Carbohydrate Binding Module Family 21 - Revision history

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

2021-12-18T21:15:10Z

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

Elizabeth Ficko-Blean at 16:05, 6 March 2018

2018-03-06T16:05:35Z

Stefan Janecek at 19:47, 8 July 2015

2015-07-08T19:47:14Z

Stefan Janecek at 15:40, 7 July 2015

2015-07-07T15:40:03Z

Stefan Janecek at 12:56, 7 July 2015

2015-07-07T12:56:27Z

Stefan Janecek at 12:54, 7 July 2015

2015-07-07T12:54:58Z

Stefan Janecek at 12:51, 7 July 2015

2015-07-07T12:51:43Z

Stefan Janecek at 11:10, 7 July 2015

2015-07-07T11:10:22Z

Stefan Janecek at 10:55, 7 July 2015

2015-07-07T10:55:39Z

Stefan Janecek at 10:54, 7 July 2015

2015-07-07T10:54:08Z

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 {{CuratorApproved}}
-* [[Author]]s: ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
+* [[Author]]s: [[User:Birte Svensson|Birte Svensson]] and [[User:Stefan Janecek|Stefan Janecek]]
-* [[Responsible Curator]]s:  ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
+* [[Responsible Curator]]s:  [[User:Birte Svensson|Birte Svensson]] and [[User:Stefan Janecek|Stefan Janecek]]
 ----

@@ Line 19: / Line 19: @@
 == Structural Features ==
-Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common β-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a CBM20 as template <cite>Chou2006</cite> and thereafter by docking onto the NMR structure determined for CBM21 from the family [[GH15]] ''Rhizopus oryzae'' glucoamylase <cite>Liu2007</cite>. The crystal structure determined for this CBM21 in complex with β-cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands <cite>Tung2008</cite>. Site I requires ligands with DP > 3 for binding <cite>Chu2014</cite>. A CBM21-like domain was identified in the crystal structure of barley family [[GH13]] limit dextrinase <cite>Moeller2012</cite>.
+Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common β-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a [[CBM20]] as template <cite>Chou2006</cite> and thereafter by docking onto the NMR structure determined for CBM21 from the family [[GH15]] ''Rhizopus oryzae'' glucoamylase <cite>Liu2007</cite>. The crystal structure determined for this CBM21 in complex with β-cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands <cite>Tung2008</cite>. Site I requires ligands with DP > 3 for binding <cite>Chu2014</cite>. A CBM21-like domain was identified in the crystal structure of barley family [[GH13]] limit dextrinase <cite>Moeller2012</cite>.
 == Functionalities ==

@@ 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]]s: ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
 * [[Responsible Curator]]s:  ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^

@@ Line 23: / Line 23: @@
 == Functionalities ==
-CBM21s are mainly associated with some fungal glucoamylases and α-amylases of the family [[GH15]] <cite>Ashikari1986 Bui1996 Houghton-Larsen2003</cite> and [[GH13]] <cite>Steyn1995 Kang2004</cite>, respectively. This was confirmed by an exhaustive evolutionary analysis of 85 fungal genomes <cite>Chen2012</cite>. In both cases, i.e. in [[GH15]] glucoamylases and [[GH13]] α-amylases, the CBM21 precedes the catalytic domain <cite>Machovic2005</cite>. The CBM21 is present also as a part of the regulatory subunit of Ser/Thr-specific protein phosphatases that directs the protein phosphatase to glycogen <cite>Bork1998</cite>. Recently, a structural comparison identified an N-terminal CBM21-like domain in the barley GH13 limit dextrinase <cite>Moeller2012</cite>, where it is followed by the module from the family [[CBM48]] succeeded by the catalytic TIM-barrel.
+CBM21s are mainly associated with some fungal glucoamylases and α-amylases of the family [[GH15]] <cite>Ashikari1986 Bui1996 Houghton-Larsen2003</cite> and [[GH13]] <cite>Steyn1995 Kang2004</cite>, respectively. This was confirmed by an exhaustive evolutionary analysis of 85 fungal genomes <cite>Chen2012</cite>. In both cases, i.e. in [[GH15]] glucoamylases and [[GH13]] α-amylases, the CBM21 precedes the catalytic domain <cite>Machovic2005</cite>. The CBM21 is present also as a part of the regulatory subunit of Ser/Thr-specific protein phosphatases that directs the protein phosphatase to glycogen <cite>Bork1998</cite>. Recently, a structural comparison identified an N-terminal CBM21-like domain in the barley [[GH13]] limit dextrinase <cite>Moeller2012</cite>, where it is followed by the module from the family [[CBM48]] succeeded by the catalytic TIM-barrel.
 == Family Firsts ==

@@ Line 20: / Line 20: @@
 == Structural Features ==
-Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common β-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a CBM20 as template <cite>Chou2006</cite> and thereafter by docking onto the NMR structure determined for CBM21 from the family [[GH15]] ''Rhizopus oryzae'' glucoamylase <cite>Liu2007</cite>. The crystal structure determined for this CBM21 in complex with β-cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands <cite>Tung2008</cite>. Site I requires ligands with DP > 3 for binding <cite>Chu2014</cite>. A CBM21-like domain was identified in the crystal structure of barley family [[GH13]] limit dextrinase <cite>Møller2012</cite>.
+Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common β-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a CBM20 as template <cite>Chou2006</cite> and thereafter by docking onto the NMR structure determined for CBM21 from the family [[GH15]] ''Rhizopus oryzae'' glucoamylase <cite>Liu2007</cite>. The crystal structure determined for this CBM21 in complex with β-cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands <cite>Tung2008</cite>. Site I requires ligands with DP > 3 for binding <cite>Chu2014</cite>. A CBM21-like domain was identified in the crystal structure of barley family [[GH13]] limit dextrinase <cite>Moeller2012</cite>.
 == Functionalities ==
-CBM21s are mainly associated with some fungal glucoamylases and α-amylases of the family [[GH15]] <cite>Ashikari1986 Bui1996 Houghton-Larsen2003</cite> and [[GH13]] <cite>Steyn1995 Kang2004</cite>, respectively. This was confirmed by an exhaustive evolutionary analysis of 85 fungal genomes <cite>Chen2012</cite>. In both cases, i.e. in [[GH15]] glucoamylases and [[GH13]] α-amylases, the CBM21 precedes the catalytic domain <cite>Machovic2005</cite>. The CBM21 is present also as a part of the regulatory subunit of Ser/Thr-specific protein phosphatases that directs the protein phosphatase to glycogen <cite>Bork1998</cite>. Recently, a structural comparison identified an N-terminal CBM21-like domain in the barley GH13 limit dextrinase <cite>Møller2012</cite>, where it is followed by the module from the family [[CBM48]] succeeded by the catalytic TIM-barrel.
+CBM21s are mainly associated with some fungal glucoamylases and α-amylases of the family [[GH15]] <cite>Ashikari1986 Bui1996 Houghton-Larsen2003</cite> and [[GH13]] <cite>Steyn1995 Kang2004</cite>, respectively. This was confirmed by an exhaustive evolutionary analysis of 85 fungal genomes <cite>Chen2012</cite>. In both cases, i.e. in [[GH15]] glucoamylases and [[GH13]] α-amylases, the CBM21 precedes the catalytic domain <cite>Machovic2005</cite>. The CBM21 is present also as a part of the regulatory subunit of Ser/Thr-specific protein phosphatases that directs the protein phosphatase to glycogen <cite>Bork1998</cite>. Recently, a structural comparison identified an N-terminal CBM21-like domain in the barley GH13 limit dextrinase <cite>Moeller2012</cite>, where it is followed by the module from the family [[CBM48]] succeeded by the catalytic TIM-barrel.
 == Family Firsts ==
@@ Line 47: / Line 47: @@
 #Steyn1995 pmid=8529895
 #Kang2004 pmid=15043869
-#Møller2012 pmid=22949184
+#Moeller2012 pmid=22949184
 #Chen2012 pmid=23166747
 #Machovic2005 pmid=16262690

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-Modules from family CBM21 bind to the α-glucan starch and oligosaccharides derived from starch or related to such oligosaccharides that contain α-1,4-linked glucose and/or α-1,6-linked glucose including maltose through maltoheptaose, β- and γ-cyclodextrins, isomaltotriose and isomaltotetraose <cite>Chou2006 Chu2014 Liu2007 Tung2008</cite>. CBM21 also interacts with amylose and alters its ultrastructure as demonstrated by atomic force microscopy <cite>Jiang2012</cite>. Circular permutation enhanced the affinity for amylose <cite>Stephen2012</cite>. The domain has been described as providing mainly glucoamylase and α-amylase with the ability to bind onto raw-starch (starch granules) <cite>Ashikari1986 Bui1996 Houghton-Larsen2003       Steyn1995 Kang2004</cite>.
+Modules from family CBM21 bind to the α-glucan starch and oligosaccharides derived from starch or related to such oligosaccharides that contain α-1,4-linked glucose and/or α-1,6-linked glucose including maltose through maltoheptaose, β- and γ-cyclodextrins, isomaltotriose and isomaltotetraose <cite>Chou2006 Chu2014 Liu2007 Tung2008</cite>. CBM21 also interacts with amylose and alters its ultrastructure as demonstrated by atomic force microscopy <cite>Jiang2012</cite>. Circular permutation enhanced the affinity for amylose <cite>Stephen2012</cite>. The domain has been described as providing mainly glucoamylase and α-amylase with the ability to bind onto raw-starch (starch granules) <cite>Ashikari1986 Bui1996 Houghton-Larsen2003 Steyn1995 Kang2004</cite>.
 == Structural Features ==
-Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common β-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a CBM20 as template <cite>Chou2006</cite> and thereafter by docking onto the NMR structure determined for CBM21 from the family GH15 ''Rhizopus oryzae'' glucoamylase <cite>Liu2007</cite>. The crystal structure determined for this CBM21 in complex with β      -cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands <cite>Tung2008</cite>. Site I requires ligands with DP > 3 for binding <cite>Chu2014</cite>. A CBM21-like domain was identified in the crystal structure of barley family [[GH13]] limit dextrinase <cite>Møller2012</cite>.
+Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common β-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a CBM20 as template <cite>Chou2006</cite> and thereafter by docking onto the NMR structure determined for CBM21 from the family [[GH15]] ''Rhizopus oryzae'' glucoamylase <cite>Liu2007</cite>. The crystal structure determined for this CBM21 in complex with β-cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands <cite>Tung2008</cite>. Site I requires ligands with DP > 3 for binding <cite>Chu2014</cite>. A CBM21-like domain was identified in the crystal structure of barley family [[GH13]] limit dextrinase <cite>Møller2012</cite>.
 == Functionalities ==
@@ Line 29: / Line 29: @@
 Family CBM21 was first observed as an N-terminally located domain in glucoamylase from ''Rhizopus oryzae'' <cite>Ashikari1986</cite>. The function was ascribed based on comparison of multiple forms of the glucoamylase <cite>Ashikari1986 Takahashi1982</cite> and amino acid sequence alignment <cite>Tanaka1986</cite>. The CBM21 sequence was revealed as related to that of the starch binding domain of ''Aspergillus niger'' glucoamylase <cite>Svensson1989</cite>, which has been assigned the family [[CBM20]] <cite>Machovic2005 Machovic2006 Christiansen2009</cite>.
 ;First Structural Characterization
-The first CBM21 three-dimensional structure was determined by NMR for the module from the family [[GH15]] glucoamylase from ''Rhizopus oryzae'' <cite>Liu2007</cite>. The first CBM21 complex structures were determined by X-ray crystallography for that domain binding to β      -cyclodextrin or maltoheptaose <cite>Tung2008</cite>.
+The first CBM21 three-dimensional structure was determined by NMR for the module from the family [[GH15]] glucoamylase from ''Rhizopus oryzae'' <cite>Liu2007</cite>. The first CBM21 complex structures were determined by X-ray crystallography for that domain binding to β-cyclodextrin or maltoheptaose <cite>Tung2008</cite>.
 == Novel Applications ==

@@ Line 17: / Line 17: @@
 == Ligand specificities ==
-Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.
+Modules from family CBM21 bind to the α-glucan starch and oligosaccharides derived from starch or related to such oligosaccharides that contain α-1,4-linked glucose and/or α-1,6-linked glucose including maltose through maltoheptaose, β- and γ-cyclodextrins, isomaltotriose and isomaltotetraose [1-4]. CBM21 also interacts with amylose and alters its ultrastructure as demonstrated by atomic force microscopy [5]. Circular permutation enhanced the affinity for amylose [6]. The domain has been described as providing mainly glucoamylase and α-amylase with the ability to bind onto raw-starch (starch granules) [7-11]      .
 ''Note: Here is an example of how to insert references in the text, together with the "biblio" section below:'' Please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.
 == Structural Features ==
-''Content in this section should include, in paragraph form, a description of:''
+Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common b-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a CBM20 as template [1] and thereafter by docking onto the NMR structure determined for CBM21 from the family GH15 Rhizopus oryzae glucoamylase [3]. The crystal structure determined for this CBM21 in complex with b-cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands [4]. Site I requires ligands with DP > 3 for binding [2]. A CBM21-like domain was identified in the crystal structure of barley family GH13 limit dextrinase [12]      .
 == Functionalities ==
-''Content in this section should include, in paragraph form, a description of:''
+     CBM21s are mainly associated with some fungal glucoamylases and α-amylases of the family GH15 [7-9] and GH13 [10,11], respectively. This was confirmed by an exhaustive evolutionary analysis of 85 fungal genomes [13]. In both cases, i.e. in GH15 glucoamylases and GH13 α-amylases, the CBM21 precedes the catalytic domain [14]. The CBM21 is present also as a part of the regulatory subunit of Ser/Thr-specific protein phosphatases that directs the protein phosphatase to glycogen [15]. Recently, a structural comparison identified an N-terminal CBM21-like domain in the barley GH13 limit dextrinase [7], where it is followed by the module from the family CBM48 succeeded by the catalytic TIM-barrel      .
 == Family Firsts ==
 ;First Identified
-:Insert archetype here, possibly including ''very brief'' synopsis.
+Family CBM21 was first observed as an N-terminally located domain in glucoamylase from Rhizopus oryzae [7]. The function was ascribed based on comparison of multiple forms of the glucoamylase [7,16] and amino acid sequence alignment [17]. The CBM21 sequence was revealed as related to that of the starch binding domain of Aspergillus niger glucoamylase [18], which has been assigned the family CBM20 [14,19,20]      .
 ;First Structural Characterization
-:Insert archetype here, possibly including ''very brief'' synopsis.
+The first CBM21 three-dimensional structure was determined by NMR for the module from the family GH15 glucoamylase from Rhizopus oryzae [3]. The first CBM21 complex structures were determined by X-ray crystallography for that domain binding to b-cyclodextrin or maltoheptaose [4]      .
 == References ==
 <biblio>
-#Cantarel2009 pmid=18838391
+#Chou2006 pmid=16509822
-#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]
+#Chu2014 pmid=24108499
-#Boraston2004 pmid=15214846
+#Liu2007 pmid=17117925
-#Hashimoto2006 pmid=17131061
+#Tung2008 pmid=18588504
-#Shoseyov2006 pmid=16760304
+#Jiang2012 pmid=22815939
-#Guillen2010 pmid=19908036
+#Stephen2012 pmid=23226294
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM021]]

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 <!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption -->
 {{UnderConstruction}}
-* [[Author]]: ^^^Alicia Lammerts van Bueren^^^
+* [[Author]]: ^^^Birte Svensson and Stefan Janecek^^^
-* [[Responsible Curator]]:  ^^^Alicia Lammerts van Bueren^^^
+* [[Responsible Curator]]:  ^^^Birte Svensson and Stefan Janecek^^^
 ----