Carbohydrate Binding Module Family 41 - Revision history

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

2021-12-18T21:17:27Z

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

Harry Brumer: /* Structural Features */ fixed typo in vanBueren2007b reference

2014-01-20T00:58:01Z

Structural Features: fixed typo in vanBueren2007b reference

Harry Brumer: removed un-used references

2014-01-20T00:48:52Z

removed un-used references

Harry Brumer: removed un-used references

2014-01-20T00:48:26Z

removed un-used references

Harry Brumer: fixed broken vanBueren2007b reference

2014-01-20T00:46:45Z

fixed broken vanBueren2007b reference

Alicia Lammerts van Bueren at 09:17, 17 January 2014

2014-01-17T09:17:55Z

Alicia Lammerts van Bueren at 09:12, 17 January 2014

2014-01-17T09:12:17Z

Alicia Lammerts van Bueren at 12:14, 8 January 2014

2014-01-08T12:14:05Z

Harry Brumer: added GH13 links

2013-10-21T07:21:16Z

added GH13 links

Alicia Lammerts van Bueren at 12:55, 18 October 2013

2013-10-18T12:55:42Z

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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]]: ^^^Alicia Lammerts van Bueren^^^
+* [[Author]]: [[User:Alicia Lammerts van Bueren|Alicia Lammerts van Bueren]]
-* [[Responsible Curator]]:  ^^^Al Boraston^^^
+* [[Responsible Curator]]:  [[User:Al Boraston|Al Boraston]]
 ----

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 CBM41s are mainly associated with pullulanases and other starch/glycogen debranching enzymes of family [[GH13]]. CBM41s are shown to direct the enzyme onto alpha-1,4-glucan chains to situate the catalytic machinery towards alpha-1,6-branch points <cite>vanBueren2011</cite>. The majority of CBM41s are found in bacteria, including several pathogenic bacterial species such as ''Streptococcus'', ''Klebsiella'' and ''Bacillus'' <cite>vanBueren2004 vanBueren2007b</cite>. They are also found in eukaryotic red and green algae. An updated list of CBM41 family members can be found in the [http://www.cazy.org/CBM41_all.html CAZy Database]
 == Structural Features ==
-There are several [http://www.cazy.org/CBM41_structure.html X-ray crystal structures of CBM41 modules] of which the majority are in complex with carbohydrate ligand. All adopt a common beta-sandwich configuration with an immunoglobulin (Ig)-like fold. A concave-shaped binding groove is formed on the side of the protein molecule to accommodate the helical structure of alpha-1,4-linked maltooligosaccharides <cite>vanBueren2007a vanbueren2007b</cite>. Typically two solvent exposed tryptophan residues form hydrophobic stacking interactions with the primary glucose molecule, with a third tryptophan creating a platform for interacting with longer maltooligosaccharide chains. The binding groove is made up of 4 binding subsites that interact with up to 4 intra-chain alpha-1,4-linked glucose molecules, classifying them as [[Carbohydrate-binding_modules|Type B CBMs]]. The CBM41 module from ''Thermotoga maritima'' was shown to accommodate either an alpha-1,4 or alpha-1,6-linked glucose residue in the fourth subsite, demonstrating that there is room for flexibility in the linkage that can be accommodated at this site <cite>vanBueren2007a</cite>.
+There are several [http://www.cazy.org/CBM41_structure.html X-ray crystal structures of CBM41 modules] of which the majority are in complex with carbohydrate ligand. All adopt a common beta-sandwich configuration with an immunoglobulin (Ig)-like fold. A concave-shaped binding groove is formed on the side of the protein molecule to accommodate the helical structure of alpha-1,4-linked maltooligosaccharides <cite>vanBueren2007a vanBueren2007b</cite>. Typically two solvent exposed tryptophan residues form hydrophobic stacking interactions with the primary glucose molecule, with a third tryptophan creating a platform for interacting with longer maltooligosaccharide chains. The binding groove is made up of 4 binding subsites that interact with up to 4 intra-chain alpha-1,4-linked glucose molecules, classifying them as [[Carbohydrate-binding_modules|Type B CBMs]]. The CBM41 module from ''Thermotoga maritima'' was shown to accommodate either an alpha-1,4 or alpha-1,6-linked glucose residue in the fourth subsite, demonstrating that there is room for flexibility in the linkage that can be accommodated at this site <cite>vanBueren2007a</cite>.
 The overall structural scaffold and mode of alpha-glucan recognition of CBM41 is similar to other starch-binding CBM families, which include CBM20, CBM21, CBM25, CBM26, CBM34, and CBM48. Although these different starch-binding module families have very little amino-acid sequence similarity to each other, that fact that they share almost identical modes of starch-binding suggests a common evolution towards maltooligosaccharide recognition by all starch-binding CBM families <cite>Christiansen2009</cite>.

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 #vanBueren2004 pmid=15581376
 #vanBueren2007b pmid=17187076
 #vanBueren2007a pmid=17095014
 #vanBueren2011 pmid=21565699

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 #Mikami2006 pmid=16650854
 #Christiansen2009 pmid=19682075
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM041]]

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 <biblio>
 #vanBueren2004 pmid=15581376
-#vanBueren20072 pmid=17187076
+#vanBueren2007b pmid=17187076
 #Gilbert2013 pmid=23769966
 #vanBueren2007a pmid=17095014

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 == Functionalities ==
-CBM41 modules are associated with alpha-glucan debranching enzymes in family GH13, including pullulanases (EC 3.2.1.41, GH13 subfamily 14) and starch/glycogen debranching enzymes (GH13 subfamily 12). They function in directing the enzyme onto alpha-1,4-glucan chains and situating the catalytic machinery towards alpha-1,6-branch points <cite>vanBueren2011</cite>. The most interesting feature of CBM41 modules is they are primarily associated with pullulanase-like enzymes originating from pathogenic bacteria, including pathogenic ''Streptococcus'', ''Klebsiella'' and ''Bacillus'' species <cite>vanBueren2004 vanBueren20072</cite>.
+CBM41 modules are associated with alpha-glucan debranching enzymes in family [[GH13]], including pullulanases (EC 3.2.1.41, [[GH13]] subfamily 14) and starch/glycogen debranching enzymes ([[GH13]] subfamily 12). They function in directing the enzyme onto alpha-1,4-glucan chains and situating the catalytic machinery towards alpha-1,6-branch points <cite>vanBueren2011</cite>. The most interesting feature of CBM41 modules is they are primarily associated with pullulanase-like enzymes originating from pathogenic bacteria, including pathogenic ''Streptococcus'', ''Klebsiella'' and ''Bacillus'' species <cite>vanBueren2004 vanBueren20072</cite>.
 == Structural Features ==
 To date there are 11 X-ray crystal structures of CBM41 modules of which seven are in complex with carbohydrate ligand. All adopt a common beta-sandwich fold and form a concave-shaped binding groove on the side of the protein molecule to accommodate the helical structure formed by alpha-1,4-linked maltooligosaccharides. Typically two solvent exposed tryptophan residues form hydrophobic stacking interactions with the primary glucose molecule, with a third tryptophan creating a platform for interacting with longer maltooligosaccharide chains. The binding groove is made up of 4 binding subsites that interact with up to 4 intra-chain alpha-1,4-linked glucose molecules, classifying them as Type B CBMs. The CBM41 module from ''Thermotoga maritima'' was shown to accommodate either an alpha-1,4 or alpha-1,6-linked glucose residue in the fourth subsite, demonstrating that there is room for flexibility in the linkage that can be accommodated at this site <cite>vanBueren2007</cite>.
@@ Line 27: / Line 27: @@
 The overall structural scaffold and mode of alpha-glucan recognition of CBM41 is similar to other starch-binding CBM families, which include CBM20, CBM21, CBM25, CBM26, CBM34, and CBM48. Although these different starch-binding module families have very little amino-acid sequence similarity to each other, that fact that they share almost identical modes of starch-binding suggests a common evolution towards maltooligosaccharide recognition by all starch-binding CBM families <cite>Christiansen2009</cite>.
-Structural data are available for several full-length pullulanases and glycogen-debranching enzymes containing both catalytic modules and associated CBMs in complex with alpha-glucan substrates which has provided details on how modularity contributes to the overall function of these enzymes. For example, the x-ray crystal structure of full length glycogen-debranching enzyme SpuA from ''Streptococcus pneumoniae'' revealed that the first of two dual, tandemly arranged N-terminal CBM41 modules directly participates in binding alpha-1,6-linked glucose branch points within the active site of the C-terminal GH13 catalytic module <cite>vanBueren2011</cite>. This is the first demonstration that a CBM directly participates in substrate binding which has so far has only been found to occur within CBM41-containing pullulanases. The second CBM41 of SpuA is available to interact with an adjacent alpha-glucan chain, suggesting a possible disruptive role for these CBMs in loosening granular glycogen and increasing the substrate availability for the catalytic module.
+Structural data are available for several full-length pullulanases and glycogen-debranching enzymes containing both catalytic modules and associated CBMs in complex with alpha-glucan substrates which has provided details on how modularity contributes to the overall function of these enzymes. For example, the x-ray crystal structure of full length glycogen-debranching enzyme SpuA from ''Streptococcus pneumoniae'' revealed that the first of two dual, tandemly arranged N-terminal CBM41 modules directly participates in binding alpha-1,6-linked glucose branch points within the active site of the C-terminal [[GH13]] catalytic module <cite>vanBueren2011</cite>. This is the first demonstration that a CBM directly participates in substrate binding which has so far has only been found to occur within CBM41-containing pullulanases. The second CBM41 of SpuA is available to interact with an adjacent alpha-glucan chain, suggesting a possible disruptive role for these CBMs in loosening granular glycogen and increasing the substrate availability for the catalytic module.
 == Family Firsts ==

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 == Ligand specificities ==
-Modules from family CBM41 bind to alpha-glucans including starch, glycogen, amylose, amylopectin and pullulan, and shorter alpha glucan oligosaccharides derived from these polysaccharides including maltose, maltotriose, longer maltooligosaccharides up to DP7, glucosyl-maltotriose and glucosyl-maltotriosyl-maltotriose <cite>vanBueren2004</cite>. CBM41 modules are specific for alpha-1,4-linked glucose chains and can accommodate a linear alpha-1,6-linked glucose moiety.
+Modules from family CBM41 bind to alpha-glucans including starch (amylopectin), glycogen, amylose (linear alpha-1,4-linked glucose), and pullulan (alpha-1,6-linked maltotriose), and shorter alpha glucan oligosaccharides derived from these polysaccharides including maltose, maltotriose, longer maltooligosaccharides up to DP7, glucosyl-maltotriose and glucosyl-maltotriosyl-maltotriose <cite>vanBueren2004</cite>. CBM41 modules are specific for alpha-1,4-linked glucose chains and may accommodate a linear alpha-1,6-linked glucose moiety.
 == Functionalities ==
-CBM41 modules are associated with alpha-glucan debranching enzymes in family GH13, including pullulanases (EC 3.2.1.41, GH13 subfamily 14) and starch/glycogen debranching enzymes (GH13 subfamily 12). They function in directing the enzyme onto alpha-1,4-glucan chains and situating the catalytic machinery towards alpha-1,6-branch points <cite>vanBueren2011</cite>. The most interesting feature of these modules is they are primarily associated with pullulanase-like enzymes originating from pathogenic bacteria, including pathogenic ''Streptococcus'', ''Klebsiella'' and ''Bacillus'' species <cite>vanBueren2004 vanBueren20072</cite>.
+CBM41 modules are associated with alpha-glucan debranching enzymes in family GH13, including pullulanases (EC 3.2.1.41, GH13 subfamily 14) and starch/glycogen debranching enzymes (GH13 subfamily 12). They function in directing the enzyme onto alpha-1,4-glucan chains and situating the catalytic machinery towards alpha-1,6-branch points <cite>vanBueren2011</cite>. The most interesting feature of CBM41 modules is they are primarily associated with pullulanase-like enzymes originating from pathogenic bacteria, including pathogenic ''Streptococcus'', ''Klebsiella'' and ''Bacillus'' species <cite>vanBueren2004 vanBueren20072</cite>.
 == Structural Features ==
 To date there are 11 X-ray crystal structures of CBM41 modules of which seven are in complex with carbohydrate ligand. All adopt a common beta-sandwich fold and form a concave-shaped binding groove on the side of the protein molecule to accommodate the helical structure formed by alpha-1,4-linked maltooligosaccharides. Typically two solvent exposed tryptophan residues form hydrophobic stacking interactions with the primary glucose molecule, with a third tryptophan creating a platform for interacting with longer maltooligosaccharide chains. The binding groove is made up of 4 binding subsites that interact with up to 4 intra-chain alpha-1,4-linked glucose molecules, classifying them as Type B CBMs. The CBM41 module from ''Thermotoga maritima'' was shown to accommodate either an alpha-1,4 or alpha-1,6-linked glucose residue in the fourth subsite, demonstrating that there is room for flexibility in the linkage that can be accommodated at this site <cite>vanBueren2007</cite>.