| anno_start anno_end anno_text entity_type sentence section | |
| 23 39 Arabinoxylanases protein_type The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans* TITLE | |
| 54 70 Highly Decorated protein_state The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans* TITLE | |
| 71 77 Xylans chemical The Mechanism by Which Arabinoxylanases Can Recognize Highly Decorated Xylans* TITLE | |
| 29 34 plant taxonomy_domain The enzymatic degradation of plant cell walls is an important biological process of increasing environmental and industrial significance. ABSTRACT | |
| 0 5 Xylan chemical Xylan, a major component of the plant cell wall, consists of a backbone of Ξ²-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. ABSTRACT | |
| 32 37 plant taxonomy_domain Xylan, a major component of the plant cell wall, consists of a backbone of Ξ²-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. ABSTRACT | |
| 75 87 Ξ²-1,4-xylose chemical Xylan, a major component of the plant cell wall, consists of a backbone of Ξ²-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. ABSTRACT | |
| 89 93 Xylp chemical Xylan, a major component of the plant cell wall, consists of a backbone of Ξ²-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. ABSTRACT | |
| 131 146 arabinofuranose chemical Xylan, a major component of the plant cell wall, consists of a backbone of Ξ²-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. ABSTRACT | |
| 148 152 Araf chemical Xylan, a major component of the plant cell wall, consists of a backbone of Ξ²-1,4-xylose (Xylp) units that are often decorated with arabinofuranose (Araf) side chains. ABSTRACT | |
| 8 28 penta-modular enzyme protein_type A large penta-modular enzyme, CtXyl5A, was shown previously to specifically target arabinoxylans. ABSTRACT | |
| 30 37 CtXyl5A protein A large penta-modular enzyme, CtXyl5A, was shown previously to specifically target arabinoxylans. ABSTRACT | |
| 83 96 arabinoxylans chemical A large penta-modular enzyme, CtXyl5A, was shown previously to specifically target arabinoxylans. ABSTRACT | |
| 19 36 crystal structure evidence Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. ABSTRACT | |
| 44 59 arabinoxylanase protein_type Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. ABSTRACT | |
| 75 90 in complex with protein_state Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. ABSTRACT | |
| 91 98 ligands chemical Here we report the crystal structure of the arabinoxylanase and the enzyme in complex with ligands. ABSTRACT | |
| 95 111 catalytic domain structure_element The data showed that four of the protein modules adopt a rigid structure, which stabilizes the catalytic domain. ABSTRACT | |
| 15 56 non-catalytic carbohydrate binding module structure_element The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure, suggesting positional flexibility. ABSTRACT | |
| 86 103 crystal structure evidence The C-terminal non-catalytic carbohydrate binding module could not be observed in the crystal structure, suggesting positional flexibility. ABSTRACT | |
| 4 13 structure evidence The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 28 43 in complex with protein_state The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 44 94 Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp chemical The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 111 115 Araf chemical The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 144 150 xylose chemical The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 158 169 active site site The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 188 194 pocket site The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 196 207 β2* subsite site The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 229 245 catalytic center site The structure of the enzyme in complex with Xylp-Ξ²-1,4-Xylp-Ξ²-1,4-Xylp-[Ξ±-1,3-Araf]-Ξ²-1,4-Xylp showed that the Araf decoration linked O3 to the xylose in the active site is located in the pocket (β2* subsite) that abuts onto the catalytic center. ABSTRACT | |
| 4 15 β2* subsite site The β2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. ABSTRACT | |
| 33 37 Xylp chemical The β2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. ABSTRACT | |
| 42 46 Arap chemical The β2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. ABSTRACT | |
| 86 92 xylose chemical The β2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. ABSTRACT | |
| 97 106 arabinose chemical The β2* subsite can also bind to Xylp and Arap, explaining why the enzyme can utilize xylose and arabinose as specificity determinants. ABSTRACT | |
| 0 20 Alanine substitution experimental_method Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the β2* subsite, abrogates catalytic activity. ABSTRACT | |
| 24 29 Glu68 residue_name_number Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the β2* subsite, abrogates catalytic activity. ABSTRACT | |
| 31 36 Tyr92 residue_name_number Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the β2* subsite, abrogates catalytic activity. ABSTRACT | |
| 41 47 Asn139 residue_name_number Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the β2* subsite, abrogates catalytic activity. ABSTRACT | |
| 69 78 arabinose chemical Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the β2* subsite, abrogates catalytic activity. ABSTRACT | |
| 83 89 xylose chemical Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the β2* subsite, abrogates catalytic activity. ABSTRACT | |
| 109 120 β2* subsite site Alanine substitution of Glu68, Tyr92, or Asn139, which interact with arabinose and xylose side chains at the β2* subsite, abrogates catalytic activity. ABSTRACT | |
| 14 25 active site site Distal to the active site, the xylan backbone makes limited apolar contacts with the enzyme, and the hydroxyls are solvent-exposed. ABSTRACT | |
| 31 36 xylan chemical Distal to the active site, the xylan backbone makes limited apolar contacts with the enzyme, and the hydroxyls are solvent-exposed. ABSTRACT | |
| 115 130 solvent-exposed protein_state Distal to the active site, the xylan backbone makes limited apolar contacts with the enzyme, and the hydroxyls are solvent-exposed. ABSTRACT | |
| 18 25 CtXyl5A protein This explains why CtXyl5A is capable of hydrolyzing xylans that are extensively decorated and that are recalcitrant to classic endo-xylanase attack. ABSTRACT | |
| 52 58 xylans chemical This explains why CtXyl5A is capable of hydrolyzing xylans that are extensively decorated and that are recalcitrant to classic endo-xylanase attack. ABSTRACT | |
| 127 140 endo-xylanase protein_type This explains why CtXyl5A is capable of hydrolyzing xylans that are extensively decorated and that are recalcitrant to classic endo-xylanase attack. ABSTRACT | |
| 4 9 plant taxonomy_domain The plant cell wall is an important biological substrate. INTRO | |
| 53 67 microorganisms taxonomy_domain This complex composite structure is depolymerized by microorganisms that occupy important highly competitive ecological niches, whereas the process makes an important contribution to the carbon cycle. INTRO | |
| 15 20 plant taxonomy_domain Given that the plant cell wall is the most abundant source of renewable organic carbon on the planet, this macromolecular substrate has substantial industrial potential. INTRO | |
| 45 50 plant taxonomy_domain An example of the chemical complexity of the plant cell wall is provided by xylan, which is the major hemicellulosic component. INTRO | |
| 76 81 xylan chemical An example of the chemical complexity of the plant cell wall is provided by xylan, which is the major hemicellulosic component. INTRO | |
| 5 19 polysaccharide chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 44 58 Ξ²-1,4-d-xylose chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 77 85 pyranose chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 101 105 Xylp chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 137 165 4-O-methyl-d-glucuronic acid chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 167 171 GlcA chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 198 217 Ξ±-l-arabinofuranose chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 219 223 Araf chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 247 261 polysaccharide chemical This polysaccharide comprises a backbone of Ξ²-1,4-d-xylose residues in their pyranose configuration (Xylp) that are decorated at O2 with 4-O-methyl-d-glucuronic acid (GlcA) and at O2 and/or O3 with Ξ±-l-arabinofuranose (Araf) residues, whereas the polysaccharide can also be extensively acetylated. INTRO | |
| 17 21 Araf chemical In addition, the Araf side chain decorations can also be esterified to ferulic acid that, in some species, provide a chemical link between hemicellulose and lignin. INTRO | |
| 71 83 ferulic acid chemical In addition, the Araf side chain decorations can also be esterified to ferulic acid that, in some species, provide a chemical link between hemicellulose and lignin. INTRO | |
| 139 152 hemicellulose chemical In addition, the Araf side chain decorations can also be esterified to ferulic acid that, in some species, provide a chemical link between hemicellulose and lignin. INTRO | |
| 157 163 lignin chemical In addition, the Araf side chain decorations can also be esterified to ferulic acid that, in some species, provide a chemical link between hemicellulose and lignin. INTRO | |
| 25 31 xylans chemical The precise structure of xylans varies between plant species, in particular in different tissues and during cellular differentiation. INTRO | |
| 47 52 plant taxonomy_domain The precise structure of xylans varies between plant species, in particular in different tissues and during cellular differentiation. INTRO | |
| 15 20 plant taxonomy_domain In specialized plant tissues, such as the outer layer of cereal grains, xylans are extremely complex, and side chains may comprise a range of other sugars including l- and d-galactose and Ξ²- and Ξ±-Xylp units. INTRO | |
| 57 63 cereal taxonomy_domain In specialized plant tissues, such as the outer layer of cereal grains, xylans are extremely complex, and side chains may comprise a range of other sugars including l- and d-galactose and Ξ²- and Ξ±-Xylp units. INTRO | |
| 72 78 xylans chemical In specialized plant tissues, such as the outer layer of cereal grains, xylans are extremely complex, and side chains may comprise a range of other sugars including l- and d-galactose and Ξ²- and Ξ±-Xylp units. INTRO | |
| 148 154 sugars chemical In specialized plant tissues, such as the outer layer of cereal grains, xylans are extremely complex, and side chains may comprise a range of other sugars including l- and d-galactose and Ξ²- and Ξ±-Xylp units. INTRO | |
| 165 183 l- and d-galactose chemical In specialized plant tissues, such as the outer layer of cereal grains, xylans are extremely complex, and side chains may comprise a range of other sugars including l- and d-galactose and Ξ²- and Ξ±-Xylp units. INTRO | |
| 188 201 Ξ²- and Ξ±-Xylp chemical In specialized plant tissues, such as the outer layer of cereal grains, xylans are extremely complex, and side chains may comprise a range of other sugars including l- and d-galactose and Ξ²- and Ξ±-Xylp units. INTRO | |
| 17 23 cereal taxonomy_domain Indeed, in these cereal brans, xylans have very few backbone Xylp units that are undecorated, and the side chains can contain up to six sugars. INTRO | |
| 31 37 xylans chemical Indeed, in these cereal brans, xylans have very few backbone Xylp units that are undecorated, and the side chains can contain up to six sugars. INTRO | |
| 61 65 Xylp chemical Indeed, in these cereal brans, xylans have very few backbone Xylp units that are undecorated, and the side chains can contain up to six sugars. INTRO | |
| 136 142 sugars chemical Indeed, in these cereal brans, xylans have very few backbone Xylp units that are undecorated, and the side chains can contain up to six sugars. INTRO | |
| 55 60 plant taxonomy_domain Reflecting the chemical and physical complexity of the plant cell wall, microorganisms that utilize these composite structures express a large number of polysaccharide-degrading enzymes, primarily glycoside hydrolases, but also polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. INTRO | |
| 72 86 microorganisms taxonomy_domain Reflecting the chemical and physical complexity of the plant cell wall, microorganisms that utilize these composite structures express a large number of polysaccharide-degrading enzymes, primarily glycoside hydrolases, but also polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. INTRO | |
| 153 185 polysaccharide-degrading enzymes protein_type Reflecting the chemical and physical complexity of the plant cell wall, microorganisms that utilize these composite structures express a large number of polysaccharide-degrading enzymes, primarily glycoside hydrolases, but also polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. INTRO | |
| 197 217 glycoside hydrolases protein_type Reflecting the chemical and physical complexity of the plant cell wall, microorganisms that utilize these composite structures express a large number of polysaccharide-degrading enzymes, primarily glycoside hydrolases, but also polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. INTRO | |
| 228 249 polysaccharide lyases protein_type Reflecting the chemical and physical complexity of the plant cell wall, microorganisms that utilize these composite structures express a large number of polysaccharide-degrading enzymes, primarily glycoside hydrolases, but also polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. INTRO | |
| 251 273 carbohydrate esterases protein_type Reflecting the chemical and physical complexity of the plant cell wall, microorganisms that utilize these composite structures express a large number of polysaccharide-degrading enzymes, primarily glycoside hydrolases, but also polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. INTRO | |
| 279 314 lytic polysaccharide monooxygenases protein_type Reflecting the chemical and physical complexity of the plant cell wall, microorganisms that utilize these composite structures express a large number of polysaccharide-degrading enzymes, primarily glycoside hydrolases, but also polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. INTRO | |
| 6 33 carbohydrate active enzymes protein_type These carbohydrate active enzymes are grouped into sequence-based families in the CAZy database. INTRO | |
| 16 21 xylan chemical With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 58 64 xylans chemical With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 82 103 endo-acting xylanases protein_type With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 142 161 glycoside hydrolase protein_type With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 163 165 GH protein_type With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 166 167 5 protein_type With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 177 181 GH10 protein_type With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 186 190 GH11 protein_type With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 226 229 GH8 protein_type With respect to xylan degradation, the backbone of simple xylans is hydrolyzed by endo-acting xylanases, the majority of which are located in glycoside hydrolase (GH)5 families GH10 and GH11, although they are also present in GH8. INTRO | |
| 32 37 xylan chemical The extensive decoration of the xylan backbone generally restricts the capacity of these enzymes to attack the polysaccharide prior to removal of the side chains by a range of Ξ±-glucuronidases, Ξ±-arabinofuranosidases, and esterases. INTRO | |
| 111 125 polysaccharide chemical The extensive decoration of the xylan backbone generally restricts the capacity of these enzymes to attack the polysaccharide prior to removal of the side chains by a range of Ξ±-glucuronidases, Ξ±-arabinofuranosidases, and esterases. INTRO | |
| 176 192 Ξ±-glucuronidases protein_type The extensive decoration of the xylan backbone generally restricts the capacity of these enzymes to attack the polysaccharide prior to removal of the side chains by a range of Ξ±-glucuronidases, Ξ±-arabinofuranosidases, and esterases. INTRO | |
| 194 216 Ξ±-arabinofuranosidases protein_type The extensive decoration of the xylan backbone generally restricts the capacity of these enzymes to attack the polysaccharide prior to removal of the side chains by a range of Ξ±-glucuronidases, Ξ±-arabinofuranosidases, and esterases. INTRO | |
| 222 231 esterases protein_type The extensive decoration of the xylan backbone generally restricts the capacity of these enzymes to attack the polysaccharide prior to removal of the side chains by a range of Ξ±-glucuronidases, Ξ±-arabinofuranosidases, and esterases. INTRO | |
| 4 13 xylanases protein_type Two xylanases, however, utilize the side chains as essential specificity determinants and thus target decorated forms of the hemicellulose. INTRO | |
| 125 138 hemicellulose chemical Two xylanases, however, utilize the side chains as essential specificity determinants and thus target decorated forms of the hemicellulose. INTRO | |
| 4 8 GH30 protein_type The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 9 27 glucuronoxylanases protein_type The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 40 44 Xylp chemical The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 45 53 bound at protein_state The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 58 60 β2 site The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 74 78 GlcA chemical The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 121 141 glycoside hydrolases protein_type The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 153 171 subsites β1 and +1 site The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 177 185 subsites site The GH30 glucuronoxylanases require the Xylp bound at the β2 to contain a GlcA side chain (the scissile bond targeted by glycoside hydrolases is between subsites β1 and +1, and subsites that extend toward the non-reducing and reducing ends of the substrate are assigned increasing negative and positive numbers, respectively). INTRO | |
| 4 7 GH5 protein_type The GH5 arabinoxylanase (CtXyl5A) derived from Clostridium thermocellum displays an absolute requirement for xylans that contain Araf side chains. INTRO | |
| 8 23 arabinoxylanase protein_type The GH5 arabinoxylanase (CtXyl5A) derived from Clostridium thermocellum displays an absolute requirement for xylans that contain Araf side chains. INTRO | |
| 25 32 CtXyl5A protein The GH5 arabinoxylanase (CtXyl5A) derived from Clostridium thermocellum displays an absolute requirement for xylans that contain Araf side chains. INTRO | |
| 47 71 Clostridium thermocellum species The GH5 arabinoxylanase (CtXyl5A) derived from Clostridium thermocellum displays an absolute requirement for xylans that contain Araf side chains. INTRO | |
| 109 115 xylans chemical The GH5 arabinoxylanase (CtXyl5A) derived from Clostridium thermocellum displays an absolute requirement for xylans that contain Araf side chains. INTRO | |
| 129 133 Araf chemical The GH5 arabinoxylanase (CtXyl5A) derived from Clostridium thermocellum displays an absolute requirement for xylans that contain Araf side chains. INTRO | |
| 55 59 Araf chemical In this enzyme, the key specificity determinant is the Araf appended to O3 of the Xylp bound in the active site (β1 subsite). INTRO | |
| 82 86 Xylp chemical In this enzyme, the key specificity determinant is the Araf appended to O3 of the Xylp bound in the active site (β1 subsite). INTRO | |
| 87 95 bound in protein_state In this enzyme, the key specificity determinant is the Araf appended to O3 of the Xylp bound in the active site (β1 subsite). INTRO | |
| 100 111 active site site In this enzyme, the key specificity determinant is the Araf appended to O3 of the Xylp bound in the active site (β1 subsite). INTRO | |
| 113 123 β1 subsite site In this enzyme, the key specificity determinant is the Araf appended to O3 of the Xylp bound in the active site (β1 subsite). INTRO | |
| 37 50 arabinoxylans chemical The reaction products generated from arabinoxylans, however, suggest that Araf can be accommodated at subsites distal to the active site. INTRO | |
| 74 78 Araf chemical The reaction products generated from arabinoxylans, however, suggest that Araf can be accommodated at subsites distal to the active site. INTRO | |
| 102 110 subsites site The reaction products generated from arabinoxylans, however, suggest that Araf can be accommodated at subsites distal to the active site. INTRO | |
| 125 136 active site site The reaction products generated from arabinoxylans, however, suggest that Araf can be accommodated at subsites distal to the active site. INTRO | |
| 0 7 CtXyl5A protein CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 64 67 GH5 protein_type CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 68 84 catalytic module structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 86 91 CtGH5 structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 100 142 non-catalytic carbohydrate binding modules structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 144 148 CBMs structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 172 173 6 protein_type CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 175 181 CtCBM6 structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 184 186 13 protein_type CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 188 195 CtCBM13 structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 202 204 62 protein_type CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 206 213 CtCBM62 structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 216 234 fibronectin type 3 protein_type CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 236 239 Fn3 structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 266 274 dockerin structure_element CtXyl5A is a multimodular enzyme containing, in addition to the GH5 catalytic module (CtGH5); three non-catalytic carbohydrate binding modules (CBMs) belonging to families 6 (CtCBM6), 13 (CtCBM13), and 62 (CtCBM62); fibronectin type 3 (Fn3) domain; and a C-terminal dockerin domain Fig. 1. INTRO | |
| 20 23 Fn3 structure_element Previous studies of Fn3 domains have indicated that they might function as ligand-binding modules, as a compact form of peptide linkers or spacers between other domains, as cellulose-disrupting modules, or as proteins that help large enzyme complexes remain soluble. INTRO | |
| 75 97 ligand-binding modules structure_element Previous studies of Fn3 domains have indicated that they might function as ligand-binding modules, as a compact form of peptide linkers or spacers between other domains, as cellulose-disrupting modules, or as proteins that help large enzyme complexes remain soluble. INTRO | |
| 173 201 cellulose-disrupting modules structure_element Previous studies of Fn3 domains have indicated that they might function as ligand-binding modules, as a compact form of peptide linkers or spacers between other domains, as cellulose-disrupting modules, or as proteins that help large enzyme complexes remain soluble. INTRO | |
| 4 12 dockerin structure_element The dockerin domain recruits the enzyme into the cellulosome, a multienzyme plant cell wall degrading complex presented on the surface of C. thermocellum. INTRO | |
| 49 60 cellulosome complex_assembly The dockerin domain recruits the enzyme into the cellulosome, a multienzyme plant cell wall degrading complex presented on the surface of C. thermocellum. INTRO | |
| 76 81 plant taxonomy_domain The dockerin domain recruits the enzyme into the cellulosome, a multienzyme plant cell wall degrading complex presented on the surface of C. thermocellum. INTRO | |
| 138 153 C. thermocellum species The dockerin domain recruits the enzyme into the cellulosome, a multienzyme plant cell wall degrading complex presented on the surface of C. thermocellum. INTRO | |
| 0 6 CtCBM6 structure_element CtCBM6 stabilizes CtGH5, and CtCBM62 binds to d-galactopyranose and l-arabinopyranose. INTRO | |
| 18 23 CtGH5 structure_element CtCBM6 stabilizes CtGH5, and CtCBM62 binds to d-galactopyranose and l-arabinopyranose. INTRO | |
| 29 36 CtCBM62 structure_element CtCBM6 stabilizes CtGH5, and CtCBM62 binds to d-galactopyranose and l-arabinopyranose. INTRO | |
| 46 63 d-galactopyranose chemical CtCBM6 stabilizes CtGH5, and CtCBM62 binds to d-galactopyranose and l-arabinopyranose. INTRO | |
| 68 85 l-arabinopyranose chemical CtCBM6 stabilizes CtGH5, and CtCBM62 binds to d-galactopyranose and l-arabinopyranose. INTRO | |
| 20 27 CtCBM13 structure_element The function of the CtCBM13 and Fn3 modules remains unclear. INTRO | |
| 32 35 Fn3 structure_element The function of the CtCBM13 and Fn3 modules remains unclear. INTRO | |
| 25 42 crystal structure evidence This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 46 52 mature protein_state This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 53 60 CtXyl5A protein This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 61 68 lacking protein_state This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 84 92 dockerin structure_element This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 101 112 CtXyl5A-Doc mutant This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 130 145 in complex with protein_state This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 146 153 ligands chemical This report exploits the crystal structure of mature CtXyl5A lacking its C-terminal dockerin domain (CtXyl5A-Doc), and the enzyme in complex with ligands, to explore the mechanism of substrate specificity. INTRO | |
| 106 112 xylans chemical The data show that the plasticity in substrate recognition enables the enzyme to hydrolyze highly complex xylans that are not accessible to classical GH10 and GH11 endo-xylanases. INTRO | |
| 150 154 GH10 protein_type The data show that the plasticity in substrate recognition enables the enzyme to hydrolyze highly complex xylans that are not accessible to classical GH10 and GH11 endo-xylanases. INTRO | |
| 159 163 GH11 protein_type The data show that the plasticity in substrate recognition enables the enzyme to hydrolyze highly complex xylans that are not accessible to classical GH10 and GH11 endo-xylanases. INTRO | |
| 164 178 endo-xylanases protein_type The data show that the plasticity in substrate recognition enables the enzyme to hydrolyze highly complex xylans that are not accessible to classical GH10 and GH11 endo-xylanases. INTRO | |
| 26 32 GH5_34 protein_type Molecular architecture of GH5_34 enzymes. FIG | |
| 20 22 GH structure_element Modules prefaced by GH, CBM, or CE are modules in the indicated glycoside hydrolase, carbohydrate binding module, or carbohydrate esterase families, respectively. FIG | |
| 24 27 CBM structure_element Modules prefaced by GH, CBM, or CE are modules in the indicated glycoside hydrolase, carbohydrate binding module, or carbohydrate esterase families, respectively. FIG | |
| 32 34 CE structure_element Modules prefaced by GH, CBM, or CE are modules in the indicated glycoside hydrolase, carbohydrate binding module, or carbohydrate esterase families, respectively. FIG | |
| 64 83 glycoside hydrolase protein_type Modules prefaced by GH, CBM, or CE are modules in the indicated glycoside hydrolase, carbohydrate binding module, or carbohydrate esterase families, respectively. FIG | |
| 85 112 carbohydrate binding module structure_element Modules prefaced by GH, CBM, or CE are modules in the indicated glycoside hydrolase, carbohydrate binding module, or carbohydrate esterase families, respectively. FIG | |
| 117 138 carbohydrate esterase protein_type Modules prefaced by GH, CBM, or CE are modules in the indicated glycoside hydrolase, carbohydrate binding module, or carbohydrate esterase families, respectively. FIG | |
| 0 11 Laminin_3_G structure_element Laminin_3_G domain belongs to the concanavalin A lectin superfamily, and FN3 denotes a fibronectin type 3 domain. FIG | |
| 34 67 concanavalin A lectin superfamily protein_type Laminin_3_G domain belongs to the concanavalin A lectin superfamily, and FN3 denotes a fibronectin type 3 domain. FIG | |
| 73 76 FN3 structure_element Laminin_3_G domain belongs to the concanavalin A lectin superfamily, and FN3 denotes a fibronectin type 3 domain. FIG | |
| 87 112 fibronectin type 3 domain structure_element Laminin_3_G domain belongs to the concanavalin A lectin superfamily, and FN3 denotes a fibronectin type 3 domain. FIG | |
| 23 31 dockerin structure_element Segments labeled D are dockerin domains. FIG | |
| 25 32 CtXyl5A protein Substrate Specificity of CtXyl5A RESULTS | |
| 29 36 CtXyl5A protein Previous studies showed that CtXyl5A is an arabinoxylan-specific xylanase that generates xylooligosaccharides with an arabinose linked O3 to the reducing end xylose. RESULTS | |
| 43 73 arabinoxylan-specific xylanase protein_type Previous studies showed that CtXyl5A is an arabinoxylan-specific xylanase that generates xylooligosaccharides with an arabinose linked O3 to the reducing end xylose. RESULTS | |
| 89 109 xylooligosaccharides chemical Previous studies showed that CtXyl5A is an arabinoxylan-specific xylanase that generates xylooligosaccharides with an arabinose linked O3 to the reducing end xylose. RESULTS | |
| 118 127 arabinose chemical Previous studies showed that CtXyl5A is an arabinoxylan-specific xylanase that generates xylooligosaccharides with an arabinose linked O3 to the reducing end xylose. RESULTS | |
| 158 164 xylose chemical Previous studies showed that CtXyl5A is an arabinoxylan-specific xylanase that generates xylooligosaccharides with an arabinose linked O3 to the reducing end xylose. RESULTS | |
| 34 39 wheat taxonomy_domain The enzyme is active against both wheat and rye arabinoxylans (abbreviated as WAX and RAX, respectively). RESULTS | |
| 44 47 rye taxonomy_domain The enzyme is active against both wheat and rye arabinoxylans (abbreviated as WAX and RAX, respectively). RESULTS | |
| 48 61 arabinoxylans chemical The enzyme is active against both wheat and rye arabinoxylans (abbreviated as WAX and RAX, respectively). RESULTS | |
| 78 81 WAX chemical The enzyme is active against both wheat and rye arabinoxylans (abbreviated as WAX and RAX, respectively). RESULTS | |
| 86 89 RAX chemical The enzyme is active against both wheat and rye arabinoxylans (abbreviated as WAX and RAX, respectively). RESULTS | |
| 21 30 arabinose chemical It was proposed that arabinose decorations make productive interactions with a pocket (β2*) that is abutted onto the active site or β1 subsite. RESULTS | |
| 79 85 pocket site It was proposed that arabinose decorations make productive interactions with a pocket (β2*) that is abutted onto the active site or β1 subsite. RESULTS | |
| 87 90 β2* site It was proposed that arabinose decorations make productive interactions with a pocket (β2*) that is abutted onto the active site or β1 subsite. RESULTS | |
| 117 128 active site site It was proposed that arabinose decorations make productive interactions with a pocket (β2*) that is abutted onto the active site or β1 subsite. RESULTS | |
| 132 142 β1 subsite site It was proposed that arabinose decorations make productive interactions with a pocket (β2*) that is abutted onto the active site or β1 subsite. RESULTS | |
| 0 9 Arabinose chemical Arabinose side chains of the other backbone xylose units in the oligosaccharides generated by CtXyl5A were essentially random. RESULTS | |
| 44 50 xylose chemical Arabinose side chains of the other backbone xylose units in the oligosaccharides generated by CtXyl5A were essentially random. RESULTS | |
| 64 80 oligosaccharides chemical Arabinose side chains of the other backbone xylose units in the oligosaccharides generated by CtXyl5A were essentially random. RESULTS | |
| 94 101 CtXyl5A protein Arabinose side chains of the other backbone xylose units in the oligosaccharides generated by CtXyl5A were essentially random. RESULTS | |
| 52 58 xylose chemical These data suggest that O3, and possibly O2, on the xylose residues at subsites distal to the active site and β2* pocket are solvent-exposed, implying that the enzyme can access highly decorated xylans. RESULTS | |
| 71 79 subsites site These data suggest that O3, and possibly O2, on the xylose residues at subsites distal to the active site and β2* pocket are solvent-exposed, implying that the enzyme can access highly decorated xylans. RESULTS | |
| 94 105 active site site These data suggest that O3, and possibly O2, on the xylose residues at subsites distal to the active site and β2* pocket are solvent-exposed, implying that the enzyme can access highly decorated xylans. RESULTS | |
| 110 120 β2* pocket site These data suggest that O3, and possibly O2, on the xylose residues at subsites distal to the active site and β2* pocket are solvent-exposed, implying that the enzyme can access highly decorated xylans. RESULTS | |
| 125 140 solvent-exposed protein_state These data suggest that O3, and possibly O2, on the xylose residues at subsites distal to the active site and β2* pocket are solvent-exposed, implying that the enzyme can access highly decorated xylans. RESULTS | |
| 195 201 xylans chemical These data suggest that O3, and possibly O2, on the xylose residues at subsites distal to the active site and β2* pocket are solvent-exposed, implying that the enzyme can access highly decorated xylans. RESULTS | |
| 41 48 CtXyl5A protein To test this hypothesis, the activity of CtXyl5A against xylans from cereal brans was assessed. RESULTS | |
| 57 63 xylans chemical To test this hypothesis, the activity of CtXyl5A against xylans from cereal brans was assessed. RESULTS | |
| 69 75 cereal taxonomy_domain To test this hypothesis, the activity of CtXyl5A against xylans from cereal brans was assessed. RESULTS | |
| 0 7 CtXyl5a protein CtXyl5a was incubated with a range of xylans for 16 h at 60 Β°C, and the limit products were visualized by TLC. RESULTS | |
| 12 21 incubated experimental_method CtXyl5a was incubated with a range of xylans for 16 h at 60 Β°C, and the limit products were visualized by TLC. RESULTS | |
| 38 44 xylans chemical CtXyl5a was incubated with a range of xylans for 16 h at 60 Β°C, and the limit products were visualized by TLC. RESULTS | |
| 106 109 TLC experimental_method CtXyl5a was incubated with a range of xylans for 16 h at 60 Β°C, and the limit products were visualized by TLC. RESULTS | |
| 6 12 xylans chemical These xylans are highly decorated not only with Araf and GlcA units but also with l-Gal, d-Gal, and d-Xyl. RESULTS | |
| 48 52 Araf chemical These xylans are highly decorated not only with Araf and GlcA units but also with l-Gal, d-Gal, and d-Xyl. RESULTS | |
| 57 61 GlcA chemical These xylans are highly decorated not only with Araf and GlcA units but also with l-Gal, d-Gal, and d-Xyl. RESULTS | |
| 82 87 l-Gal chemical These xylans are highly decorated not only with Araf and GlcA units but also with l-Gal, d-Gal, and d-Xyl. RESULTS | |
| 89 94 d-Gal chemical These xylans are highly decorated not only with Araf and GlcA units but also with l-Gal, d-Gal, and d-Xyl. RESULTS | |
| 100 105 d-Xyl chemical These xylans are highly decorated not only with Araf and GlcA units but also with l-Gal, d-Gal, and d-Xyl. RESULTS | |
| 17 23 xylose chemical Indeed, very few xylose units in the backbone of bran xylans lack side chains. RESULTS | |
| 54 60 xylans chemical Indeed, very few xylose units in the backbone of bran xylans lack side chains. RESULTS | |
| 42 49 CtXyl5A protein The data presented in Table 1 showed that CtXyl5A was active against corn bran xylan (CX). RESULTS | |
| 69 73 corn taxonomy_domain The data presented in Table 1 showed that CtXyl5A was active against corn bran xylan (CX). RESULTS | |
| 79 84 xylan chemical The data presented in Table 1 showed that CtXyl5A was active against corn bran xylan (CX). RESULTS | |
| 86 88 CX chemical The data presented in Table 1 showed that CtXyl5A was active against corn bran xylan (CX). RESULTS | |
| 20 34 endo-xylanases protein_type In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 40 44 GH10 protein_type In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 49 53 GH11 protein_type In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 76 78 CX chemical In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 95 102 lack of protein_state In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 115 121 xylose chemical In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 149 160 active site site In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 187 194 bind to protein_state In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 211 217 xylose chemical In contrast typical endo-xylanases from GH10 and GH11 were unable to attack CX, reflecting the lack of undecorated xylose units in the backbone (the active site of these enzymes can only bind to non-substituted xylose residues). RESULTS | |
| 32 39 CtXyl5A protein The limit products generated by CtXyl5A from CX consisted of an extensive range of oligosaccharides. RESULTS | |
| 45 47 CX chemical The limit products generated by CtXyl5A from CX consisted of an extensive range of oligosaccharides. RESULTS | |
| 83 99 oligosaccharides chemical The limit products generated by CtXyl5A from CX consisted of an extensive range of oligosaccharides. RESULTS | |
| 36 44 subsites site These data support the view that in subsites out with the active site the O2 and O3 groups of the bound xylose units are solvent-exposed and will thus tolerate decoration. RESULTS | |
| 58 69 active site site These data support the view that in subsites out with the active site the O2 and O3 groups of the bound xylose units are solvent-exposed and will thus tolerate decoration. RESULTS | |
| 104 110 xylose chemical These data support the view that in subsites out with the active site the O2 and O3 groups of the bound xylose units are solvent-exposed and will thus tolerate decoration. RESULTS | |
| 121 136 solvent-exposed protein_state These data support the view that in subsites out with the active site the O2 and O3 groups of the bound xylose units are solvent-exposed and will thus tolerate decoration. RESULTS | |
| 0 8 Kinetics evidence Kinetics of GH5_34 arabinoxylanases TABLE | |
| 12 18 GH5_34 protein_type Kinetics of GH5_34 arabinoxylanases TABLE | |
| 19 35 arabinoxylanases protein_type Kinetics of GH5_34 arabinoxylanases TABLE | |
| 15 19 kcat evidence "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 20 22 Km evidence "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 25 28 WAX chemical "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 29 32 RAX chemical "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 33 35 CX chemical "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 54 61 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 62 88 CtGH5-CBM6-CBM13-Fn3-CBM62 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 102 109 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 110 130 CtGH5-CBM6-CBM13-Fn3 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 146 153 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 154 170 CtGH5-CBM6-CBM13 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 186 193 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 194 204 CtGH5-CBM6 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 218 225 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 226 236 CtGH5-CBM6 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 238 242 E68A mutant "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 254 261 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 262 272 CtGH5-CBM6 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 274 278 Y92A mutant "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 290 297 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 298 308 CtGH5-CBM6 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 310 315 N135A mutant "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 328 335 CtXyl5A protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 336 346 CtGH5-CBM6 structure_element "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 348 353 N139A mutant "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 365 370 AcGH5 protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 371 380 Wild type protein_state "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 397 402 GpGH5 protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 403 412 Wild type protein_state "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 431 436 VbGH5 protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 437 446 Wild type protein_state "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 458 463 VbGH5 protein "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 464 468 D45A mutant "Enzyme Variant kcat/Km WAX RAX CX minβ1mgβ1ml CtXyl5A CtGH5-CBM6-CBM13-Fn3-CBM62 800 ND 460 CtXyl5A CtGH5-CBM6-CBM13-Fn3 1,232 ND 659 CtXyl5A CtGH5-CBM6-CBM13 1,307 ND 620 CtXyl5A CtGH5-CBM6 488 ND 102 CtXyl5A CtGH5-CBM6: E68A NA NA NA CtXyl5A CtGH5-CBM6: Y92A NA NA NA CtXyl5A CtGH5-CBM6: N135A 260 ND ND CtXyl5A CtGH5-CBM6: N139A NA NA NA AcGH5 Wild type 628 1,641 289 GpGH5 Wild type 2,600 9,986 314 VbGH5 Wild type ND ND ND VbGH5 D45A 102 203 23 " TABLE | |
| 29 42 bound only at protein_state To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 43 46 β2* site To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 51 53 β1 site To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 61 78 negative subsites site To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 97 104 CtXyl5A protein To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 128 130 CX chemical To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 147 162 arabinoxylanase protein_type To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 181 210 size exclusion chromatography experimental_method To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 249 265 oligosaccharides chemical To explore whether substrate bound only at β2* and β1 in the negative subsites was hydrolyzed by CtXyl5A, the limit products of CX digested by the arabinoxylanase were subjected to size exclusion chromatography using a Bio-Gel P-2, and the smallest oligosaccharides (largest elution volume) were chosen for further study. RESULTS | |
| 0 5 HPAEC experimental_method HPAEC analysis of the smallest oligosaccharide fraction (pool 4) contained two species with retention times of 14.0 min (oligosaccharide 1) and 20.8 min (oligosaccharide 2) (Fig. 2). RESULTS | |
| 31 46 oligosaccharide chemical HPAEC analysis of the smallest oligosaccharide fraction (pool 4) contained two species with retention times of 14.0 min (oligosaccharide 1) and 20.8 min (oligosaccharide 2) (Fig. 2). RESULTS | |
| 121 136 oligosaccharide chemical HPAEC analysis of the smallest oligosaccharide fraction (pool 4) contained two species with retention times of 14.0 min (oligosaccharide 1) and 20.8 min (oligosaccharide 2) (Fig. 2). RESULTS | |
| 154 169 oligosaccharide chemical HPAEC analysis of the smallest oligosaccharide fraction (pool 4) contained two species with retention times of 14.0 min (oligosaccharide 1) and 20.8 min (oligosaccharide 2) (Fig. 2). RESULTS | |
| 0 44 Positive mode electrospray mass spectrometry experimental_method Positive mode electrospray mass spectrometry showed that pool 4 contained exclusively molecular ions with a m/z = 305 [M + Na]+, which corresponds to a pentose-pentose disaccharide (molecular mass = 282 Da) as a sodium ion adduct, whereas a dimer of the disaccharide with a sodium adduct (m/z = 587 [2M+Na]+) was also evident. RESULTS | |
| 152 159 pentose chemical Positive mode electrospray mass spectrometry showed that pool 4 contained exclusively molecular ions with a m/z = 305 [M + Na]+, which corresponds to a pentose-pentose disaccharide (molecular mass = 282 Da) as a sodium ion adduct, whereas a dimer of the disaccharide with a sodium adduct (m/z = 587 [2M+Na]+) was also evident. RESULTS | |
| 160 167 pentose chemical Positive mode electrospray mass spectrometry showed that pool 4 contained exclusively molecular ions with a m/z = 305 [M + Na]+, which corresponds to a pentose-pentose disaccharide (molecular mass = 282 Da) as a sodium ion adduct, whereas a dimer of the disaccharide with a sodium adduct (m/z = 587 [2M+Na]+) was also evident. RESULTS | |
| 168 180 disaccharide chemical Positive mode electrospray mass spectrometry showed that pool 4 contained exclusively molecular ions with a m/z = 305 [M + Na]+, which corresponds to a pentose-pentose disaccharide (molecular mass = 282 Da) as a sodium ion adduct, whereas a dimer of the disaccharide with a sodium adduct (m/z = 587 [2M+Na]+) was also evident. RESULTS | |
| 254 266 disaccharide chemical Positive mode electrospray mass spectrometry showed that pool 4 contained exclusively molecular ions with a m/z = 305 [M + Na]+, which corresponds to a pentose-pentose disaccharide (molecular mass = 282 Da) as a sodium ion adduct, whereas a dimer of the disaccharide with a sodium adduct (m/z = 587 [2M+Na]+) was also evident. RESULTS | |
| 55 69 TFA hydrolysis experimental_method The monosaccharide composition of pool 4 determined by TFA hydrolysis contained xylose and arabinose in a 3:1 ratio. RESULTS | |
| 80 86 xylose chemical The monosaccharide composition of pool 4 determined by TFA hydrolysis contained xylose and arabinose in a 3:1 ratio. RESULTS | |
| 91 100 arabinose chemical The monosaccharide composition of pool 4 determined by TFA hydrolysis contained xylose and arabinose in a 3:1 ratio. RESULTS | |
| 27 43 oligosaccharides chemical This suggests that the two oligosaccharides consist of two disaccharides: one consisting of two xylose residues and the other consisting of an arabinose linked to a xylose. RESULTS | |
| 59 72 disaccharides chemical This suggests that the two oligosaccharides consist of two disaccharides: one consisting of two xylose residues and the other consisting of an arabinose linked to a xylose. RESULTS | |
| 96 102 xylose chemical This suggests that the two oligosaccharides consist of two disaccharides: one consisting of two xylose residues and the other consisting of an arabinose linked to a xylose. RESULTS | |
| 143 152 arabinose chemical This suggests that the two oligosaccharides consist of two disaccharides: one consisting of two xylose residues and the other consisting of an arabinose linked to a xylose. RESULTS | |
| 165 171 xylose chemical This suggests that the two oligosaccharides consist of two disaccharides: one consisting of two xylose residues and the other consisting of an arabinose linked to a xylose. RESULTS | |
| 29 60 nonspecific arabinofuranosidase protein_type Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 62 70 CjAbf51A protein Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 96 111 oligosaccharide chemical Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 141 147 xylose chemical Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 152 161 arabinose chemical Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 179 191 disaccharide chemical Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 195 201 xylose chemical Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 206 215 arabinose chemical Treatment of pool 4 with the nonspecific arabinofuranosidase, CjAbf51A, resulted in the loss of oligosaccharide 2 and the production of both xylose and arabinose, indicative of a disaccharide of xylose and arabinose. RESULTS | |
| 28 44 Ξ²-1,3-xylosidase protein_type Incubation of pool 4 with a Ξ²-1,3-xylosidase (XynB) converted oligosaccharide 1 into xylose, demonstrating that this molecule is the disaccharide Ξ²-1,3-xylobiose. RESULTS | |
| 46 50 XynB protein Incubation of pool 4 with a Ξ²-1,3-xylosidase (XynB) converted oligosaccharide 1 into xylose, demonstrating that this molecule is the disaccharide Ξ²-1,3-xylobiose. RESULTS | |
| 62 77 oligosaccharide chemical Incubation of pool 4 with a Ξ²-1,3-xylosidase (XynB) converted oligosaccharide 1 into xylose, demonstrating that this molecule is the disaccharide Ξ²-1,3-xylobiose. RESULTS | |
| 85 91 xylose chemical Incubation of pool 4 with a Ξ²-1,3-xylosidase (XynB) converted oligosaccharide 1 into xylose, demonstrating that this molecule is the disaccharide Ξ²-1,3-xylobiose. RESULTS | |
| 133 145 disaccharide chemical Incubation of pool 4 with a Ξ²-1,3-xylosidase (XynB) converted oligosaccharide 1 into xylose, demonstrating that this molecule is the disaccharide Ξ²-1,3-xylobiose. RESULTS | |
| 146 161 Ξ²-1,3-xylobiose chemical Incubation of pool 4 with a Ξ²-1,3-xylosidase (XynB) converted oligosaccharide 1 into xylose, demonstrating that this molecule is the disaccharide Ξ²-1,3-xylobiose. RESULTS | |
| 45 70 Ξ²-1,4-specific xylosidase protein_type This view is supported by the inability of a Ξ²-1,4-specific xylosidase to hydrolyze oligosaccharide 1 or oligosaccharide 2 (data not shown). RESULTS | |
| 84 99 oligosaccharide chemical This view is supported by the inability of a Ξ²-1,4-specific xylosidase to hydrolyze oligosaccharide 1 or oligosaccharide 2 (data not shown). RESULTS | |
| 105 120 oligosaccharide chemical This view is supported by the inability of a Ξ²-1,4-specific xylosidase to hydrolyze oligosaccharide 1 or oligosaccharide 2 (data not shown). RESULTS | |
| 43 53 β2* pocket site The crucial importance of occupancy of the β2* pocket for catalytic competence is illustrated by the inability of the enzyme to hydrolyze linear Ξ²-1,4-xylooligosaccharides. RESULTS | |
| 145 171 Ξ²-1,4-xylooligosaccharides chemical The crucial importance of occupancy of the β2* pocket for catalytic competence is illustrated by the inability of the enzyme to hydrolyze linear Ξ²-1,4-xylooligosaccharides. RESULTS | |
| 18 27 Araf-Xylp chemical The generation of Araf-Xylp and Xyl-Ξ²-1,3-Xyl as reaction products demonstrates that occupancy of the β2 subsite is not essential for catalytic activity, which is in contrast to all endo-acting xylanases where this subsite plays a critical role in enzyme activity. RESULTS | |
| 32 45 Xyl-Ξ²-1,3-Xyl chemical The generation of Araf-Xylp and Xyl-Ξ²-1,3-Xyl as reaction products demonstrates that occupancy of the β2 subsite is not essential for catalytic activity, which is in contrast to all endo-acting xylanases where this subsite plays a critical role in enzyme activity. RESULTS | |
| 102 112 β2 subsite site The generation of Araf-Xylp and Xyl-Ξ²-1,3-Xyl as reaction products demonstrates that occupancy of the β2 subsite is not essential for catalytic activity, which is in contrast to all endo-acting xylanases where this subsite plays a critical role in enzyme activity. RESULTS | |
| 182 203 endo-acting xylanases protein_type The generation of Araf-Xylp and Xyl-Ξ²-1,3-Xyl as reaction products demonstrates that occupancy of the β2 subsite is not essential for catalytic activity, which is in contrast to all endo-acting xylanases where this subsite plays a critical role in enzyme activity. RESULTS | |
| 215 222 subsite site The generation of Araf-Xylp and Xyl-Ξ²-1,3-Xyl as reaction products demonstrates that occupancy of the β2 subsite is not essential for catalytic activity, which is in contrast to all endo-acting xylanases where this subsite plays a critical role in enzyme activity. RESULTS | |
| 34 37 β2* site Indeed, the data demonstrate that β2* plays a more important role in productive substrate binding than the β2 subsite. RESULTS | |
| 107 117 β2 subsite site Indeed, the data demonstrate that β2* plays a more important role in productive substrate binding than the β2 subsite. RESULTS | |
| 57 89 (Xyl-Ξ²-1,4)n-[Ξ²-1,3-Xyl/Ara]-Xyl chemical Unfortunately, the inability to generate highly purified (Xyl-Ξ²-1,4)n-[Ξ²-1,3-Xyl/Ara]-Xyl oligosaccharides from arabinoxylans prevented the precise binding energies at the negative subsites to be determined. RESULTS | |
| 90 106 oligosaccharides chemical Unfortunately, the inability to generate highly purified (Xyl-Ξ²-1,4)n-[Ξ²-1,3-Xyl/Ara]-Xyl oligosaccharides from arabinoxylans prevented the precise binding energies at the negative subsites to be determined. RESULTS | |
| 112 125 arabinoxylans chemical Unfortunately, the inability to generate highly purified (Xyl-Ξ²-1,4)n-[Ξ²-1,3-Xyl/Ara]-Xyl oligosaccharides from arabinoxylans prevented the precise binding energies at the negative subsites to be determined. RESULTS | |
| 22 34 disaccharide chemical Identification of the disaccharide reaction products generated from CX. FIG | |
| 68 70 CX chemical Identification of the disaccharide reaction products generated from CX. FIG | |
| 48 77 size exclusion chromatography experimental_method The smallest reaction products were purified by size exclusion chromatography and analyzed by HPAEC (A) and positive mode ESI-MS (B), respectively. FIG | |
| 94 99 HPAEC experimental_method The smallest reaction products were purified by size exclusion chromatography and analyzed by HPAEC (A) and positive mode ESI-MS (B), respectively. FIG | |
| 122 128 ESI-MS experimental_method The smallest reaction products were purified by size exclusion chromatography and analyzed by HPAEC (A) and positive mode ESI-MS (B), respectively. FIG | |
| 32 63 nonspecific arabinofuranosidase protein_type The samples were treated with a nonspecific arabinofuranosidase (CjAbf51A) and a GH3 xylosidase (XynB) that targeted Ξ²-1,3-xylosidic bonds. FIG | |
| 65 73 CjAbf51A protein The samples were treated with a nonspecific arabinofuranosidase (CjAbf51A) and a GH3 xylosidase (XynB) that targeted Ξ²-1,3-xylosidic bonds. FIG | |
| 81 95 GH3 xylosidase protein_type The samples were treated with a nonspecific arabinofuranosidase (CjAbf51A) and a GH3 xylosidase (XynB) that targeted Ξ²-1,3-xylosidic bonds. FIG | |
| 97 101 XynB protein The samples were treated with a nonspecific arabinofuranosidase (CjAbf51A) and a GH3 xylosidase (XynB) that targeted Ξ²-1,3-xylosidic bonds. FIG | |
| 3 9 xylose chemical X, xylose; A, arabinose. FIG | |
| 14 23 arabinose chemical X, xylose; A, arabinose. FIG | |
| 32 39 pentose chemical The m/z = 305 species denotes a pentose disaccharide as a sodium adduct [M + Na]+, whereas the m/z = 587 signal corresponds to an ESI-MS dimer of the pentose disaccharide also as a sodium adduct [2M + Na]+. FIG | |
| 40 52 disaccharide chemical The m/z = 305 species denotes a pentose disaccharide as a sodium adduct [M + Na]+, whereas the m/z = 587 signal corresponds to an ESI-MS dimer of the pentose disaccharide also as a sodium adduct [2M + Na]+. FIG | |
| 130 136 ESI-MS experimental_method The m/z = 305 species denotes a pentose disaccharide as a sodium adduct [M + Na]+, whereas the m/z = 587 signal corresponds to an ESI-MS dimer of the pentose disaccharide also as a sodium adduct [2M + Na]+. FIG | |
| 150 157 pentose chemical The m/z = 305 species denotes a pentose disaccharide as a sodium adduct [M + Na]+, whereas the m/z = 587 signal corresponds to an ESI-MS dimer of the pentose disaccharide also as a sodium adduct [2M + Na]+. FIG | |
| 158 170 disaccharide chemical The m/z = 305 species denotes a pentose disaccharide as a sodium adduct [M + Na]+, whereas the m/z = 587 signal corresponds to an ESI-MS dimer of the pentose disaccharide also as a sodium adduct [2M + Na]+. FIG | |
| 0 17 Crystal Structure evidence Crystal Structure of the Catalytic Module of CtXyl5A in Complex with Ligands RESULTS | |
| 25 41 Catalytic Module structure_element Crystal Structure of the Catalytic Module of CtXyl5A in Complex with Ligands RESULTS | |
| 45 52 CtXyl5A protein Crystal Structure of the Catalytic Module of CtXyl5A in Complex with Ligands RESULTS | |
| 53 68 in Complex with protein_state Crystal Structure of the Catalytic Module of CtXyl5A in Complex with Ligands RESULTS | |
| 69 76 Ligands chemical Crystal Structure of the Catalytic Module of CtXyl5A in Complex with Ligands RESULTS | |
| 69 76 CtXyl5A protein To understand the structural basis for the biochemical properties of CtXyl5A, the crystal structure of the enzyme with ligands that occupy the substrate binding cleft and the critical β2* subsite were sought. RESULTS | |
| 82 99 crystal structure evidence To understand the structural basis for the biochemical properties of CtXyl5A, the crystal structure of the enzyme with ligands that occupy the substrate binding cleft and the critical β2* subsite were sought. RESULTS | |
| 143 166 substrate binding cleft site To understand the structural basis for the biochemical properties of CtXyl5A, the crystal structure of the enzyme with ligands that occupy the substrate binding cleft and the critical β2* subsite were sought. RESULTS | |
| 184 195 β2* subsite site To understand the structural basis for the biochemical properties of CtXyl5A, the crystal structure of the enzyme with ligands that occupy the substrate binding cleft and the critical β2* subsite were sought. RESULTS | |
| 39 48 structure evidence The data presented in Fig. 3A show the structure of the CtXyl5A derivative CtGH5-CtCBM6 in complex with arabinose bound in the β2* pocket. RESULTS | |
| 56 63 CtXyl5A protein The data presented in Fig. 3A show the structure of the CtXyl5A derivative CtGH5-CtCBM6 in complex with arabinose bound in the β2* pocket. RESULTS | |
| 75 87 CtGH5-CtCBM6 structure_element The data presented in Fig. 3A show the structure of the CtXyl5A derivative CtGH5-CtCBM6 in complex with arabinose bound in the β2* pocket. RESULTS | |
| 88 103 in complex with protein_state The data presented in Fig. 3A show the structure of the CtXyl5A derivative CtGH5-CtCBM6 in complex with arabinose bound in the β2* pocket. RESULTS | |
| 104 113 arabinose chemical The data presented in Fig. 3A show the structure of the CtXyl5A derivative CtGH5-CtCBM6 in complex with arabinose bound in the β2* pocket. RESULTS | |
| 114 122 bound in protein_state The data presented in Fig. 3A show the structure of the CtXyl5A derivative CtGH5-CtCBM6 in complex with arabinose bound in the β2* pocket. RESULTS | |
| 127 137 β2* pocket site The data presented in Fig. 3A show the structure of the CtXyl5A derivative CtGH5-CtCBM6 in complex with arabinose bound in the β2* pocket. RESULTS | |
| 19 24 bound protein_state Interestingly, the bound arabinose was in the pyranose conformation rather than in its furanose form found in arabinoxylans. RESULTS | |
| 25 34 arabinose chemical Interestingly, the bound arabinose was in the pyranose conformation rather than in its furanose form found in arabinoxylans. RESULTS | |
| 46 54 pyranose chemical Interestingly, the bound arabinose was in the pyranose conformation rather than in its furanose form found in arabinoxylans. RESULTS | |
| 87 95 furanose chemical Interestingly, the bound arabinose was in the pyranose conformation rather than in its furanose form found in arabinoxylans. RESULTS | |
| 110 123 arabinoxylans chemical Interestingly, the bound arabinose was in the pyranose conformation rather than in its furanose form found in arabinoxylans. RESULTS | |
| 25 36 active site site O1 was facing toward the active site β1 subsite, indicative of the bound arabinose being in the right orientation to be linked to the xylan backbone via an Ξ±-1,3 linkage. RESULTS | |
| 37 47 β1 subsite site O1 was facing toward the active site β1 subsite, indicative of the bound arabinose being in the right orientation to be linked to the xylan backbone via an Ξ±-1,3 linkage. RESULTS | |
| 67 72 bound protein_state O1 was facing toward the active site β1 subsite, indicative of the bound arabinose being in the right orientation to be linked to the xylan backbone via an Ξ±-1,3 linkage. RESULTS | |
| 73 82 arabinose chemical O1 was facing toward the active site β1 subsite, indicative of the bound arabinose being in the right orientation to be linked to the xylan backbone via an Ξ±-1,3 linkage. RESULTS | |
| 134 139 xylan chemical O1 was facing toward the active site β1 subsite, indicative of the bound arabinose being in the right orientation to be linked to the xylan backbone via an Ξ±-1,3 linkage. RESULTS | |
| 43 47 Arap chemical As discussed on below, the axial O4 of the Arap did not interact with the β2* subsite, suggesting that the pocket might be capable of binding a xylose molecule. RESULTS | |
| 74 85 β2* subsite site As discussed on below, the axial O4 of the Arap did not interact with the β2* subsite, suggesting that the pocket might be capable of binding a xylose molecule. RESULTS | |
| 107 113 pocket site As discussed on below, the axial O4 of the Arap did not interact with the β2* subsite, suggesting that the pocket might be capable of binding a xylose molecule. RESULTS | |
| 144 150 xylose chemical As discussed on below, the axial O4 of the Arap did not interact with the β2* subsite, suggesting that the pocket might be capable of binding a xylose molecule. RESULTS | |
| 8 15 soaking experimental_method Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 16 19 apo protein_state Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 20 28 crystals evidence Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 34 40 xylose chemical Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 57 64 pentose chemical Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 65 70 sugar chemical Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 76 84 bound in protein_state Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 89 100 β2* subsite site Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 108 116 pyranose chemical Indeed, soaking apo crystals with xylose showed that the pentose sugar also bound in the β2* subsite in its pyranose conformation (Fig. 3B). RESULTS | |
| 6 24 crystal structures evidence These crystal structures support the biochemical data presented above showing that the enzyme generated Ξ²-1,3-xylobiose from CX, which would require the disaccharide to bind at the β1 and β2* subsites. RESULTS | |
| 104 119 Ξ²-1,3-xylobiose chemical These crystal structures support the biochemical data presented above showing that the enzyme generated Ξ²-1,3-xylobiose from CX, which would require the disaccharide to bind at the β1 and β2* subsites. RESULTS | |
| 125 127 CX chemical These crystal structures support the biochemical data presented above showing that the enzyme generated Ξ²-1,3-xylobiose from CX, which would require the disaccharide to bind at the β1 and β2* subsites. RESULTS | |
| 153 165 disaccharide chemical These crystal structures support the biochemical data presented above showing that the enzyme generated Ξ²-1,3-xylobiose from CX, which would require the disaccharide to bind at the β1 and β2* subsites. RESULTS | |
| 181 200 β1 and β2* subsites site These crystal structures support the biochemical data presented above showing that the enzyme generated Ξ²-1,3-xylobiose from CX, which would require the disaccharide to bind at the β1 and β2* subsites. RESULTS | |
| 41 57 co-crystallizing experimental_method A third product complex was generated by co-crystallizing the nucleophile inactive mutant CtGH5E279S-CtCBM6 with a WAX-derived oligosaccharide (Fig. 3C). RESULTS | |
| 62 82 nucleophile inactive protein_state A third product complex was generated by co-crystallizing the nucleophile inactive mutant CtGH5E279S-CtCBM6 with a WAX-derived oligosaccharide (Fig. 3C). RESULTS | |
| 83 89 mutant protein_state A third product complex was generated by co-crystallizing the nucleophile inactive mutant CtGH5E279S-CtCBM6 with a WAX-derived oligosaccharide (Fig. 3C). RESULTS | |
| 90 100 CtGH5E279S mutant A third product complex was generated by co-crystallizing the nucleophile inactive mutant CtGH5E279S-CtCBM6 with a WAX-derived oligosaccharide (Fig. 3C). RESULTS | |
| 101 107 CtCBM6 structure_element A third product complex was generated by co-crystallizing the nucleophile inactive mutant CtGH5E279S-CtCBM6 with a WAX-derived oligosaccharide (Fig. 3C). RESULTS | |
| 115 118 WAX chemical A third product complex was generated by co-crystallizing the nucleophile inactive mutant CtGH5E279S-CtCBM6 with a WAX-derived oligosaccharide (Fig. 3C). RESULTS | |
| 127 142 oligosaccharide chemical A third product complex was generated by co-crystallizing the nucleophile inactive mutant CtGH5E279S-CtCBM6 with a WAX-derived oligosaccharide (Fig. 3C). RESULTS | |
| 20 35 pentasaccharide chemical The data revealed a pentasaccharide bound to the enzyme, comprising Ξ²-1,4-xylotetraose with an Araf linked Ξ±-1,3 to the reducing end xylose. RESULTS | |
| 36 44 bound to protein_state The data revealed a pentasaccharide bound to the enzyme, comprising Ξ²-1,4-xylotetraose with an Araf linked Ξ±-1,3 to the reducing end xylose. RESULTS | |
| 68 86 Ξ²-1,4-xylotetraose chemical The data revealed a pentasaccharide bound to the enzyme, comprising Ξ²-1,4-xylotetraose with an Araf linked Ξ±-1,3 to the reducing end xylose. RESULTS | |
| 95 99 Araf chemical The data revealed a pentasaccharide bound to the enzyme, comprising Ξ²-1,4-xylotetraose with an Araf linked Ξ±-1,3 to the reducing end xylose. RESULTS | |
| 133 139 xylose chemical The data revealed a pentasaccharide bound to the enzyme, comprising Ξ²-1,4-xylotetraose with an Araf linked Ξ±-1,3 to the reducing end xylose. RESULTS | |
| 4 16 xylotetraose chemical The xylotetraose was positioned in subsites β1 to β4 and the Araf in the β2* pocket. RESULTS | |
| 35 52 subsites β1 to β4 site The xylotetraose was positioned in subsites β1 to β4 and the Araf in the β2* pocket. RESULTS | |
| 61 65 Araf chemical The xylotetraose was positioned in subsites β1 to β4 and the Araf in the β2* pocket. RESULTS | |
| 73 83 β2* pocket site The xylotetraose was positioned in subsites β1 to β4 and the Araf in the β2* pocket. RESULTS | |
| 22 32 structures evidence Analysis of the three structures showed that O1, O2, O3, and the endocyclic oxygen occupied identical positions in the Arap, Araf, and Xylp ligands bound in the β2* subsite and thus made identical interactions with the pocket. RESULTS | |
| 119 123 Arap chemical Analysis of the three structures showed that O1, O2, O3, and the endocyclic oxygen occupied identical positions in the Arap, Araf, and Xylp ligands bound in the β2* subsite and thus made identical interactions with the pocket. RESULTS | |
| 125 129 Araf chemical Analysis of the three structures showed that O1, O2, O3, and the endocyclic oxygen occupied identical positions in the Arap, Araf, and Xylp ligands bound in the β2* subsite and thus made identical interactions with the pocket. RESULTS | |
| 135 139 Xylp chemical Analysis of the three structures showed that O1, O2, O3, and the endocyclic oxygen occupied identical positions in the Arap, Araf, and Xylp ligands bound in the β2* subsite and thus made identical interactions with the pocket. RESULTS | |
| 148 156 bound in protein_state Analysis of the three structures showed that O1, O2, O3, and the endocyclic oxygen occupied identical positions in the Arap, Araf, and Xylp ligands bound in the β2* subsite and thus made identical interactions with the pocket. RESULTS | |
| 161 172 β2* subsite site Analysis of the three structures showed that O1, O2, O3, and the endocyclic oxygen occupied identical positions in the Arap, Araf, and Xylp ligands bound in the β2* subsite and thus made identical interactions with the pocket. RESULTS | |
| 219 225 pocket site Analysis of the three structures showed that O1, O2, O3, and the endocyclic oxygen occupied identical positions in the Arap, Araf, and Xylp ligands bound in the β2* subsite and thus made identical interactions with the pocket. RESULTS | |
| 11 24 polar contact bond_interaction O1 makes a polar contact with NΞ΄2 of Asn139, O2 is within hydrogen bonding distance with OΞ΄1 of Asn139 and the backbone N of Asn135, and O3 interacts with the N of Gly136 and OΟ΅2 of Glu68. RESULTS | |
| 37 43 Asn139 residue_name_number O1 makes a polar contact with NΞ΄2 of Asn139, O2 is within hydrogen bonding distance with OΞ΄1 of Asn139 and the backbone N of Asn135, and O3 interacts with the N of Gly136 and OΟ΅2 of Glu68. RESULTS | |
| 58 74 hydrogen bonding bond_interaction O1 makes a polar contact with NΞ΄2 of Asn139, O2 is within hydrogen bonding distance with OΞ΄1 of Asn139 and the backbone N of Asn135, and O3 interacts with the N of Gly136 and OΟ΅2 of Glu68. RESULTS | |
| 96 102 Asn139 residue_name_number O1 makes a polar contact with NΞ΄2 of Asn139, O2 is within hydrogen bonding distance with OΞ΄1 of Asn139 and the backbone N of Asn135, and O3 interacts with the N of Gly136 and OΟ΅2 of Glu68. RESULTS | |
| 125 131 Asn135 residue_name_number O1 makes a polar contact with NΞ΄2 of Asn139, O2 is within hydrogen bonding distance with OΞ΄1 of Asn139 and the backbone N of Asn135, and O3 interacts with the N of Gly136 and OΟ΅2 of Glu68. RESULTS | |
| 164 170 Gly136 residue_name_number O1 makes a polar contact with NΞ΄2 of Asn139, O2 is within hydrogen bonding distance with OΞ΄1 of Asn139 and the backbone N of Asn135, and O3 interacts with the N of Gly136 and OΟ΅2 of Glu68. RESULTS | |
| 182 187 Glu68 residue_name_number O1 makes a polar contact with NΞ΄2 of Asn139, O2 is within hydrogen bonding distance with OΞ΄1 of Asn139 and the backbone N of Asn135, and O3 interacts with the N of Gly136 and OΟ΅2 of Glu68. RESULTS | |
| 15 19 Arap chemical Although O4 of Arap does not make a direct interaction with the enzyme, O4 and O5 of Xylp and Araf, respectively, form hydrogen bonds with OΟ΅1 of Glu68. RESULTS | |
| 85 89 Xylp chemical Although O4 of Arap does not make a direct interaction with the enzyme, O4 and O5 of Xylp and Araf, respectively, form hydrogen bonds with OΟ΅1 of Glu68. RESULTS | |
| 94 98 Araf chemical Although O4 of Arap does not make a direct interaction with the enzyme, O4 and O5 of Xylp and Araf, respectively, form hydrogen bonds with OΟ΅1 of Glu68. RESULTS | |
| 119 133 hydrogen bonds bond_interaction Although O4 of Arap does not make a direct interaction with the enzyme, O4 and O5 of Xylp and Araf, respectively, form hydrogen bonds with OΟ΅1 of Glu68. RESULTS | |
| 146 151 Glu68 residue_name_number Although O4 of Arap does not make a direct interaction with the enzyme, O4 and O5 of Xylp and Araf, respectively, form hydrogen bonds with OΟ΅1 of Glu68. RESULTS | |
| 8 13 Tyr92 residue_name_number Finally Tyr92 makes apolar parallel interactions with the pyranose or furanose rings of the three sugars. RESULTS | |
| 27 48 parallel interactions bond_interaction Finally Tyr92 makes apolar parallel interactions with the pyranose or furanose rings of the three sugars. RESULTS | |
| 58 66 pyranose chemical Finally Tyr92 makes apolar parallel interactions with the pyranose or furanose rings of the three sugars. RESULTS | |
| 70 78 furanose chemical Finally Tyr92 makes apolar parallel interactions with the pyranose or furanose rings of the three sugars. RESULTS | |
| 74 85 β2* subsite site Representation of the residues involved in the ligands recognition at the β2* subsite. FIG | |
| 63 81 catalytic residues site Interacting residues are represented as stick in blue, and the catalytic residues and the mutated glutamate (into a serine) are in magenta. FIG | |
| 90 97 mutated experimental_method Interacting residues are represented as stick in blue, and the catalytic residues and the mutated glutamate (into a serine) are in magenta. FIG | |
| 98 107 glutamate residue_name Interacting residues are represented as stick in blue, and the catalytic residues and the mutated glutamate (into a serine) are in magenta. FIG | |
| 116 122 serine residue_name Interacting residues are represented as stick in blue, and the catalytic residues and the mutated glutamate (into a serine) are in magenta. FIG | |
| 3 13 CtGH5-CBM6 structure_element A, CtGH5-CBM6 in complex with an arabinopyranose. FIG | |
| 14 29 in complex with protein_state A, CtGH5-CBM6 in complex with an arabinopyranose. FIG | |
| 33 48 arabinopyranose chemical A, CtGH5-CBM6 in complex with an arabinopyranose. FIG | |
| 3 13 CtGH5-CBM6 structure_element B, CtGH5-CBM6 in complex with a xylopyranose. FIG | |
| 14 29 in complex with protein_state B, CtGH5-CBM6 in complex with a xylopyranose. FIG | |
| 32 44 xylopyranose chemical B, CtGH5-CBM6 in complex with a xylopyranose. FIG | |
| 3 13 CtGH5E279S mutant C, CtGH5E279S-CBM6 in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 14 18 CBM6 structure_element C, CtGH5E279S-CBM6 in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 19 34 in complex with protein_state C, CtGH5E279S-CBM6 in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 37 52 pentasaccharide chemical C, CtGH5E279S-CBM6 in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 54 71 Ξ²1,4-xylotetraose chemical C, CtGH5E279S-CBM6 in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 80 86 l-Araf chemical C, CtGH5E279S-CBM6 in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 119 125 xylose chemical C, CtGH5E279S-CBM6 in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 4 9 xylan chemical The xylan backbone is shown transparently for more clarity. FIG | |
| 0 9 Densities evidence Densities shown in blue are RefMac maximum-likelihood ΟA-weighted 2Fo β Fc at 1.5 Ο. FIG | |
| 35 83 maximum-likelihood ΟA-weighted 2Fo β Fc at 1.5 Ο evidence Densities shown in blue are RefMac maximum-likelihood ΟA-weighted 2Fo β Fc at 1.5 Ο. FIG | |
| 98 108 β2* pocket site The importance of the interactions between the ligands and the side chains of the residues in the β2* pocket were evaluated by alanine substitution of these amino acids. RESULTS | |
| 127 147 alanine substitution experimental_method The importance of the interactions between the ligands and the side chains of the residues in the β2* pocket were evaluated by alanine substitution of these amino acids. RESULTS | |
| 4 11 mutants protein_state The mutants E68A, Y92A, and N139A were all inactive (Table 1), demonstrating the importance of the interactions of these residues with the substrate and reinforcing the critical role the β2* subsite plays in the activity of the enzyme. RESULTS | |
| 12 16 E68A mutant The mutants E68A, Y92A, and N139A were all inactive (Table 1), demonstrating the importance of the interactions of these residues with the substrate and reinforcing the critical role the β2* subsite plays in the activity of the enzyme. RESULTS | |
| 18 22 Y92A mutant The mutants E68A, Y92A, and N139A were all inactive (Table 1), demonstrating the importance of the interactions of these residues with the substrate and reinforcing the critical role the β2* subsite plays in the activity of the enzyme. RESULTS | |
| 28 33 N139A mutant The mutants E68A, Y92A, and N139A were all inactive (Table 1), demonstrating the importance of the interactions of these residues with the substrate and reinforcing the critical role the β2* subsite plays in the activity of the enzyme. RESULTS | |
| 43 51 inactive protein_state The mutants E68A, Y92A, and N139A were all inactive (Table 1), demonstrating the importance of the interactions of these residues with the substrate and reinforcing the critical role the β2* subsite plays in the activity of the enzyme. RESULTS | |
| 187 198 β2* subsite site The mutants E68A, Y92A, and N139A were all inactive (Table 1), demonstrating the importance of the interactions of these residues with the substrate and reinforcing the critical role the β2* subsite plays in the activity of the enzyme. RESULTS | |
| 0 5 N135A mutant N135A retained wild type activity because the O2 of the sugars interacts with the backbone N of Asn135 and not with the side chain. RESULTS | |
| 15 24 wild type protein_state N135A retained wild type activity because the O2 of the sugars interacts with the backbone N of Asn135 and not with the side chain. RESULTS | |
| 96 102 Asn135 residue_name_number N135A retained wild type activity because the O2 of the sugars interacts with the backbone N of Asn135 and not with the side chain. RESULTS | |
| 25 29 Xylp chemical Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 33 37 Araf chemical Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 45 55 β2* pocket site Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 64 79 solvent-exposed protein_state Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 85 96 active site site Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 104 119 arabinoxylanase protein_type Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 137 143 xylose chemical Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 175 181 xylose chemical Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 185 194 arabinose chemical Because the hydroxyls of Xylp or Araf in the β2* pocket are not solvent-exposed, the active site of the arabinoxylanase can only bind to xylose residues that contain a single xylose or arabinose O3 decoration. RESULTS | |
| 25 29 kcat evidence This may explain why the kcat/Km for CtXyl5A against WAX was 2-fold higher than against CX (Table 1). RESULTS | |
| 30 32 Km evidence This may explain why the kcat/Km for CtXyl5A against WAX was 2-fold higher than against CX (Table 1). RESULTS | |
| 37 44 CtXyl5A protein This may explain why the kcat/Km for CtXyl5A against WAX was 2-fold higher than against CX (Table 1). RESULTS | |
| 53 56 WAX chemical This may explain why the kcat/Km for CtXyl5A against WAX was 2-fold higher than against CX (Table 1). RESULTS | |
| 88 90 CX chemical This may explain why the kcat/Km for CtXyl5A against WAX was 2-fold higher than against CX (Table 1). RESULTS | |
| 0 3 WAX chemical WAX is likely to have a higher concentration of single Araf decorations compared with CX and thus contain more substrate available to the arabinoxylanase. RESULTS | |
| 55 59 Araf chemical WAX is likely to have a higher concentration of single Araf decorations compared with CX and thus contain more substrate available to the arabinoxylanase. RESULTS | |
| 86 88 CX chemical WAX is likely to have a higher concentration of single Araf decorations compared with CX and thus contain more substrate available to the arabinoxylanase. RESULTS | |
| 138 153 arabinoxylanase protein_type WAX is likely to have a higher concentration of single Araf decorations compared with CX and thus contain more substrate available to the arabinoxylanase. RESULTS | |
| 7 18 active site site In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 22 29 CtXyl5A protein In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 34 42 Ξ±-d-Xylp chemical In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 153 167 hydrogen bonds bond_interaction In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 184 190 His253 residue_name_number In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 202 208 Glu171 residue_name_number In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 257 270 polar contact bond_interaction In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 286 292 Tyr255 residue_name_number In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 303 309 Ser279 residue_name_number In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 354 368 hydrogen bonds bond_interaction In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 381 387 Asn170 residue_name_number In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 398 403 Tyr92 residue_name_number In the active site of CtXyl5A the Ξ±-d-Xylp, which is in its relaxed 4C1 conformation, makes the following interactions with the enzyme (Fig. 4, AβC): O1 hydrogen bonds with the NΞ΄1 of His253 and OΟ΅2 of Glu171 (catalytic acid-base) and makes a possible weak polar contact with the OH of Tyr255 and OΞ³ of Ser279 (mutation of the catalytic nucleophile); O2 hydrogen bonds with NΞ΄2 of Asn170 and OH of Tyr92. RESULTS | |
| 14 18 Araf chemical O3 (O1 of the Araf at the β2* subsite) makes a polar contact with NΞ΄2 of Asn139; the endocyclic oxygen hydrogens bonds with the OH of Tyr255. RESULTS | |
| 26 37 β2* subsite site O3 (O1 of the Araf at the β2* subsite) makes a polar contact with NΞ΄2 of Asn139; the endocyclic oxygen hydrogens bonds with the OH of Tyr255. RESULTS | |
| 47 60 polar contact bond_interaction O3 (O1 of the Araf at the β2* subsite) makes a polar contact with NΞ΄2 of Asn139; the endocyclic oxygen hydrogens bonds with the OH of Tyr255. RESULTS | |
| 73 79 Asn139 residue_name_number O3 (O1 of the Araf at the β2* subsite) makes a polar contact with NΞ΄2 of Asn139; the endocyclic oxygen hydrogens bonds with the OH of Tyr255. RESULTS | |
| 103 118 hydrogens bonds bond_interaction O3 (O1 of the Araf at the β2* subsite) makes a polar contact with NΞ΄2 of Asn139; the endocyclic oxygen hydrogens bonds with the OH of Tyr255. RESULTS | |
| 134 140 Tyr255 residue_name_number O3 (O1 of the Araf at the β2* subsite) makes a polar contact with NΞ΄2 of Asn139; the endocyclic oxygen hydrogens bonds with the OH of Tyr255. RESULTS | |
| 4 8 Xylp chemical The Xylp in the active site makes strong parallel apolar interactions with Phe310. RESULTS | |
| 16 27 active site site The Xylp in the active site makes strong parallel apolar interactions with Phe310. RESULTS | |
| 41 69 parallel apolar interactions bond_interaction The Xylp in the active site makes strong parallel apolar interactions with Phe310. RESULTS | |
| 75 81 Phe310 residue_name_number The Xylp in the active site makes strong parallel apolar interactions with Phe310. RESULTS | |
| 29 40 active site site Substrate recognition in the active site is conserved between CtXyl5A and the closest GH5 structural homolog, the endoglucanase BaCel5A (PDB code 1qi2) as noted previously. RESULTS | |
| 44 53 conserved protein_state Substrate recognition in the active site is conserved between CtXyl5A and the closest GH5 structural homolog, the endoglucanase BaCel5A (PDB code 1qi2) as noted previously. RESULTS | |
| 62 69 CtXyl5A protein Substrate recognition in the active site is conserved between CtXyl5A and the closest GH5 structural homolog, the endoglucanase BaCel5A (PDB code 1qi2) as noted previously. RESULTS | |
| 86 89 GH5 protein_type Substrate recognition in the active site is conserved between CtXyl5A and the closest GH5 structural homolog, the endoglucanase BaCel5A (PDB code 1qi2) as noted previously. RESULTS | |
| 114 127 endoglucanase protein_type Substrate recognition in the active site is conserved between CtXyl5A and the closest GH5 structural homolog, the endoglucanase BaCel5A (PDB code 1qi2) as noted previously. RESULTS | |
| 128 135 BaCel5A protein Substrate recognition in the active site is conserved between CtXyl5A and the closest GH5 structural homolog, the endoglucanase BaCel5A (PDB code 1qi2) as noted previously. RESULTS | |
| 51 68 negative subsites site Comparison of the ligand recognition at the distal negative subsites between CtGH5E279S-CBM6, the cellulase BaCel5A, and the xylanase GH10. FIG | |
| 77 87 CtGH5E279S mutant Comparison of the ligand recognition at the distal negative subsites between CtGH5E279S-CBM6, the cellulase BaCel5A, and the xylanase GH10. FIG | |
| 88 92 CBM6 structure_element Comparison of the ligand recognition at the distal negative subsites between CtGH5E279S-CBM6, the cellulase BaCel5A, and the xylanase GH10. FIG | |
| 98 107 cellulase protein_type Comparison of the ligand recognition at the distal negative subsites between CtGH5E279S-CBM6, the cellulase BaCel5A, and the xylanase GH10. FIG | |
| 108 115 BaCel5A protein Comparison of the ligand recognition at the distal negative subsites between CtGH5E279S-CBM6, the cellulase BaCel5A, and the xylanase GH10. FIG | |
| 125 133 xylanase protein_type Comparison of the ligand recognition at the distal negative subsites between CtGH5E279S-CBM6, the cellulase BaCel5A, and the xylanase GH10. FIG | |
| 134 138 GH10 protein_type Comparison of the ligand recognition at the distal negative subsites between CtGH5E279S-CBM6, the cellulase BaCel5A, and the xylanase GH10. FIG | |
| 10 20 CtGH5E279S mutant AβC show CtGH5E279S-CBM6 is in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 29 44 in complex with protein_state AβC show CtGH5E279S-CBM6 is in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 47 62 pentasaccharide chemical AβC show CtGH5E279S-CBM6 is in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 64 81 Ξ²1,4-xylotetraose chemical AβC show CtGH5E279S-CBM6 is in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 90 96 l-Araf chemical AβC show CtGH5E279S-CBM6 is in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 129 135 xylose chemical AβC show CtGH5E279S-CBM6 is in complex with a pentasaccharide (Ξ²1,4-xylotetraose with an l-Araf linked Ξ±1,3 to the reducing end xylose). FIG | |
| 44 60 hydrogen bonding bond_interaction A, Poseview representation highlighting the hydrogen bonding and the hydrophobic interactions that occur in the negative subsites. FIG | |
| 69 93 hydrophobic interactions bond_interaction A, Poseview representation highlighting the hydrogen bonding and the hydrophobic interactions that occur in the negative subsites. FIG | |
| 112 129 negative subsites site A, Poseview representation highlighting the hydrogen bonding and the hydrophobic interactions that occur in the negative subsites. FIG | |
| 3 10 density evidence C, density of the ligand shown in blue is RefMac maximum-likelihood ΟA-weighted 2Fo β Fc at 1.5 Ο. FIG | |
| 49 97 maximum-likelihood ΟA-weighted 2Fo β Fc at 1.5 Ο evidence C, density of the ligand shown in blue is RefMac maximum-likelihood ΟA-weighted 2Fo β Fc at 1.5 Ο. FIG | |
| 16 23 BaCel5A protein D and E display BaCel5A in complex with deoxy-2-fluoro-Ξ²-d-cellotrioside (PDB code 1qi2), and F and G show CmXyn10B in complex with a xylotriose (PDB code 1uqy). FIG | |
| 24 39 in complex with protein_state D and E display BaCel5A in complex with deoxy-2-fluoro-Ξ²-d-cellotrioside (PDB code 1qi2), and F and G show CmXyn10B in complex with a xylotriose (PDB code 1uqy). FIG | |
| 40 72 deoxy-2-fluoro-Ξ²-d-cellotrioside chemical D and E display BaCel5A in complex with deoxy-2-fluoro-Ξ²-d-cellotrioside (PDB code 1qi2), and F and G show CmXyn10B in complex with a xylotriose (PDB code 1uqy). FIG | |
| 107 115 CmXyn10B protein D and E display BaCel5A in complex with deoxy-2-fluoro-Ξ²-d-cellotrioside (PDB code 1qi2), and F and G show CmXyn10B in complex with a xylotriose (PDB code 1uqy). FIG | |
| 116 131 in complex with protein_state D and E display BaCel5A in complex with deoxy-2-fluoro-Ξ²-d-cellotrioside (PDB code 1qi2), and F and G show CmXyn10B in complex with a xylotriose (PDB code 1uqy). FIG | |
| 134 144 xylotriose chemical D and E display BaCel5A in complex with deoxy-2-fluoro-Ξ²-d-cellotrioside (PDB code 1qi2), and F and G show CmXyn10B in complex with a xylotriose (PDB code 1uqy). FIG | |
| 41 51 CtGH5E279S mutant B, D, and F are surface representations (CtGH5E279S-CBM6 in gray, BaCel5A in cyan, and the xylanase GH10 in light brown). FIG | |
| 66 73 BaCel5A protein B, D, and F are surface representations (CtGH5E279S-CBM6 in gray, BaCel5A in cyan, and the xylanase GH10 in light brown). FIG | |
| 91 99 xylanase protein_type B, D, and F are surface representations (CtGH5E279S-CBM6 in gray, BaCel5A in cyan, and the xylanase GH10 in light brown). FIG | |
| 100 104 GH10 protein_type B, D, and F are surface representations (CtGH5E279S-CBM6 in gray, BaCel5A in cyan, and the xylanase GH10 in light brown). FIG | |
| 31 45 hydrogen bonds bond_interaction The black dashes represent the hydrogen bonds. FIG | |
| 31 45 hydrogen bonds bond_interaction The black dashes represent the hydrogen bonds. FIG | |
| 16 23 CtXyl5A protein The capacity of CtXyl5A to act on the highly decorated xylan CX indicates that O3 and possibly O2 of the backbone Xylp units are solvent-exposed. RESULTS | |
| 55 60 xylan chemical The capacity of CtXyl5A to act on the highly decorated xylan CX indicates that O3 and possibly O2 of the backbone Xylp units are solvent-exposed. RESULTS | |
| 61 63 CX chemical The capacity of CtXyl5A to act on the highly decorated xylan CX indicates that O3 and possibly O2 of the backbone Xylp units are solvent-exposed. RESULTS | |
| 114 118 Xylp chemical The capacity of CtXyl5A to act on the highly decorated xylan CX indicates that O3 and possibly O2 of the backbone Xylp units are solvent-exposed. RESULTS | |
| 129 144 solvent-exposed protein_state The capacity of CtXyl5A to act on the highly decorated xylan CX indicates that O3 and possibly O2 of the backbone Xylp units are solvent-exposed. RESULTS | |
| 47 59 xylotetraose chemical This is consistent with the interaction of the xylotetraose backbone with the enzyme distal to the active site. RESULTS | |
| 99 110 active site site This is consistent with the interaction of the xylotetraose backbone with the enzyme distal to the active site. RESULTS | |
| 73 79 xylose chemical A surface representation of the enzyme (Fig. 4B) shows that O3 and O2 of xylose units at subsites β2 to β4 are solvent-exposed and are thus available for decoration. RESULTS | |
| 89 106 subsites β2 to β4 site A surface representation of the enzyme (Fig. 4B) shows that O3 and O2 of xylose units at subsites β2 to β4 are solvent-exposed and are thus available for decoration. RESULTS | |
| 111 126 solvent-exposed protein_state A surface representation of the enzyme (Fig. 4B) shows that O3 and O2 of xylose units at subsites β2 to β4 are solvent-exposed and are thus available for decoration. RESULTS | |
| 14 22 pyranose chemical Indeed, these pyranose sugars make very weak apolar interactions with the arabinoxylanase. RESULTS | |
| 23 29 sugars chemical Indeed, these pyranose sugars make very weak apolar interactions with the arabinoxylanase. RESULTS | |
| 45 64 apolar interactions bond_interaction Indeed, these pyranose sugars make very weak apolar interactions with the arabinoxylanase. RESULTS | |
| 74 89 arabinoxylanase protein_type Indeed, these pyranose sugars make very weak apolar interactions with the arabinoxylanase. RESULTS | |
| 3 5 β2 site At β2, Xylp makes planar apolar interactions with the Araf bound to the β2* subsite (Fig. 4C). RESULTS | |
| 7 11 Xylp chemical At β2, Xylp makes planar apolar interactions with the Araf bound to the β2* subsite (Fig. 4C). RESULTS | |
| 18 44 planar apolar interactions bond_interaction At β2, Xylp makes planar apolar interactions with the Araf bound to the β2* subsite (Fig. 4C). RESULTS | |
| 54 58 Araf chemical At β2, Xylp makes planar apolar interactions with the Araf bound to the β2* subsite (Fig. 4C). RESULTS | |
| 59 67 bound to protein_state At β2, Xylp makes planar apolar interactions with the Araf bound to the β2* subsite (Fig. 4C). RESULTS | |
| 72 83 β2* subsite site At β2, Xylp makes planar apolar interactions with the Araf bound to the β2* subsite (Fig. 4C). RESULTS | |
| 0 4 Xylp chemical Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 8 26 subsites β2 and β3 site Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 52 71 hydrophobic contact bond_interaction Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 77 83 Val318 residue_name_number Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 89 91 β3 site Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 92 96 Xylp chemical Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 103 129 planar apolar interactions bond_interaction Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 135 141 Ala137 residue_name_number Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 155 161 xylose chemical Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 165 167 β4 site Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 174 198 parallel apolar contacts bond_interaction Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 204 209 Trp69 residue_name_number Xylp at subsites β2 and β3, respectively, make weak hydrophobic contact with Val318, the β3 Xylp makes planar apolar interactions with Ala137, whereas the xylose at β4 forms parallel apolar contacts with Trp69. RESULTS | |
| 25 42 negative subsites site Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 46 53 CtXyl5A protein Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 59 66 BaCel5A protein Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 81 85 GH10 protein_type Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 86 94 xylanase protein_type Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 96 104 CmXyn10B protein Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 172 187 arabinoxylanase protein_type Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 219 230 active site site Comparison of the distal negative subsites of CtXyl5A with BaCel5A and a typical GH10 xylanase (CmXyn10B, PDB code 1uqy) highlights the paucity of interactions between the arabinoxylanase and its substrate out with the active site (Fig. 4). RESULTS | |
| 10 19 cellulase protein_type Thus, the cellulase contains three negative subsites and the sugars bound in the β2 and β3 subsites make a total of 9 polar interactions with the enzyme (Fig. 4, D and E). RESULTS | |
| 35 52 negative subsites site Thus, the cellulase contains three negative subsites and the sugars bound in the β2 and β3 subsites make a total of 9 polar interactions with the enzyme (Fig. 4, D and E). RESULTS | |
| 61 67 sugars chemical Thus, the cellulase contains three negative subsites and the sugars bound in the β2 and β3 subsites make a total of 9 polar interactions with the enzyme (Fig. 4, D and E). RESULTS | |
| 68 76 bound in protein_state Thus, the cellulase contains three negative subsites and the sugars bound in the β2 and β3 subsites make a total of 9 polar interactions with the enzyme (Fig. 4, D and E). RESULTS | |
| 81 99 β2 and β3 subsites site Thus, the cellulase contains three negative subsites and the sugars bound in the β2 and β3 subsites make a total of 9 polar interactions with the enzyme (Fig. 4, D and E). RESULTS | |
| 118 136 polar interactions bond_interaction Thus, the cellulase contains three negative subsites and the sugars bound in the β2 and β3 subsites make a total of 9 polar interactions with the enzyme (Fig. 4, D and E). RESULTS | |
| 4 8 GH10 protein_type The GH10 xylanase also contains a β2 subsite that, similar to the cellulase, makes numerous interactions with the substrate (Fig. 4, F and G). RESULTS | |
| 9 17 xylanase protein_type The GH10 xylanase also contains a β2 subsite that, similar to the cellulase, makes numerous interactions with the substrate (Fig. 4, F and G). RESULTS | |
| 34 44 β2 subsite site The GH10 xylanase also contains a β2 subsite that, similar to the cellulase, makes numerous interactions with the substrate (Fig. 4, F and G). RESULTS | |
| 66 75 cellulase protein_type The GH10 xylanase also contains a β2 subsite that, similar to the cellulase, makes numerous interactions with the substrate (Fig. 4, F and G). RESULTS | |
| 45 52 CtXyl5A protein The Influence of the Modular Architecture of CtXyl5A on Catalytic Activity RESULTS | |
| 0 7 CtXyl5A protein CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 28 44 catalytic module structure_element CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 61 65 CBMs structure_element CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 67 73 CtCBM6 structure_element CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 75 82 CtCBM13 structure_element CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 88 95 CtCBM62 structure_element CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 103 121 fibronectin domain structure_element CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 123 128 CtFn3 structure_element CtXyl5A, in addition to its catalytic module, contains three CBMs (CtCBM6, CtCBM13, and CtCBM62) and a fibronectin domain (CtFn3). RESULTS | |
| 42 46 CBM6 structure_element A previous study showed that although the CBM6 bound in an exo-mode to xylo- and cellulooligosaccharides, the primary role of this module was to stabilize the structure of the GH5 catalytic module. RESULTS | |
| 47 55 bound in protein_state A previous study showed that although the CBM6 bound in an exo-mode to xylo- and cellulooligosaccharides, the primary role of this module was to stabilize the structure of the GH5 catalytic module. RESULTS | |
| 59 67 exo-mode protein_state A previous study showed that although the CBM6 bound in an exo-mode to xylo- and cellulooligosaccharides, the primary role of this module was to stabilize the structure of the GH5 catalytic module. RESULTS | |
| 71 104 xylo- and cellulooligosaccharides chemical A previous study showed that although the CBM6 bound in an exo-mode to xylo- and cellulooligosaccharides, the primary role of this module was to stabilize the structure of the GH5 catalytic module. RESULTS | |
| 176 179 GH5 protein_type A previous study showed that although the CBM6 bound in an exo-mode to xylo- and cellulooligosaccharides, the primary role of this module was to stabilize the structure of the GH5 catalytic module. RESULTS | |
| 180 196 catalytic module structure_element A previous study showed that although the CBM6 bound in an exo-mode to xylo- and cellulooligosaccharides, the primary role of this module was to stabilize the structure of the GH5 catalytic module. RESULTS | |
| 41 62 non-catalytic modules structure_element To explore the contribution of the other non-catalytic modules to CtXyl5A function, the activity of a series of truncated derivatives of the arabinoxylanase were assessed. RESULTS | |
| 66 73 CtXyl5A protein To explore the contribution of the other non-catalytic modules to CtXyl5A function, the activity of a series of truncated derivatives of the arabinoxylanase were assessed. RESULTS | |
| 112 121 truncated protein_state To explore the contribution of the other non-catalytic modules to CtXyl5A function, the activity of a series of truncated derivatives of the arabinoxylanase were assessed. RESULTS | |
| 141 156 arabinoxylanase protein_type To explore the contribution of the other non-catalytic modules to CtXyl5A function, the activity of a series of truncated derivatives of the arabinoxylanase were assessed. RESULTS | |
| 30 40 removal of experimental_method The data in Table 1 show that removal of CtCBM62 caused a modest increase in activity against both WAX and CX, whereas deletion of the Fn3 domain had no further impact on catalytic performance. RESULTS | |
| 41 48 CtCBM62 structure_element The data in Table 1 show that removal of CtCBM62 caused a modest increase in activity against both WAX and CX, whereas deletion of the Fn3 domain had no further impact on catalytic performance. RESULTS | |
| 99 102 WAX chemical The data in Table 1 show that removal of CtCBM62 caused a modest increase in activity against both WAX and CX, whereas deletion of the Fn3 domain had no further impact on catalytic performance. RESULTS | |
| 107 109 CX chemical The data in Table 1 show that removal of CtCBM62 caused a modest increase in activity against both WAX and CX, whereas deletion of the Fn3 domain had no further impact on catalytic performance. RESULTS | |
| 119 130 deletion of experimental_method The data in Table 1 show that removal of CtCBM62 caused a modest increase in activity against both WAX and CX, whereas deletion of the Fn3 domain had no further impact on catalytic performance. RESULTS | |
| 135 138 Fn3 structure_element The data in Table 1 show that removal of CtCBM62 caused a modest increase in activity against both WAX and CX, whereas deletion of the Fn3 domain had no further impact on catalytic performance. RESULTS | |
| 0 10 Truncation experimental_method Truncation of CtCBM13, however, caused a 4β5-fold reduction in activity against both substrates. RESULTS | |
| 14 21 CtCBM13 structure_element Truncation of CtCBM13, however, caused a 4β5-fold reduction in activity against both substrates. RESULTS | |
| 11 16 CBM13 structure_element Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 44 50 xylans chemical Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 52 59 mannose chemical Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 65 74 galactose chemical Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 87 102 complex glycans chemical Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 133 140 CtCBM13 structure_element Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 190 206 catalytic module structure_element Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 210 217 CtXyl5A protein Members of CBM13 have been shown to bind to xylans, mannose, and galactose residues in complex glycans, hinting that the function of CtCBM13 is to increase the proximity of substrate to the catalytic module of CtXyl5A. RESULTS | |
| 0 15 Binding studies experimental_method Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 38 45 CtCBM13 structure_element Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 92 99 glycans chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 110 113 WAX chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 115 117 CX chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 119 125 xylose chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 127 134 mannose chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 136 145 galactose chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 151 166 birchwood xylan chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 168 170 BX chemical Binding studies, however, showed that CtCBM13 displayed no affinity for a range of relevant glycans including WAX, CX, xylose, mannose, galactose, and birchwood xylan (BX) (data not shown). RESULTS | |
| 33 40 CtCBM13 structure_element It would appear, therefore, that CtCBM13 makes a structural contribution to the function of CtXyl5A. RESULTS | |
| 92 99 CtXyl5A protein It would appear, therefore, that CtCBM13 makes a structural contribution to the function of CtXyl5A. RESULTS | |
| 0 17 Crystal Structure evidence Crystal Structure of CtXyl5A-D RESULTS | |
| 21 30 CtXyl5A-D mutant Crystal Structure of CtXyl5A-D RESULTS | |
| 35 56 non-catalytic modules structure_element To explore further the role of the non-catalytic modules in CtXyl5A the crystal structure of CtXyl5A extending from CtGH5 to CtCBM62 was sought. RESULTS | |
| 60 67 CtXyl5A protein To explore further the role of the non-catalytic modules in CtXyl5A the crystal structure of CtXyl5A extending from CtGH5 to CtCBM62 was sought. RESULTS | |
| 72 89 crystal structure evidence To explore further the role of the non-catalytic modules in CtXyl5A the crystal structure of CtXyl5A extending from CtGH5 to CtCBM62 was sought. RESULTS | |
| 93 100 CtXyl5A protein To explore further the role of the non-catalytic modules in CtXyl5A the crystal structure of CtXyl5A extending from CtGH5 to CtCBM62 was sought. RESULTS | |
| 116 121 CtGH5 structure_element To explore further the role of the non-catalytic modules in CtXyl5A the crystal structure of CtXyl5A extending from CtGH5 to CtCBM62 was sought. RESULTS | |
| 125 132 CtCBM62 structure_element To explore further the role of the non-catalytic modules in CtXyl5A the crystal structure of CtXyl5A extending from CtGH5 to CtCBM62 was sought. RESULTS | |
| 48 60 crystallized experimental_method To obtain a construct that could potentially be crystallized, the protein was generated without the C-terminal dockerin domain because it is known to be unstable and prone to cleavage. RESULTS | |
| 88 95 without protein_state To obtain a construct that could potentially be crystallized, the protein was generated without the C-terminal dockerin domain because it is known to be unstable and prone to cleavage. RESULTS | |
| 111 119 dockerin structure_element To obtain a construct that could potentially be crystallized, the protein was generated without the C-terminal dockerin domain because it is known to be unstable and prone to cleavage. RESULTS | |
| 22 31 CtXyl5A-D mutant Using this construct (CtXyl5A-D) the crystal structure of the arabinoxylanase was determined by molecular replacement to a resolution of 2.64 β« with Rwork and Rfree at 23.7% and 27.8%, respectively. RESULTS | |
| 37 54 crystal structure evidence Using this construct (CtXyl5A-D) the crystal structure of the arabinoxylanase was determined by molecular replacement to a resolution of 2.64 β« with Rwork and Rfree at 23.7% and 27.8%, respectively. RESULTS | |
| 62 77 arabinoxylanase protein_type Using this construct (CtXyl5A-D) the crystal structure of the arabinoxylanase was determined by molecular replacement to a resolution of 2.64 β« with Rwork and Rfree at 23.7% and 27.8%, respectively. RESULTS | |
| 96 117 molecular replacement experimental_method Using this construct (CtXyl5A-D) the crystal structure of the arabinoxylanase was determined by molecular replacement to a resolution of 2.64 β« with Rwork and Rfree at 23.7% and 27.8%, respectively. RESULTS | |
| 149 154 Rwork evidence Using this construct (CtXyl5A-D) the crystal structure of the arabinoxylanase was determined by molecular replacement to a resolution of 2.64 β« with Rwork and Rfree at 23.7% and 27.8%, respectively. RESULTS | |
| 159 164 Rfree evidence Using this construct (CtXyl5A-D) the crystal structure of the arabinoxylanase was determined by molecular replacement to a resolution of 2.64 β« with Rwork and Rfree at 23.7% and 27.8%, respectively. RESULTS | |
| 4 13 structure evidence The structure comprises a continuous polypeptide extending from Ala36 to Trp742 displaying four modules GH5-CBM6-CBM13-Fn3. RESULTS | |
| 64 79 Ala36 to Trp742 residue_range The structure comprises a continuous polypeptide extending from Ala36 to Trp742 displaying four modules GH5-CBM6-CBM13-Fn3. RESULTS | |
| 104 122 GH5-CBM6-CBM13-Fn3 structure_element The structure comprises a continuous polypeptide extending from Ala36 to Trp742 displaying four modules GH5-CBM6-CBM13-Fn3. RESULTS | |
| 24 40 electron density evidence Although there was some electron density for CtCBM62, it was not sufficient to confidently build the module (Fig. 5). RESULTS | |
| 45 52 CtCBM62 structure_element Although there was some electron density for CtCBM62, it was not sufficient to confidently build the module (Fig. 5). RESULTS | |
| 29 44 crystal packing evidence Further investigation of the crystal packing revealed a large solvent channel adjacent to the area the CBM62 occupies. RESULTS | |
| 62 77 solvent channel site Further investigation of the crystal packing revealed a large solvent channel adjacent to the area the CBM62 occupies. RESULTS | |
| 103 108 CBM62 structure_element Further investigation of the crystal packing revealed a large solvent channel adjacent to the area the CBM62 occupies. RESULTS | |
| 42 58 electron density evidence We postulate that the reason for the poor electron density is due to the CtCBM62 being mobile compared with the rest of the protein. RESULTS | |
| 73 80 CtCBM62 structure_element We postulate that the reason for the poor electron density is due to the CtCBM62 being mobile compared with the rest of the protein. RESULTS | |
| 87 93 mobile protein_state We postulate that the reason for the poor electron density is due to the CtCBM62 being mobile compared with the rest of the protein. RESULTS | |
| 4 14 structures evidence The structures of CtGH5 and CtCBM6 have been described previously. RESULTS | |
| 18 23 CtGH5 structure_element The structures of CtGH5 and CtCBM6 have been described previously. RESULTS | |
| 28 34 CtCBM6 structure_element The structures of CtGH5 and CtCBM6 have been described previously. RESULTS | |
| 44 59 arabinoxylanase protein_type Surface representation of the tetra-modular arabinoxylanase and zoom view on the CtGH5 loop. FIG | |
| 81 86 CtGH5 structure_element Surface representation of the tetra-modular arabinoxylanase and zoom view on the CtGH5 loop. FIG | |
| 87 91 loop structure_element Surface representation of the tetra-modular arabinoxylanase and zoom view on the CtGH5 loop. FIG | |
| 23 28 CtGH5 structure_element The blue module is the CtGH5 catalytic domain, the green module corresponds to the CtCBM6, the yellow module is the CtCBM13, and the salmon module is the fibronectin domain. FIG | |
| 29 45 catalytic domain structure_element The blue module is the CtGH5 catalytic domain, the green module corresponds to the CtCBM6, the yellow module is the CtCBM13, and the salmon module is the fibronectin domain. FIG | |
| 83 89 CtCBM6 structure_element The blue module is the CtGH5 catalytic domain, the green module corresponds to the CtCBM6, the yellow module is the CtCBM13, and the salmon module is the fibronectin domain. FIG | |
| 116 123 CtCBM13 structure_element The blue module is the CtGH5 catalytic domain, the green module corresponds to the CtCBM6, the yellow module is the CtCBM13, and the salmon module is the fibronectin domain. FIG | |
| 154 172 fibronectin domain structure_element The blue module is the CtGH5 catalytic domain, the green module corresponds to the CtCBM6, the yellow module is the CtCBM13, and the salmon module is the fibronectin domain. FIG | |
| 4 9 CtGH5 structure_element The CtGH5 loop is stabilized between the CtCBM6 and the CtCBM13 modules. FIG | |
| 10 14 loop structure_element The CtGH5 loop is stabilized between the CtCBM6 and the CtCBM13 modules. FIG | |
| 41 47 CtCBM6 structure_element The CtGH5 loop is stabilized between the CtCBM6 and the CtCBM13 modules. FIG | |
| 56 63 CtCBM13 structure_element The CtGH5 loop is stabilized between the CtCBM6 and the CtCBM13 modules. FIG | |
| 0 7 CtCBM13 structure_element CtCBM13 extends from Gly567 to Pro648. RESULTS | |
| 21 37 Gly567 to Pro648 residue_range CtCBM13 extends from Gly567 to Pro648. RESULTS | |
| 11 16 CBM13 protein_type Typical of CBM13 proteins CtCBM13 displays a Ξ²-trefoil fold comprising the canonical pseudo 3-fold symmetry with a 3-fold repeating unit of 40β50 amino acid residues characteristic of the Ricin superfamily. RESULTS | |
| 26 33 CtCBM13 structure_element Typical of CBM13 proteins CtCBM13 displays a Ξ²-trefoil fold comprising the canonical pseudo 3-fold symmetry with a 3-fold repeating unit of 40β50 amino acid residues characteristic of the Ricin superfamily. RESULTS | |
| 45 59 Ξ²-trefoil fold structure_element Typical of CBM13 proteins CtCBM13 displays a Ξ²-trefoil fold comprising the canonical pseudo 3-fold symmetry with a 3-fold repeating unit of 40β50 amino acid residues characteristic of the Ricin superfamily. RESULTS | |
| 115 136 3-fold repeating unit structure_element Typical of CBM13 proteins CtCBM13 displays a Ξ²-trefoil fold comprising the canonical pseudo 3-fold symmetry with a 3-fold repeating unit of 40β50 amino acid residues characteristic of the Ricin superfamily. RESULTS | |
| 140 156 40β50 amino acid residue_range Typical of CBM13 proteins CtCBM13 displays a Ξ²-trefoil fold comprising the canonical pseudo 3-fold symmetry with a 3-fold repeating unit of 40β50 amino acid residues characteristic of the Ricin superfamily. RESULTS | |
| 188 205 Ricin superfamily protein_type Typical of CBM13 proteins CtCBM13 displays a Ξ²-trefoil fold comprising the canonical pseudo 3-fold symmetry with a 3-fold repeating unit of 40β50 amino acid residues characteristic of the Ricin superfamily. RESULTS | |
| 5 11 repeat structure_element Each repeat contains two pairs of antiparallel Ξ²-strands. RESULTS | |
| 34 56 antiparallel Ξ²-strands structure_element Each repeat contains two pairs of antiparallel Ξ²-strands. RESULTS | |
| 2 13 Dali search experimental_method A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 52 57 CBM13 protein_type A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 73 99 root mean square deviation evidence A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 205 220 C. thermocellum species A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 221 242 exo-Ξ²-1,3-galactanase protein_type A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 260 284 Streptomyces avermitilis species A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 285 308 Ξ²-l-arabinopyranosidase protein_type A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 326 347 Streptomyces lividans species A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 348 360 xylanase 10A protein A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 383 416 Streptomyces olivaceoviridis E-86 species A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 417 429 xylanase 10A protein A Dali search revealed structural homologs from the CBM13 family with an root mean square deviation less than 2.0 β« and sequence identities of less than 20% that include the functionally relevant homologs C. thermocellum exo-Ξ²-1,3-galactanase (PDB code 3vsz), Streptomyces avermitilis Ξ²-l-arabinopyranosidase (PDB code 3a21), Streptomyces lividans xylanase 10A (PDB code, 1mc9), and Streptomyces olivaceoviridis E-86 xylanase 10A (PDB code 1v6v). RESULTS | |
| 4 7 Fn3 structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 34 49 Ξ²-sandwich fold structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 63 69 sheets structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 99 119 antiparallel strands structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 133 141 Ξ²1-Ξ²2-Ξ²5 structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 145 154 Ξ²-sheet 1 structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 159 167 Ξ²4-Ξ²3-Ξ²6 structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 171 180 Ξ²-sheet 2 structure_element The Fn3 module displays a typical Ξ²-sandwich fold with the two sheets comprising, primarily, three antiparallel strands in the order Ξ²1-Ξ²2-Ξ²5 in Ξ²-sheet 1 and Ξ²4-Ξ²3-Ξ²6 in Ξ²-sheet 2. RESULTS | |
| 9 18 Ξ²-sheet 2 structure_element Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 30 35 cleft site Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 62 79 endo-binding CBMs protein_type Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 187 198 full-length protein_state Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 199 205 enzyme protein Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 211 216 cleft site Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 228 235 CtCBM13 structure_element Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 290 304 polysaccharide chemical Although Ξ²-sheet 2 presents a cleft-like topology, typical of endo-binding CBMs, the surface lacks aromatic residues that play a key role in ligand recognition, and in the context of the full-length enzyme, the cleft abuts into CtCBM13 and thus would not be able to accommodate an extended polysaccharide chain (see below). RESULTS | |
| 7 16 structure evidence In the structure of CtXyl5A-D, the four modules form a three-leaf clover-like structure (Fig. 5). RESULTS | |
| 20 29 CtXyl5A-D mutant In the structure of CtXyl5A-D, the four modules form a three-leaf clover-like structure (Fig. 5). RESULTS | |
| 40 47 modules structure_element In the structure of CtXyl5A-D, the four modules form a three-leaf clover-like structure (Fig. 5). RESULTS | |
| 12 22 interfaces site Between the interfaces of CtGH5-CBM6-CBM13 there are a number of interactions that maintain the modules in a fixed position relative to each other. RESULTS | |
| 26 42 CtGH5-CBM6-CBM13 structure_element Between the interfaces of CtGH5-CBM6-CBM13 there are a number of interactions that maintain the modules in a fixed position relative to each other. RESULTS | |
| 19 24 CtGH5 structure_element The interaction of CtGH5 and CtCBM6, which buries a substantial apolar solvent-exposed surface of the two modules, has been described previously. RESULTS | |
| 29 35 CtCBM6 structure_element The interaction of CtGH5 and CtCBM6, which buries a substantial apolar solvent-exposed surface of the two modules, has been described previously. RESULTS | |
| 64 94 apolar solvent-exposed surface site The interaction of CtGH5 and CtCBM6, which buries a substantial apolar solvent-exposed surface of the two modules, has been described previously. RESULTS | |
| 4 22 polar interactions bond_interaction The polar interactions between these two modules comprise 14 hydrogen bonds and 5 salt bridges. RESULTS | |
| 61 75 hydrogen bonds bond_interaction The polar interactions between these two modules comprise 14 hydrogen bonds and 5 salt bridges. RESULTS | |
| 82 94 salt bridges bond_interaction The polar interactions between these two modules comprise 14 hydrogen bonds and 5 salt bridges. RESULTS | |
| 4 33 apolar and polar interactions bond_interaction The apolar and polar interactions between these two modules likely explaining why they do not fold independently compared with other glycoside hydrolases that contain CBMs. RESULTS | |
| 133 153 glycoside hydrolases protein_type The apolar and polar interactions between these two modules likely explaining why they do not fold independently compared with other glycoside hydrolases that contain CBMs. RESULTS | |
| 167 171 CBMs structure_element The apolar and polar interactions between these two modules likely explaining why they do not fold independently compared with other glycoside hydrolases that contain CBMs. RESULTS | |
| 0 7 CtCBM13 structure_element CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 20 34 central domain structure_element CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 42 56 interacts with protein_state CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 57 62 CtGH5 structure_element CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 64 70 CtCBM6 structure_element CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 76 81 CtFn3 structure_element CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 98 112 hydrogen bonds bond_interaction CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 201 208 compact protein_state CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 209 223 heterotetramer oligomeric_state CtCBM13 acts as the central domain, which interacts with CtGH5, CtCBM6, and CtFn3 via 2, 5, and 4 hydrogen bonds, respectively, burying a surface area of βΌ450, 350, and 500 β«2, respectively, to form a compact heterotetramer. RESULTS | |
| 20 42 CtCBM6-CBM13 interface site With respect to the CtCBM6-CBM13 interface, the linker (SPISTGTIP) between the two modules, extending from Ser514 to Pro522, adopts a fixed conformation. RESULTS | |
| 48 54 linker structure_element With respect to the CtCBM6-CBM13 interface, the linker (SPISTGTIP) between the two modules, extending from Ser514 to Pro522, adopts a fixed conformation. RESULTS | |
| 56 65 SPISTGTIP structure_element With respect to the CtCBM6-CBM13 interface, the linker (SPISTGTIP) between the two modules, extending from Ser514 to Pro522, adopts a fixed conformation. RESULTS | |
| 83 90 modules structure_element With respect to the CtCBM6-CBM13 interface, the linker (SPISTGTIP) between the two modules, extending from Ser514 to Pro522, adopts a fixed conformation. RESULTS | |
| 107 113 Ser514 residue_name_number With respect to the CtCBM6-CBM13 interface, the linker (SPISTGTIP) between the two modules, extending from Ser514 to Pro522, adopts a fixed conformation. RESULTS | |
| 117 123 Pro522 residue_name_number With respect to the CtCBM6-CBM13 interface, the linker (SPISTGTIP) between the two modules, extending from Ser514 to Pro522, adopts a fixed conformation. RESULTS | |
| 134 152 fixed conformation protein_state With respect to the CtCBM6-CBM13 interface, the linker (SPISTGTIP) between the two modules, extending from Ser514 to Pro522, adopts a fixed conformation. RESULTS | |
| 65 68 Ile residue_name Such sequences are normally extremely flexible; however, the two Ile residues make extensive apolar contacts within the linker and with the two CBMs, leading to conformational stabilization. RESULTS | |
| 93 108 apolar contacts bond_interaction Such sequences are normally extremely flexible; however, the two Ile residues make extensive apolar contacts within the linker and with the two CBMs, leading to conformational stabilization. RESULTS | |
| 120 126 linker structure_element Such sequences are normally extremely flexible; however, the two Ile residues make extensive apolar contacts within the linker and with the two CBMs, leading to conformational stabilization. RESULTS | |
| 144 148 CBMs structure_element Such sequences are normally extremely flexible; however, the two Ile residues make extensive apolar contacts within the linker and with the two CBMs, leading to conformational stabilization. RESULTS | |
| 25 30 CtGH5 structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 43 47 CBMs structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 86 90 loop structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 99 102 Ξ²-7 structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 107 110 Ξ±-7 structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 112 118 loop 7 structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 123 128 CtGH5 structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 153 170 trimodular clover structure_element The interactions between CtGH5 and the two CBMs, which are mediated by the tip of the loop between Ξ²-7 and Ξ±-7 (loop 7) of CtGH5, not only stabilize the trimodular clover-like structure but also make a contribution to catalytic function. RESULTS | |
| 46 53 modules structure_element Central to the interactions between the three modules is Trp285, which is intercalated between the two CBMs. RESULTS | |
| 57 63 Trp285 residue_name_number Central to the interactions between the three modules is Trp285, which is intercalated between the two CBMs. RESULTS | |
| 74 94 intercalated between bond_interaction Central to the interactions between the three modules is Trp285, which is intercalated between the two CBMs. RESULTS | |
| 103 107 CBMs structure_element Central to the interactions between the three modules is Trp285, which is intercalated between the two CBMs. RESULTS | |
| 38 52 hydrogen bonds bond_interaction The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 83 89 Val615 residue_name_number The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 94 100 Gly616 residue_name_number The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 104 111 CtCBM13 structure_element The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 147 162 apolar contacts bond_interaction The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 168 174 CtCBM6 structure_element The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 176 182 Pro440 residue_name_number The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 184 190 Phe489 residue_name_number The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 192 198 Gly491 residue_name_number The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 204 210 Ala492 residue_name_number The NΟ΅ of this aromatic residue makes hydrogen bonds with the backbone carbonyl of Val615 and Gly616 in CtCBM13, and the indole ring makes several apolar contacts with CtCBM6 (Pro440, Phe489, Gly491, and Ala492) (Fig. 5). RESULTS | |
| 8 14 loop 7 structure_element Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 18 39 completely disordered protein_state Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 47 56 truncated protein_state Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 71 78 CtXyl5A protein Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 90 95 CtGH5 structure_element Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 100 106 CtCBM6 structure_element Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 149 156 CtCBM13 structure_element Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 192 196 loop structure_element Indeed, loop 7 is completely disordered in the truncated derivative of CtXyl5A comprising CtGH5 and CtCBM6, demonstrating that the interactions with CtCBM13 stabilize the conformation of this loop. RESULTS | |
| 20 26 loop 7 structure_element Although the tip of loop 7 does not directly contribute to the topology of the active site, it is only βΌ12 β« from the catalytic nucleophile Glu279. RESULTS | |
| 79 90 active site site Although the tip of loop 7 does not directly contribute to the topology of the active site, it is only βΌ12 β« from the catalytic nucleophile Glu279. RESULTS | |
| 140 146 Glu279 residue_name_number Although the tip of loop 7 does not directly contribute to the topology of the active site, it is only βΌ12 β« from the catalytic nucleophile Glu279. RESULTS | |
| 30 34 loop structure_element Thus, any perturbation of the loop (through the removal of CtCBM13) is likely to influence the electrostatic and apolar environment of the catalytic apparatus, which could explain the reduction in activity associated with the deletion of CtCBM13. RESULTS | |
| 48 55 removal experimental_method Thus, any perturbation of the loop (through the removal of CtCBM13) is likely to influence the electrostatic and apolar environment of the catalytic apparatus, which could explain the reduction in activity associated with the deletion of CtCBM13. RESULTS | |
| 59 66 CtCBM13 structure_element Thus, any perturbation of the loop (through the removal of CtCBM13) is likely to influence the electrostatic and apolar environment of the catalytic apparatus, which could explain the reduction in activity associated with the deletion of CtCBM13. RESULTS | |
| 226 234 deletion experimental_method Thus, any perturbation of the loop (through the removal of CtCBM13) is likely to influence the electrostatic and apolar environment of the catalytic apparatus, which could explain the reduction in activity associated with the deletion of CtCBM13. RESULTS | |
| 238 245 CtCBM13 structure_element Thus, any perturbation of the loop (through the removal of CtCBM13) is likely to influence the electrostatic and apolar environment of the catalytic apparatus, which could explain the reduction in activity associated with the deletion of CtCBM13. RESULTS | |
| 36 42 CtCBM6 structure_element Similar to the interactions between CtCBM6 and CtCBM13, there are extensive hydrophobic interactions between CtCBM13 and CtFn3, resulting in very little flexibility between these modules. RESULTS | |
| 47 54 CtCBM13 structure_element Similar to the interactions between CtCBM6 and CtCBM13, there are extensive hydrophobic interactions between CtCBM13 and CtFn3, resulting in very little flexibility between these modules. RESULTS | |
| 76 100 hydrophobic interactions bond_interaction Similar to the interactions between CtCBM6 and CtCBM13, there are extensive hydrophobic interactions between CtCBM13 and CtFn3, resulting in very little flexibility between these modules. RESULTS | |
| 109 116 CtCBM13 structure_element Similar to the interactions between CtCBM6 and CtCBM13, there are extensive hydrophobic interactions between CtCBM13 and CtFn3, resulting in very little flexibility between these modules. RESULTS | |
| 121 126 CtFn3 structure_element Similar to the interactions between CtCBM6 and CtCBM13, there are extensive hydrophobic interactions between CtCBM13 and CtFn3, resulting in very little flexibility between these modules. RESULTS | |
| 179 186 modules structure_element Similar to the interactions between CtCBM6 and CtCBM13, there are extensive hydrophobic interactions between CtCBM13 and CtFn3, resulting in very little flexibility between these modules. RESULTS | |
| 21 31 absence of protein_state As stated above, the absence of CtCBM62 in the structure suggests that the module can adopt multiple positions with respect to the rest of the protein. RESULTS | |
| 32 39 CtCBM62 structure_element As stated above, the absence of CtCBM62 in the structure suggests that the module can adopt multiple positions with respect to the rest of the protein. RESULTS | |
| 47 56 structure evidence As stated above, the absence of CtCBM62 in the structure suggests that the module can adopt multiple positions with respect to the rest of the protein. RESULTS | |
| 75 81 module structure_element As stated above, the absence of CtCBM62 in the structure suggests that the module can adopt multiple positions with respect to the rest of the protein. RESULTS | |
| 4 11 CtCBM62 structure_element The CtCBM62, by binding to its ligands (d-Galp and l-Arap) in plant cell walls, may be able to recruit the enzyme onto its target substrate. RESULTS | |
| 16 26 binding to protein_state The CtCBM62, by binding to its ligands (d-Galp and l-Arap) in plant cell walls, may be able to recruit the enzyme onto its target substrate. RESULTS | |
| 40 46 d-Galp chemical The CtCBM62, by binding to its ligands (d-Galp and l-Arap) in plant cell walls, may be able to recruit the enzyme onto its target substrate. RESULTS | |
| 51 57 l-Arap chemical The CtCBM62, by binding to its ligands (d-Galp and l-Arap) in plant cell walls, may be able to recruit the enzyme onto its target substrate. RESULTS | |
| 62 67 plant taxonomy_domain The CtCBM62, by binding to its ligands (d-Galp and l-Arap) in plant cell walls, may be able to recruit the enzyme onto its target substrate. RESULTS | |
| 0 6 Xylans chemical Xylans are not generally thought to contain such sugars. RESULTS | |
| 49 55 sugars chemical Xylans are not generally thought to contain such sugars. RESULTS | |
| 0 6 d-Galp chemical d-Galp, however, has been detected in xylans in the outer layer of cereal grains and in eucalyptus trees, which are substrates used by CtXyl5A. RESULTS | |
| 38 44 xylans chemical d-Galp, however, has been detected in xylans in the outer layer of cereal grains and in eucalyptus trees, which are substrates used by CtXyl5A. RESULTS | |
| 67 73 cereal taxonomy_domain d-Galp, however, has been detected in xylans in the outer layer of cereal grains and in eucalyptus trees, which are substrates used by CtXyl5A. RESULTS | |
| 88 104 eucalyptus trees taxonomy_domain d-Galp, however, has been detected in xylans in the outer layer of cereal grains and in eucalyptus trees, which are substrates used by CtXyl5A. RESULTS | |
| 135 142 CtXyl5A protein d-Galp, however, has been detected in xylans in the outer layer of cereal grains and in eucalyptus trees, which are substrates used by CtXyl5A. RESULTS | |
| 6 13 CtCBM62 structure_element Thus, CtCBM62 may direct the enzyme to particularly complex xylans containing d-Galp at the non-reducing termini of the side chains, consistent with the open substrate binding cleft of the arabinoxylanase that is optimized to bind highly decorated forms of the hemicellulose. RESULTS | |
| 60 66 xylans chemical Thus, CtCBM62 may direct the enzyme to particularly complex xylans containing d-Galp at the non-reducing termini of the side chains, consistent with the open substrate binding cleft of the arabinoxylanase that is optimized to bind highly decorated forms of the hemicellulose. RESULTS | |
| 78 84 d-Galp chemical Thus, CtCBM62 may direct the enzyme to particularly complex xylans containing d-Galp at the non-reducing termini of the side chains, consistent with the open substrate binding cleft of the arabinoxylanase that is optimized to bind highly decorated forms of the hemicellulose. RESULTS | |
| 153 157 open protein_state Thus, CtCBM62 may direct the enzyme to particularly complex xylans containing d-Galp at the non-reducing termini of the side chains, consistent with the open substrate binding cleft of the arabinoxylanase that is optimized to bind highly decorated forms of the hemicellulose. RESULTS | |
| 158 181 substrate binding cleft site Thus, CtCBM62 may direct the enzyme to particularly complex xylans containing d-Galp at the non-reducing termini of the side chains, consistent with the open substrate binding cleft of the arabinoxylanase that is optimized to bind highly decorated forms of the hemicellulose. RESULTS | |
| 189 204 arabinoxylanase protein_type Thus, CtCBM62 may direct the enzyme to particularly complex xylans containing d-Galp at the non-reducing termini of the side chains, consistent with the open substrate binding cleft of the arabinoxylanase that is optimized to bind highly decorated forms of the hemicellulose. RESULTS | |
| 261 274 hemicellulose chemical Thus, CtCBM62 may direct the enzyme to particularly complex xylans containing d-Galp at the non-reducing termini of the side chains, consistent with the open substrate binding cleft of the arabinoxylanase that is optimized to bind highly decorated forms of the hemicellulose. RESULTS | |
| 11 15 CBMs structure_element In general CBMs have little influence on enzyme activity against soluble substrates but have a significant impact on glycans within plant cell walls. RESULTS | |
| 117 124 glycans chemical In general CBMs have little influence on enzyme activity against soluble substrates but have a significant impact on glycans within plant cell walls. RESULTS | |
| 132 137 plant taxonomy_domain In general CBMs have little influence on enzyme activity against soluble substrates but have a significant impact on glycans within plant cell walls. RESULTS | |
| 18 23 CBM62 structure_element Thus, the role of CBM62 will likely only be evident against insoluble composite substrates. RESULTS | |
| 10 26 GH5 Subfamily 34 protein_type Exploring GH5 Subfamily 34 RESULTS | |
| 0 7 CtXyl5A protein CtXyl5A is a member of a seven-protein subfamily of GH5, GH5_34. RESULTS | |
| 52 55 GH5 protein_type CtXyl5A is a member of a seven-protein subfamily of GH5, GH5_34. RESULTS | |
| 57 63 GH5_34 protein_type CtXyl5A is a member of a seven-protein subfamily of GH5, GH5_34. RESULTS | |
| 130 145 C. thermocellum species Four of these proteins are distinct, whereas the other three members are essentially identical (derived from different strains of C. thermocellum). RESULTS | |
| 110 116 GH5_34 protein_type To investigate further the substrate specificity within this subfamily, recombinant forms of three members of GH5_34 that were distinct from CtXyl5A were generated. RESULTS | |
| 141 148 CtXyl5A protein To investigate further the substrate specificity within this subfamily, recombinant forms of three members of GH5_34 that were distinct from CtXyl5A were generated. RESULTS | |
| 0 5 AcGH5 protein AcGH5 has a similar molecular architecture to CtXyl5A with the exception of an additional carbohydrate esterase family 6 module at the C terminus (Fig. 1). RESULTS | |
| 46 53 CtXyl5A protein AcGH5 has a similar molecular architecture to CtXyl5A with the exception of an additional carbohydrate esterase family 6 module at the C terminus (Fig. 1). RESULTS | |
| 90 127 carbohydrate esterase family 6 module structure_element AcGH5 has a similar molecular architecture to CtXyl5A with the exception of an additional carbohydrate esterase family 6 module at the C terminus (Fig. 1). RESULTS | |
| 4 10 GH5_34 protein_type The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 16 32 Verrucomicrobiae taxonomy_domain The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 33 42 bacterium taxonomy_domain The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 44 49 VbGH5 protein The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 64 78 GH5-CBM6-CBM13 structure_element The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 114 132 Fn3-CBM62-dockerin structure_element The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 153 160 CtXyl5A protein The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 182 200 Laminin_3_G domain structure_element The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 283 296 carbohydrates chemical The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 312 318 glycan chemical The GH5_34 from Verrucomicrobiae bacterium, VbGH5, contains the GH5-CBM6-CBM13 core structure, but the C-terminal Fn3-CBM62-dockerin modules, present in CtXyl5A, are replaced with a Laminin_3_G domain, which, by analogy to homologous domains in other proteins that have affinity for carbohydrates, may display a glycan binding function. RESULTS | |
| 4 19 Verrucomicobiae taxonomy_domain The Verrucomicobiae enzyme also has an N-terminal GH43 subfamily 10 (GH43_10) catalytic module. RESULTS | |
| 50 67 GH43 subfamily 10 protein_type The Verrucomicobiae enzyme also has an N-terminal GH43 subfamily 10 (GH43_10) catalytic module. RESULTS | |
| 69 76 GH43_10 protein_type The Verrucomicobiae enzyme also has an N-terminal GH43 subfamily 10 (GH43_10) catalytic module. RESULTS | |
| 78 94 catalytic module structure_element The Verrucomicobiae enzyme also has an N-terminal GH43 subfamily 10 (GH43_10) catalytic module. RESULTS | |
| 4 10 fungal taxonomy_domain The fungal GH5_34, GpGH5, unlike the two bacterial homologs, comprises a single GH5 catalytic module lacking all of the other accessory modules (Fig. 1). RESULTS | |
| 11 17 GH5_34 protein_type The fungal GH5_34, GpGH5, unlike the two bacterial homologs, comprises a single GH5 catalytic module lacking all of the other accessory modules (Fig. 1). RESULTS | |
| 19 24 GpGH5 protein The fungal GH5_34, GpGH5, unlike the two bacterial homologs, comprises a single GH5 catalytic module lacking all of the other accessory modules (Fig. 1). RESULTS | |
| 41 50 bacterial taxonomy_domain The fungal GH5_34, GpGH5, unlike the two bacterial homologs, comprises a single GH5 catalytic module lacking all of the other accessory modules (Fig. 1). RESULTS | |
| 80 83 GH5 protein_type The fungal GH5_34, GpGH5, unlike the two bacterial homologs, comprises a single GH5 catalytic module lacking all of the other accessory modules (Fig. 1). RESULTS | |
| 84 100 catalytic module structure_element The fungal GH5_34, GpGH5, unlike the two bacterial homologs, comprises a single GH5 catalytic module lacking all of the other accessory modules (Fig. 1). RESULTS | |
| 0 5 GpGh5 protein GpGh5 is particularly interesting as Gonapodya prolifera is the only fungus of the several hundred fungal genomes that encodes a GH5_34 enzyme. RESULTS | |
| 37 56 Gonapodya prolifera species GpGh5 is particularly interesting as Gonapodya prolifera is the only fungus of the several hundred fungal genomes that encodes a GH5_34 enzyme. RESULTS | |
| 69 75 fungus taxonomy_domain GpGh5 is particularly interesting as Gonapodya prolifera is the only fungus of the several hundred fungal genomes that encodes a GH5_34 enzyme. RESULTS | |
| 99 105 fungal taxonomy_domain GpGh5 is particularly interesting as Gonapodya prolifera is the only fungus of the several hundred fungal genomes that encodes a GH5_34 enzyme. RESULTS | |
| 129 135 GH5_34 protein_type GpGh5 is particularly interesting as Gonapodya prolifera is the only fungus of the several hundred fungal genomes that encodes a GH5_34 enzyme. RESULTS | |
| 33 39 GH5_34 protein_type In fact there are four potential GH5_34 sequences in the G. prolifera genome, all of which show high sequence homology to Clostridium GH5_34 sequences. RESULTS | |
| 57 69 G. prolifera species In fact there are four potential GH5_34 sequences in the G. prolifera genome, all of which show high sequence homology to Clostridium GH5_34 sequences. RESULTS | |
| 122 133 Clostridium taxonomy_domain In fact there are four potential GH5_34 sequences in the G. prolifera genome, all of which show high sequence homology to Clostridium GH5_34 sequences. RESULTS | |
| 134 140 GH5_34 protein_type In fact there are four potential GH5_34 sequences in the G. prolifera genome, all of which show high sequence homology to Clostridium GH5_34 sequences. RESULTS | |
| 0 12 G. prolifera species G. prolifera and Clostridium occupy similar environments, suggesting that the GpGH5_34 gene was acquired from a Clostridium species, which was followed by duplication of the gene in the fungal genome. RESULTS | |
| 17 28 Clostridium taxonomy_domain G. prolifera and Clostridium occupy similar environments, suggesting that the GpGH5_34 gene was acquired from a Clostridium species, which was followed by duplication of the gene in the fungal genome. RESULTS | |
| 78 86 GpGH5_34 protein G. prolifera and Clostridium occupy similar environments, suggesting that the GpGH5_34 gene was acquired from a Clostridium species, which was followed by duplication of the gene in the fungal genome. RESULTS | |
| 112 123 Clostridium taxonomy_domain G. prolifera and Clostridium occupy similar environments, suggesting that the GpGH5_34 gene was acquired from a Clostridium species, which was followed by duplication of the gene in the fungal genome. RESULTS | |
| 186 192 fungal taxonomy_domain G. prolifera and Clostridium occupy similar environments, suggesting that the GpGH5_34 gene was acquired from a Clostridium species, which was followed by duplication of the gene in the fungal genome. RESULTS | |
| 29 35 GH5_34 protein_type The sequence identity of the GH5_34 catalytic modules with CtXyl5A ranged from 55 to 80% (supplemental Fig. S1). RESULTS | |
| 36 53 catalytic modules structure_element The sequence identity of the GH5_34 catalytic modules with CtXyl5A ranged from 55 to 80% (supplemental Fig. S1). RESULTS | |
| 59 66 CtXyl5A protein The sequence identity of the GH5_34 catalytic modules with CtXyl5A ranged from 55 to 80% (supplemental Fig. S1). RESULTS | |
| 8 14 GH5_34 protein_type All the GH5_34 enzymes were active on the arabinoxylans RAX, WAX, and CX but displayed no activity on BX (Table 1 and Fig. 6) and are thus defined as arabinoxylanases. RESULTS | |
| 42 55 arabinoxylans chemical All the GH5_34 enzymes were active on the arabinoxylans RAX, WAX, and CX but displayed no activity on BX (Table 1 and Fig. 6) and are thus defined as arabinoxylanases. RESULTS | |
| 56 59 RAX chemical All the GH5_34 enzymes were active on the arabinoxylans RAX, WAX, and CX but displayed no activity on BX (Table 1 and Fig. 6) and are thus defined as arabinoxylanases. RESULTS | |
| 61 64 WAX chemical All the GH5_34 enzymes were active on the arabinoxylans RAX, WAX, and CX but displayed no activity on BX (Table 1 and Fig. 6) and are thus defined as arabinoxylanases. RESULTS | |
| 70 72 CX chemical All the GH5_34 enzymes were active on the arabinoxylans RAX, WAX, and CX but displayed no activity on BX (Table 1 and Fig. 6) and are thus defined as arabinoxylanases. RESULTS | |
| 102 104 BX chemical All the GH5_34 enzymes were active on the arabinoxylans RAX, WAX, and CX but displayed no activity on BX (Table 1 and Fig. 6) and are thus defined as arabinoxylanases. RESULTS | |
| 150 166 arabinoxylanases protein_type All the GH5_34 enzymes were active on the arabinoxylans RAX, WAX, and CX but displayed no activity on BX (Table 1 and Fig. 6) and are thus defined as arabinoxylanases. RESULTS | |
| 32 39 CtXyl5A protein The limit products generated by CtXyl5A, AcGH5, and GpGH5 comprised a range of oligosaccharides with some high molecular weight material. RESULTS | |
| 41 46 AcGH5 protein The limit products generated by CtXyl5A, AcGH5, and GpGH5 comprised a range of oligosaccharides with some high molecular weight material. RESULTS | |
| 52 57 GpGH5 protein The limit products generated by CtXyl5A, AcGH5, and GpGH5 comprised a range of oligosaccharides with some high molecular weight material. RESULTS | |
| 79 95 oligosaccharides chemical The limit products generated by CtXyl5A, AcGH5, and GpGH5 comprised a range of oligosaccharides with some high molecular weight material. RESULTS | |
| 4 20 oligosaccharides chemical The oligosaccharides with low degrees of polymerization were absent in the VbGH5 reaction products. RESULTS | |
| 75 80 VbGH5 protein The oligosaccharides with low degrees of polymerization were absent in the VbGH5 reaction products. RESULTS | |
| 48 57 arabinose chemical However, the enzyme generated a large amount of arabinose, which was not produced by the other arabinoxylanases. RESULTS | |
| 95 111 arabinoxylanases protein_type However, the enzyme generated a large amount of arabinose, which was not produced by the other arabinoxylanases. RESULTS | |
| 11 18 GH43_10 protein_type Given that GH43_10 is predominantly an arabinofuranosidase subfamily of GH43, the arabinose generated by VbGH5 is likely mediated by the N-terminal catalytic module (see below). RESULTS | |
| 39 58 arabinofuranosidase protein_type Given that GH43_10 is predominantly an arabinofuranosidase subfamily of GH43, the arabinose generated by VbGH5 is likely mediated by the N-terminal catalytic module (see below). RESULTS | |
| 72 76 GH43 protein_type Given that GH43_10 is predominantly an arabinofuranosidase subfamily of GH43, the arabinose generated by VbGH5 is likely mediated by the N-terminal catalytic module (see below). RESULTS | |
| 82 91 arabinose chemical Given that GH43_10 is predominantly an arabinofuranosidase subfamily of GH43, the arabinose generated by VbGH5 is likely mediated by the N-terminal catalytic module (see below). RESULTS | |
| 105 110 VbGH5 protein Given that GH43_10 is predominantly an arabinofuranosidase subfamily of GH43, the arabinose generated by VbGH5 is likely mediated by the N-terminal catalytic module (see below). RESULTS | |
| 148 164 catalytic module structure_element Given that GH43_10 is predominantly an arabinofuranosidase subfamily of GH43, the arabinose generated by VbGH5 is likely mediated by the N-terminal catalytic module (see below). RESULTS | |
| 29 34 AcGH5 protein Kinetic analysis showed that AcGH5 displayed similar activity to CtXyl5A against both WAX and RAX and was 2-fold less active against CX. RESULTS | |
| 65 72 CtXyl5A protein Kinetic analysis showed that AcGH5 displayed similar activity to CtXyl5A against both WAX and RAX and was 2-fold less active against CX. RESULTS | |
| 86 89 WAX chemical Kinetic analysis showed that AcGH5 displayed similar activity to CtXyl5A against both WAX and RAX and was 2-fold less active against CX. RESULTS | |
| 94 97 RAX chemical Kinetic analysis showed that AcGH5 displayed similar activity to CtXyl5A against both WAX and RAX and was 2-fold less active against CX. RESULTS | |
| 133 135 CX chemical Kinetic analysis showed that AcGH5 displayed similar activity to CtXyl5A against both WAX and RAX and was 2-fold less active against CX. RESULTS | |
| 41 50 wild type protein_state When initially measuring the activity of wild type VbGH5 against the different substrates, no clear data could be obtained, regardless of the concentration of enzyme used the reaction appeared to cease after a few minutes. RESULTS | |
| 51 56 VbGH5 protein When initially measuring the activity of wild type VbGH5 against the different substrates, no clear data could be obtained, regardless of the concentration of enzyme used the reaction appeared to cease after a few minutes. RESULTS | |
| 36 43 GH43_10 protein_type We hypothesized that the N-terminal GH43_10 rapidly removed single arabinose decorations from the arabinoxylans depleting the substrate available to the arabinoxylanase, explaining why this activity was short lived. RESULTS | |
| 67 76 arabinose chemical We hypothesized that the N-terminal GH43_10 rapidly removed single arabinose decorations from the arabinoxylans depleting the substrate available to the arabinoxylanase, explaining why this activity was short lived. RESULTS | |
| 98 111 arabinoxylans chemical We hypothesized that the N-terminal GH43_10 rapidly removed single arabinose decorations from the arabinoxylans depleting the substrate available to the arabinoxylanase, explaining why this activity was short lived. RESULTS | |
| 153 168 arabinoxylanase protein_type We hypothesized that the N-terminal GH43_10 rapidly removed single arabinose decorations from the arabinoxylans depleting the substrate available to the arabinoxylanase, explaining why this activity was short lived. RESULTS | |
| 29 38 conserved protein_state To test this hypothesis, the conserved catalytic base (Asp45) of the GH43_10 module of VbGH5 was substituted with alanine, which is predicted to inactivate this catalytic module. RESULTS | |
| 55 60 Asp45 residue_name_number To test this hypothesis, the conserved catalytic base (Asp45) of the GH43_10 module of VbGH5 was substituted with alanine, which is predicted to inactivate this catalytic module. RESULTS | |
| 69 76 GH43_10 structure_element To test this hypothesis, the conserved catalytic base (Asp45) of the GH43_10 module of VbGH5 was substituted with alanine, which is predicted to inactivate this catalytic module. RESULTS | |
| 87 92 VbGH5 protein To test this hypothesis, the conserved catalytic base (Asp45) of the GH43_10 module of VbGH5 was substituted with alanine, which is predicted to inactivate this catalytic module. RESULTS | |
| 97 113 substituted with experimental_method To test this hypothesis, the conserved catalytic base (Asp45) of the GH43_10 module of VbGH5 was substituted with alanine, which is predicted to inactivate this catalytic module. RESULTS | |
| 114 121 alanine residue_name To test this hypothesis, the conserved catalytic base (Asp45) of the GH43_10 module of VbGH5 was substituted with alanine, which is predicted to inactivate this catalytic module. RESULTS | |
| 161 177 catalytic module structure_element To test this hypothesis, the conserved catalytic base (Asp45) of the GH43_10 module of VbGH5 was substituted with alanine, which is predicted to inactivate this catalytic module. RESULTS | |
| 4 8 D45A mutant The D45A mutant did not produce arabinose consistent with the arabinofuranosidase activity displayed by the GH43_10 module in the wild type enzyme (Fig. 6). RESULTS | |
| 9 15 mutant protein_state The D45A mutant did not produce arabinose consistent with the arabinofuranosidase activity displayed by the GH43_10 module in the wild type enzyme (Fig. 6). RESULTS | |
| 32 41 arabinose chemical The D45A mutant did not produce arabinose consistent with the arabinofuranosidase activity displayed by the GH43_10 module in the wild type enzyme (Fig. 6). RESULTS | |
| 62 81 arabinofuranosidase protein_type The D45A mutant did not produce arabinose consistent with the arabinofuranosidase activity displayed by the GH43_10 module in the wild type enzyme (Fig. 6). RESULTS | |
| 108 115 GH43_10 structure_element The D45A mutant did not produce arabinose consistent with the arabinofuranosidase activity displayed by the GH43_10 module in the wild type enzyme (Fig. 6). RESULTS | |
| 130 139 wild type protein_state The D45A mutant did not produce arabinose consistent with the arabinofuranosidase activity displayed by the GH43_10 module in the wild type enzyme (Fig. 6). RESULTS | |
| 4 12 kinetics evidence The kinetics of the GH5_34 arabinoxylanase catalytic module was now measurable, and activities were determined to be between βΌ6- and 10-fold lower than that of CtXyl5A. RESULTS | |
| 20 26 GH5_34 protein_type The kinetics of the GH5_34 arabinoxylanase catalytic module was now measurable, and activities were determined to be between βΌ6- and 10-fold lower than that of CtXyl5A. RESULTS | |
| 27 42 arabinoxylanase protein_type The kinetics of the GH5_34 arabinoxylanase catalytic module was now measurable, and activities were determined to be between βΌ6- and 10-fold lower than that of CtXyl5A. RESULTS | |
| 43 59 catalytic module structure_element The kinetics of the GH5_34 arabinoxylanase catalytic module was now measurable, and activities were determined to be between βΌ6- and 10-fold lower than that of CtXyl5A. RESULTS | |
| 160 167 CtXyl5A protein The kinetics of the GH5_34 arabinoxylanase catalytic module was now measurable, and activities were determined to be between βΌ6- and 10-fold lower than that of CtXyl5A. RESULTS | |
| 19 25 fungal taxonomy_domain Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 26 41 arabinoxylanase protein_type Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 82 85 WAX chemical Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 90 93 RAX chemical Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 137 144 CtXyl5A protein Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 215 225 eukaryotic taxonomy_domain Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 230 241 prokaryotic taxonomy_domain Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 258 260 CX chemical Interestingly, the fungal arabinoxylanase displays the highest activities against WAX and RAX, βΌ4- and 6-fold higher, respectively, than CtXyl5A; however, there is very little difference in the activity between the eukaryotic and prokaryotic enzymes against CX. RESULTS | |
| 70 75 AcGH5 protein Attempts to express individual modules of a variety of truncations of AcGH5 and VbGH5 were unsuccessful. RESULTS | |
| 80 85 VbGH5 protein Attempts to express individual modules of a variety of truncations of AcGH5 and VbGH5 were unsuccessful. RESULTS | |
| 97 108 full-length protein_state This may indicate that the individual modules can only fold correctly when incorporated into the full-length enzyme, demonstrating the importance of intermodule interactions to maintain the structural integrity of these enzymes. RESULTS | |
| 30 36 GH5_34 protein_type Products profile generated of GH5_34 enzymes. FIG | |
| 25 34 incubated experimental_method The enzymes at 1 ΞΌm were incubated with the four different xylans at 1% in 50 mm sodium phosphate buffer for 16 h at 37 Β°C (GpGH5, VbGH5, and AcGH5) or 60 Β°C. FIG | |
| 59 65 xylans chemical The enzymes at 1 ΞΌm were incubated with the four different xylans at 1% in 50 mm sodium phosphate buffer for 16 h at 37 Β°C (GpGH5, VbGH5, and AcGH5) or 60 Β°C. FIG | |
| 124 129 GpGH5 protein The enzymes at 1 ΞΌm were incubated with the four different xylans at 1% in 50 mm sodium phosphate buffer for 16 h at 37 Β°C (GpGH5, VbGH5, and AcGH5) or 60 Β°C. FIG | |
| 131 136 VbGH5 protein The enzymes at 1 ΞΌm were incubated with the four different xylans at 1% in 50 mm sodium phosphate buffer for 16 h at 37 Β°C (GpGH5, VbGH5, and AcGH5) or 60 Β°C. FIG | |
| 142 147 AcGH5 protein The enzymes at 1 ΞΌm were incubated with the four different xylans at 1% in 50 mm sodium phosphate buffer for 16 h at 37 Β°C (GpGH5, VbGH5, and AcGH5) or 60 Β°C. FIG | |
| 37 40 TLC experimental_method The limit products were separated by TLC. FIG | |
| 4 23 xylooligosaccharide chemical The xylooligosaccharide standards (X) are indicated by their degrees of polymerization. FIG | |
| 52 57 plant taxonomy_domain A characteristic feature of enzymes that attack the plant cell wall is their complex molecular architecture. DISCUSS | |
| 4 8 CBMs structure_element The CBMs in these enzymes generally play a role in substrate targeting and are appended to the catalytic modules through flexible linker sequences. DISCUSS | |
| 95 112 catalytic modules structure_element The CBMs in these enzymes generally play a role in substrate targeting and are appended to the catalytic modules through flexible linker sequences. DISCUSS | |
| 121 146 flexible linker sequences structure_element The CBMs in these enzymes generally play a role in substrate targeting and are appended to the catalytic modules through flexible linker sequences. DISCUSS | |
| 0 7 CtXyl5A protein CtXyl5A provides a rare visualization of the structure of multiple modules within a single enzyme. DISCUSS | |
| 45 54 structure evidence CtXyl5A provides a rare visualization of the structure of multiple modules within a single enzyme. DISCUSS | |
| 78 82 CBMs structure_element The central feature of these data is the structural role played by two of the CBMs, CtCBM6 and CtCBM13, in maintaining the active conformation of the catalytic module, CtGH5. DISCUSS | |
| 84 90 CtCBM6 structure_element The central feature of these data is the structural role played by two of the CBMs, CtCBM6 and CtCBM13, in maintaining the active conformation of the catalytic module, CtGH5. DISCUSS | |
| 95 102 CtCBM13 structure_element The central feature of these data is the structural role played by two of the CBMs, CtCBM6 and CtCBM13, in maintaining the active conformation of the catalytic module, CtGH5. DISCUSS | |
| 123 129 active protein_state The central feature of these data is the structural role played by two of the CBMs, CtCBM6 and CtCBM13, in maintaining the active conformation of the catalytic module, CtGH5. DISCUSS | |
| 150 166 catalytic module structure_element The central feature of these data is the structural role played by two of the CBMs, CtCBM6 and CtCBM13, in maintaining the active conformation of the catalytic module, CtGH5. DISCUSS | |
| 168 173 CtGH5 structure_element The central feature of these data is the structural role played by two of the CBMs, CtCBM6 and CtCBM13, in maintaining the active conformation of the catalytic module, CtGH5. DISCUSS | |
| 4 25 crystallographic data evidence The crystallographic data described here are supported by biochemical data showing either that these two modules do not bind to glycans (CtCBM13) or that the recognition of the non-reducing end of xylan or cellulose chains (CtCBM6) is unlikely to be biologically significant. DISCUSS | |
| 128 135 glycans chemical The crystallographic data described here are supported by biochemical data showing either that these two modules do not bind to glycans (CtCBM13) or that the recognition of the non-reducing end of xylan or cellulose chains (CtCBM6) is unlikely to be biologically significant. DISCUSS | |
| 137 144 CtCBM13 structure_element The crystallographic data described here are supported by biochemical data showing either that these two modules do not bind to glycans (CtCBM13) or that the recognition of the non-reducing end of xylan or cellulose chains (CtCBM6) is unlikely to be biologically significant. DISCUSS | |
| 197 202 xylan chemical The crystallographic data described here are supported by biochemical data showing either that these two modules do not bind to glycans (CtCBM13) or that the recognition of the non-reducing end of xylan or cellulose chains (CtCBM6) is unlikely to be biologically significant. DISCUSS | |
| 206 215 cellulose chemical The crystallographic data described here are supported by biochemical data showing either that these two modules do not bind to glycans (CtCBM13) or that the recognition of the non-reducing end of xylan or cellulose chains (CtCBM6) is unlikely to be biologically significant. DISCUSS | |
| 224 230 CtCBM6 structure_element The crystallographic data described here are supported by biochemical data showing either that these two modules do not bind to glycans (CtCBM13) or that the recognition of the non-reducing end of xylan or cellulose chains (CtCBM6) is unlikely to be biologically significant. DISCUSS | |
| 39 45 glycan chemical It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 105 116 full-length protein_state It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 172 177 plant taxonomy_domain It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 215 220 CBM46 structure_element It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 235 243 Bacillus taxonomy_domain It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 244 257 xyloglucanase protein_type It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 258 280 mixed linked glucanase protein_type It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 281 288 BhCel5B protein It should be emphasized, however, that glycan binding and substrate targeting may only be evident in the full-length enzyme acting on highly complex structures such as the plant cell wall, as observed recently by a CBM46 module in the Bacillus xyloglucanase/mixed linked glucanase BhCel5B. DISCUSS | |
| 0 7 CtXyl5A protein CtXyl5A is a member of GH5 that contains 6644 members. DISCUSS | |
| 23 26 GH5 protein_type CtXyl5A is a member of GH5 that contains 6644 members. DISCUSS | |
| 0 7 CtXyl5A protein CtXyl5A is a member of subfamily GH5_34. DISCUSS | |
| 33 39 GH5_34 protein_type CtXyl5A is a member of subfamily GH5_34. DISCUSS | |
| 78 94 arabinoxylanases protein_type Despite differences in sequence identity all of the homologs were shown to be arabinoxylanases. DISCUSS | |
| 68 74 GH5_34 protein_type Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 89 113 specificity determinants site Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 114 119 Glu68 residue_name_number Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 121 126 Tyr92 residue_name_number Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 132 138 Asn139 residue_name_number Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 182 188 xylose chemical Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 192 201 arabinose chemical Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 209 220 β2* subsite site Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 250 256 xylose chemical Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 275 286 active site site Consistent with the conserved substrate specificity, all members of GH5_34 contained the specificity determinants Glu68, Tyr92, and Asn139, which make critical interactions with the xylose or arabinose in the β2* subsite, which are 1,3-linked to the xylose positioned in the active site. DISCUSS | |
| 18 23 CBM62 structure_element The presence of a CBM62 in CtXyl5A and AcGH5 suggests that these enzymes target highly complex xylans that contain d-galactose in their side chains. DISCUSS | |
| 27 34 CtXyl5A protein The presence of a CBM62 in CtXyl5A and AcGH5 suggests that these enzymes target highly complex xylans that contain d-galactose in their side chains. DISCUSS | |
| 39 44 AcGH5 protein The presence of a CBM62 in CtXyl5A and AcGH5 suggests that these enzymes target highly complex xylans that contain d-galactose in their side chains. DISCUSS | |
| 95 101 xylans chemical The presence of a CBM62 in CtXyl5A and AcGH5 suggests that these enzymes target highly complex xylans that contain d-galactose in their side chains. DISCUSS | |
| 115 126 d-galactose chemical The presence of a CBM62 in CtXyl5A and AcGH5 suggests that these enzymes target highly complex xylans that contain d-galactose in their side chains. DISCUSS | |
| 4 14 absence of protein_state The absence of a βnon-structuralβ CBM in GpGH5 may indicate that this arabinoxylanase is designed to target simpler arabinoxylans present in the endosperm of cereals. DISCUSS | |
| 34 37 CBM structure_element The absence of a βnon-structuralβ CBM in GpGH5 may indicate that this arabinoxylanase is designed to target simpler arabinoxylans present in the endosperm of cereals. DISCUSS | |
| 41 46 GpGH5 protein The absence of a βnon-structuralβ CBM in GpGH5 may indicate that this arabinoxylanase is designed to target simpler arabinoxylans present in the endosperm of cereals. DISCUSS | |
| 70 85 arabinoxylanase protein_type The absence of a βnon-structuralβ CBM in GpGH5 may indicate that this arabinoxylanase is designed to target simpler arabinoxylans present in the endosperm of cereals. DISCUSS | |
| 116 129 arabinoxylans chemical The absence of a βnon-structuralβ CBM in GpGH5 may indicate that this arabinoxylanase is designed to target simpler arabinoxylans present in the endosperm of cereals. DISCUSS | |
| 158 165 cereals taxonomy_domain The absence of a βnon-structuralβ CBM in GpGH5 may indicate that this arabinoxylanase is designed to target simpler arabinoxylans present in the endosperm of cereals. DISCUSS | |
| 48 54 GH5_34 protein_type Although the characterization of all members of GH5_34 suggests that this subfamily is monospecific, differences in specificity are observed in other subfamilies of GHs including GH43 and GH5. DISCUSS | |
| 165 168 GHs protein_type Although the characterization of all members of GH5_34 suggests that this subfamily is monospecific, differences in specificity are observed in other subfamilies of GHs including GH43 and GH5. DISCUSS | |
| 179 183 GH43 protein_type Although the characterization of all members of GH5_34 suggests that this subfamily is monospecific, differences in specificity are observed in other subfamilies of GHs including GH43 and GH5. DISCUSS | |
| 188 191 GH5 protein_type Although the characterization of all members of GH5_34 suggests that this subfamily is monospecific, differences in specificity are observed in other subfamilies of GHs including GH43 and GH5. DISCUSS | |
| 24 30 GH5_34 protein_type Thus, as new members of GH5_34 are identified from genomic sequence data and subsequently characterized, the specificity of this family may require reinterpretation. DISCUSS | |
| 25 30 VbGH5 protein An intriguing feature of VbGH5 is that the limited products generated by this enzymes are much larger than those produced by the other arabinoxylanases. DISCUSS | |
| 135 151 arabinoxylanases protein_type An intriguing feature of VbGH5 is that the limited products generated by this enzymes are much larger than those produced by the other arabinoxylanases. DISCUSS | |
| 28 37 arabinose chemical This suggests that although arabinose decorations contribute to enzyme specificity (VbGH5 is not active on xylans lacking arabinose side chains), the enzyme requires other specificity determinants that occur less frequently in arabinoxylans. DISCUSS | |
| 84 89 VbGH5 protein This suggests that although arabinose decorations contribute to enzyme specificity (VbGH5 is not active on xylans lacking arabinose side chains), the enzyme requires other specificity determinants that occur less frequently in arabinoxylans. DISCUSS | |
| 107 113 xylans chemical This suggests that although arabinose decorations contribute to enzyme specificity (VbGH5 is not active on xylans lacking arabinose side chains), the enzyme requires other specificity determinants that occur less frequently in arabinoxylans. DISCUSS | |
| 122 131 arabinose chemical This suggests that although arabinose decorations contribute to enzyme specificity (VbGH5 is not active on xylans lacking arabinose side chains), the enzyme requires other specificity determinants that occur less frequently in arabinoxylans. DISCUSS | |
| 227 240 arabinoxylans chemical This suggests that although arabinose decorations contribute to enzyme specificity (VbGH5 is not active on xylans lacking arabinose side chains), the enzyme requires other specificity determinants that occur less frequently in arabinoxylans. DISCUSS | |
| 50 54 GH98 protein_type This has some resonance with a recently described GH98 xylanase that also exploits specificity determinants that occur infrequently and are only evident in highly complex xylans (e.g. CX). DISCUSS | |
| 55 63 xylanase protein_type This has some resonance with a recently described GH98 xylanase that also exploits specificity determinants that occur infrequently and are only evident in highly complex xylans (e.g. CX). DISCUSS | |
| 171 177 xylans chemical This has some resonance with a recently described GH98 xylanase that also exploits specificity determinants that occur infrequently and are only evident in highly complex xylans (e.g. CX). DISCUSS | |
| 184 186 CX chemical This has some resonance with a recently described GH98 xylanase that also exploits specificity determinants that occur infrequently and are only evident in highly complex xylans (e.g. CX). DISCUSS | |
| 86 102 arabinoxylanases protein_type To conclude, this study provides the molecular basis for the specificity displayed by arabinoxylanases. DISCUSS | |
| 42 48 pocket site Substrate specificity is dominated by the pocket that binds single arabinose or xylose side chains. DISCUSS | |
| 67 76 arabinose chemical Substrate specificity is dominated by the pocket that binds single arabinose or xylose side chains. DISCUSS | |
| 80 86 xylose chemical Substrate specificity is dominated by the pocket that binds single arabinose or xylose side chains. DISCUSS | |
| 4 8 open protein_state The open xylan binding cleft explains why the enzyme is able to attack highly decorated forms of the hemicellulose. DISCUSS | |
| 9 28 xylan binding cleft site The open xylan binding cleft explains why the enzyme is able to attack highly decorated forms of the hemicellulose. DISCUSS | |
| 101 114 hemicellulose chemical The open xylan binding cleft explains why the enzyme is able to attack highly decorated forms of the hemicellulose. DISCUSS | |
| 45 62 catalytic modules structure_element It is also evident that appending additional catalytic modules and CBMs onto the core components of these enzymes generates bespoke arabinoxylanases with activities optimized for specific functions. DISCUSS | |
| 67 71 CBMs structure_element It is also evident that appending additional catalytic modules and CBMs onto the core components of these enzymes generates bespoke arabinoxylanases with activities optimized for specific functions. DISCUSS | |
| 132 148 arabinoxylanases protein_type It is also evident that appending additional catalytic modules and CBMs onto the core components of these enzymes generates bespoke arabinoxylanases with activities optimized for specific functions. DISCUSS | |
| 25 41 arabinoxylanases protein_type The specificities of the arabinoxylanases described here are distinct from the classical endo-xylanases and thus have the potential to contribute to the toolbox of biocatalysts required by industries that exploit the plant cell wall as a sustainable substrate. DISCUSS | |
| 89 103 endo-xylanases protein_type The specificities of the arabinoxylanases described here are distinct from the classical endo-xylanases and thus have the potential to contribute to the toolbox of biocatalysts required by industries that exploit the plant cell wall as a sustainable substrate. DISCUSS | |
| 217 222 plant taxonomy_domain The specificities of the arabinoxylanases described here are distinct from the classical endo-xylanases and thus have the potential to contribute to the toolbox of biocatalysts required by industries that exploit the plant cell wall as a sustainable substrate. DISCUSS | |
| 0 41 Data collection and refinement statistics evidence Data collection and refinement statistics TABLE | |
| 1 10 CtXyl5A-D mutant " CtXyl5A-D GH5-CBM6-Arap GH5-CBM6-Xylp GH5-CBM6- (Araf-Xylp4) Data collection ββββSource ESRF-ID14-1 Diamond I04β1 Diamond I24 Diamond I02 ββββWavelength (Γ ) 0.9334 0.9173 0.9772 0.9791 ββββSpace group P21212 P212121 P212121 P212121 ββββCell dimensions ββββββββa, b, c (Γ ) 147.4, 191.7, 50.7 67.1, 72.4, 109.1 67.9, 72.5, 109.5 76.3, 123.2, 125.4 ββββββββΞ±, Ξ², Ξ³ (Β°) 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 ββββNo. of measured reflections 244,475 (29,324) 224,842 (11,281) 152,004 (4,996) 463,237 (23,068) ββββNo. of independent reflections 42246 (5,920) 63,523 (3,175) 42,716 (2,334) 140,288 (6,879) ββββResolution (Γ ) 50.70β2.64 (2.78β2.64) 44.85β1.65 (1.68β1.65) 45.16β1.90 (1.94β1.90) 48.43β1.65 (1.68β1.65) ββββRmerge (%) 16.5 (69.5) 6.7 (65.1) 2.8 (8.4) 5.7 (74.9) ββββCC1/2 0.985 (0.478) 0.998 (0.594) 0.999 (0.982) 0.998 (0.484) ββββI/ΟI 8.0 (2.0) 13 (1.6) 26.6 (8.0) 11.2 (1.6) ββββCompleteness (%) 98.5 (96.4) 98.5 (99.4) 98.6 (85.0) 98.8 (99.4) ββββRedundancy 5.8 (5.0) 3.5 (3.6) 3.6 (2.1) 3.3 (3.4) Refinement ββββRwork/Rfree 23.7/27.8 12.2/17.0 12.9/16.1 14.5/19.9 ββββNo. atoms ββββββββProtein 5446 3790 3729 7333 ββββββββLigand 19 20 20 92 ββββββββWater 227 579 601 923 ββββB-factors ββββββββProtein 41.6 17.8 15.8 21.0 ββββββββLigand 65.0 19.4 24.2 39.5 ββββββββWater 35.4 38.5 32.2 37.6 ββββR.m.s deviations ββββββββBond lengths (Γ ) 0.008 0.015 0.012 0.012 ββββββββBond angles (Β°) 1.233 1.502 1.624 1.554 ββββProtein Data Bank code 5G56 5LA0 5LA1 2LA2 " TABLE | |
| 11 24 GH5-CBM6-Arap complex_assembly " CtXyl5A-D GH5-CBM6-Arap GH5-CBM6-Xylp GH5-CBM6- (Araf-Xylp4) Data collection ββββSource ESRF-ID14-1 Diamond I04β1 Diamond I24 Diamond I02 ββββWavelength (Γ ) 0.9334 0.9173 0.9772 0.9791 ββββSpace group P21212 P212121 P212121 P212121 ββββCell dimensions ββββββββa, b, c (Γ ) 147.4, 191.7, 50.7 67.1, 72.4, 109.1 67.9, 72.5, 109.5 76.3, 123.2, 125.4 ββββββββΞ±, Ξ², Ξ³ (Β°) 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 ββββNo. of measured reflections 244,475 (29,324) 224,842 (11,281) 152,004 (4,996) 463,237 (23,068) ββββNo. of independent reflections 42246 (5,920) 63,523 (3,175) 42,716 (2,334) 140,288 (6,879) ββββResolution (Γ ) 50.70β2.64 (2.78β2.64) 44.85β1.65 (1.68β1.65) 45.16β1.90 (1.94β1.90) 48.43β1.65 (1.68β1.65) ββββRmerge (%) 16.5 (69.5) 6.7 (65.1) 2.8 (8.4) 5.7 (74.9) ββββCC1/2 0.985 (0.478) 0.998 (0.594) 0.999 (0.982) 0.998 (0.484) ββββI/ΟI 8.0 (2.0) 13 (1.6) 26.6 (8.0) 11.2 (1.6) ββββCompleteness (%) 98.5 (96.4) 98.5 (99.4) 98.6 (85.0) 98.8 (99.4) ββββRedundancy 5.8 (5.0) 3.5 (3.6) 3.6 (2.1) 3.3 (3.4) Refinement ββββRwork/Rfree 23.7/27.8 12.2/17.0 12.9/16.1 14.5/19.9 ββββNo. atoms ββββββββProtein 5446 3790 3729 7333 ββββββββLigand 19 20 20 92 ββββββββWater 227 579 601 923 ββββB-factors ββββββββProtein 41.6 17.8 15.8 21.0 ββββββββLigand 65.0 19.4 24.2 39.5 ββββββββWater 35.4 38.5 32.2 37.6 ββββR.m.s deviations ββββββββBond lengths (Γ ) 0.008 0.015 0.012 0.012 ββββββββBond angles (Β°) 1.233 1.502 1.624 1.554 ββββProtein Data Bank code 5G56 5LA0 5LA1 2LA2 " TABLE | |
| 25 38 GH5-CBM6-Xylp complex_assembly " CtXyl5A-D GH5-CBM6-Arap GH5-CBM6-Xylp GH5-CBM6- (Araf-Xylp4) Data collection ββββSource ESRF-ID14-1 Diamond I04β1 Diamond I24 Diamond I02 ββββWavelength (Γ ) 0.9334 0.9173 0.9772 0.9791 ββββSpace group P21212 P212121 P212121 P212121 ββββCell dimensions ββββββββa, b, c (Γ ) 147.4, 191.7, 50.7 67.1, 72.4, 109.1 67.9, 72.5, 109.5 76.3, 123.2, 125.4 ββββββββΞ±, Ξ², Ξ³ (Β°) 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 ββββNo. of measured reflections 244,475 (29,324) 224,842 (11,281) 152,004 (4,996) 463,237 (23,068) ββββNo. of independent reflections 42246 (5,920) 63,523 (3,175) 42,716 (2,334) 140,288 (6,879) ββββResolution (Γ ) 50.70β2.64 (2.78β2.64) 44.85β1.65 (1.68β1.65) 45.16β1.90 (1.94β1.90) 48.43β1.65 (1.68β1.65) ββββRmerge (%) 16.5 (69.5) 6.7 (65.1) 2.8 (8.4) 5.7 (74.9) ββββCC1/2 0.985 (0.478) 0.998 (0.594) 0.999 (0.982) 0.998 (0.484) ββββI/ΟI 8.0 (2.0) 13 (1.6) 26.6 (8.0) 11.2 (1.6) ββββCompleteness (%) 98.5 (96.4) 98.5 (99.4) 98.6 (85.0) 98.8 (99.4) ββββRedundancy 5.8 (5.0) 3.5 (3.6) 3.6 (2.1) 3.3 (3.4) Refinement ββββRwork/Rfree 23.7/27.8 12.2/17.0 12.9/16.1 14.5/19.9 ββββNo. atoms ββββββββProtein 5446 3790 3729 7333 ββββββββLigand 19 20 20 92 ββββββββWater 227 579 601 923 ββββB-factors ββββββββProtein 41.6 17.8 15.8 21.0 ββββββββLigand 65.0 19.4 24.2 39.5 ββββββββWater 35.4 38.5 32.2 37.6 ββββR.m.s deviations ββββββββBond lengths (Γ ) 0.008 0.015 0.012 0.012 ββββββββBond angles (Β°) 1.233 1.502 1.624 1.554 ββββProtein Data Bank code 5G56 5LA0 5LA1 2LA2 " TABLE | |
| 39 61 GH5-CBM6- (Araf-Xylp4) complex_assembly " CtXyl5A-D GH5-CBM6-Arap GH5-CBM6-Xylp GH5-CBM6- (Araf-Xylp4) Data collection ββββSource ESRF-ID14-1 Diamond I04β1 Diamond I24 Diamond I02 ββββWavelength (Γ ) 0.9334 0.9173 0.9772 0.9791 ββββSpace group P21212 P212121 P212121 P212121 ββββCell dimensions ββββββββa, b, c (Γ ) 147.4, 191.7, 50.7 67.1, 72.4, 109.1 67.9, 72.5, 109.5 76.3, 123.2, 125.4 ββββββββΞ±, Ξ², Ξ³ (Β°) 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 ββββNo. of measured reflections 244,475 (29,324) 224,842 (11,281) 152,004 (4,996) 463,237 (23,068) ββββNo. of independent reflections 42246 (5,920) 63,523 (3,175) 42,716 (2,334) 140,288 (6,879) ββββResolution (Γ ) 50.70β2.64 (2.78β2.64) 44.85β1.65 (1.68β1.65) 45.16β1.90 (1.94β1.90) 48.43β1.65 (1.68β1.65) ββββRmerge (%) 16.5 (69.5) 6.7 (65.1) 2.8 (8.4) 5.7 (74.9) ββββCC1/2 0.985 (0.478) 0.998 (0.594) 0.999 (0.982) 0.998 (0.484) ββββI/ΟI 8.0 (2.0) 13 (1.6) 26.6 (8.0) 11.2 (1.6) ββββCompleteness (%) 98.5 (96.4) 98.5 (99.4) 98.6 (85.0) 98.8 (99.4) ββββRedundancy 5.8 (5.0) 3.5 (3.6) 3.6 (2.1) 3.3 (3.4) Refinement ββββRwork/Rfree 23.7/27.8 12.2/17.0 12.9/16.1 14.5/19.9 ββββNo. atoms ββββββββProtein 5446 3790 3729 7333 ββββββββLigand 19 20 20 92 ββββββββWater 227 579 601 923 ββββB-factors ββββββββProtein 41.6 17.8 15.8 21.0 ββββββββLigand 65.0 19.4 24.2 39.5 ββββββββWater 35.4 38.5 32.2 37.6 ββββR.m.s deviations ββββββββBond lengths (Γ ) 0.008 0.015 0.012 0.012 ββββββββBond angles (Β°) 1.233 1.502 1.624 1.554 ββββProtein Data Bank code 5G56 5LA0 5LA1 2LA2 " TABLE | |
| 1079 1084 Rwork evidence " CtXyl5A-D GH5-CBM6-Arap GH5-CBM6-Xylp GH5-CBM6- (Araf-Xylp4) Data collection ββββSource ESRF-ID14-1 Diamond I04β1 Diamond I24 Diamond I02 ββββWavelength (Γ ) 0.9334 0.9173 0.9772 0.9791 ββββSpace group P21212 P212121 P212121 P212121 ββββCell dimensions ββββββββa, b, c (Γ ) 147.4, 191.7, 50.7 67.1, 72.4, 109.1 67.9, 72.5, 109.5 76.3, 123.2, 125.4 ββββββββΞ±, Ξ², Ξ³ (Β°) 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 ββββNo. of measured reflections 244,475 (29,324) 224,842 (11,281) 152,004 (4,996) 463,237 (23,068) ββββNo. of independent reflections 42246 (5,920) 63,523 (3,175) 42,716 (2,334) 140,288 (6,879) ββββResolution (Γ ) 50.70β2.64 (2.78β2.64) 44.85β1.65 (1.68β1.65) 45.16β1.90 (1.94β1.90) 48.43β1.65 (1.68β1.65) ββββRmerge (%) 16.5 (69.5) 6.7 (65.1) 2.8 (8.4) 5.7 (74.9) ββββCC1/2 0.985 (0.478) 0.998 (0.594) 0.999 (0.982) 0.998 (0.484) ββββI/ΟI 8.0 (2.0) 13 (1.6) 26.6 (8.0) 11.2 (1.6) ββββCompleteness (%) 98.5 (96.4) 98.5 (99.4) 98.6 (85.0) 98.8 (99.4) ββββRedundancy 5.8 (5.0) 3.5 (3.6) 3.6 (2.1) 3.3 (3.4) Refinement ββββRwork/Rfree 23.7/27.8 12.2/17.0 12.9/16.1 14.5/19.9 ββββNo. atoms ββββββββProtein 5446 3790 3729 7333 ββββββββLigand 19 20 20 92 ββββββββWater 227 579 601 923 ββββB-factors ββββββββProtein 41.6 17.8 15.8 21.0 ββββββββLigand 65.0 19.4 24.2 39.5 ββββββββWater 35.4 38.5 32.2 37.6 ββββR.m.s deviations ββββββββBond lengths (Γ ) 0.008 0.015 0.012 0.012 ββββββββBond angles (Β°) 1.233 1.502 1.624 1.554 ββββProtein Data Bank code 5G56 5LA0 5LA1 2LA2 " TABLE | |
| 1085 1090 Rfree evidence " CtXyl5A-D GH5-CBM6-Arap GH5-CBM6-Xylp GH5-CBM6- (Araf-Xylp4) Data collection ββββSource ESRF-ID14-1 Diamond I04β1 Diamond I24 Diamond I02 ββββWavelength (Γ ) 0.9334 0.9173 0.9772 0.9791 ββββSpace group P21212 P212121 P212121 P212121 ββββCell dimensions ββββββββa, b, c (Γ ) 147.4, 191.7, 50.7 67.1, 72.4, 109.1 67.9, 72.5, 109.5 76.3, 123.2, 125.4 ββββββββΞ±, Ξ², Ξ³ (Β°) 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 ββββNo. of measured reflections 244,475 (29,324) 224,842 (11,281) 152,004 (4,996) 463,237 (23,068) ββββNo. of independent reflections 42246 (5,920) 63,523 (3,175) 42,716 (2,334) 140,288 (6,879) ββββResolution (Γ ) 50.70β2.64 (2.78β2.64) 44.85β1.65 (1.68β1.65) 45.16β1.90 (1.94β1.90) 48.43β1.65 (1.68β1.65) ββββRmerge (%) 16.5 (69.5) 6.7 (65.1) 2.8 (8.4) 5.7 (74.9) ββββCC1/2 0.985 (0.478) 0.998 (0.594) 0.999 (0.982) 0.998 (0.484) ββββI/ΟI 8.0 (2.0) 13 (1.6) 26.6 (8.0) 11.2 (1.6) ββββCompleteness (%) 98.5 (96.4) 98.5 (99.4) 98.6 (85.0) 98.8 (99.4) ββββRedundancy 5.8 (5.0) 3.5 (3.6) 3.6 (2.1) 3.3 (3.4) Refinement ββββRwork/Rfree 23.7/27.8 12.2/17.0 12.9/16.1 14.5/19.9 ββββNo. atoms ββββββββProtein 5446 3790 3729 7333 ββββββββLigand 19 20 20 92 ββββββββWater 227 579 601 923 ββββB-factors ββββββββProtein 41.6 17.8 15.8 21.0 ββββββββLigand 65.0 19.4 24.2 39.5 ββββββββWater 35.4 38.5 32.2 37.6 ββββR.m.s deviations ββββββββBond lengths (Γ ) 0.008 0.015 0.012 0.012 ββββββββBond angles (Β°) 1.233 1.502 1.624 1.554 ββββProtein Data Bank code 5G56 5LA0 5LA1 2LA2 " TABLE | |
| 0 2 GH protein_type GH SUPPL | |
| 0 19 glycoside hydrolase protein_type glycoside hydrolase SUPPL | |
| 0 7 CtXyl5A protein CtXyl5A SUPPL | |
| 0 15 C. thermocellum species C. thermocellum arabinoxylanase SUPPL | |
| 16 31 arabinoxylanase protein_type C. thermocellum arabinoxylanase SUPPL | |
| 0 3 CBM structure_element CBM SUPPL | |
| 0 41 non-catalytic carbohydrate binding module structure_element non-catalytic carbohydrate binding module SUPPL | |
| 0 2 Fn protein_type Fn SUPPL | |
| 0 11 fibronectin protein_type fibronectin SUPPL | |
| 0 3 WAX chemical WAX SUPPL | |
| 0 5 wheat taxonomy_domain wheat arabinoxylan SUPPL | |
| 6 18 arabinoxylan chemical wheat arabinoxylan SUPPL | |
| 0 3 RAX chemical RAX SUPPL | |
| 0 3 rye taxonomy_domain rye arabinoxylan SUPPL | |
| 4 16 arabinoxylan chemical rye arabinoxylan SUPPL | |
| 0 2 CX chemical CX SUPPL | |
| 0 4 corn taxonomy_domain corn bran xylan SUPPL | |
| 10 15 xylan chemical corn bran xylan SUPPL | |
| 0 5 HPAEC experimental_method HPAEC SUPPL | |
| 0 46 high performance anion exchange chromatography experimental_method high performance anion exchange chromatography SUPPL | |
| 0 9 birchwood taxonomy_domain birchwood xylan SUPPL | |
| 10 15 xylan chemical birchwood xylan SUPPL | |
| 0 23 electrospray ionization experimental_method electrospray ionization. SUPPL | |