https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&feed=atom&action=historyCarbohydrate Binding Module Family 66 - Revision history2024-03-28T14:21:10ZRevision history for this page on the wikiMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=16556&oldid=prevHarry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"2021-12-18T21:16:29Z<p>Text replacement - "\^\^\^(.*)\^\^\^" to "<a href="/index.php?title=User:$1&action=edit&redlink=1" class="new" title="User:$1 (page does not exist)">$1</a>"</p>
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</table>Harry Brumerhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12667&oldid=prevElizabeth Ficko-Blean: /* Ligand specificities */2018-03-06T16:23:07Z<p><span dir="auto"><span class="autocomment">Ligand specificities</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Ligand specificities ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Ligand specificities ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>CBM66 is predominantly a bacterial family that comprises protein modules of around 160 amino acids. The C-terminal module of the ''Bacillus subtilis'' exo-levanase (SacC; locus tag BSU27030) is a CBM66 module, defined as BsCBM66, which was shown to bind weakly to fructose (''K''<sub>A</sub> ~100 M<sup>-1</sup>) but with higher affinity to inulin, levan and their respectively oligosaccharides (''K''<sub>A</sub> 0.1-1 x 10<sup>3</sup> M<sup>-1</sup>) <cite>Cuskin2012</cite>. The affinity of the CBM66 for its ligands was enthalpically driven. To determine whether BsCBM66 recognizes internal or terminal regions of levan, the stoichiometry of binding was compared with that of an inactive form (lacking the catalytic nucleophile) of the exo-acting &beta;-fructosidase BT3082 that attacks the non-reducing fructose termini in inulin and levan <cite>Sonnenburg2010</cite>. The data showed that both proteins bind to ''Erwinia herbicola'' levan at the same frequency <cite>Cuskin2012</cite>. It would appear, therefore, that BsCBM66 binds to the non-reducing fructose termini present in levan molecules, a view consistent with the crystal structure of the protein in complex with its target ligands, described below. BsCBM66 is thus a type C CBM.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>CBM66 is predominantly a bacterial family that comprises protein modules of around 160 amino acids. The C-terminal module of the ''Bacillus subtilis'' exo-levanase (SacC; locus tag BSU27030) is a CBM66 module, defined as BsCBM66, which was shown to bind weakly to fructose (''K''<sub>A</sub> ~100 M<sup>-1</sup>) but with higher affinity to inulin, levan and their respectively oligosaccharides (''K''<sub>A</sub> 0.1-1 x 10<sup>3</sup> M<sup>-1</sup>) <cite>Cuskin2012</cite>. The affinity of the CBM66 for its ligands was enthalpically driven. To determine whether BsCBM66 recognizes internal or terminal regions of levan, the stoichiometry of binding was compared with that of an inactive form (lacking the catalytic nucleophile) of the exo-acting &beta;-fructosidase BT3082 that attacks the non-reducing fructose termini in inulin and levan <cite>Sonnenburg2010</cite>. The data showed that both proteins bind to ''Erwinia herbicola'' levan at the same frequency <cite>Cuskin2012</cite>. It would appear, therefore, that BsCBM66 binds to the non-reducing fructose termini present in levan molecules, a view consistent with the crystal structure of the protein in complex with its target ligands, described below. BsCBM66 is thus a <ins class="diffchange diffchange-inline">[[Carbohydrate-binding_modules#Types|</ins>type C<ins class="diffchange diffchange-inline">]] </ins>CBM.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Structural Features ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Structural Features ==</div></td></tr>
</table>Elizabeth Ficko-Bleanhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12337&oldid=prevHarry Brumer: /* Structural Features */2018-02-05T23:42:05Z<p><span dir="auto"><span class="autocomment">Structural Features</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Structural Features ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Structural Features ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[File:CBM66fold.jpg|thumb|<del class="diffchange diffchange-inline">300px</del>|right|'''Figure 1.''' The crystal structure of BsCBM60 in complex with levanotriose ([{{PDBlink}}4B1M PDB ID 4B1M]), highlighting the location of the ligand binding site on the concave &beta;-sheet (A). B shows the surface representation of the CBM. In the fructose located in the ligand binding site O2 and O6 (both in cyan) are pointing at the surface of the protein and thus the sugar cannot be extended in the non-reducing direction.]]</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[File:CBM66fold.jpg|thumb|<ins class="diffchange diffchange-inline">450px</ins>|right|'''Figure 1.''' The crystal structure of BsCBM60 in complex with levanotriose ([{{PDBlink}}4B1M PDB ID 4B1M]), highlighting the location of the ligand binding site on the concave &beta;-sheet (A). B shows the surface representation of the CBM. In the fructose located in the ligand binding site O2 and O6 (both in cyan) are pointing at the surface of the protein and thus the sugar cannot be extended in the non-reducing direction.]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of the apo form of BsCBM66 showed that the protein adopts a β-sandwich fold in which the two β-sheets contain seven and six antiparallel β-strands, respectively ([{{PDBlink}}AZZ PDB ID AZZ]). The surface of the protein reveals a broad pocket centered on the concave β-sheet (Figure 1A). In complex with fructose ([{{PDBlink}}4B1L PDB ID 4B1L]) or levantriose ([{{PDBlink}}4B1M PDB ID 4B1M]) the sugars were located in the broad pocket demonstrating that it comprises the ligand binding site. Fructose, which is in its furanose form, is sandwiched between two aromatic residues, which make non-polar interactions with the ligand. These hydrophobic contacts are augmented by polar interactions with a lysine, asparagine and two aspartates.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of the apo form of BsCBM66 showed that the protein adopts a β-sandwich fold in which the two β-sheets contain seven and six antiparallel β-strands, respectively ([{{PDBlink}}AZZ PDB ID AZZ]). The surface of the protein reveals a broad pocket centered on the concave β-sheet (Figure 1A). In complex with fructose ([{{PDBlink}}4B1L PDB ID 4B1L]) or levantriose ([{{PDBlink}}4B1M PDB ID 4B1M]) the sugars were located in the broad pocket demonstrating that it comprises the ligand binding site. Fructose, which is in its furanose form, is sandwiched between two aromatic residues, which make non-polar interactions with the ligand. These hydrophobic contacts are augmented by polar interactions with a lysine, asparagine and two aspartates.</div></td></tr>
</table>Harry Brumerhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12335&oldid=prevHarry Gilbert: /* Functionalities */2018-02-05T22:56:17Z<p><span dir="auto"><span class="autocomment">Functionalities</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Functionalities == </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Functionalities == </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The vast majority of CBM66s are located in GH32 enzymes that target fructans. Based on this observation it was suggested that the predominant role of CBM66 is in binding fructans. The remaining CBM66 members are linked to a range of CAZy enzymes, primarily glycoside hydrolases and lyases, associated with plant cell-wall degradation, although the binding properties of these modules are unknown <cite>Cuskin2012</cite>. Biochemical analysis revealed that SacC displayed ∼100-fold-higher activity for levan (&beta;-2,6–glycosidic linkages) compared with inulin (&beta;-2,1–glycosidic linkages) or oligosaccharides [with a degree of polymerization (DP) <6] of either fructan. Truncation experiments showed that this elevated activity against levan was conferred by BsCBM66 <cite>Cuskin2012</cite>. Fusion of BsCBM66 onto a non-specific fructosidase caused a 100-fold increase in the activity of the enzyme against levan but did not influence the activity of the glycoside hydrolase against oligosaccharides or inulin <cite>Cuskin2012</cite>. It was argued that increased activity against levan reflects its highly branched structure compared to inulin; levan consists of multiple non-reducing fructose residues, similar to glycogen and amylopectin. Thus, the BsCBM66 and the GH32 catalytic module within SacC would be able to bind to different non-reducing terminal terminal fructose residues of the same polysaccharide molecule. It was proposed that the ensuing avidity effect resulted in much tighter binding of SacC to levan, compared to the catalytic module as a discrete entity, leading to increased catalytic activity. It was proposed that the avidity, and thus increase in substrate binding of the levanase, may be greater in the many GH32 enzymes that contain two or more CBM66 modules. It was also suggested that the proposed avidity mechanism for BsCBM66 function may be a generic feature of CBMs that bind to the terminal residues of glycans and are linked to exo-acting glycanases. Examples cited include [[GH84]] exo-GlcNAcases, which often contain [[CBM32]]s that target terminal Gal-GlcNAc structures present on the surface of red blood cells <cite>Ficko-Blean2006</cite>.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The vast majority of CBM66s are located in GH32 enzymes that target fructans. Based on this observation it was suggested that the predominant role of CBM66 is in binding fructans. The remaining CBM66 members are linked to a range of CAZy enzymes, primarily glycoside hydrolases and lyases, associated with plant cell-wall degradation, although the binding properties of these modules are unknown <cite>Cuskin2012</cite>. Biochemical analysis revealed that SacC displayed ∼100-fold-higher activity for levan (&beta;-2,6–glycosidic linkages) compared with inulin (&beta;-2,1–glycosidic linkages) or oligosaccharides [with a degree of polymerization (DP) <6] of either fructan. Truncation experiments showed that this elevated activity against levan was conferred by BsCBM66 <cite>Cuskin2012</cite>. Fusion of BsCBM66 onto a non-specific fructosidase caused a 100-fold increase in the activity of the enzyme against levan but did not influence the activity of the glycoside hydrolase against oligosaccharides or inulin <cite>Cuskin2012</cite>.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>It was argued that increased activity <ins class="diffchange diffchange-inline">of the CBM66-containing fructosidase </ins>against levan reflects its highly branched structure compared to inulin; levan consists of multiple non-reducing fructose residues, similar to glycogen and amylopectin. Thus, the BsCBM66 and the GH32 catalytic module within SacC would be able to bind to different non-reducing terminal terminal fructose residues of the same polysaccharide molecule. It was proposed that the ensuing avidity effect resulted in much tighter binding of SacC to levan, compared to the catalytic module as a discrete entity, leading to increased catalytic activity. It was proposed that the avidity, and thus increase in substrate binding of the levanase, may be greater in the many GH32 enzymes that contain two or more CBM66 modules. It was also suggested that the proposed avidity mechanism for BsCBM66 function may be a generic feature of CBMs that bind to the terminal residues of glycans and are linked to exo-acting glycanases. Examples cited include [[GH84]] exo-GlcNAcases, which often contain [[CBM32]]s that target terminal Gal-GlcNAc structures present on the surface of red blood cells <cite>Ficko-Blean2006</cite>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
</table>Harry Gilberthttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12334&oldid=prevHarry Gilbert: /* Structural Features */2018-02-05T22:54:39Z<p><span dir="auto"><span class="autocomment">Structural Features</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:CBM66fold.jpg|thumb|300px|right|'''Figure 1.''' The crystal structure of BsCBM60 in complex with levanotriose ([{{PDBlink}}4B1M PDB ID 4B1M]), highlighting the location of the ligand binding site on the concave &beta;-sheet (A). B shows the surface representation of the CBM. In the fructose located in the ligand binding site O2 and O6 (both in cyan) are pointing at the surface of the protein and thus the sugar cannot be extended in the non-reducing direction.]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[File:CBM66fold.jpg|thumb|300px|right|'''Figure 1.''' The crystal structure of BsCBM60 in complex with levanotriose ([{{PDBlink}}4B1M PDB ID 4B1M]), highlighting the location of the ligand binding site on the concave &beta;-sheet (A). B shows the surface representation of the CBM. In the fructose located in the ligand binding site O2 and O6 (both in cyan) are pointing at the surface of the protein and thus the sugar cannot be extended in the non-reducing direction.]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of the apo form of BsCBM66 showed that the protein adopts a β-sandwich fold in which the two β-sheets contain seven and six antiparallel β-strands, respectively ([{{PDBlink}}AZZ PDB ID AZZ]). The surface of the protein reveals a broad pocket centered on the concave β-sheet (Figure 1A). In complex with fructose ([{{PDBlink}}4B1L PDB ID 4B1L]) or levantriose ([{{PDBlink}}4B1M PDB ID 4B1M]) the sugars were located in the broad pocket demonstrating that it comprises the ligand binding site. Fructose, which is in its furanose form, is sandwiched between two aromatic residues, which make non-polar interactions with the ligand. These hydrophobic contacts are augmented by polar interactions with a lysine, asparagine and two aspartates. Mutagenesis showed that all <del class="diffchange diffchange-inline">these </del>residues are essential for <del class="diffchange diffchange-inline">ligand </del>binding. The O1 and O6 of the bound fructose are pointing at the surface of BsCBM66 (Figure 1B), preventing extension of the ligand in the non-reducing direction (levan and inulin are linked &beta;-2,6– and &beta;-2,1, respectively), whereas O2 is pointing into solvent, consistent with the protein binding to the non-reducing fructose termini of &beta;-2,6– and &beta;-2,1–linked fructans. This confirms the designation of BsCBM66 as a type C CBM. The ligand-binding residues identified above are conserved in 37 CBM66 members, and thus it is likely that these protein modules display specificity for the non-reducing fructose termini of levan and inulin and bind through a common mechanism. In the complex with levantriose the non-reducing fructose makes the same interactions with BsCBM66 as fructose. The central and terminal fructose in the trisaccharide do not make biologically significant interactions with the protein.</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The crystal structure of the apo form of BsCBM66 showed that the protein adopts a β-sandwich fold in which the two β-sheets contain seven and six antiparallel β-strands, respectively ([{{PDBlink}}AZZ PDB ID AZZ]). The surface of the protein reveals a broad pocket centered on the concave β-sheet (Figure 1A). In complex with fructose ([{{PDBlink}}4B1L PDB ID 4B1L]) or levantriose ([{{PDBlink}}4B1M PDB ID 4B1M]) the sugars were located in the broad pocket demonstrating that it comprises the ligand binding site. Fructose, which is in its furanose form, is sandwiched between two aromatic residues, which make non-polar interactions with the ligand. These hydrophobic contacts are augmented by polar interactions with a lysine, asparagine and two aspartates.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Mutagenesis showed that all <ins class="diffchange diffchange-inline">the polar and aromatic </ins>residues are essential for <ins class="diffchange diffchange-inline">the </ins>binding <ins class="diffchange diffchange-inline">of the CBM66 to its ligands</ins>. The O1 and O6 of the bound fructose are pointing at the surface of BsCBM66 (Figure 1B), preventing extension of the ligand in the non-reducing direction (levan and inulin are linked &beta;-2,6– and &beta;-2,1, respectively), whereas O2 is pointing into solvent, consistent with the protein binding to the non-reducing fructose termini of &beta;-2,6– and &beta;-2,1–linked fructans. This confirms the designation of BsCBM66 as a type C CBM. The ligand-binding residues identified above are conserved in 37 CBM66 members, and thus it is likely that these protein modules display specificity for the non-reducing fructose termini of levan and inulin and bind through a common mechanism. In the complex with levantriose the non-reducing fructose makes the same interactions with BsCBM66 as fructose. The central and terminal fructose in the trisaccharide do not make biologically significant interactions with the protein.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Functionalities == </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Functionalities == </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The vast majority of CBM66s are located in GH32 enzymes that target fructans. Based on this observation it was suggested that the predominant role of CBM66 is in binding fructans. The remaining CBM66 members are linked to a range of CAZy enzymes, primarily glycoside hydrolases and lyases, associated with plant cell-wall degradation, although the binding properties of these modules are unknown <cite>Cuskin2012</cite>. Biochemical analysis revealed that SacC displayed ∼100-fold-higher activity for levan (&beta;-2,6–glycosidic linkages) compared with inulin (&beta;-2,1–glycosidic linkages) or oligosaccharides [with a degree of polymerization (DP) <6] of either fructan. Truncation experiments showed that this elevated activity against levan was conferred by BsCBM66 <cite>Cuskin2012</cite>. Fusion of BsCBM66 onto a non-specific fructosidase caused a 100-fold increase in the activity of the enzyme against levan but did not influence the activity of the glycoside hydrolase against oligosaccharides or inulin <cite>Cuskin2012</cite>. It was argued that increased activity against levan reflects its highly branched structure compared to inulin; levan consists of multiple non-reducing fructose residues, similar to glycogen and amylopectin. Thus, the BsCBM66 and the GH32 catalytic module within SacC would be able to bind to different non-reducing terminal terminal fructose residues of the same polysaccharide molecule. It was proposed that the ensuing avidity effect resulted in much tighter binding of SacC to levan, compared to the catalytic module as a discrete entity, leading to increased catalytic activity. It was proposed that the avidity, and thus increase in substrate binding of the levanase, may be greater in the many GH32 enzymes that contain two or more CBM66 modules. It was also suggested that the proposed avidity mechanism for BsCBM66 function may be a generic feature of CBMs that bind to the terminal residues of glycans and are linked to exo-acting glycanases. Examples cited include [[GH84]] exo-GlcNAcases, which often contain [[CBM32]]s that target terminal Gal-GlcNAc structures present on the surface of red blood cells <cite>Ficko-Blean2006</cite>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The vast majority of CBM66s are located in GH32 enzymes that target fructans. Based on this observation it was suggested that the predominant role of CBM66 is in binding fructans. The remaining CBM66 members are linked to a range of CAZy enzymes, primarily glycoside hydrolases and lyases, associated with plant cell-wall degradation, although the binding properties of these modules are unknown <cite>Cuskin2012</cite>. Biochemical analysis revealed that SacC displayed ∼100-fold-higher activity for levan (&beta;-2,6–glycosidic linkages) compared with inulin (&beta;-2,1–glycosidic linkages) or oligosaccharides [with a degree of polymerization (DP) <6] of either fructan. Truncation experiments showed that this elevated activity against levan was conferred by BsCBM66 <cite>Cuskin2012</cite>. Fusion of BsCBM66 onto a non-specific fructosidase caused a 100-fold increase in the activity of the enzyme against levan but did not influence the activity of the glycoside hydrolase against oligosaccharides or inulin <cite>Cuskin2012</cite>. It was argued that increased activity against levan reflects its highly branched structure compared to inulin; levan consists of multiple non-reducing fructose residues, similar to glycogen and amylopectin. Thus, the BsCBM66 and the GH32 catalytic module within SacC would be able to bind to different non-reducing terminal terminal fructose residues of the same polysaccharide molecule. It was proposed that the ensuing avidity effect resulted in much tighter binding of SacC to levan, compared to the catalytic module as a discrete entity, leading to increased catalytic activity. It was proposed that the avidity, and thus increase in substrate binding of the levanase, may be greater in the many GH32 enzymes that contain two or more CBM66 modules. It was also suggested that the proposed avidity mechanism for BsCBM66 function may be a generic feature of CBMs that bind to the terminal residues of glycans and are linked to exo-acting glycanases. Examples cited include [[GH84]] exo-GlcNAcases, which often contain [[CBM32]]s that target terminal Gal-GlcNAc structures present on the surface of red blood cells <cite>Ficko-Blean2006</cite>.</div></td></tr>
</table>Harry Gilberthttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12284&oldid=prevHarry Brumer: /* Family Firsts */2018-01-31T19:02:29Z<p><span dir="auto"><span class="autocomment">Family Firsts</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Family Firsts ==</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>;First Identified</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>;First Identified<ins class="diffchange diffchange-inline">: </ins>BsCBM66 from the ''B. subtilis<ins class="diffchange diffchange-inline">'</ins>' exo-levanase SacC was the first member of the family to be identified and characterized <cite>Cuskin2012</cite>. </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>BsCBM66 from the ''B. subtilis' exo-levanase SacC was the first member of the family to be identified and characterized <cite>Cuskin2012</cite>. </div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>;First Structural Characterization<ins class="diffchange diffchange-inline">: </ins>The first structural characterization of a member of family CBM66 was BsCBM66 <cite>Cuskin2012</cite>.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>;First Structural Characterization</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The first structural characterization of a member of family CBM66 was BsCBM66 <cite>Cuskin2012</cite>.</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== References ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== References ==</div></td></tr>
</table>Harry Brumerhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12229&oldid=prevHarry Gilbert at 17:42, 25 January 20182018-01-25T17:42:18Z<p></p>
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</table>Harry Gilberthttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12228&oldid=prevHarry Gilbert at 17:41, 25 January 20182018-01-25T17:41:58Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Author]]: ^^^Harry Gilbert^^^</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Author]]: ^^^Harry Gilbert^^^</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [[Responsible Curator]]: ^^^<del class="diffchange diffchange-inline">Harry Gilbert</del>^^^</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [[Responsible Curator]]: ^^^<ins class="diffchange diffchange-inline">Fiona Cuskin</ins>^^^</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>Harry Gilberthttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12227&oldid=prevHarry Gilbert at 17:41, 25 January 20182018-01-25T17:41:37Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:41, 25 January 2018</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>{{<del class="diffchange diffchange-inline">Curator Approved</del>}}</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>{{<ins class="diffchange diffchange-inline">CuratorApproved</ins>}}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Author]]: ^^^Harry Gilbert^^^</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Author]]: ^^^Harry Gilbert^^^</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Responsible Curator]]: ^^^Harry Gilbert^^^</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Responsible Curator]]: ^^^Harry Gilbert^^^</div></td></tr>
</table>Harry Gilberthttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_66&diff=12226&oldid=prevHarry Gilbert at 17:40, 25 January 20182018-01-25T17:40:24Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:40, 25 January 2018</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Author]]: ^^^Harry Gilbert^^^</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Author]]: ^^^Harry Gilbert^^^</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [[Responsible Curator]]: ^^^<del class="diffchange diffchange-inline">Fiona Cuskin</del>^^^</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [[Responsible Curator]]: ^^^<ins class="diffchange diffchange-inline">Harry Gilbert</ins>^^^</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>----</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
</table>Harry Gilbert