Carbohydrate Binding Module Family 28 - Revision history

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

2021-12-18T21:15:21Z

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

Shinya Fushinobu at 02:19, 12 August 2016

2016-08-12T02:19:11Z

Alicia Lammerts van Bueren at 07:45, 16 May 2014

2014-05-16T07:45:36Z

Alicia Lammerts van Bueren at 07:33, 16 May 2014

2014-05-16T07:33:22Z

Shinya Fushinobu at 16:20, 14 May 2014

2014-05-14T16:20:44Z

Shinya Fushinobu at 09:09, 14 May 2014

2014-05-14T09:09:21Z

Shinya Fushinobu at 09:07, 14 May 2014

2014-05-14T09:07:42Z

Shinya Fushinobu at 09:05, 14 May 2014

2014-05-14T09:05:31Z

Shinya Fushinobu at 08:57, 14 May 2014

2014-05-14T08:57:11Z

Shinya Fushinobu at 08:34, 14 May 2014

2014-05-14T08:34:59Z

@@ Line 1: / Line 1: @@
 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{CuratorApproved}}
-* [[Author]]:  ^^^Shinya Fushinobu^^^
+* [[Author]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
-* [[Responsible Curator]]:  ^^^Shinya Fushinobu^^^
+* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
 ----

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-This module was first classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. All known CBM28s are so far derrived from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or &beta;-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.
+This module was first classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. All known CBM28s are so far derived from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or &beta;-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.
 == Structural Features ==

← Older revision		Revision as of 07:45, 16 May 2014
Line 22:		Line 22:
	[[Image:CBM28-17-4.png\|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca<sup>2+</sup> ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). \|frame\|right]]		[[Image:CBM28-17-4.png\|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca<sup>2+</sup> ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). \|frame\|right]]

−	CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the concave face of the β-sandwich fold. A Ca<sup>2+</sup> ion is bound on the back side of molecule. The Ca<sup>2+</sup> ion is not involved in ligand binding but appears to play a structural stabilization role. These modules are typical endo-type [[Carbohydrate-binding_modules#Types\|Type B CBMs]] that accommodate a single glycan chain in an open cleft.	+	CBM28s have a β-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the concave face of the β-sandwich fold. A Ca<sup>2+</sup> ion is bound on the back side of molecule. The Ca<sup>2+</sup> ion is not involved in ligand binding but appears to play a structural stabilization role. These modules are typical endo-type [[Carbohydrate-binding_modules#Types\|Type B CBMs]] that accommodate a single glycan chain in an open cleft. '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on the concave face (side) of the β-sandwich fold, not within the variable loop region ([[Carbohydrate-binding_modules#Fold\|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.
−
−	'''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on the concave face (side) of the β-sandwich fold, not within the variable loop region ([[Carbohydrate-binding_modules#Fold\|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78, W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-This module was firstly classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. Currently known CBM28s are solely from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or &beta;-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.
+This module was first classified in 2002 by a characterization study of the C-terminal module in [[GH5]] Cel5A from ''Bacillus'' sp. 1139 (''Bsp''CBM28) <cite>Boraston2002</cite>. All known CBM28s are so far derrived from bacterial origins, mostly attached to cellulosomal endoglucanases in tandem with [[CBM17]]. They bind non-crystalline (or amorphous) part of cellulose, cellooligosaccharides, or &beta;-1,3-1,4-glucans <cite>Boraston2002 Boraston2003</cite>.
 == Structural Features ==
 [[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca<sup>2+</sup> ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). |frame|right]]
-CBM28s have a &beta;-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the &beta;-sandwich fold. A Ca<sup>2+</sup> ion is bound on the back side of molecule. The Ca<sup>2+</sup> ion is not involved in ligand binding but appears to play a structural stabilization role.
+CBM28s have a &beta;-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the concave face of the &beta;-sandwich fold. A Ca<sup>2+</sup> ion is bound on the back side of molecule. The Ca<sup>2+</sup> ion is not involved in ligand binding but appears to play a structural stabilization role. These modules are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain in an open cleft.
-CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
+'''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on the concave face (side) of the &beta;-sandwich fold, not within the variable loop region ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78,  W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.
 == Functionalities ==
-CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
+CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>. They are exclusively associated with [[GH5]] endo-&beta;-1,4-glucanases and a survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains. As a typical endo-type (Type B) CBM, CBM28s show the <i>K</i><sub>a</sub> values of 0.7-5.2 &times;10<sup>4</sup> M<sup>-1</sup> for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (<i>K</i><sub>a</sub> = 9.9 &times;10<sup>5</sup> M<sup>-1</sup>) and low-affinity (<i>K</i><sub>a</sub> = 2.1 &times;10<sup>4</sup> M<sup>-1</sup>) cites <cite>Boraston2003</cite>. A novel application of CBM28 molecules was recently published where ''Bsp''CBM28 was used as a marker to identify amorphous regions in cellulose in photoactivated localization microscopy (PALM) studies <cite>Fox2013</cite>.
 == Family Firsts ==
@@ Line 43: / Line 35: @@
 ;First Structural Characterization
-Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in a ligand-free form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.
+Partial assignment of the NMR data of a CBM28 in Cel5I from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1521 ''Clostridium cellulolyticum''] was reported in 2002 <cite>Mosbah2002</cite> but its three-dimensional structure is not reported yet. The first crystal structure was reported in 2004 for ''Bsp''CBM28 in apo form ([{{PDBlink}}1uww 1uww]) <cite>Jamal2004</cite>. The first ligand complex structures were reported in 2010 for CBM28 in Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''C. josui''] (''Cj''CBM28) ([{{PDBlink}}3acf 3acf] [{{PDBlink}}3acg 3acg] [{{PDBlink}}3ach 3ach] [{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite>.
 == References ==

@@ Line 22: / Line 22: @@
 [[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. Ca<sup>2+</sup> ions in CBM28 and CBM17 are shown as green spheres in the ribbon representations (upper). Important residues in the cleft are colored yellow (aromatic), red (acidic), blue (basic), and green (neutral) on the molecular surfaces (lower). |frame|right]]
-* '''Fold:''' CBM28s have a &beta;-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the &beta;-sandwich fold. A Ca<sup>2+</sup> ion is bound on the back side of molecule. The Ca<sup>2+</sup> ion is not involved in ligand binding but appears to play a structural stabilization role.
+CBM28s have a &beta;-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the &beta;-sandwich fold. A Ca<sup>2+</sup> ion is bound on the back side of molecule. The Ca<sup>2+</sup> ion is not involved in ligand binding but appears to play a structural stabilization role.
-* '''Type:''' CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
-* '''Features of ligand binding:''' '''Figure 1''' shows the cellopentaose complex structure ([{{PDBlink}}3aci 3aci]) of CBM28 in [[GH5]] Cel5A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1499 ''Clostridium josui''] (''Cj''CBM28). The long binding cleft runs at the center of the molecule. Therefore, the binding pocket location of CBM28 is on a face (side) of the &beta;-sandwich fold, not on an apex/edge ([[Carbohydrate-binding_modules#Fold|CBM Fold]]). The shallow cleft of CBM28 binds one side of the cellooligosaccharides (face-on) in contrast with the case of [[CBM4]] (side-on). There are at at least five subsites (A-E from the non-reducing end to the reducing end) in ''Cj''CBM28. Interestingly, the direction of the cellooligosaccharides bound to CBM28 is opposite to those in [[CBM17]] and [[CBM4]]. Subsites B, C, and E form stacking interactions with aromatic residues (W78,  W129, and F128 in ''Cj''CBM28). The flanking hydroxyl groups are extensively recognized by direct or water-mediated hydrogen bonds. Therefore, CBM28 has a relatively wide cleft.
+CBM28s are typical endo-type [[Carbohydrate-binding_modules#Types|Type B CBMs]] that accommodate a single glycan chain because both ends of the cleft are open.
 == Functionalities ==
-* '''Functional role of CBM:''' CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
+CBM28s are thought to target catalytic modules (endoglucanases) to non-crystalline region of cellulose. Deletion mutants of CBM28 in Cel5A from ''Bacillus'' sp. 1139 showed significantly decreased amounts of the soluble products from amorphous cellulose <cite>Boraston2003</cite>.
-* '''Most Common Associated Modules:''' Endo-&beta;-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
-* '''Binding affinities:''' As a typical endo-type (Type B) CBM, CBM28s show the <i>K</i><sub>a</sub> values of 0.7-5.2 &times;10<sup>4</sup> M<sup>-1</sup> for the binding of cellooligosaccharides (cellotetraose to cellohexaose), and it is enthalpically driven <cite>Boraston2002 Araki2009</cite>. ''Bsp''CBM28 binds amorphous (regenerated) cellulose with high-affinity (<i>K</i><sub>a</sub> = 9.9 &times;10<sup>5</sup> M<sup>-1</sup>) and low-affinity (<i>K</i><sub>a</sub> = 2.1 &times;10<sup>4</sup> M<sup>-1</sup>) cites <cite>Boraston2003</cite>.
+CBM28s are associated with endo-&beta;-1,4-glucanases of [[GH5]]. A survey using the [http://www.ahv.dk/index.php/bioinformatic/cazy-tools/gh-cbm GH-CBM tool] shows that CBM28s are not associated with other GH family domains.
-* '''Novel Applications:''' ''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.
+''Bsp''CBM28 was used as the most amorphous-specific CBM in a study of photoactivated localization microscopy (PALM) <cite>Fox2013</cite>.
 == Family Firsts ==

@@ Line 20: / Line 20: @@
 == Structural Features ==
-[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-D (+E) from the non-reducing end to the reducing end. |frame|right]]
+[[Image:CBM28-17-4.png|'''Figure 1:''' CBM28 ([{{PDBlink}}3aci 3aci]) <cite>Tsukimoto2010</cite> in comparison with CBM17 ([{{PDBlink}}1j84 1j84]) <cite>Notenboom2011</cite> and CBM4 ([{{PDBlink}}1gu3 1gu3]) <cite>Boraston2002-2</cite>. Sugars of cellooligosaccharides (cellopentaose or cellotetraose) are designated as A-E from the non-reducing end to the reducing end. |frame|right]]
 * '''Fold:''' CBM28s have a &beta;-sandwich fold (approximately 200 amino acids) that is similar to [[CBM17]] and [[CBM4]] ('''Figure 1'''). The module has a straight cleft that binds a cellulose glycan chain at the center of the &beta;-sandwich fold.