Carbohydrate Binding Module Family 20 - Revision history

Harry Brumer: Text replacement - "User:Marie Sofie Møller" to "User:Marie Sofie Moeller"

2021-12-18T21:24:53Z

Text replacement - "User:Marie Sofie Møller" to "User:Marie Sofie Moeller"

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

2021-12-18T21:21:01Z

Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer: Text replacement - "Stephan Janecek" to "Stefan Janecek"

2021-12-18T21:04:21Z

Text replacement - "Stephan Janecek" to "Stefan Janecek"

Elizabeth Ficko-Blean: /* Family Firsts */

2020-05-14T12:27:11Z

Family Firsts

Elizabeth Ficko-Blean: /* Functionalities */

2020-05-14T12:26:15Z

Functionalities

Elizabeth Ficko-Blean: /* Functionalities */

2020-05-14T12:02:51Z

Functionalities

Elizabeth Ficko-Blean: /* Structural Features */

2020-05-14T11:43:30Z

Structural Features

Elizabeth Ficko-Blean: /* Structural Features */

2020-05-14T11:39:40Z

Structural Features

Elizabeth Ficko-Blean: /* Structural Features */

2020-05-14T11:31:22Z

Structural Features

Elizabeth Ficko-Blean: /* Structural Features */

2020-05-14T11:24:13Z

Structural Features

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: [[User:Marie Sofie Møller|Marie Sofie Møller]]
+* [[Author]]: [[User:Marie Sofie Moeller|Marie Sofie Møller]]
 * [[Responsible Curator]]s:  [[User:Birte Svensson|Birte Svensson]] and [[User:Stefan Janecek|Stefan Janecek]]
 ----

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]: ^^^Marie Sofie Møller^^^
+* [[Author]]: [[User:Marie Sofie Møller|Marie Sofie Møller]]
-* [[Responsible Curator]]s:  ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
+* [[Responsible Curator]]s:  [[User:Birte Svensson|Birte Svensson]] and [[User:Stefan Janecek|Stefan Janecek]]
 ----

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 {{CuratorApproved}}
 * [[Author]]: ^^^Marie Sofie Møller^^^
-* [[Responsible Curator]]s:  ^^^Birte Svensson^^^ and ^^^Stephan Janecek^^^
+* [[Responsible Curator]]s:  ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
 ----

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 == Family Firsts ==
-;First Identified
+;First Identified:The first CBM20 was recognised in the early 1980s at the C-termini of glucoamylases from <i>A. awamori</i> <cite>Hayashida1982</cite> and <i>A. niger</i> <cite>Svensson1982 Svensson1983 Boel1984</cite>.
-:The first CBM20 was recognised in the early 1980s at the C-termini of glucoamylases from <i>A. awamori</i> <cite>Hayashida1982</cite> and <i>A. niger</i> <cite>Svensson1982 Svensson1983 Boel1984</cite>.
+;First Structural Characterization:The first structure of CBM20 was the structure of a [[GH13]] CGTase from <i>Bacillus circulans</i> 8 (PDB entry [{{PDBlink}}1cgt 1CGT]) <cite>Klein1991</cite>. The first CBM20 structure with a ligand bound was the structure of the [[GH13]] CGTase from <i>Bacillus circulans</i> 251 (PDB entry [{{PDBlink}}1cdg 1CDG]) <cite>Lawson1994</cite>.
 <!-- :Insert archetype here, possibly including ''very brief'' synopsis. -->

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 <!-- ''Content in this section should include, in paragraph form, a description of:'' -->
 The CBM20 from the <i>A. niger</i> glucoamylase has been shown not only to bind starch but also to disrupt its surface, thereby enhancing the amylolytic rate <cite>Southhall1999</cite>. A CBM20 from an auxiliary activities family [[AA13]] starch polysaccharide monooxygenase was shown to be important for amylose binding and activity on amylose <cite>Vu2019</cite>. <!-- Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate. -->
-The enzymes, of which the CBM20 module constitutes a domain, have predominantly specificities from the ɑ-amylase family [[GH13]] or enzymes from [[GH77]], but can also belong to [[GH14]] β-amylases and [[GH15]] glucoamylases <cite>Janecek2011</cite>. Among other CAZy GH families, the CBM20 is in some cases found associated with enzymes from [[GH31]], [[GH57]], [[GH119]] and the auxiliary activities family [[AA13]]. Furthermore, CBM20 modules have been recognised in enzymes of which the catalytic domain is not classified in CAZy. Examples are phosphoglucan, water dikinase, glycerophosphodiester phosphodiesterase-5, laforin, and genethonin-1 <cite>Janecek2019</cite>. The modules of family CBM20 have commonly been found in a single copy and usually appear without SBDs from other CBM families within the same protein, although co-occurence has been observed with [[CBM25]], [[CBM34]], and [[CBM48]] <cite>Janecek2019</cite>.
+The enzymes which have CBM20 modules have specificities predominantly from the ɑ-amylase families [[GH13]] and [[GH77]], but can also belong to the [[GH14]] β-amylases and [[GH15]] glucoamylases <cite>Janecek2011</cite>. Among other CAZy GH families, the CBM20 is in some cases found associated with enzymes from [[GH31]], [[GH57]], [[GH119]] and the auxiliary activities family [[AA13]]. Furthermore, CBM20 modules have been recognised in enzymes where the catalytic domain is not classified in CAZy. Examples are phosphoglucan water dikinase, glycerophosphodiester phosphodiesterase-5, laforin, and genethonin-1 <cite>Janecek2019</cite>. The CBM20 modules are commonly found as a single copy and usually appear without SBDs (starch-binding domains) from other CBM families within the same protein, although co-occurence has been observed with [[CBM25]], [[CBM34]], and [[CBM48]] <cite>Janecek2019</cite>.
 == Family Firsts ==

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 [[File:CBM20_structure_1AC0.png|thumb|300px|right|'''Figure 1.'''  The NMR structure of the CBM20 from the <i>Aspergillus niger</i> [[GH15]] glucoamylase with β-cyclodextrin bound to both binding sites (PDB ID [{{PDBlink}}1ac0 1AC0] <cite>Sorimachi1997</cite>). The prominent binding site residues are shown as sticks.]]
 <!-- ''Content in this section should include, in paragraph form, a description of:'' -->
-The CBM20 members are [[Carbohydrate-binding_modules#Types|type B]] CBMs and their overall fold is a β-sandwich (Fig. 1). At least one but more typically two binding sites have been found in structures with CBM20 in complex with bound carbohydrate. Such complexes have been studied for modules originating from several amylolytic enzymes, e.g. [[GH13]]_2 cyclodextrin glucanotransferase (CGTase) from <i>Bacillus circulans</i> <cite>Penninga1996</cite>, [[GH14]] β-amylase from <i>Bacillus cereus</i> <cite>Mikami1999</cite> and [[GH15]] glucoamylase from <i>Aspergillus niger</i> <cite>Sorimachi1997</cite>, as well as the human glucan phosphatase laforin <cite>Raththagala2015</cite>. The two binding sites of CBM20 have been best illustrated in the NMR structure of the isolated module from <i>A. niger</i> glucoamylase complexed with β-cyclodextrin (Fig. 1) <cite>Sorimachi1997</cite> and the X-ray structure of the module of the intact <i>B. circulans</i> CGTase in complex with maltose <cite>Penninga1996</cite>. Binding site 1, important for raw starch binding ability, is formed from two tryptophan residues (Trp543 and Trp590 in the glucoamylase and Trp616 and Trp662 in the CGTase) making a compact and rigid hydrophobic site exposed on the surface that is well adapted to bind glucose residues in the cyclodextrin ligands, considered as starch mimics. This small and easily accessible site may function as the place where the starch is initially recognized and it does not change conformation after β-cyclodextrin binding when compared to the ligand-free CBM20 <cite>Sorimachi1996</cite>. It is worth mentioning that both tryptophan residues make stacking interactions with glucose rings and are conserved in the sequence alignment of CBM20s <cite>Janecek2019</cite>. This is not the case, however, for the aromatic residues stacked against glucose rings in binding site 2, which may function to guide the starch chains to the active site and is thus more extended and flexible. Binding site 2 aromatic amino acids undergo a larger conformational rearrangement when binding the β-cyclodextrin <cite>Sorimachi1997</cite>.  While there are two tyrosines (Tyr527 and Tyr556) in the glucoamylase binding site 2, only one aromatic residue (Tyr633 in CGTase, corresponding to Tyr556 in glucoamylase) is believed to play the analogous role in the CGTase. On the other hand, a third well-conserved tryptophan residue (Trp636 in CGTase and Trp563 in glucoamylase ), although buried and thus not able to interact with β-cyclodextrin directly, was found to be involved in making contacts with several residues at binding site 2 <cite>Sorimachi1997</cite>.  <!-- Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. -->
+The CBM20 members are [[Carbohydrate-binding_modules#Types|type B]] CBMs and their overall fold is a β-sandwich (Fig. 1). At least one but more typically two binding sites have been found in structures with CBM20 in complex with bound carbohydrate. Such complexes have been studied for modules originating from several amylolytic enzymes, e.g. [[GH13]]_2 cyclodextrin glucanotransferase (CGTase) from <i>Bacillus circulans</i> <cite>Penninga1996</cite>, [[GH14]] β-amylase from <i>Bacillus cereus</i> <cite>Mikami1999</cite> and [[GH15]] glucoamylase from <i>Aspergillus niger</i> <cite>Sorimachi1997</cite>, as well as the human glucan phosphatase laforin <cite>Raththagala2015</cite>. The two binding sites of CBM20 have been best illustrated in the NMR structure of the isolated module from <i>A. niger</i> glucoamylase complexed with β-cyclodextrin (Fig. 1) <cite>Sorimachi1997</cite> and the X-ray structure of the module of the intact <i>B. circulans</i> CGTase in complex with maltose <cite>Penninga1996</cite>. Binding site 1, important for raw starch binding ability, is formed from two tryptophan residues (Trp543 and Trp590 in the glucoamylase and Trp616 and Trp662 in the CGTase) making a compact and rigid hydrophobic site exposed on the surface that is well adapted to bind glucose residues in the cyclodextrin ligands, considered as starch mimics. This small and easily accessible site may function as the place where the starch is initially recognized and it does not change conformation after β-cyclodextrin binding when compared to the ligand-free CBM20 <cite>Sorimachi1996</cite>. It is worth mentioning that both tryptophan residues make stacking interactions with glucose rings and are conserved in the sequence alignment of CBM20s <cite>Janecek2019</cite>. This is not the case, however, for the aromatic residues stacked against glucose rings in binding site 2, which may function to guide the starch chains to the active site and is thus more extended and flexible. Binding site 2 aromatic amino acids undergo a larger conformational rearrangement when binding the β-cyclodextrin <cite>Sorimachi1997</cite>.  While there are two tyrosines (Tyr527 and Tyr556) in the glucoamylase binding site 2, only one aromatic residue (Tyr633 in CGTase, corresponding to Tyr556 in glucoamylase) is believed to play the analogous role in the CGTase. On the other hand, a third well-conserved tryptophan residue (Trp636 in CGTase, corresponding to Trp563 in glucoamylase), although buried and thus not able to interact with β-cyclodextrin directly, was found to be involved in making contacts with several residues at binding site 2 <cite>Sorimachi1997</cite>.  <!-- Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. -->
 == Functionalities ==

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 == Structural Features ==
-[[File:CBM20_structure_1AC0.png|thumb|300px|right|'''Figure 1.'''  The NMR structure of the CBM20 from the <i>Aspergillus niger</i> GH15 glucoamylase with β-cyclodextrin bound to both binding sites (PDB ID [{{PDBlink}}1ac0 1AC0] <cite>Sorimachi1997</cite>). The prominent binding site residues are shown as sticks.]]
+[[File:CBM20_structure_1AC0.png|thumb|300px|right|'''Figure 1.'''  The NMR structure of the CBM20 from the <i>Aspergillus niger</i> [[GH15]] glucoamylase with β-cyclodextrin bound to both binding sites (PDB ID [{{PDBlink}}1ac0 1AC0] <cite>Sorimachi1997</cite>). The prominent binding site residues are shown as sticks.]]
 <!-- ''Content in this section should include, in paragraph form, a description of:'' -->
-The CBM20 members are [[Carbohydrate-binding_modules#Types|type B]] CBMs and their overall fold is a β-sandwich (Fig. 1). At least one but more typically two binding sites have been found in determined structures having the CBM20 complexed with bound carbohydrate. Such complexes have been studied for modules originating from several amylolytic enzymes, e.g. GH13_2 cyclodextrin glucanotransferase (CGTase) from <i>Bacillus circulans</i> <cite>Penninga1996</cite>, GH14 β-amylase from <i>Bacillus cereus</i> <cite>Mikami1999</cite> and GH15 glucoamylase from <i>Aspergillus niger</i> <cite>Sorimachi1997</cite>, as well as the human glucan phosphatase laforin <cite>Raththagala2015</cite>. The two binding sites of CBM20 have been best illustrated in the NMR structure of the isolated module from <i>A. niger</i> glucoamylase complexed with β-cyclodextrin (Fig. 1) <cite>Sorimachi1997</cite> and the X-ray structure of the module of the intact <i>B. circulans</i> CGTase in complex with maltose <cite>Penninga1996</cite>. Binding site 1, important for raw starch binding ability, is formed from two tryptophan residues (Trp543 and Trp590 in the glucoamylase and Trp616 and Trp662 in the CGTase) making a compact and rigid hydrophobic site exposed on the surface and well adapted to bind glucose residues in the cyclodextrin ligands, considered as starch mimics. This small and easily accessible site may function as the place where the starch is initially recognized and it in fact does not change conformation after β-cyclodextrin binding compared to the free CBM20 <cite>Sorimachi1996</cite>. It is worth mentioning that both tryptophan residues make stacking interactions with glucose rings and are conserved in the sequence alignment of CBM20s <cite>Janecek2019</cite>. This is not the case, however, for aromatic residues stacked against glucose rings in binding site 2, which may function to guide the starch chains to the active site and is thus more extended and flexible, undergoing a larger conformational rearrangement when binding the β-cyclodextrin <cite>Sorimachi1997</cite>.  While there are two tyrosines (Tyr527 and Tyr556) in the glucoamylase binding site 2, only one aromatic residue (Tyr633, corresponding to the Tyr556) is believed to play the analogous role in the CGTase. On the other hand, a third well-conserved tryptophan residue (Trp563 in glucoamylase and Trp636 in CGTase), although buried and thus not able to interact with β-cyclodextrin directly, was found to be involved in making contacts with several residues at binding site 2 <cite>Sorimachi1997</cite>.  <!-- Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. -->
+The CBM20 members are [[Carbohydrate-binding_modules#Types|type B]] CBMs and their overall fold is a β-sandwich (Fig. 1). At least one but more typically two binding sites have been found in structures with CBM20 in complex with bound carbohydrate. Such complexes have been studied for modules originating from several amylolytic enzymes, e.g. [[GH13]]_2 cyclodextrin glucanotransferase (CGTase) from <i>Bacillus circulans</i> <cite>Penninga1996</cite>, [[GH14]] β-amylase from <i>Bacillus cereus</i> <cite>Mikami1999</cite> and [[GH15]] glucoamylase from <i>Aspergillus niger</i> <cite>Sorimachi1997</cite>, as well as the human glucan phosphatase laforin <cite>Raththagala2015</cite>. The two binding sites of CBM20 have been best illustrated in the NMR structure of the isolated module from <i>A. niger</i> glucoamylase complexed with β-cyclodextrin (Fig. 1) <cite>Sorimachi1997</cite> and the X-ray structure of the module of the intact <i>B. circulans</i> CGTase in complex with maltose <cite>Penninga1996</cite>. Binding site 1, important for raw starch binding ability, is formed from two tryptophan residues (Trp543 and Trp590 in the glucoamylase and Trp616 and Trp662 in the CGTase) making a compact and rigid hydrophobic site exposed on the surface that is well adapted to bind glucose residues in the cyclodextrin ligands, considered as starch mimics. This small and easily accessible site may function as the place where the starch is initially recognized and it does not change conformation after β-cyclodextrin binding when compared to the ligand-free CBM20 <cite>Sorimachi1996</cite>. It is worth mentioning that both tryptophan residues make stacking interactions with glucose rings and are conserved in the sequence alignment of CBM20s <cite>Janecek2019</cite>. This is not the case, however, for aromatic residues stacked against glucose rings in binding site 2, which may function to guide the starch chains to the active site and is thus more extended and flexible, undergoing a larger conformational rearrangement when binding the β-cyclodextrin <cite>Sorimachi1997</cite>.  While there are two tyrosines (Tyr527 and Tyr556) in the glucoamylase binding site 2, only one aromatic residue (Tyr633, corresponding to the Tyr556) is believed to play the analogous role in the CGTase. On the other hand, a third well-conserved tryptophan residue (Trp563 in glucoamylase and Trp636 in CGTase), although buried and thus not able to interact with β-cyclodextrin directly, was found to be involved in making contacts with several residues at binding site 2 <cite>Sorimachi1997</cite>.  <!-- Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc. -->
 == Functionalities ==