 substrate-binding site site Because of minor variations in the loops located distal to the substrate-binding site, a root mean squared deviation (rmsd) of 0.33 Å between the complexed and substrate-free structures was observed. RESULTS | |
| 89 116 root mean squared deviation evidence Because of minor variations in the loops located distal to the substrate-binding site, a root mean squared deviation (rmsd) of 0.33 Å between the complexed and substrate-free structures was observed. RESULTS | |
| 118 122 rmsd evidence Because of minor variations in the loops located distal to the substrate-binding site, a root mean squared deviation (rmsd) of 0.33 Å between the complexed and substrate-free structures was observed. RESULTS | |
| 146 155 complexed protein_state Because of minor variations in the loops located distal to the substrate-binding site, a root mean squared deviation (rmsd) of 0.33 Å between the complexed and substrate-free structures was observed. RESULTS | |
| 160 174 substrate-free protein_state Because of minor variations in the loops located distal to the substrate-binding site, a root mean squared deviation (rmsd) of 0.33 Å between the complexed and substrate-free structures was observed. RESULTS | |
| 175 185 structures evidence Because of minor variations in the loops located distal to the substrate-binding site, a root mean squared deviation (rmsd) of 0.33 Å between the complexed and substrate-free structures was observed. RESULTS | |
| 116 133 first 17 residues residue_range A single protein chain occupies the asymmetric unit, and most of the residues were built, with the exception of the first 17 residues and those in the loop between L398 and P405 due to weak electron density. RESULTS | |
| 151 155 loop structure_element A single protein chain occupies the asymmetric unit, and most of the residues were built, with the exception of the first 17 residues and those in the loop between L398 and P405 due to weak electron density. RESULTS | |
| 164 168 L398 residue_name_number A single protein chain occupies the asymmetric unit, and most of the residues were built, with the exception of the first 17 residues and those in the loop between L398 and P405 due to weak electron density. RESULTS | |
| 173 177 P405 residue_name_number A single protein chain occupies the asymmetric unit, and most of the residues were built, with the exception of the first 17 residues and those in the loop between L398 and P405 due to weak electron density. RESULTS | |
| 190 206 electron density evidence A single protein chain occupies the asymmetric unit, and most of the residues were built, with the exception of the first 17 residues and those in the loop between L398 and P405 due to weak electron density. RESULTS | |
| 4 11 BlCel5B protein The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 12 21 structure evidence The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 70 72 CD structure_element The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 83 92 18 to 330 residue_range The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 98 112 Ig-like module structure_element The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 123 133 335 to 428 residue_range The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 141 154 family 46 CBM structure_element The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 165 175 432 to 533 residue_range The BlCel5B structure comprises three distinct domains: an N-terminal CD (residues 18 to 330), an Ig-like module (residues 335 to 428) and a family 46 CBM (residues 432 to 533) (Fig. 1A,B). RESULTS | |
| 34 37 GH5 protein_type Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 50 52 CD structure_element Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 56 63 BlCel5B protein Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 78 93 TIM barrel fold structure_element Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 111 120 β-strands structure_element Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 137 146 α helices structure_element Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 174 179 loops structure_element Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 196 205 α helices structure_element Similarly to other members of the GH5 family, the CD of BlCel5B has a typical TIM barrel fold with eight inner β-strands and eight outer α helices that are interconnected by loops and three short α helices. RESULTS | |
| 11 18 linkers structure_element Very short linkers, D429-D430-P431 and V331-P332-N333-A334, connect the CBM46 to the Ig-like module and the Ig-like module to the CD, respectively. RESULTS | |
| 20 34 D429-D430-P431 structure_element Very short linkers, D429-D430-P431 and V331-P332-N333-A334, connect the CBM46 to the Ig-like module and the Ig-like module to the CD, respectively. RESULTS | |
| 39 58 V331-P332-N333-A334 structure_element Very short linkers, D429-D430-P431 and V331-P332-N333-A334, connect the CBM46 to the Ig-like module and the Ig-like module to the CD, respectively. RESULTS | |
| 72 77 CBM46 structure_element Very short linkers, D429-D430-P431 and V331-P332-N333-A334, connect the CBM46 to the Ig-like module and the Ig-like module to the CD, respectively. RESULTS | |
| 85 99 Ig-like module structure_element Very short linkers, D429-D430-P431 and V331-P332-N333-A334, connect the CBM46 to the Ig-like module and the Ig-like module to the CD, respectively. RESULTS | |
| 108 122 Ig-like module structure_element Very short linkers, D429-D430-P431 and V331-P332-N333-A334, connect the CBM46 to the Ig-like module and the Ig-like module to the CD, respectively. RESULTS | |
| 130 132 CD structure_element Very short linkers, D429-D430-P431 and V331-P332-N333-A334, connect the CBM46 to the Ig-like module and the Ig-like module to the CD, respectively. RESULTS | |
| 5 19 Ig-like module structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 24 29 CBM46 structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 37 52 β-sandwich fold structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 69 77 β-sheets structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 96 118 antiparallel β-strands structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 137 142 loops structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 155 162 α helix structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 171 178 strands structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 179 181 β3 structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 186 188 β4 structure_element Both Ig-like module and CBM46 have a β-sandwich fold composed of two β-sheets of four and three antiparallel β-strands interconnected by loops and a short α helix between strands β3 and β4 (Fig. 1C). RESULTS | |
| 2 23 structural comparison experimental_method A structural comparison between the Ig-like module and the CBM46 using the Dali server yielded an rmsd of 2.3 Å and a Z-score of 10.2. RESULTS | |
| 36 50 Ig-like module structure_element A structural comparison between the Ig-like module and the CBM46 using the Dali server yielded an rmsd of 2.3 Å and a Z-score of 10.2. RESULTS | |
| 59 64 CBM46 structure_element A structural comparison between the Ig-like module and the CBM46 using the Dali server yielded an rmsd of 2.3 Å and a Z-score of 10.2. RESULTS | |
| 75 86 Dali server experimental_method A structural comparison between the Ig-like module and the CBM46 using the Dali server yielded an rmsd of 2.3 Å and a Z-score of 10.2. RESULTS | |
| 98 102 rmsd evidence A structural comparison between the Ig-like module and the CBM46 using the Dali server yielded an rmsd of 2.3 Å and a Z-score of 10.2. RESULTS | |
| 118 125 Z-score evidence A structural comparison between the Ig-like module and the CBM46 using the Dali server yielded an rmsd of 2.3 Å and a Z-score of 10.2. RESULTS | |
| 2 24 structure-based search experimental_method A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 73 87 Ig-like module structure_element A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 106 120 Ig-like module structure_element A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 137 143 solved experimental_method A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 144 161 crystal structure evidence A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 167 178 tri-modular structure_element A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 179 184 GH5_4 protein_type A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 197 216 Bacillus halodurans species A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 218 225 BhCel5B protein A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 232 236 rmsd evidence A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 249 256 Z-score evidence A structure-based search performed using the same server showed that the Ig-like module is similar to the Ig-like module from a recently solved crystal structure of a tri-modular GH5_4 enzyme from Bacillus halodurans, BhCel5B, with rmsd = 1.3 Å and Z-score = 15.3. RESULTS | |
| 4 9 CBM46 structure_element The CBM46 from BhCel5B is the most structurally similar to BlCel5B CBM46, with rmsd = 1.6 Å and Z-score = 12.4. RESULTS | |
| 15 22 BhCel5B protein The CBM46 from BhCel5B is the most structurally similar to BlCel5B CBM46, with rmsd = 1.6 Å and Z-score = 12.4. RESULTS | |
| 59 66 BlCel5B protein The CBM46 from BhCel5B is the most structurally similar to BlCel5B CBM46, with rmsd = 1.6 Å and Z-score = 12.4. RESULTS | |
| 67 72 CBM46 structure_element The CBM46 from BhCel5B is the most structurally similar to BlCel5B CBM46, with rmsd = 1.6 Å and Z-score = 12.4. RESULTS | |
| 79 83 rmsd evidence The CBM46 from BhCel5B is the most structurally similar to BlCel5B CBM46, with rmsd = 1.6 Å and Z-score = 12.4. RESULTS | |
| 96 103 Z-score evidence The CBM46 from BhCel5B is the most structurally similar to BlCel5B CBM46, with rmsd = 1.6 Å and Z-score = 12.4. RESULTS | |
| 34 41 BhCel5B protein The sequence identity relative to BhCel5B, however, is low (28% for Ig-like and 25% for CBM46). RESULTS | |
| 68 75 Ig-like structure_element The sequence identity relative to BhCel5B, however, is low (28% for Ig-like and 25% for CBM46). RESULTS | |
| 88 93 CBM46 structure_element The sequence identity relative to BhCel5B, however, is low (28% for Ig-like and 25% for CBM46). RESULTS | |
| 4 18 Ig-like module structure_element The Ig-like module, adjacent to the CD, contains only one tyrosine (Y367) exposed to solvent and no tryptophan residues. RESULTS | |
| 36 38 CD structure_element The Ig-like module, adjacent to the CD, contains only one tyrosine (Y367) exposed to solvent and no tryptophan residues. RESULTS | |
| 58 66 tyrosine residue_name The Ig-like module, adjacent to the CD, contains only one tyrosine (Y367) exposed to solvent and no tryptophan residues. RESULTS | |
| 68 72 Y367 residue_name_number The Ig-like module, adjacent to the CD, contains only one tyrosine (Y367) exposed to solvent and no tryptophan residues. RESULTS | |
| 100 110 tryptophan residue_name The Ig-like module, adjacent to the CD, contains only one tyrosine (Y367) exposed to solvent and no tryptophan residues. RESULTS | |
| 47 54 glucose chemical Because aromatic residues play a major role in glucose recognition, this observation suggests that substrate binding may not be the primary function of Ig-like module. RESULTS | |
| 152 166 Ig-like module structure_element Because aromatic residues play a major role in glucose recognition, this observation suggests that substrate binding may not be the primary function of Ig-like module. RESULTS | |
| 17 22 CBM46 structure_element In contrast, the CBM46 has three tryptophan residues, two of which face the CD substrate binding site (Fig. 1A), indicating that it may be actively engaged in the carbohydrate binding. RESULTS | |
| 33 43 tryptophan residue_name In contrast, the CBM46 has three tryptophan residues, two of which face the CD substrate binding site (Fig. 1A), indicating that it may be actively engaged in the carbohydrate binding. RESULTS | |
| 76 78 CD structure_element In contrast, the CBM46 has three tryptophan residues, two of which face the CD substrate binding site (Fig. 1A), indicating that it may be actively engaged in the carbohydrate binding. RESULTS | |
| 79 101 substrate binding site site In contrast, the CBM46 has three tryptophan residues, two of which face the CD substrate binding site (Fig. 1A), indicating that it may be actively engaged in the carbohydrate binding. RESULTS | |
| 163 175 carbohydrate chemical In contrast, the CBM46 has three tryptophan residues, two of which face the CD substrate binding site (Fig. 1A), indicating that it may be actively engaged in the carbohydrate binding. RESULTS | |
| 0 21 Electron density maps evidence Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 41 52 presence of protein_state Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 55 68 cellotetraose chemical Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 70 72 C4 chemical Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 91 104 cellopentaose chemical Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 106 108 C5 chemical Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 117 119 CD structure_element Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 120 155 negative substrate-binding subsites site Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 183 190 BlCel5B protein Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 194 214 catalytically active protein_state Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 257 259 C5 chemical Electron density maps clearly reveal the presence of a cellotetraose (C4) and not a soaked cellopentaose (C5) in the CD negative substrate-binding subsites (Fig. 1D), indicating that BlCel5B is catalytically active in the crystal state and able to cleave a C5 molecule. RESULTS | |
| 4 28 lack of electron density evidence The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 42 52 absence of protein_state The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 57 62 fifth residue_number The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 63 70 glucose chemical The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 94 96 C5 chemical The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 129 138 structure evidence The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 158 169 presence of protein_state The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 172 177 fifth residue_number The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 178 185 glucose chemical The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 227 245 catalytic residues site The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 281 285 R234 residue_name_number The lack of electron density verifies the absence of the fifth glucose moiety from the soaked C5, and a closer inspection of the structure confirmed that the presence of a fifth glucose unit would be sterically hindered by the catalytic residues on the reducing end and by residue R234 of a symmetry-related enzyme molecule on the non-reducing end. RESULTS | |
| 15 22 BlCel5B protein The ability of BlCel5B to cleave C5 into glucose and C4 molecules in solution was demonstrated by enzymatic product profile mass spectrometry analysis (Fig. 2A). RESULTS | |
| 33 35 C5 chemical The ability of BlCel5B to cleave C5 into glucose and C4 molecules in solution was demonstrated by enzymatic product profile mass spectrometry analysis (Fig. 2A). RESULTS | |
| 41 48 glucose chemical The ability of BlCel5B to cleave C5 into glucose and C4 molecules in solution was demonstrated by enzymatic product profile mass spectrometry analysis (Fig. 2A). RESULTS | |
| 53 55 C4 chemical The ability of BlCel5B to cleave C5 into glucose and C4 molecules in solution was demonstrated by enzymatic product profile mass spectrometry analysis (Fig. 2A). RESULTS | |
| 98 141 enzymatic product profile mass spectrometry experimental_method The ability of BlCel5B to cleave C5 into glucose and C4 molecules in solution was demonstrated by enzymatic product profile mass spectrometry analysis (Fig. 2A). RESULTS | |
| 4 6 C4 chemical The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 23 30 BlCel5B protein The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 31 43 binding site site The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 47 58 coordinated bond_interaction The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 62 76 hydrogen bonds bond_interaction The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 89 92 N36 residue_name_number The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 94 98 H113 residue_name_number The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 100 104 H114 residue_name_number The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 106 110 N158 residue_name_number The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 112 116 W301 residue_name_number The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 122 126 N303 residue_name_number The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 136 152 CH-π interaction bond_interaction The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 166 169 W47 residue_name_number The C4 oligomer in the BlCel5B binding site is coordinated by hydrogen bonds to residues N36, H113, H114, N158, W301, and N303 and by a CH-π interaction with residue W47 (Fig. 1D). RESULTS | |
| 29 31 CD structure_element These residues belong to the CD and are conserved in the GH5 family. RESULTS | |
| 40 49 conserved protein_state These residues belong to the CD and are conserved in the GH5 family. RESULTS | |
| 57 60 GH5 protein_type These residues belong to the CD and are conserved in the GH5 family. RESULTS | |
| 0 7 BlCel5B protein BlCel5B enzymatic activity RESULTS | |
| 0 7 BlCel5B protein BlCel5B exhibits optimum activity toward carboxymethylcellulose (CMC; 8.7 U/mg) at a pH of 4.0 and 55 °C and retains approximately half of its maximum activity at 80 °C, demonstrating considerable thermal stability (Fig. 2B,C). RESULTS | |
| 41 63 carboxymethylcellulose chemical BlCel5B exhibits optimum activity toward carboxymethylcellulose (CMC; 8.7 U/mg) at a pH of 4.0 and 55 °C and retains approximately half of its maximum activity at 80 °C, demonstrating considerable thermal stability (Fig. 2B,C). RESULTS | |
| 65 68 CMC chemical BlCel5B exhibits optimum activity toward carboxymethylcellulose (CMC; 8.7 U/mg) at a pH of 4.0 and 55 °C and retains approximately half of its maximum activity at 80 °C, demonstrating considerable thermal stability (Fig. 2B,C). RESULTS | |
| 0 7 BlCel5B protein BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 16 22 active protein_state BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 26 34 β-glucan chemical BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 46 54 lichenan chemical BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 71 81 xyloglucan chemical BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 152 165 galactomannan chemical BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 167 170 rye taxonomy_domain BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 171 183 arabinoxylan chemical BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 185 197 1,4-β-mannan chemical BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 225 235 Azo-Avicel chemical BlCel5B is also active on β-glucan (34 U/mg), lichenan (17.8 U/mg) and xyloglucan (15.7 U/mg) substrates (Table 1), whereas no activity was detected on galactomannan, rye arabinoxylan, 1,4-β-mannan or the insoluble substrate Azo-Avicel. RESULTS | |
| 44 69 Michaelis-Menten behavior experimental_method Kinetic parameters were calculated assuming Michaelis-Menten behavior with CMC as substrate: KM = 1.78 g L−1 and Vmax = 1.41 × 10−4 g s−1 mg protein−1 (Fig. 2D). RESULTS | |
| 75 78 CMC chemical Kinetic parameters were calculated assuming Michaelis-Menten behavior with CMC as substrate: KM = 1.78 g L−1 and Vmax = 1.41 × 10−4 g s−1 mg protein−1 (Fig. 2D). RESULTS | |
| 93 95 KM evidence Kinetic parameters were calculated assuming Michaelis-Menten behavior with CMC as substrate: KM = 1.78 g L−1 and Vmax = 1.41 × 10−4 g s−1 mg protein−1 (Fig. 2D). RESULTS | |
| 113 117 Vmax evidence Kinetic parameters were calculated assuming Michaelis-Menten behavior with CMC as substrate: KM = 1.78 g L−1 and Vmax = 1.41 × 10−4 g s−1 mg protein−1 (Fig. 2D). RESULTS | |
| 9 16 BlCel5B protein Although BlCel5B is not a highly active enzyme against one specific substrate as compared to others GH5_4, it has the advantage of being active against different substrates with β-1,3 and/or β-1,4 glycosidic linkages. RESULTS | |
| 33 39 active protein_state Although BlCel5B is not a highly active enzyme against one specific substrate as compared to others GH5_4, it has the advantage of being active against different substrates with β-1,3 and/or β-1,4 glycosidic linkages. RESULTS | |
| 100 105 GH5_4 protein_type Although BlCel5B is not a highly active enzyme against one specific substrate as compared to others GH5_4, it has the advantage of being active against different substrates with β-1,3 and/or β-1,4 glycosidic linkages. RESULTS | |
| 137 143 active protein_state Although BlCel5B is not a highly active enzyme against one specific substrate as compared to others GH5_4, it has the advantage of being active against different substrates with β-1,3 and/or β-1,4 glycosidic linkages. RESULTS | |
| 36 53 ancillary modules structure_element To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 58 65 BlCel5B protein To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 76 92 enzymatic assays experimental_method To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 128 135 mutants protein_state To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 139 144 CBM46 structure_element To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 145 153 deletion experimental_method To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 155 161 ΔCBM46 mutant To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 170 177 Ig-like structure_element To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 180 185 CBM46 structure_element To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 186 194 deletion experimental_method To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 196 205 ΔIg-CBM46 mutant To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 218 233 point mutations experimental_method To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 241 246 CBM46 structure_element To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 270 275 W479A mutant To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 280 285 W481A mutant To understand the importance of the ancillary modules for BlCel5B activity, enzymatic assays were carried out using four enzyme mutants: a CBM46 deletion (ΔCBM46) and an Ig-like + CBM46 deletion (ΔIg-CBM46) as well as point mutations of the CBM46 inner surface residues W479A and W481A. RESULTS | |
| 6 13 mutants protein_state These mutants were expressed and purified as described for the wild-type enzyme. RESULTS | |
| 19 41 expressed and purified experimental_method These mutants were expressed and purified as described for the wild-type enzyme. RESULTS | |
| 63 72 wild-type protein_state These mutants were expressed and purified as described for the wild-type enzyme. RESULTS | |
| 27 44 deletion variants protein_state Strikingly, neither of the deletion variants exhibited detectable activity toward any of the substrates tested using full-length BlCel5B (Table 1), demonstrating that the Ig-like module and the CBM46 are essential for BlCel5B activity. RESULTS | |
| 117 128 full-length protein_state Strikingly, neither of the deletion variants exhibited detectable activity toward any of the substrates tested using full-length BlCel5B (Table 1), demonstrating that the Ig-like module and the CBM46 are essential for BlCel5B activity. RESULTS | |
| 129 136 BlCel5B protein Strikingly, neither of the deletion variants exhibited detectable activity toward any of the substrates tested using full-length BlCel5B (Table 1), demonstrating that the Ig-like module and the CBM46 are essential for BlCel5B activity. RESULTS | |
| 171 185 Ig-like module structure_element Strikingly, neither of the deletion variants exhibited detectable activity toward any of the substrates tested using full-length BlCel5B (Table 1), demonstrating that the Ig-like module and the CBM46 are essential for BlCel5B activity. RESULTS | |
| 194 199 CBM46 structure_element Strikingly, neither of the deletion variants exhibited detectable activity toward any of the substrates tested using full-length BlCel5B (Table 1), demonstrating that the Ig-like module and the CBM46 are essential for BlCel5B activity. RESULTS | |
| 218 225 BlCel5B protein Strikingly, neither of the deletion variants exhibited detectable activity toward any of the substrates tested using full-length BlCel5B (Table 1), demonstrating that the Ig-like module and the CBM46 are essential for BlCel5B activity. RESULTS | |
| 0 20 Thermal shift assays experimental_method Thermal shift assays were conducted to confirm structural stability of the mutants (Supplementary Fig. 1). RESULTS | |
| 75 82 mutants protein_state Thermal shift assays were conducted to confirm structural stability of the mutants (Supplementary Fig. 1). RESULTS | |
| 37 57 melting temperatures evidence All of the constructs showed similar melting temperatures: 62 °C for BlCel5B, 58 °C for BlCel5BΔCBM46, 56 °C for BlCel5BΔIg-CBM46, 65 °C for BlCel5BW479A and 59 °C for BlCel5BW479A, thus confirming their proper overall fold. RESULTS | |
| 69 76 BlCel5B protein All of the constructs showed similar melting temperatures: 62 °C for BlCel5B, 58 °C for BlCel5BΔCBM46, 56 °C for BlCel5BΔIg-CBM46, 65 °C for BlCel5BW479A and 59 °C for BlCel5BW479A, thus confirming their proper overall fold. RESULTS | |
| 88 101 BlCel5BΔCBM46 mutant All of the constructs showed similar melting temperatures: 62 °C for BlCel5B, 58 °C for BlCel5BΔCBM46, 56 °C for BlCel5BΔIg-CBM46, 65 °C for BlCel5BW479A and 59 °C for BlCel5BW479A, thus confirming their proper overall fold. RESULTS | |
| 113 129 BlCel5BΔIg-CBM46 mutant All of the constructs showed similar melting temperatures: 62 °C for BlCel5B, 58 °C for BlCel5BΔCBM46, 56 °C for BlCel5BΔIg-CBM46, 65 °C for BlCel5BW479A and 59 °C for BlCel5BW479A, thus confirming their proper overall fold. RESULTS | |
| 141 153 BlCel5BW479A mutant All of the constructs showed similar melting temperatures: 62 °C for BlCel5B, 58 °C for BlCel5BΔCBM46, 56 °C for BlCel5BΔIg-CBM46, 65 °C for BlCel5BW479A and 59 °C for BlCel5BW479A, thus confirming their proper overall fold. RESULTS | |
| 168 180 BlCel5BW479A mutant All of the constructs showed similar melting temperatures: 62 °C for BlCel5B, 58 °C for BlCel5BΔCBM46, 56 °C for BlCel5BΔIg-CBM46, 65 °C for BlCel5BW479A and 59 °C for BlCel5BW479A, thus confirming their proper overall fold. RESULTS | |
| 37 42 CBM46 structure_element We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 49 56 surface site We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 66 70 W479 residue_name_number We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 75 79 W481 residue_name_number We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 93 100 BlCel5B protein We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 124 140 enzymatic assays experimental_method We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 146 151 W479A mutant We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 156 161 W481A mutant We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 162 169 mutants protein_state We also examined the function of the CBM46 inner surface residues W479 and W481 (Fig. 1A) in BlCel5B activity by performing enzymatic assays with W479A and W481A mutants. RESULTS | |
| 5 14 mutations experimental_method Both mutations reduced enzymatic activity toward all tested substrates (Table 1), with W481A having a stronger effect than W479A (~64% vs. 79% activity relative to wt BlCel5B using β-glucan and ~10% vs. 50% using CMC). RESULTS | |
| 87 92 W481A mutant Both mutations reduced enzymatic activity toward all tested substrates (Table 1), with W481A having a stronger effect than W479A (~64% vs. 79% activity relative to wt BlCel5B using β-glucan and ~10% vs. 50% using CMC). RESULTS | |
| 123 128 W479A mutant Both mutations reduced enzymatic activity toward all tested substrates (Table 1), with W481A having a stronger effect than W479A (~64% vs. 79% activity relative to wt BlCel5B using β-glucan and ~10% vs. 50% using CMC). RESULTS | |
| 164 166 wt protein_state Both mutations reduced enzymatic activity toward all tested substrates (Table 1), with W481A having a stronger effect than W479A (~64% vs. 79% activity relative to wt BlCel5B using β-glucan and ~10% vs. 50% using CMC). RESULTS | |
| 167 174 BlCel5B protein Both mutations reduced enzymatic activity toward all tested substrates (Table 1), with W481A having a stronger effect than W479A (~64% vs. 79% activity relative to wt BlCel5B using β-glucan and ~10% vs. 50% using CMC). RESULTS | |
| 181 189 β-glucan chemical Both mutations reduced enzymatic activity toward all tested substrates (Table 1), with W481A having a stronger effect than W479A (~64% vs. 79% activity relative to wt BlCel5B using β-glucan and ~10% vs. 50% using CMC). RESULTS | |
| 213 216 CMC chemical Both mutations reduced enzymatic activity toward all tested substrates (Table 1), with W481A having a stronger effect than W479A (~64% vs. 79% activity relative to wt BlCel5B using β-glucan and ~10% vs. 50% using CMC). RESULTS | |
| 20 25 CBM46 structure_element This indicates that CBM46 must interact with the substrate via residues W479 and W481. RESULTS | |
| 72 76 W479 residue_name_number This indicates that CBM46 must interact with the substrate via residues W479 and W481. RESULTS | |
| 81 85 W481 residue_name_number This indicates that CBM46 must interact with the substrate via residues W479 and W481. RESULTS | |
| 19 26 BlCel5B protein However, since the BlCel5B crystal structure exhibits no close contact between these residues and the substrate, these results suggest the existence of large-amplitude interdomain motions that may enable direct interactions between CBM46 and the carbohydrate. RESULTS | |
| 27 44 crystal structure evidence However, since the BlCel5B crystal structure exhibits no close contact between these residues and the substrate, these results suggest the existence of large-amplitude interdomain motions that may enable direct interactions between CBM46 and the carbohydrate. RESULTS | |
| 57 62 close protein_state However, since the BlCel5B crystal structure exhibits no close contact between these residues and the substrate, these results suggest the existence of large-amplitude interdomain motions that may enable direct interactions between CBM46 and the carbohydrate. RESULTS | |
| 232 237 CBM46 structure_element However, since the BlCel5B crystal structure exhibits no close contact between these residues and the substrate, these results suggest the existence of large-amplitude interdomain motions that may enable direct interactions between CBM46 and the carbohydrate. RESULTS | |
| 246 258 carbohydrate chemical However, since the BlCel5B crystal structure exhibits no close contact between these residues and the substrate, these results suggest the existence of large-amplitude interdomain motions that may enable direct interactions between CBM46 and the carbohydrate. RESULTS | |
| 0 7 BlCelB5 protein BlCelB5 dynamics and binding-site architecture RESULTS | |
| 21 33 binding-site site BlCelB5 dynamics and binding-site architecture RESULTS | |
| 0 18 Molecular dynamics experimental_method Molecular dynamics (MD) simulations were performed to investigate the conformational mobility of BlCel5B. RESULTS | |
| 20 22 MD experimental_method Molecular dynamics (MD) simulations were performed to investigate the conformational mobility of BlCel5B. RESULTS | |
| 24 35 simulations experimental_method Molecular dynamics (MD) simulations were performed to investigate the conformational mobility of BlCel5B. RESULTS | |
| 97 104 BlCel5B protein Molecular dynamics (MD) simulations were performed to investigate the conformational mobility of BlCel5B. RESULTS | |
| 7 18 simulations experimental_method In the simulations of the crystal structure for BlCel5B bound to C4, the substrate dissociates from the protein within the first 100 ns of the simulation time (Supplementary Fig. 2A). RESULTS | |
| 26 43 crystal structure evidence In the simulations of the crystal structure for BlCel5B bound to C4, the substrate dissociates from the protein within the first 100 ns of the simulation time (Supplementary Fig. 2A). RESULTS | |
| 48 55 BlCel5B protein In the simulations of the crystal structure for BlCel5B bound to C4, the substrate dissociates from the protein within the first 100 ns of the simulation time (Supplementary Fig. 2A). RESULTS | |
| 56 64 bound to protein_state In the simulations of the crystal structure for BlCel5B bound to C4, the substrate dissociates from the protein within the first 100 ns of the simulation time (Supplementary Fig. 2A). RESULTS | |
| 65 67 C4 chemical In the simulations of the crystal structure for BlCel5B bound to C4, the substrate dissociates from the protein within the first 100 ns of the simulation time (Supplementary Fig. 2A). RESULTS | |
| 143 153 simulation experimental_method In the simulations of the crystal structure for BlCel5B bound to C4, the substrate dissociates from the protein within the first 100 ns of the simulation time (Supplementary Fig. 2A). RESULTS | |
| 31 44 cellotetraose chemical This observation suggests that cellotetraose does not exhibit detectable affinity for this specific BlCel5B conformation in solution, as one might otherwise expect for a reaction product. RESULTS | |
| 100 107 BlCel5B protein This observation suggests that cellotetraose does not exhibit detectable affinity for this specific BlCel5B conformation in solution, as one might otherwise expect for a reaction product. RESULTS | |
| 71 78 BlCel5B protein No changes beyond local fluctuations were observed in any of the three BlCel5B domains within the time scale of these runs (400 ns; Supplementary Fig. 2B). RESULTS | |
| 13 18 CBM46 structure_element However, the CBM46 and Ig-like domains did exhibit rigid body-like motions relative to the CD, with rmsd values around 2.3 Å and 1.8 Å, respectively, suggesting that BlCel5B may execute large-amplitude interdomain motions over longer time scales (Supplementary Fig. 2B,C). RESULTS | |
| 23 38 Ig-like domains structure_element However, the CBM46 and Ig-like domains did exhibit rigid body-like motions relative to the CD, with rmsd values around 2.3 Å and 1.8 Å, respectively, suggesting that BlCel5B may execute large-amplitude interdomain motions over longer time scales (Supplementary Fig. 2B,C). RESULTS | |
| 91 93 CD structure_element However, the CBM46 and Ig-like domains did exhibit rigid body-like motions relative to the CD, with rmsd values around 2.3 Å and 1.8 Å, respectively, suggesting that BlCel5B may execute large-amplitude interdomain motions over longer time scales (Supplementary Fig. 2B,C). RESULTS | |
| 100 104 rmsd evidence However, the CBM46 and Ig-like domains did exhibit rigid body-like motions relative to the CD, with rmsd values around 2.3 Å and 1.8 Å, respectively, suggesting that BlCel5B may execute large-amplitude interdomain motions over longer time scales (Supplementary Fig. 2B,C). RESULTS | |
| 166 173 BlCel5B protein However, the CBM46 and Ig-like domains did exhibit rigid body-like motions relative to the CD, with rmsd values around 2.3 Å and 1.8 Å, respectively, suggesting that BlCel5B may execute large-amplitude interdomain motions over longer time scales (Supplementary Fig. 2B,C). RESULTS | |
| 13 24 simulations experimental_method Accordingly, simulations were then performed using accelerated molecular dynamics (aMD) techniques to probe BlCel5B interdomain motions. RESULTS | |
| 51 81 accelerated molecular dynamics experimental_method Accordingly, simulations were then performed using accelerated molecular dynamics (aMD) techniques to probe BlCel5B interdomain motions. RESULTS | |
| 83 86 aMD experimental_method Accordingly, simulations were then performed using accelerated molecular dynamics (aMD) techniques to probe BlCel5B interdomain motions. RESULTS | |
| 108 115 BlCel5B protein Accordingly, simulations were then performed using accelerated molecular dynamics (aMD) techniques to probe BlCel5B interdomain motions. RESULTS | |
| 0 3 aMD experimental_method aMD enhances conformational sampling by raising the basins of the dihedral potential energy surface without affecting the general form of the atomistic potential, thereby increasing transition rates between different local minima. RESULTS | |
| 66 99 dihedral potential energy surface evidence aMD enhances conformational sampling by raising the basins of the dihedral potential energy surface without affecting the general form of the atomistic potential, thereby increasing transition rates between different local minima. RESULTS | |
| 0 3 aMD experimental_method aMD trajectories corresponding to more than 1.0 μs of conventional MD runs were generated. RESULTS | |
| 4 16 trajectories evidence aMD trajectories corresponding to more than 1.0 μs of conventional MD runs were generated. RESULTS | |
| 67 69 MD experimental_method aMD trajectories corresponding to more than 1.0 μs of conventional MD runs were generated. RESULTS | |
| 13 24 simulations experimental_method During these simulations, we observed occlusive conformations between CBM46 and CD that resulted in a rearrangement of the enzyme’s architecture around the active site (Video S1). RESULTS | |
| 70 75 CBM46 structure_element During these simulations, we observed occlusive conformations between CBM46 and CD that resulted in a rearrangement of the enzyme’s architecture around the active site (Video S1). RESULTS | |
| 80 82 CD structure_element During these simulations, we observed occlusive conformations between CBM46 and CD that resulted in a rearrangement of the enzyme’s architecture around the active site (Video S1). RESULTS | |
| 156 167 active site site During these simulations, we observed occlusive conformations between CBM46 and CD that resulted in a rearrangement of the enzyme’s architecture around the active site (Video S1). RESULTS | |
| 16 23 BlCel5B protein Figure 3A shows BlCel5B in the crystallographic conformation (red) and in a selected configuration obtained with aMD (blue) in the absence of the substrate. RESULTS | |
| 31 47 crystallographic experimental_method Figure 3A shows BlCel5B in the crystallographic conformation (red) and in a selected configuration obtained with aMD (blue) in the absence of the substrate. RESULTS | |
| 113 116 aMD experimental_method Figure 3A shows BlCel5B in the crystallographic conformation (red) and in a selected configuration obtained with aMD (blue) in the absence of the substrate. RESULTS | |
| 131 141 absence of protein_state Figure 3A shows BlCel5B in the crystallographic conformation (red) and in a selected configuration obtained with aMD (blue) in the absence of the substrate. RESULTS | |
| 61 69 distance evidence Interdomain motions were gauged by the time evolution of the distance between the α carbons of residues I120 and E477 (represented as spheres in Fig. 3A), belonging to the CD and CBM46, respectively. RESULTS | |
| 104 108 I120 residue_name_number Interdomain motions were gauged by the time evolution of the distance between the α carbons of residues I120 and E477 (represented as spheres in Fig. 3A), belonging to the CD and CBM46, respectively. RESULTS | |
| 113 117 E477 residue_name_number Interdomain motions were gauged by the time evolution of the distance between the α carbons of residues I120 and E477 (represented as spheres in Fig. 3A), belonging to the CD and CBM46, respectively. RESULTS | |
| 172 174 CD structure_element Interdomain motions were gauged by the time evolution of the distance between the α carbons of residues I120 and E477 (represented as spheres in Fig. 3A), belonging to the CD and CBM46, respectively. RESULTS | |
| 179 184 CBM46 structure_element Interdomain motions were gauged by the time evolution of the distance between the α carbons of residues I120 and E477 (represented as spheres in Fig. 3A), belonging to the CD and CBM46, respectively. RESULTS | |
| 25 29 I120 residue_name_number Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 30 34 E477 residue_name_number Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 35 43 distance evidence Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 131 134 aMD experimental_method Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 135 145 trajectory evidence Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 183 192 semi-open protein_state Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 194 210 crystallographic experimental_method Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 216 224 occluded protein_state Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 226 229 aMD experimental_method Figure 3C shows that the I120-E477 distance (red curve) gradually decreases from ~35 Å to ~7 Å within the first half of the 1.0 μs aMD trajectory, indicating a transition between the semi-open (crystallographic) and occluded (aMD sampled) configurations. RESULTS | |
| 30 44 aMD simulation experimental_method During the second half of the aMD simulation, the full-length enzyme remained in the closed conformation, with the CBM46 covering the carbohydrate-binding site. RESULTS | |
| 50 61 full-length protein_state During the second half of the aMD simulation, the full-length enzyme remained in the closed conformation, with the CBM46 covering the carbohydrate-binding site. RESULTS | |
| 85 91 closed protein_state During the second half of the aMD simulation, the full-length enzyme remained in the closed conformation, with the CBM46 covering the carbohydrate-binding site. RESULTS | |
| 115 120 CBM46 structure_element During the second half of the aMD simulation, the full-length enzyme remained in the closed conformation, with the CBM46 covering the carbohydrate-binding site. RESULTS | |
| 134 159 carbohydrate-binding site site During the second half of the aMD simulation, the full-length enzyme remained in the closed conformation, with the CBM46 covering the carbohydrate-binding site. RESULTS | |
| 27 34 BlCel5B protein These results suggest that BlCel5B undergoes large-scale interdomain movements that enable interactions between CBM46 and the substrate bound to the CD. RESULTS | |
| 112 117 CBM46 structure_element These results suggest that BlCel5B undergoes large-scale interdomain movements that enable interactions between CBM46 and the substrate bound to the CD. RESULTS | |
| 136 144 bound to protein_state These results suggest that BlCel5B undergoes large-scale interdomain movements that enable interactions between CBM46 and the substrate bound to the CD. RESULTS | |
| 149 151 CD structure_element These results suggest that BlCel5B undergoes large-scale interdomain movements that enable interactions between CBM46 and the substrate bound to the CD. RESULTS | |
| 29 36 BlCel5B protein To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 59 65 glucan chemical To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 90 99 structure evidence To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 107 119 cellooctaose chemical To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 121 123 C8 chemical To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 151 170 positive (+1 to +4) site To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 175 194 negative (−4 to −1) site To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 195 203 subsites site To study the interactions of BlCel5B with a non-hydrolyzed glucan chain, we built a model structure with a cellooctaose (C8) chain spanning the entire positive (+1 to +4) and negative (−4 to −1) subsites of the enzyme. RESULTS | |
| 35 42 BlCel5B protein Starting from the crystallographic BlCel5B conformation, the C8 molecule deviated significantly from the active site and assumed a non-productive binding mode (Supplementary Fig. 2D). RESULTS | |
| 61 63 C8 chemical Starting from the crystallographic BlCel5B conformation, the C8 molecule deviated significantly from the active site and assumed a non-productive binding mode (Supplementary Fig. 2D). RESULTS | |
| 105 116 active site site Starting from the crystallographic BlCel5B conformation, the C8 molecule deviated significantly from the active site and assumed a non-productive binding mode (Supplementary Fig. 2D). RESULTS | |
| 35 39 open protein_state This observation suggests that the open conformation of BlCel5B is not able to hold the substrate in a position suitable for hydrolysis (Supplementary Fig. 2E). RESULTS | |
| 56 63 BlCel5B protein This observation suggests that the open conformation of BlCel5B is not able to hold the substrate in a position suitable for hydrolysis (Supplementary Fig. 2E). RESULTS | |
| 30 40 BlCel5B-C8 complex_assembly However, after subjecting the BlCel5B-C8 complex to a 0.5 μs aMD simulation with harmonic restraints on the C8 chain to prevent it from deviating from the productive binding mode, the CBM46 readily closed over the CD and trapped the C8 chain in position for hydrolysis (Fig. 3B). RESULTS | |
| 61 75 aMD simulation experimental_method However, after subjecting the BlCel5B-C8 complex to a 0.5 μs aMD simulation with harmonic restraints on the C8 chain to prevent it from deviating from the productive binding mode, the CBM46 readily closed over the CD and trapped the C8 chain in position for hydrolysis (Fig. 3B). RESULTS | |
| 108 110 C8 chemical However, after subjecting the BlCel5B-C8 complex to a 0.5 μs aMD simulation with harmonic restraints on the C8 chain to prevent it from deviating from the productive binding mode, the CBM46 readily closed over the CD and trapped the C8 chain in position for hydrolysis (Fig. 3B). RESULTS | |
| 184 189 CBM46 structure_element However, after subjecting the BlCel5B-C8 complex to a 0.5 μs aMD simulation with harmonic restraints on the C8 chain to prevent it from deviating from the productive binding mode, the CBM46 readily closed over the CD and trapped the C8 chain in position for hydrolysis (Fig. 3B). RESULTS | |
| 198 204 closed protein_state However, after subjecting the BlCel5B-C8 complex to a 0.5 μs aMD simulation with harmonic restraints on the C8 chain to prevent it from deviating from the productive binding mode, the CBM46 readily closed over the CD and trapped the C8 chain in position for hydrolysis (Fig. 3B). RESULTS | |
| 214 216 CD structure_element However, after subjecting the BlCel5B-C8 complex to a 0.5 μs aMD simulation with harmonic restraints on the C8 chain to prevent it from deviating from the productive binding mode, the CBM46 readily closed over the CD and trapped the C8 chain in position for hydrolysis (Fig. 3B). RESULTS | |
| 233 235 C8 chemical However, after subjecting the BlCel5B-C8 complex to a 0.5 μs aMD simulation with harmonic restraints on the C8 chain to prevent it from deviating from the productive binding mode, the CBM46 readily closed over the CD and trapped the C8 chain in position for hydrolysis (Fig. 3B). RESULTS | |
| 7 18 presence of protein_state In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 34 39 CBM46 structure_element In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 93 119 crystallographic structure evidence In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 145 159 substrate-free protein_state In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 160 167 BlCel5B protein In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 168 183 aMD simulations experimental_method In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 212 216 I120 residue_name_number In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 217 221 E477 residue_name_number In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 222 230 distance evidence In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 266 272 closed protein_state In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 302 304 C8 chemical In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 339 353 substrate-free protein_state In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 354 361 BlCel5B protein In the presence of the substrate, CBM46 adopts a final conformation intermediate between the crystallographic structure and that observed in the substrate-free BlCel5B aMD simulations; this is illustrated by the I120-E477 distance, which stabilizes near 20 Å in the closed configuration that traps the C8 molecule (in contrast to ~7 Å for substrate-free BlCel5B) (Fig. 3C). RESULTS | |
| 5 15 BlCel5B-C8 complex_assembly This BlCel5B-C8 configuration remains stable over an additional 500 ns of conventional MD simulation with no restraints (Fig. 3C cyan line, Supplementary Fig. 2E,F). RESULTS | |
| 87 100 MD simulation experimental_method This BlCel5B-C8 configuration remains stable over an additional 500 ns of conventional MD simulation with no restraints (Fig. 3C cyan line, Supplementary Fig. 2E,F). RESULTS | |
| 81 92 simulations experimental_method A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 110 115 CBM46 structure_element A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 116 126 tryptophan residue_name A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 136 140 W479 residue_name_number A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 145 149 W481 residue_name_number A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 162 164 CD structure_element A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 165 175 tryptophan residue_name A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 210 222 carbohydrate chemical A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 265 271 tunnel site A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 296 303 BlCel5B protein A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 304 317 binding cleft site A closer inspection of the productive binding mode obtained from these extensive simulations reveals that the CBM46 tryptophan residues W479 and W481 (along with CD tryptophan residues) play important roles in carbohydrate recognition and orientation by creating a tunnel-like topology along the BlCel5B binding cleft, as depicted in Fig. 3D. RESULTS | |
| 38 43 CBM46 structure_element Together, these results indicate that CBM46 is a key component of the catalytic active complex, providing an explanation as to why CBM46 is essential for the enzymatic activity of BlCel5B. RESULTS | |
| 70 86 catalytic active protein_state Together, these results indicate that CBM46 is a key component of the catalytic active complex, providing an explanation as to why CBM46 is essential for the enzymatic activity of BlCel5B. RESULTS | |
| 131 136 CBM46 structure_element Together, these results indicate that CBM46 is a key component of the catalytic active complex, providing an explanation as to why CBM46 is essential for the enzymatic activity of BlCel5B. RESULTS | |
| 180 187 BlCel5B protein Together, these results indicate that CBM46 is a key component of the catalytic active complex, providing an explanation as to why CBM46 is essential for the enzymatic activity of BlCel5B. RESULTS | |
| 55 76 atomistic simulations experimental_method To enable substantially longer time scales compared to atomistic simulations, we further explored the dynamics of BlCel5B using coarse-grained MD (CG-MD) simulations. RESULTS | |
| 114 121 BlCel5B protein To enable substantially longer time scales compared to atomistic simulations, we further explored the dynamics of BlCel5B using coarse-grained MD (CG-MD) simulations. RESULTS | |
| 128 145 coarse-grained MD experimental_method To enable substantially longer time scales compared to atomistic simulations, we further explored the dynamics of BlCel5B using coarse-grained MD (CG-MD) simulations. RESULTS | |
| 147 152 CG-MD experimental_method To enable substantially longer time scales compared to atomistic simulations, we further explored the dynamics of BlCel5B using coarse-grained MD (CG-MD) simulations. RESULTS | |
| 154 165 simulations experimental_method To enable substantially longer time scales compared to atomistic simulations, we further explored the dynamics of BlCel5B using coarse-grained MD (CG-MD) simulations. RESULTS | |
| 39 56 CG-MD simulations experimental_method We performed three independent ~120 μs CG-MD simulations, for a total of approximately 360 μs of sampling. RESULTS | |
| 4 12 distance evidence The distance between the α carbons of two residues centrally positioned in the CD and CBM46 (Fig. 4A) was monitored, and the results shown in Fig. 4B indicate that the wide-amplitude events described above frequently appear in this time scale. RESULTS | |
| 79 81 CD structure_element The distance between the α carbons of two residues centrally positioned in the CD and CBM46 (Fig. 4A) was monitored, and the results shown in Fig. 4B indicate that the wide-amplitude events described above frequently appear in this time scale. RESULTS | |
| 86 91 CBM46 structure_element The distance between the α carbons of two residues centrally positioned in the CD and CBM46 (Fig. 4A) was monitored, and the results shown in Fig. 4B indicate that the wide-amplitude events described above frequently appear in this time scale. RESULTS | |
| 4 34 computed distance distribution evidence The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 115 121 closed protein_state The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 172 186 substrate-free protein_state The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 187 202 aMD simulations experimental_method The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 213 218 CBM46 structure_element The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 238 240 CD structure_element The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 254 276 substrate binding site site The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 286 295 semi-open protein_state The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 325 351 crystallographic structure evidence The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 363 371 extended protein_state The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 372 379 BlCel5B protein The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 407 409 CD structure_element The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 414 419 CBM46 structure_element The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 455 472 crystal structure evidence The computed distance distribution depicted in Fig. 4C indicates three main conformational states ranging from (I) closed conformations similar to those encountered in the substrate-free aMD simulations, in which CBM46 interacts with the CD to shape the substrate binding site, to (II) semi-open conformations similar to the crystallographic structure, and (III) extended BlCel5B conformations in which the CD and CBM46 are even further apart than in the crystal structure. RESULTS | |
| 0 7 BlCel5B protein BlCel5B conformers fit the SAXS envelope RESULTS | |
| 27 31 SAXS experimental_method BlCel5B conformers fit the SAXS envelope RESULTS | |
| 32 40 envelope evidence BlCel5B conformers fit the SAXS envelope RESULTS | |
| 0 4 SAXS experimental_method SAXS experiments were conducted to assess BlCel5B conformational states in solution, and the results revealed the enzyme in its monomeric form, with average values of Rg = 27.17 Å and Dmax = 87.59 Å (Supplementary Table 2). RESULTS | |
| 42 49 BlCel5B protein SAXS experiments were conducted to assess BlCel5B conformational states in solution, and the results revealed the enzyme in its monomeric form, with average values of Rg = 27.17 Å and Dmax = 87.59 Å (Supplementary Table 2). RESULTS | |
| 128 137 monomeric oligomeric_state SAXS experiments were conducted to assess BlCel5B conformational states in solution, and the results revealed the enzyme in its monomeric form, with average values of Rg = 27.17 Å and Dmax = 87.59 Å (Supplementary Table 2). RESULTS | |
| 167 169 Rg evidence SAXS experiments were conducted to assess BlCel5B conformational states in solution, and the results revealed the enzyme in its monomeric form, with average values of Rg = 27.17 Å and Dmax = 87.59 Å (Supplementary Table 2). RESULTS | |
| 184 188 Dmax evidence SAXS experiments were conducted to assess BlCel5B conformational states in solution, and the results revealed the enzyme in its monomeric form, with average values of Rg = 27.17 Å and Dmax = 87.59 Å (Supplementary Table 2). RESULTS | |
| 4 30 ab initio dummy atom model experimental_method The ab initio dummy atom model (DAM) demonstrated that the SAXS-derived BlCel5B molecular envelope could not be single-handedly filled by any of the main conformational states encountered in the simulations (Fig. 4D). RESULTS | |
| 32 35 DAM experimental_method The ab initio dummy atom model (DAM) demonstrated that the SAXS-derived BlCel5B molecular envelope could not be single-handedly filled by any of the main conformational states encountered in the simulations (Fig. 4D). RESULTS | |
| 59 63 SAXS experimental_method The ab initio dummy atom model (DAM) demonstrated that the SAXS-derived BlCel5B molecular envelope could not be single-handedly filled by any of the main conformational states encountered in the simulations (Fig. 4D). RESULTS | |
| 72 79 BlCel5B protein The ab initio dummy atom model (DAM) demonstrated that the SAXS-derived BlCel5B molecular envelope could not be single-handedly filled by any of the main conformational states encountered in the simulations (Fig. 4D). RESULTS | |
| 90 98 envelope evidence The ab initio dummy atom model (DAM) demonstrated that the SAXS-derived BlCel5B molecular envelope could not be single-handedly filled by any of the main conformational states encountered in the simulations (Fig. 4D). RESULTS | |
| 195 206 simulations experimental_method The ab initio dummy atom model (DAM) demonstrated that the SAXS-derived BlCel5B molecular envelope could not be single-handedly filled by any of the main conformational states encountered in the simulations (Fig. 4D). RESULTS | |
| 19 30 Kratky plot evidence It is known that a Kratky plot exhibits a peak with an elevated baseline at high q for a monodisperse system composed of multi-domain particles with flexible extensions. RESULTS | |
| 85 92 BlCel5B protein Indeed, an elevation of the baseline toward a hyperbolic-like curve was observed for BlCel5B, indicating a considerable degree of molecular mobility in solution (Supplementary Fig. 3). RESULTS | |
| 151 182 crystallographic and MD studies experimental_method Thus, the conformational heterogeneity of the enzyme can be decomposed in structural terms as a combination of conformational states identified in our crystallographic and MD studies. RESULTS | |
| 18 22 SAXS experimental_method We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 23 31 envelope evidence We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 75 90 superimposition experimental_method We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 152 159 BlCel5B protein We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 173 179 closed protein_state We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 183 188 CBM46 structure_element We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 189 191 CD structure_element We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 192 200 occluded protein_state We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 233 244 simulations experimental_method We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 278 287 semi-open protein_state We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 320 337 crystal structure evidence We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 367 375 extended protein_state We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 398 409 simulations experimental_method We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 445 449 SAXS experimental_method We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 450 458 envelope evidence We found that the SAXS envelope can be well represented by considering the superimposition of three different representative molecular conformations of BlCel5B (Fig. 4E): a closed or CBM46/CD-occluded conformation extracted from the simulations with a relative weight of 26%, a semi-open conformation represented by the crystal structure corresponding to 40%, and an extended conformation based on simulations that is responsible for 34% of the SAXS envelope. RESULTS | |
| 14 38 average scattering curve evidence The resulting average scattering curve from this model fits the experimental protein scattering intensity, with χ = 1.89 (Supplementary Fig. 3). RESULTS | |
| 85 105 scattering intensity evidence The resulting average scattering curve from this model fits the experimental protein scattering intensity, with χ = 1.89 (Supplementary Fig. 3). RESULTS | |
| 112 113 χ evidence The resulting average scattering curve from this model fits the experimental protein scattering intensity, with χ = 1.89 (Supplementary Fig. 3). RESULTS | |
| 0 5 GH5_4 protein_type GH5_4 phylogenetic analysis RESULTS | |
| 6 27 phylogenetic analysis experimental_method GH5_4 phylogenetic analysis RESULTS | |
| 150 161 277 and 400 residue_range After the exclusion of partial sequences and the suppression of highly identical members (higher than 90% identity), 144 sequences containing between 277 and 400 residues were aligned and used to construct a phylogenetic tree (Supplementary Fig. 4A). RESULTS | |
| 176 183 aligned experimental_method After the exclusion of partial sequences and the suppression of highly identical members (higher than 90% identity), 144 sequences containing between 277 and 400 residues were aligned and used to construct a phylogenetic tree (Supplementary Fig. 4A). RESULTS | |
| 208 225 phylogenetic tree evidence After the exclusion of partial sequences and the suppression of highly identical members (higher than 90% identity), 144 sequences containing between 277 and 400 residues were aligned and used to construct a phylogenetic tree (Supplementary Fig. 4A). RESULTS | |
| 64 67 GH5 protein_type According to PFAM database conserved domain classification, 128 GH5 enzymes have an architecture consisting of an N-terminal catalytic module, a CBM_X2 module and an unknown module of approximately 100 residues at the C-terminus (Supplementary Fig. 4B). RESULTS | |
| 125 141 catalytic module structure_element According to PFAM database conserved domain classification, 128 GH5 enzymes have an architecture consisting of an N-terminal catalytic module, a CBM_X2 module and an unknown module of approximately 100 residues at the C-terminus (Supplementary Fig. 4B). RESULTS | |
| 145 151 CBM_X2 structure_element According to PFAM database conserved domain classification, 128 GH5 enzymes have an architecture consisting of an N-terminal catalytic module, a CBM_X2 module and an unknown module of approximately 100 residues at the C-terminus (Supplementary Fig. 4B). RESULTS | |
| 40 44 CBM1 structure_element Of these, 12 enzymes have an additional CBM1, and 5 have a CBM2 at the N-terminal region. RESULTS | |
| 59 63 CBM2 structure_element Of these, 12 enzymes have an additional CBM1, and 5 have a CBM2 at the N-terminal region. RESULTS | |
| 98 105 BlCel5B protein Based on this PFAM architecture and CAZy subfamily classification, all the 144 enzymes (including BlCel5B) belong to the GH5_4 subfamily and group together in the same branch of the phylogenetic tree, evidencing a common ancestor. RESULTS | |
| 121 126 GH5_4 protein_type Based on this PFAM architecture and CAZy subfamily classification, all the 144 enzymes (including BlCel5B) belong to the GH5_4 subfamily and group together in the same branch of the phylogenetic tree, evidencing a common ancestor. RESULTS | |
| 182 199 phylogenetic tree evidence Based on this PFAM architecture and CAZy subfamily classification, all the 144 enzymes (including BlCel5B) belong to the GH5_4 subfamily and group together in the same branch of the phylogenetic tree, evidencing a common ancestor. RESULTS | |
| 217 222 CBM46 structure_element These results support the hypothesis that the enzymes may employ the same mechanism by which ligand binding is mediated by an extensive conformational breathing of the enzyme that involves the large-scale movement of CBM46 around the Ig-like module (CBM_X2) as a structural hinge. RESULTS | |
| 234 248 Ig-like module structure_element These results support the hypothesis that the enzymes may employ the same mechanism by which ligand binding is mediated by an extensive conformational breathing of the enzyme that involves the large-scale movement of CBM46 around the Ig-like module (CBM_X2) as a structural hinge. RESULTS | |
| 250 256 CBM_X2 structure_element These results support the hypothesis that the enzymes may employ the same mechanism by which ligand binding is mediated by an extensive conformational breathing of the enzyme that involves the large-scale movement of CBM46 around the Ig-like module (CBM_X2) as a structural hinge. RESULTS | |
| 263 279 structural hinge structure_element These results support the hypothesis that the enzymes may employ the same mechanism by which ligand binding is mediated by an extensive conformational breathing of the enzyme that involves the large-scale movement of CBM46 around the Ig-like module (CBM_X2) as a structural hinge. RESULTS | |
| 23 33 trimodular protein_state Here, we elucidate the trimodular molecular architecture of the full-length BlCel5B, a member of the GH5_4 subfamily, for which large-scale conformational dynamics appears to play a central role in its enzymatic activity. DISCUSS | |
| 64 75 full-length protein_state Here, we elucidate the trimodular molecular architecture of the full-length BlCel5B, a member of the GH5_4 subfamily, for which large-scale conformational dynamics appears to play a central role in its enzymatic activity. DISCUSS | |
| 76 83 BlCel5B protein Here, we elucidate the trimodular molecular architecture of the full-length BlCel5B, a member of the GH5_4 subfamily, for which large-scale conformational dynamics appears to play a central role in its enzymatic activity. DISCUSS | |
| 101 106 GH5_4 protein_type Here, we elucidate the trimodular molecular architecture of the full-length BlCel5B, a member of the GH5_4 subfamily, for which large-scale conformational dynamics appears to play a central role in its enzymatic activity. DISCUSS | |
| 0 11 Full-length protein_state Full-length BlCel5B is active on both cellulosic and hemicellulosic substrates and auxiliary modules are crucial for its activity. DISCUSS | |
| 12 19 BlCel5B protein Full-length BlCel5B is active on both cellulosic and hemicellulosic substrates and auxiliary modules are crucial for its activity. DISCUSS | |
| 23 29 active protein_state Full-length BlCel5B is active on both cellulosic and hemicellulosic substrates and auxiliary modules are crucial for its activity. DISCUSS | |
| 38 48 cellulosic chemical Full-length BlCel5B is active on both cellulosic and hemicellulosic substrates and auxiliary modules are crucial for its activity. DISCUSS | |
| 53 67 hemicellulosic chemical Full-length BlCel5B is active on both cellulosic and hemicellulosic substrates and auxiliary modules are crucial for its activity. DISCUSS | |
| 5 32 carbohydrate-active enzymes protein_type Most carbohydrate-active enzymes are modular and consist of a catalytic domain appended to one or more separate AMs. DISCUSS | |
| 62 78 catalytic domain structure_element Most carbohydrate-active enzymes are modular and consist of a catalytic domain appended to one or more separate AMs. DISCUSS | |
| 112 115 AMs structure_element Most carbohydrate-active enzymes are modular and consist of a catalytic domain appended to one or more separate AMs. DISCUSS | |
| 0 3 AMs structure_element AMs, such as CBMs, typically recognize carbohydrates and target their cognate catalytic domains toward the substrate. DISCUSS | |
| 13 17 CBMs structure_element AMs, such as CBMs, typically recognize carbohydrates and target their cognate catalytic domains toward the substrate. DISCUSS | |
| 39 52 carbohydrates chemical AMs, such as CBMs, typically recognize carbohydrates and target their cognate catalytic domains toward the substrate. DISCUSS | |
| 78 95 catalytic domains structure_element AMs, such as CBMs, typically recognize carbohydrates and target their cognate catalytic domains toward the substrate. DISCUSS | |
| 12 31 structural analysis experimental_method Because the structural analysis of the protein is challenging if the linkers connecting the structural subunits of the enzyme are long and flexible, the standard approach is to study the domains separately. DISCUSS | |
| 69 76 linkers structure_element Because the structural analysis of the protein is challenging if the linkers connecting the structural subunits of the enzyme are long and flexible, the standard approach is to study the domains separately. DISCUSS | |
| 31 54 protein crystallography experimental_method In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 56 88 computational molecular dynamics experimental_method In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 94 98 SAXS experimental_method In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 209 212 GH5 protein_type In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 213 229 catalytic domain structure_element In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 238 241 AMs structure_element In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 245 256 full-length protein_state In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 257 264 BlCel5B protein In this work, a combination of protein crystallography, computational molecular dynamics, and SAXS analyses enabled the identification of a new conformational selection-based molecular mechanism that involves GH5 catalytic domain and two AMs in full-length BlCel5B. DISCUSS | |
| 21 28 BlCel5B protein We observed that the BlCel5B distal CBM46 is directly involved in shaping the local architecture of the substrate-binding site. DISCUSS | |
| 36 41 CBM46 structure_element We observed that the BlCel5B distal CBM46 is directly involved in shaping the local architecture of the substrate-binding site. DISCUSS | |
| 104 126 substrate-binding site site We observed that the BlCel5B distal CBM46 is directly involved in shaping the local architecture of the substrate-binding site. DISCUSS | |
| 13 15 CD structure_element Although the CD alone appears unable to bind the substrate for catalysis, the AMs exhibit open-close motions that allow the substrate to be captured in a suitable position for hydrolysis. DISCUSS | |
| 16 21 alone protein_state Although the CD alone appears unable to bind the substrate for catalysis, the AMs exhibit open-close motions that allow the substrate to be captured in a suitable position for hydrolysis. DISCUSS | |
| 78 81 AMs structure_element Although the CD alone appears unable to bind the substrate for catalysis, the AMs exhibit open-close motions that allow the substrate to be captured in a suitable position for hydrolysis. DISCUSS | |
| 90 94 open protein_state Although the CD alone appears unable to bind the substrate for catalysis, the AMs exhibit open-close motions that allow the substrate to be captured in a suitable position for hydrolysis. DISCUSS | |
| 95 100 close protein_state Although the CD alone appears unable to bind the substrate for catalysis, the AMs exhibit open-close motions that allow the substrate to be captured in a suitable position for hydrolysis. DISCUSS | |
| 50 53 AMs structure_element Here, we advocate that large-amplitude motions of AMs are crucial for assembling the enzyme into its active conformation, highlighting a new function of CBMs. DISCUSS | |
| 101 107 active protein_state Here, we advocate that large-amplitude motions of AMs are crucial for assembling the enzyme into its active conformation, highlighting a new function of CBMs. DISCUSS | |
| 153 157 CBMs structure_element Here, we advocate that large-amplitude motions of AMs are crucial for assembling the enzyme into its active conformation, highlighting a new function of CBMs. DISCUSS | |
| 58 66 extended protein_state This mechanism of substrate binding closely resembles the extended conformational selection model, with the induced-fit mechanism of reaction as its limiting case. DISCUSS | |
| 96 98 GH protein_type To the best of our knowledge, this enzymatic mechanism has not been proposed previously for any GH. DISCUSS | |
| 4 19 CD binding site site The CD binding site of BlCel5B is open and relatively flat and is thus barely able to properly hold the substrate in position for catalysis without assistance from the CBM46. DISCUSS | |
| 23 30 BlCel5B protein The CD binding site of BlCel5B is open and relatively flat and is thus barely able to properly hold the substrate in position for catalysis without assistance from the CBM46. DISCUSS | |
| 168 173 CBM46 structure_element The CD binding site of BlCel5B is open and relatively flat and is thus barely able to properly hold the substrate in position for catalysis without assistance from the CBM46. DISCUSS | |
| 19 23 GH5s protein_type In contrast, other GH5s belonging to subfamily 4 listed in the Protein Data Bank exhibit a deep binding cleft or tunnel that can effectively entrap the substrate for catalysis (Fig. 5). DISCUSS | |
| 96 109 binding cleft site In contrast, other GH5s belonging to subfamily 4 listed in the Protein Data Bank exhibit a deep binding cleft or tunnel that can effectively entrap the substrate for catalysis (Fig. 5). DISCUSS | |
| 113 119 tunnel site In contrast, other GH5s belonging to subfamily 4 listed in the Protein Data Bank exhibit a deep binding cleft or tunnel that can effectively entrap the substrate for catalysis (Fig. 5). DISCUSS | |
| 75 86 simulations experimental_method Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 92 97 CBM46 structure_element Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 119 131 binding site site Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 135 142 BlCel5B protein Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 162 174 binding site site Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 201 204 GH5 protein_type Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 218 222 lack protein_state Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 223 226 AMs structure_element Due to the marked interdomain conformational rearrangement observed in our simulations, the CBM46 generates a confined binding site in BlCel5B that resembles the binding site architecture of the other GH5 enzymes that lack AMs. DISCUSS | |
| 6 13 BlCel5B protein Thus, BlCel5B appears to have adopted a strategy of CBM46-mediated interactions for proper functioning. DISCUSS | |
| 52 57 CBM46 structure_element Thus, BlCel5B appears to have adopted a strategy of CBM46-mediated interactions for proper functioning. DISCUSS | |
| 24 31 BhCel5B protein Although the homologous BhCel5B has the same domain architecture of BlCel5B and belongs to the same subfamily (a comparison of the sequence and structure of BlCel5B and BhCel5B is presented in Supplementary Fig. 5), its binding site exhibits important differences that may impact the catalytic mechanism. DISCUSS | |
| 68 75 BlCel5B protein Although the homologous BhCel5B has the same domain architecture of BlCel5B and belongs to the same subfamily (a comparison of the sequence and structure of BlCel5B and BhCel5B is presented in Supplementary Fig. 5), its binding site exhibits important differences that may impact the catalytic mechanism. DISCUSS | |
| 144 153 structure evidence Although the homologous BhCel5B has the same domain architecture of BlCel5B and belongs to the same subfamily (a comparison of the sequence and structure of BlCel5B and BhCel5B is presented in Supplementary Fig. 5), its binding site exhibits important differences that may impact the catalytic mechanism. DISCUSS | |
| 157 164 BlCel5B protein Although the homologous BhCel5B has the same domain architecture of BlCel5B and belongs to the same subfamily (a comparison of the sequence and structure of BlCel5B and BhCel5B is presented in Supplementary Fig. 5), its binding site exhibits important differences that may impact the catalytic mechanism. DISCUSS | |
| 169 176 BhCel5B protein Although the homologous BhCel5B has the same domain architecture of BlCel5B and belongs to the same subfamily (a comparison of the sequence and structure of BlCel5B and BhCel5B is presented in Supplementary Fig. 5), its binding site exhibits important differences that may impact the catalytic mechanism. DISCUSS | |
| 220 232 binding site site Although the homologous BhCel5B has the same domain architecture of BlCel5B and belongs to the same subfamily (a comparison of the sequence and structure of BlCel5B and BhCel5B is presented in Supplementary Fig. 5), its binding site exhibits important differences that may impact the catalytic mechanism. DISCUSS | |
| 4 11 BhCel5B protein The BhCel5B binding site is V-shaped and deeper than the BlCel5B binding site (Figs 5 and 6). DISCUSS | |
| 12 24 binding site site The BhCel5B binding site is V-shaped and deeper than the BlCel5B binding site (Figs 5 and 6). DISCUSS | |
| 28 36 V-shaped protein_state The BhCel5B binding site is V-shaped and deeper than the BlCel5B binding site (Figs 5 and 6). DISCUSS | |
| 57 64 BlCel5B protein The BhCel5B binding site is V-shaped and deeper than the BlCel5B binding site (Figs 5 and 6). DISCUSS | |
| 65 77 binding site site The BhCel5B binding site is V-shaped and deeper than the BlCel5B binding site (Figs 5 and 6). DISCUSS | |
| 19 23 loop structure_element This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 41 45 F177 residue_name_number This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 50 54 R185 residue_name_number This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 60 67 BhCel5B protein This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 69 75 absent protein_state This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 83 90 BlCel5B protein This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 116 120 W181 residue_name_number This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 144 157 binding cleft site This is due to the loop between residues F177 and R185 from BhCel5B (absent in the BlCel5B), which contains residue W181 that forms part of the binding cleft (Fig. 6). DISCUSS | |
| 23 30 BhCel5B protein Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 31 36 CBM46 structure_element Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 54 70 β-1,3-1,4-glucan chemical Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 83 90 BhCel5B protein Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 113 119 active protein_state Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 120 127 without protein_state Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 128 133 CBM46 structure_element Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 140 149 truncated protein_state Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 171 177 active protein_state Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 186 196 xyloglucan chemical Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 218 223 CBM46 structure_element Consistently, although BhCel5B CBM46 is important for β-1,3-1,4-glucan hydrolysis (BhCel5B is about 60-fold less active without CBM46), the truncated enzyme is completely active against xyloglucan, suggesting that the CBM46, in this case, is necessary for the binding to specific substrates. DISCUSS | |
| 38 59 phylogenetic analysis experimental_method A closer inspection of results of the phylogenetic analysis, more specifically of the clade composed by GH5_4 enzymes with trimodular architecture (Supplementary Fig. 4C), reveals subclades whose main characteristic is the varying length of the loop located between residues 161 and 163 (BlCel5B residue numbering). DISCUSS | |
| 104 109 GH5_4 protein_type A closer inspection of results of the phylogenetic analysis, more specifically of the clade composed by GH5_4 enzymes with trimodular architecture (Supplementary Fig. 4C), reveals subclades whose main characteristic is the varying length of the loop located between residues 161 and 163 (BlCel5B residue numbering). DISCUSS | |
| 123 133 trimodular protein_state A closer inspection of results of the phylogenetic analysis, more specifically of the clade composed by GH5_4 enzymes with trimodular architecture (Supplementary Fig. 4C), reveals subclades whose main characteristic is the varying length of the loop located between residues 161 and 163 (BlCel5B residue numbering). DISCUSS | |
| 245 249 loop structure_element A closer inspection of results of the phylogenetic analysis, more specifically of the clade composed by GH5_4 enzymes with trimodular architecture (Supplementary Fig. 4C), reveals subclades whose main characteristic is the varying length of the loop located between residues 161 and 163 (BlCel5B residue numbering). DISCUSS | |
| 275 286 161 and 163 residue_range A closer inspection of results of the phylogenetic analysis, more specifically of the clade composed by GH5_4 enzymes with trimodular architecture (Supplementary Fig. 4C), reveals subclades whose main characteristic is the varying length of the loop located between residues 161 and 163 (BlCel5B residue numbering). DISCUSS | |
| 288 295 BlCel5B protein A closer inspection of results of the phylogenetic analysis, more specifically of the clade composed by GH5_4 enzymes with trimodular architecture (Supplementary Fig. 4C), reveals subclades whose main characteristic is the varying length of the loop located between residues 161 and 163 (BlCel5B residue numbering). DISCUSS | |
| 33 40 BlCel5B protein Therefore, our results show that BlCel5B represents a smaller group of enzymes that are completely dependent on its AMs for hydrolysis of plant cell wall polysaccharides, and that the underlying mechanism may rely on large-scale interdomain motions. DISCUSS | |
| 116 119 AMs structure_element Therefore, our results show that BlCel5B represents a smaller group of enzymes that are completely dependent on its AMs for hydrolysis of plant cell wall polysaccharides, and that the underlying mechanism may rely on large-scale interdomain motions. DISCUSS | |
| 138 143 plant taxonomy_domain Therefore, our results show that BlCel5B represents a smaller group of enzymes that are completely dependent on its AMs for hydrolysis of plant cell wall polysaccharides, and that the underlying mechanism may rely on large-scale interdomain motions. DISCUSS | |
| 154 169 polysaccharides chemical Therefore, our results show that BlCel5B represents a smaller group of enzymes that are completely dependent on its AMs for hydrolysis of plant cell wall polysaccharides, and that the underlying mechanism may rely on large-scale interdomain motions. DISCUSS | |
| 31 38 BlCel5B protein The amino acid sequence of the BlCel5B Ig-like module is recognized by BLASTP as belonging to CBM_X2, a poorly described group that has been compared with CBM-like accessory modules without a defined function. DISCUSS | |
| 39 53 Ig-like module structure_element The amino acid sequence of the BlCel5B Ig-like module is recognized by BLASTP as belonging to CBM_X2, a poorly described group that has been compared with CBM-like accessory modules without a defined function. DISCUSS | |
| 71 77 BLASTP experimental_method The amino acid sequence of the BlCel5B Ig-like module is recognized by BLASTP as belonging to CBM_X2, a poorly described group that has been compared with CBM-like accessory modules without a defined function. DISCUSS | |
| 94 100 CBM_X2 structure_element The amino acid sequence of the BlCel5B Ig-like module is recognized by BLASTP as belonging to CBM_X2, a poorly described group that has been compared with CBM-like accessory modules without a defined function. DISCUSS | |
| 155 181 CBM-like accessory modules structure_element The amino acid sequence of the BlCel5B Ig-like module is recognized by BLASTP as belonging to CBM_X2, a poorly described group that has been compared with CBM-like accessory modules without a defined function. DISCUSS | |
| 26 33 BlCel5B protein Despite the similarity of BlCel5B Ig-like module to CBMs, it lacks an identifiable aromatic residue-rich carbohydrate-binding site. DISCUSS | |
| 34 48 Ig-like module structure_element Despite the similarity of BlCel5B Ig-like module to CBMs, it lacks an identifiable aromatic residue-rich carbohydrate-binding site. DISCUSS | |
| 52 56 CBMs structure_element Despite the similarity of BlCel5B Ig-like module to CBMs, it lacks an identifiable aromatic residue-rich carbohydrate-binding site. DISCUSS | |
| 105 130 carbohydrate-binding site site Despite the similarity of BlCel5B Ig-like module to CBMs, it lacks an identifiable aromatic residue-rich carbohydrate-binding site. DISCUSS | |
| 43 57 Ig-like module structure_element Nonetheless, according to our results, the Ig-like module seems to play an important function as a structural hinge, dynamically holding the CBM46 and CD in positions that are appropriate for enzymatic activity. DISCUSS | |
| 99 115 structural hinge structure_element Nonetheless, according to our results, the Ig-like module seems to play an important function as a structural hinge, dynamically holding the CBM46 and CD in positions that are appropriate for enzymatic activity. DISCUSS | |
| 141 146 CBM46 structure_element Nonetheless, according to our results, the Ig-like module seems to play an important function as a structural hinge, dynamically holding the CBM46 and CD in positions that are appropriate for enzymatic activity. DISCUSS | |
| 151 153 CD structure_element Nonetheless, according to our results, the Ig-like module seems to play an important function as a structural hinge, dynamically holding the CBM46 and CD in positions that are appropriate for enzymatic activity. DISCUSS | |
| 28 65 crystallographic, computer simulation experimental_method Based on the results of our crystallographic, computer simulation, and SAXS structural analyses, as well as site-directed mutagenesis and activity assays, we propose a molecular mechanism for BlCel5B substrate binding, which might apply to other GH5_4 subfamily enzymes that share this tri-modular architecture. DISCUSS | |
| 71 95 SAXS structural analyses experimental_method Based on the results of our crystallographic, computer simulation, and SAXS structural analyses, as well as site-directed mutagenesis and activity assays, we propose a molecular mechanism for BlCel5B substrate binding, which might apply to other GH5_4 subfamily enzymes that share this tri-modular architecture. DISCUSS | |
| 108 133 site-directed mutagenesis experimental_method Based on the results of our crystallographic, computer simulation, and SAXS structural analyses, as well as site-directed mutagenesis and activity assays, we propose a molecular mechanism for BlCel5B substrate binding, which might apply to other GH5_4 subfamily enzymes that share this tri-modular architecture. DISCUSS | |
| 138 153 activity assays experimental_method Based on the results of our crystallographic, computer simulation, and SAXS structural analyses, as well as site-directed mutagenesis and activity assays, we propose a molecular mechanism for BlCel5B substrate binding, which might apply to other GH5_4 subfamily enzymes that share this tri-modular architecture. DISCUSS | |
| 192 199 BlCel5B protein Based on the results of our crystallographic, computer simulation, and SAXS structural analyses, as well as site-directed mutagenesis and activity assays, we propose a molecular mechanism for BlCel5B substrate binding, which might apply to other GH5_4 subfamily enzymes that share this tri-modular architecture. DISCUSS | |
| 246 251 GH5_4 protein_type Based on the results of our crystallographic, computer simulation, and SAXS structural analyses, as well as site-directed mutagenesis and activity assays, we propose a molecular mechanism for BlCel5B substrate binding, which might apply to other GH5_4 subfamily enzymes that share this tri-modular architecture. DISCUSS | |
| 286 297 tri-modular structure_element Based on the results of our crystallographic, computer simulation, and SAXS structural analyses, as well as site-directed mutagenesis and activity assays, we propose a molecular mechanism for BlCel5B substrate binding, which might apply to other GH5_4 subfamily enzymes that share this tri-modular architecture. DISCUSS | |
| 0 7 BlCel5B protein BlCel5B can be found in several different conformational states ranging from CBM46/CD closed (or occluded) to extended conformations (Fig. 7). DISCUSS | |
| 77 82 CBM46 structure_element BlCel5B can be found in several different conformational states ranging from CBM46/CD closed (or occluded) to extended conformations (Fig. 7). DISCUSS | |
| 83 85 CD structure_element BlCel5B can be found in several different conformational states ranging from CBM46/CD closed (or occluded) to extended conformations (Fig. 7). DISCUSS | |
| 86 92 closed protein_state BlCel5B can be found in several different conformational states ranging from CBM46/CD closed (or occluded) to extended conformations (Fig. 7). DISCUSS | |
| 97 105 occluded protein_state BlCel5B can be found in several different conformational states ranging from CBM46/CD closed (or occluded) to extended conformations (Fig. 7). DISCUSS | |
| 110 118 extended protein_state BlCel5B can be found in several different conformational states ranging from CBM46/CD closed (or occluded) to extended conformations (Fig. 7). DISCUSS | |
| 3 11 extended protein_state In extended configurations, the substrate may dock at the shallow substrate binding site of CD in one of the semi-closed conformations of the enzyme; however, its binding is properly stabilized for hydrolysis only with the aid of induced-fit repositioning mediated by CBM46. DISCUSS | |
| 66 88 substrate binding site site In extended configurations, the substrate may dock at the shallow substrate binding site of CD in one of the semi-closed conformations of the enzyme; however, its binding is properly stabilized for hydrolysis only with the aid of induced-fit repositioning mediated by CBM46. DISCUSS | |
| 92 94 CD structure_element In extended configurations, the substrate may dock at the shallow substrate binding site of CD in one of the semi-closed conformations of the enzyme; however, its binding is properly stabilized for hydrolysis only with the aid of induced-fit repositioning mediated by CBM46. DISCUSS | |
| 109 120 semi-closed protein_state In extended configurations, the substrate may dock at the shallow substrate binding site of CD in one of the semi-closed conformations of the enzyme; however, its binding is properly stabilized for hydrolysis only with the aid of induced-fit repositioning mediated by CBM46. DISCUSS | |
| 268 273 CBM46 structure_element In extended configurations, the substrate may dock at the shallow substrate binding site of CD in one of the semi-closed conformations of the enzyme; however, its binding is properly stabilized for hydrolysis only with the aid of induced-fit repositioning mediated by CBM46. DISCUSS | |
| 42 49 BlCel5B protein After cleavage, the intrinsic dynamics of BlCel5B would eventually allow the opening of the active site for product release. DISCUSS | |
| 92 103 active site site After cleavage, the intrinsic dynamics of BlCel5B would eventually allow the opening of the active site for product release. DISCUSS | |
| 46 87 mutagenesis and enzymatic activity assays experimental_method The proposed mechanism is consistent with our mutagenesis and enzymatic activity assays, which show that the Ig-like module and CBM46 are indispensable for BlCel5B catalytic activity and, together with the CD, form the unique catalytic domain of the enzyme. DISCUSS | |
| 109 123 Ig-like module structure_element The proposed mechanism is consistent with our mutagenesis and enzymatic activity assays, which show that the Ig-like module and CBM46 are indispensable for BlCel5B catalytic activity and, together with the CD, form the unique catalytic domain of the enzyme. DISCUSS | |
| 128 133 CBM46 structure_element The proposed mechanism is consistent with our mutagenesis and enzymatic activity assays, which show that the Ig-like module and CBM46 are indispensable for BlCel5B catalytic activity and, together with the CD, form the unique catalytic domain of the enzyme. DISCUSS | |
| 156 163 BlCel5B protein The proposed mechanism is consistent with our mutagenesis and enzymatic activity assays, which show that the Ig-like module and CBM46 are indispensable for BlCel5B catalytic activity and, together with the CD, form the unique catalytic domain of the enzyme. DISCUSS | |
| 206 208 CD structure_element The proposed mechanism is consistent with our mutagenesis and enzymatic activity assays, which show that the Ig-like module and CBM46 are indispensable for BlCel5B catalytic activity and, together with the CD, form the unique catalytic domain of the enzyme. DISCUSS | |
| 219 225 unique protein_state The proposed mechanism is consistent with our mutagenesis and enzymatic activity assays, which show that the Ig-like module and CBM46 are indispensable for BlCel5B catalytic activity and, together with the CD, form the unique catalytic domain of the enzyme. DISCUSS | |
| 226 242 catalytic domain structure_element The proposed mechanism is consistent with our mutagenesis and enzymatic activity assays, which show that the Ig-like module and CBM46 are indispensable for BlCel5B catalytic activity and, together with the CD, form the unique catalytic domain of the enzyme. DISCUSS | |
| 46 50 CBMs structure_element These experiments reveal a novel function for CBMs in which they are intimately involved in the assembly of the active site and catalytic process. DISCUSS | |
| 112 123 active site site These experiments reveal a novel function for CBMs in which they are intimately involved in the assembly of the active site and catalytic process. DISCUSS | |
| 0 20 Computer simulations experimental_method Computer simulations suggest that large-scale motions of the CBM46 and Ig-like domains mediate conformational selection and final induced-fit adjustments to trap the substrate at the active site and promote hydrolysis. DISCUSS | |
| 61 66 CBM46 structure_element Computer simulations suggest that large-scale motions of the CBM46 and Ig-like domains mediate conformational selection and final induced-fit adjustments to trap the substrate at the active site and promote hydrolysis. DISCUSS | |
| 71 86 Ig-like domains structure_element Computer simulations suggest that large-scale motions of the CBM46 and Ig-like domains mediate conformational selection and final induced-fit adjustments to trap the substrate at the active site and promote hydrolysis. DISCUSS | |
| 183 194 active site site Computer simulations suggest that large-scale motions of the CBM46 and Ig-like domains mediate conformational selection and final induced-fit adjustments to trap the substrate at the active site and promote hydrolysis. DISCUSS | |
| 0 4 SAXS experimental_method SAXS data support the modeling results, providing compelling evidence for highly mobile domains in solution. DISCUSS | |
| 22 30 modeling experimental_method SAXS data support the modeling results, providing compelling evidence for highly mobile domains in solution. DISCUSS | |
| 74 87 highly mobile protein_state SAXS data support the modeling results, providing compelling evidence for highly mobile domains in solution. DISCUSS | |
| 9 17 spectrum evidence A single spectrum was obtained by averaging four independent spectra generated by 300 laser shots at 60% potency. METHODS | |
| 61 68 spectra evidence A single spectrum was obtained by averaging four independent spectra generated by 300 laser shots at 60% potency. METHODS | |
| 41 44 apo protein_state The missing residues were taken from the apo BlCel5B structure after structural alignment using the LovoAlign server. METHODS | |
| 0 20 BlCel5B-cellooctaose complex_assembly BlCel5B-cellooctaose METHODS | |
| 22 42 BlCel5B-cellooctaose complex_assembly To get a model of the BlCel5B-cellooctaose complex in the closed conformation, we took the configuration after 80 ns of the restrained 200-ns MD simulation as the starting point for a 500-ns-long restrained aMD simulation, in which the CBM46 moved towards the CD in the presence of the harmonically-restrained cellooctaose chain. METHODS | |
| 75 95 BlCel5B-cellooctaose complex_assembly After this procedure, we released the restraints and propagated the closed BlCel5B-cellooctaose complex for additional 500 ns of conventional, restraint-free MD simulation. METHODS | |
| 0 14 Crystal models evidence Crystal models of BlCel5B. FIG | |
| 18 25 BlCel5B protein Crystal models of BlCel5B. FIG | |
| 9 18 structure evidence Complete structure is shown as a cartoon illustration in (a) and a van der Waals surface in (b). FIG | |
| 4 6 CD structure_element The CD module (red) has a typical TIM-barrel fold, and its substrate-binding site is adjacent to CBM46 (blue). FIG | |
| 34 49 TIM-barrel fold structure_element The CD module (red) has a typical TIM-barrel fold, and its substrate-binding site is adjacent to CBM46 (blue). FIG | |
| 59 81 substrate-binding site site The CD module (red) has a typical TIM-barrel fold, and its substrate-binding site is adjacent to CBM46 (blue). FIG | |
| 97 102 CBM46 structure_element The CD module (red) has a typical TIM-barrel fold, and its substrate-binding site is adjacent to CBM46 (blue). FIG | |
| 29 41 binding site site Despite the proximity of the binding site in the crystallographic model, the CBM46 residues W479 and W481 are distant from the substrate cellotetraose (yellow). FIG | |
| 77 82 CBM46 structure_element Despite the proximity of the binding site in the crystallographic model, the CBM46 residues W479 and W481 are distant from the substrate cellotetraose (yellow). FIG | |
| 92 96 W479 residue_name_number Despite the proximity of the binding site in the crystallographic model, the CBM46 residues W479 and W481 are distant from the substrate cellotetraose (yellow). FIG | |
| 101 105 W481 residue_name_number Despite the proximity of the binding site in the crystallographic model, the CBM46 residues W479 and W481 are distant from the substrate cellotetraose (yellow). FIG | |
| 137 150 cellotetraose chemical Despite the proximity of the binding site in the crystallographic model, the CBM46 residues W479 and W481 are distant from the substrate cellotetraose (yellow). FIG | |
| 4 18 Ig-like domain structure_element The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 86 88 CD structure_element The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 93 98 CBM46 structure_element The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 106 119 superposition experimental_method The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 127 141 Ig-like domain structure_element The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 146 151 CBM46 structure_element The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 248 252 loop structure_element The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 286 299 Cellotetraose chemical The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 309 326 subsites -1 to -3 site The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 344 355 coordinated bond_interaction The Ig-like domain (green) has a lateral position, serving as a connector between the CD and CBM46. (c) A superposition of the Ig-like domain and CBM46 illustrates their structural similarity, with most of the structural differences present in the loop highlighted by a red circle. (d) Cellotetraose occupies subsites -1 to -3 and is primarily coordinated by the residues represented in gray. FIG | |
| 0 7 BlCel5B protein BlCel5B enzymatic activity characterization. FIG | |
| 8 43 enzymatic activity characterization experimental_method BlCel5B enzymatic activity characterization. FIG | |
| 4 16 MALDI/TOF-MS experimental_method (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 17 24 spectra evidence (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 70 77 BlCel5B protein (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 90 109 deletion constructs experimental_method (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 111 117 ΔCBM46 mutant (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 122 131 ΔIg-CBM46 mutant (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 152 165 cellopentaose chemical (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 167 169 C5 chemical (a) MALDI/TOF-MS spectra of the products released after incubation of BlCel5B and its two deletion constructs (ΔCBM46 and ΔIg-CBM46) with the substrate cellopentaose (C5). FIG | |
| 16 23 spectra evidence The first three spectra show the substrate, enzyme and buffer controls. FIG | |
| 10 18 spectrum evidence The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 32 43 full length protein_state The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 44 51 BlCel5B protein The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 90 92 C5 chemical The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 106 122 oligosaccharides chemical The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 131 133 C4 chemical The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 135 137 C3 chemical The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 142 144 C2 chemical The forth spectrum reveals that full length BlCel5B is capable of enzymatic hydrolysis of C5 into smaller oligosaccharides such as C4, C3 and C2. FIG | |
| 13 20 spectra evidence The last two spectra show that the C-terminal deletions eliminate the enzyme activity. FIG | |
| 56 85 eliminate the enzyme activity protein_state The last two spectra show that the C-terminal deletions eliminate the enzyme activity. FIG | |
| 0 7 BlCel5B protein BlCel5B activities on CMC as functions of pH and temperature are shown in (b) and (c), respectively. FIG | |
| 22 25 CMC chemical BlCel5B activities on CMC as functions of pH and temperature are shown in (b) and (c), respectively. FIG | |
| 4 26 Michaelis-Menten curve evidence (d) Michaelis-Menten curve using CMC as a substrate. FIG | |
| 33 36 CMC chemical (d) Michaelis-Menten curve using CMC as a substrate. FIG | |
| 0 4 Open protein_state Open-close transitions of BlCel5B. FIG | |
| 5 10 close protein_state Open-close transitions of BlCel5B. FIG | |
| 26 33 BlCel5B protein Open-close transitions of BlCel5B. FIG | |
| 4 11 BlCel5B protein (a) BlCel5B in the absence of substrate and (b) in the presence of cellooctaose, as observed in our aMD simulations. FIG | |
| 19 29 absence of protein_state (a) BlCel5B in the absence of substrate and (b) in the presence of cellooctaose, as observed in our aMD simulations. FIG | |
| 55 66 presence of protein_state (a) BlCel5B in the absence of substrate and (b) in the presence of cellooctaose, as observed in our aMD simulations. FIG | |
| 67 79 cellooctaose chemical (a) BlCel5B in the absence of substrate and (b) in the presence of cellooctaose, as observed in our aMD simulations. FIG | |
| 100 115 aMD simulations experimental_method (a) BlCel5B in the absence of substrate and (b) in the presence of cellooctaose, as observed in our aMD simulations. FIG | |
| 4 12 distance evidence The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 46 50 I120 residue_name_number The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 52 54 CD structure_element The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 60 64 E477 residue_name_number The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 66 71 CBM46 structure_element The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 170 178 distance evidence The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 197 211 substrate-free protein_state The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 225 236 presence of protein_state The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 237 249 cellooctaose chemical The distance between the α carbon of residues I120 (CD) and E477 (CBM46), illustrated as spheres in (a), is plotted in (c), revealing a transition by the decrease in the distance from 40 Å to 7 Å (substrate-free) or 20 Å (in presence of cellooctaose). FIG | |
| 8 22 substrate-free protein_state For the substrate-free enzyme, the red line refers to a 1 μs-long aMD; for the BlCel5B-cellooctaose complex, the first 500 ns refers to aMD (in blue) and the second 500 ns to conventional MD (in turquoise). FIG | |
| 66 69 aMD experimental_method For the substrate-free enzyme, the red line refers to a 1 μs-long aMD; for the BlCel5B-cellooctaose complex, the first 500 ns refers to aMD (in blue) and the second 500 ns to conventional MD (in turquoise). FIG | |
| 79 99 BlCel5B-cellooctaose complex_assembly For the substrate-free enzyme, the red line refers to a 1 μs-long aMD; for the BlCel5B-cellooctaose complex, the first 500 ns refers to aMD (in blue) and the second 500 ns to conventional MD (in turquoise). FIG | |
| 136 139 aMD experimental_method For the substrate-free enzyme, the red line refers to a 1 μs-long aMD; for the BlCel5B-cellooctaose complex, the first 500 ns refers to aMD (in blue) and the second 500 ns to conventional MD (in turquoise). FIG | |
| 188 190 MD experimental_method For the substrate-free enzyme, the red line refers to a 1 μs-long aMD; for the BlCel5B-cellooctaose complex, the first 500 ns refers to aMD (in blue) and the second 500 ns to conventional MD (in turquoise). FIG | |
| 22 42 BlCel5B-cellooctaose complex_assembly (d) A snapshot of the BlCel5B-cellooctaose complex, highlighting the tryptophan residues that interact with the glucan chain in subsites −4 to +4. FIG | |
| 69 79 tryptophan residue_name (d) A snapshot of the BlCel5B-cellooctaose complex, highlighting the tryptophan residues that interact with the glucan chain in subsites −4 to +4. FIG | |
| 112 118 glucan chemical (d) A snapshot of the BlCel5B-cellooctaose complex, highlighting the tryptophan residues that interact with the glucan chain in subsites −4 to +4. FIG | |
| 128 145 subsites −4 to +4 site (d) A snapshot of the BlCel5B-cellooctaose complex, highlighting the tryptophan residues that interact with the glucan chain in subsites −4 to +4. FIG | |
| 9 13 W479 residue_name_number Residues W479 and W481 belong to CBM46 and only become available for substrate interactions in the closed configuration of BlCel5B. FIG | |
| 18 22 W481 residue_name_number Residues W479 and W481 belong to CBM46 and only become available for substrate interactions in the closed configuration of BlCel5B. FIG | |
| 33 38 CBM46 structure_element Residues W479 and W481 belong to CBM46 and only become available for substrate interactions in the closed configuration of BlCel5B. FIG | |
| 99 105 closed protein_state Residues W479 and W481 belong to CBM46 and only become available for substrate interactions in the closed configuration of BlCel5B. FIG | |
| 123 130 BlCel5B protein Residues W479 and W481 belong to CBM46 and only become available for substrate interactions in the closed configuration of BlCel5B. FIG | |
| 25 32 BlCel5B protein Large-scale movements of BlCel5B modules and superposition of their representative conformations with the SAXS envelope. FIG | |
| 45 58 superposition experimental_method Large-scale movements of BlCel5B modules and superposition of their representative conformations with the SAXS envelope. FIG | |
| 106 110 SAXS experimental_method Large-scale movements of BlCel5B modules and superposition of their representative conformations with the SAXS envelope. FIG | |
| 111 119 envelope evidence Large-scale movements of BlCel5B modules and superposition of their representative conformations with the SAXS envelope. FIG | |
| 4 11 BlCel5B protein (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 12 21 structure evidence (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 34 42 distance evidence (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 82 86 I120 residue_name_number (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 91 95 E477 residue_name_number (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 128 130 CD structure_element (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 135 140 CBM46 structure_element (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 246 250 I120 residue_name_number (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 251 255 E477 residue_name_number (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 256 264 distance evidence (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 280 297 CG-MD simulations experimental_method (a) BlCel5B structure showing the distance between the backbone beads of residues I120 and E477, which are centrally located in CD and CBM46, respectively, as a metric for the relative disposition between the two domains. (b) Time history of the I120-E477 distance computed using CG-MD simulations. FIG | |
| 71 82 simulations experimental_method Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 116 137 distance distribution evidence Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 167 173 closed protein_state Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 177 185 occluded protein_state Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 186 191 CBM46 structure_element Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 192 194 CD structure_element Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 214 223 semi-open protein_state Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 254 280 crystallographic structure evidence Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 286 294 extended protein_state Different colors separated by vertical lines correspond to independent simulations of approximately 120 μs. (c) The distance distribution indicates three major peaks: closed or occluded CBM46/CD conformations (I); semi-open (II), which is similar to the crystallographic structure; and extended conformers (III). FIG | |
| 4 19 Superimposition experimental_method (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 75 82 BlCel5B protein (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 92 96 SAXS experimental_method (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 97 102 model evidence (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 116 126 structures evidence (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 145 155 simulation experimental_method (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 230 240 superposed experimental_method (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 248 252 SAXS experimental_method (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 253 261 envelope evidence (d) Superimposition of the three representative molecular conformations of BlCel5B with the SAXS model. (e) Average structures obtained from the simulation segments corresponding to population groups I-III, which are individually superposed on the SAXS envelope. FIG | |
| 0 10 Comparison experimental_method Comparison of the binding site shape of GH5_4 enzymes available on the Protein Data Bank. FIG | |
| 18 30 binding site site Comparison of the binding site shape of GH5_4 enzymes available on the Protein Data Bank. FIG | |
| 40 45 GH5_4 protein_type Comparison of the binding site shape of GH5_4 enzymes available on the Protein Data Bank. FIG | |
| 4 11 BlCel5B protein (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 19 35 crystallographic experimental_method (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 40 46 closed protein_state (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 66 85 Bacillus halodurans species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 86 91 Cel5B protein (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 93 100 BhCel5B protein (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 121 142 Piromyces rhizinflata species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 143 146 GH5 protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 147 160 endoglucanase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 181 207 Clostridium cellulolyticum species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 208 211 GH5 protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 212 225 endoglucanase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 246 271 Clostridium cellulovorans species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 272 275 GH5 protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 276 289 endoglucanase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 310 328 Bacteroides ovatus species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 329 332 GH5 protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 333 346 xyloglucanase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 367 387 Paenibacillus pabuli species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 388 391 GH5 protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 392 405 xyloglucanase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 426 445 Prevotella bryantii species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 446 449 GH5 protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 450 463 endoglucanase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 484 514 Ruminiclostridium thermocellum species (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 531 534 GH5 protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 535 544 cellulase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 546 554 xylanase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 559 566 mannase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 587 610 Bacteroidetes bacterium taxonomy_domain (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 611 615 AC2a protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 616 629 endocellulase protein_type (a) BlCel5B in the crystallographic and closed configuration; (b) Bacillus halodurans Cel5B (BhCel5B) (PDB id: 4V2X) (c) Piromyces rhizinflata GH5 endoglucanase (PDB id: 3AYR); (d) Clostridium cellulolyticum GH5 endoglucanase (PDB id: 1EDG); (e) Clostridium cellulovorans GH5 endoglucanase (PDB id: 3NDY); (f) Bacteroides ovatus GH5 xyloglucanase (PDB id: 3ZMR); (g) Paenibacillus pabuli GH5 xyloglucanase (PDB id: 2JEP); (h) Prevotella bryantii GH5 endoglucanase (PDB id: 3VDH); (i) Ruminiclostridium thermocellum multifunctional GH5 cellulase, xylanase and mannase (PDB id: 4IM4); (j) Bacteroidetes bacterium AC2a endocellulase (PDB id: 4YHE). FIG | |
| 0 10 Comparison experimental_method Comparison of the binding cleft of the BlCel5B and BhCel5B. FIG | |
| 18 31 binding cleft site Comparison of the binding cleft of the BlCel5B and BhCel5B. FIG | |
| 39 46 BlCel5B protein Comparison of the binding cleft of the BlCel5B and BhCel5B. FIG | |
| 51 58 BhCel5B protein Comparison of the binding cleft of the BlCel5B and BhCel5B. FIG | |
| 28 35 BlCel5B protein The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 40 47 BhCel5B protein The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 85 90 cleft site The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 102 113 presence of protein_state The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 122 126 W181 residue_name_number The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 134 138 loop structure_element The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 147 151 F177 residue_name_number The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 156 160 R185 residue_name_number The main difference between BlCel5B and BhCel5B is that the latter exhibits a deeper cleft due to the presence of residue W181 in the loop between F177 and R185. FIG | |
| 42 54 binding site site We conjecture that this difference in the binding site architecture relates to the importance that the CBM46 plays in the BlCel5B enzymatic mechanism. FIG | |
| 103 108 CBM46 structure_element We conjecture that this difference in the binding site architecture relates to the importance that the CBM46 plays in the BlCel5B enzymatic mechanism. FIG | |
| 122 129 BlCel5B protein We conjecture that this difference in the binding site architecture relates to the importance that the CBM46 plays in the BlCel5B enzymatic mechanism. FIG | |
| 32 39 BlCel5B protein Proposed molecular mechanism of BlCel5B conformational selection. FIG | |
| 20 31 simulations experimental_method As suggested by the simulations and SAXS data, BlCel5B spans multiple conformations ranging from closed to extended CBM46/CD states. FIG | |
| 36 40 SAXS experimental_method As suggested by the simulations and SAXS data, BlCel5B spans multiple conformations ranging from closed to extended CBM46/CD states. FIG | |
| 47 54 BlCel5B protein As suggested by the simulations and SAXS data, BlCel5B spans multiple conformations ranging from closed to extended CBM46/CD states. FIG | |
| 97 103 closed protein_state As suggested by the simulations and SAXS data, BlCel5B spans multiple conformations ranging from closed to extended CBM46/CD states. FIG | |
| 107 115 extended protein_state As suggested by the simulations and SAXS data, BlCel5B spans multiple conformations ranging from closed to extended CBM46/CD states. FIG | |
| 116 121 CBM46 structure_element As suggested by the simulations and SAXS data, BlCel5B spans multiple conformations ranging from closed to extended CBM46/CD states. FIG | |
| 122 124 CD structure_element As suggested by the simulations and SAXS data, BlCel5B spans multiple conformations ranging from closed to extended CBM46/CD states. FIG | |
| 11 15 open protein_state In a given open state, the substrate may reach the active site and become entrapped by the capping of CBM46 onto CD and induced-fit conformational adjustments. FIG | |
| 51 62 active site site In a given open state, the substrate may reach the active site and become entrapped by the capping of CBM46 onto CD and induced-fit conformational adjustments. FIG | |
| 102 107 CBM46 structure_element In a given open state, the substrate may reach the active site and become entrapped by the capping of CBM46 onto CD and induced-fit conformational adjustments. FIG | |
| 113 115 CD structure_element In a given open state, the substrate may reach the active site and become entrapped by the capping of CBM46 onto CD and induced-fit conformational adjustments. FIG | |
| 60 63 apo protein_state After hydrolysis, the reaction product is released to yield apo-BlCel5B, which becomes ready for a new cycle. FIG | |
| 64 71 BlCel5B protein After hydrolysis, the reaction product is released to yield apo-BlCel5B, which becomes ready for a new cycle. FIG | |
| 12 19 BlCel5B protein Activity of BlCel5B constructs against tested substrates. TABLE | |
| 39 41 WT protein_state "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 43 48 W479A mutant "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 49 54 W481A mutant "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 55 61 ΔCBM46 mutant "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 62 71 ΔIg-CBM46 mutant "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 74 82 β-glucan chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 105 108 CMC chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 131 139 Lichenan chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 161 171 Xyloglucan chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 195 205 Azo-Avicel chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 225 237 Arabinoxylan chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 255 268 Galactomannan chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 286 298 1,4-β-mannan chemical "Substrate (1%) Relative Activity (%) WT* W479A W481A ΔCBM46 ΔIg-CBM46 β-glucan 100 79.1 63.6 nd nd CMC 25.5 12.2 2.4 nd nd Lichenan 52.4 41 28.6 nd nd Xyloglucan 45.2 41.2 30.8 nd nd Azo-Avicel nd** nd nd nd nd Arabinoxylan nd nd nd nd nd Galactomannan nd nd nd nd nd 1,4-β-mannan nd nd nd nd nd " TABLE | |
| 1 3 WT protein_state *WT = wild type. TABLE | |
| 6 15 wild type protein_state *WT = wild type. TABLE | |