Difference between revisions of "Carbohydrate Binding Module Family 48"

Latest revision as of 13:15, 18 December 2021

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Authors: Stefan Janecek and Birte Svensson
Responsible Curators: Stefan Janecek and Birte Svensson

CAZy DB link
https://www.cazy.org/CBM48.html

Ligand specificities

Family CBM48 contains modules able to bind various linear and cyclic α-glucans related to and derived from starch and glycogen having both the α-1,4- and α-1,6-linkages including, e.g., glucose and maltopentaose [1], maltooligosaccharides [2], maltoheptaose [3], β-cyclodextrin [4], single α-1,6-branched glucosyl, maltosyl and maltoteatraosyl maltoheptaose [2] and single α-1,6-branched glucosyl β-cyclodextrin [5].

Structural Features

There is a number of family CBM48 structures solved mostly by X-ray crystallography [1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30], but also by NMR [5]. The structure is a typical β-sandwich with one well-defined binding site [4]. As seen in the β1 subunit of the rat AMP-activated protein kinase (AMPK) [4], the crucial role in binding is played by residues W100, F112, K126 and W133. As a complex exhibiting carbohydrate binding, the CBM48 has been determined only for β-subunits of mammalian AMPK [2, 4, 5], and family GH13 branching enzyme [1] and starch excess4 (SEX4) protein [3] both from plants. Notably, in complexes of the rice starch branching enzyme [1] and the SEX4 protein [3] with maltopentaose and maltoheptaose, respectively, the ligand interacts with both the CBM48 and the catalytic domain. In this light CBM48 possesses two binding sites including a canonical site 1 seen in the closely related CBM20 and which in CBM48 is occupied by ligands that at the same time interact with the active site area of the catalytic domain. There are many homologous CBM48 structures present in several enzyme specificities from the α-amylase family GH13 [31], but of these only the CBM48 from rice starch branching enzyme has been solved in complex with carbohydrate ligands [1].

Functionalities

The CBM48 in amylolytic enzymes from the family GH13 precedes the catalytic TIM-barrel. This is the case of isoamylase [6, 26], maltooligosyltrehalohydrolase [7, 9, 10], branching enzyme [1, 8, 16, 20, 32], debranching enzyme [13, 17], pullulanase [11, 14, 15, 27], limit dextrinase [19, 21, 29, 30] and a bifunctional α-amylase/cyclomaltodextrinase [23]. In the non-amylolytic SEX4 proteins from plants and green algae, the module is positioned C-terminally with respect to the catalytic glucan phosphatase domain [3, 18, 33]. A special case is represented by mammalian AMPKs that possess the CBM48 within the β-subunits of its αβγ heterotrimer molecule [2, 4, 5, 24, 25, 28]; the same applies for AMPK’s yeast homologue SNF1 [12]. A C-terminal position is also found for CBM48 in FLO6, a protein involved in starch biosynthesis [34]. With regard to sequence/structure relationships and the way of carbohydrate binding, the modules from the family CBM48 are most closely related to those from the family CBM20 [31] and, in a wider sense, also to those from families CBM21, CBM53 [35, 36] and the recently established family CBM69 [37].

Family Firsts

First Identified

The family CBM48 was first referred to as (CBM20+CBM21)-related groups based on the in silico analysis of various proteins and taxa [35] and then defined within the CAZy database as an independent CBM family [38, 39].

First Structural Characterization

Based on current knowledge [31, 38, 39], the first CBM48 structure without any carbohydrate bound was solved as the N-terminal domain of the isoamylase from Pseudomonas amyloderamosa [6]. The first CBM48 structure confirming its carbohydrate binding ability (a complex with β-cyclodextrin) was determined for the β1 subunit of the rat AMPK [4], but it is of note that at that time the family CBM48 was not established [40].

References

All Medline abstracts: PubMed

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+* [[Author]]s: [[User:Stefan Janecek|Stefan Janecek]] and [[User:Birte Svensson|Birte Svensson]]
-* [[Author]]s: ^^^Stefan Janecek^^^ and ^^^Birte Svensson^^^
+* [[Responsible Curator]]s: [[User:Stefan Janecek|Stefan Janecek]] and [[User:Birte Svensson|Birte Svensson]]
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 == Ligand specificities ==
-Family CBM48 contains modules able to bind various linear and cyclic α-glucans related to and derived from starch and glycogen having both the α-1,4- and α-1,6-linkages including, e.g., glucose and maltopentaose [1], maltooligosaccharides [2], maltoheptaose [3], β-cyclodextrin [4], single α-1,6-branched glucosyl, maltosyl and maltoteatraosyl maltoheptaose [2] and single α-1,6-branched glucosyl β-cyclodextrin [5].
+Family CBM48 contains modules able to bind various linear and cyclic α-glucans related to and derived from starch and glycogen having both the α-1,4- and α-1,6-linkages including, e.g., glucose and maltopentaose <cite>Chaen2012</cite>, maltooligosaccharides <cite>Koay2010</cite>, maltoheptaose <cite>Meekins2014</cite>, β-cyclodextrin <cite>Polekhina2005</cite>, single α-1,6-branched glucosyl, maltosyl and maltoteatraosyl maltoheptaose <cite>Koay2010</cite> and single α-1,6-branched glucosyl β-cyclodextrin <cite>Mobbs2015</cite>.
-''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 ==
-There is a number of family CBM48 structures solved mostly by X-ray crystallography [1-4,6-30], but also by NMR [5]. The structure is a typical β-sandwich with one well-defined binding site [4]. As seen in the β1 subunit of the rat AMP-activated protein kinase (AMPK) [4], the crucial role in binding is played by residues W100, F112, K126 and W133. As a complex exhibiting carbohydrate binding, the CBM48 has been determined only for β-subunits of mammalian AMPK [2,4,5], and family GH13 branching enzyme [1] and starch excess4 (SEX4) protein [3] both from plants. Notably, in complexes of the rice starch branching enzyme [1] and the SEX4 protein [3] with maltopentaose and maltoheptaose, respectively, the ligand interacts with both the CBM48 and the catalytic domain. In this light CBM48 possesses two binding sites including a canonical site 1 seen in the closely related CBM20 and which in CBM48 is occupied by ligands that at the same time interact with the active site area of the catalytic domain. There are many homologous CBM48 structures present in several enzyme specificities from the α-amylase family GH13 [31], but of these only the CBM48 from rice starch branching enzyme has been solved in complex with carbohydrate ligands [1].
+There is a number of family CBM48 structures solved mostly by X-ray crystallography <cite>Chaen2012 Koay2010 Meekins2014 Polekhina2005 Katsuya1998 Feese2000 Abad2002 Timmis2005 Leiros2006 Mikami2006 Amodeo2007 Woo2008 Gourlay2009 Turkenburg2009 Pal2010 Song2010 Vander-Kooi2010 Vester-Christensen2010 Noguchi2011 Moeller2012 Okazaki2012 Park2013 Xiao2013 Calabrese2014 Sim2014 Xu2014 Li2015 Moeller2015a Moeller2015b</cite>, but also by NMR <cite>Mobbs2015</cite>. The structure is a typical β-sandwich with one well-defined binding site <cite>Polekhina2005</cite>. As seen in the β1 subunit of the rat AMP-activated protein kinase (AMPK) <cite>Polekhina2005</cite>, the crucial role in binding is played by residues W100, F112, K126 and W133. As a complex exhibiting carbohydrate binding, the CBM48 has been determined only for β-subunits of mammalian AMPK <cite>Koay2010 Polekhina2005 Mobbs2015</cite>, and family [[GH13]] branching enzyme <cite>Chaen2012</cite> and starch excess4 (SEX4) protein <cite>Meekins2014</cite> both from plants. Notably, in complexes of the rice starch branching enzyme <cite>Chaen2012</cite> and the SEX4 protein <cite>Meekins2014</cite> with maltopentaose and maltoheptaose, respectively, the ligand interacts with both the CBM48 and the catalytic domain. In this light CBM48 possesses two binding sites including a canonical site 1 seen in the closely related [[CBM20]] and which in CBM48 is occupied by ligands that at the same time interact with the active site area of the catalytic domain. There are many homologous CBM48 structures present in several enzyme specificities from the α-amylase family [[GH13]] <cite>Janecek2011</cite>, but of these only the CBM48 from rice starch branching enzyme has been solved in complex with carbohydrate ligands <cite>Chaen2012</cite>.
 == Functionalities ==
- The CBM48 in amylolytic enzymes from the family GH13 precedes the catalytic TIM-barrel. This is the case of isoamylase [6,26], maltooligosyltrehalohydrolase [7,9,10], branching enzyme [1,8,16,20,32], debranching enzyme [13,17], pullulanase [11,14,15,27], limit dextrinase [19,21,29,30] and a bifunctional α-amylase/cyclomaltodextrinase [23]. In the non-amylolytic SEX4 proteins from plants and green algae, the module is positioned C-terminally with respect to the catalytic glucan phosphatase domain [3,18,33]. A special case is represented by mammalian AMPKs that possess the CBM48 within the β-subunits of its αβγ heterotrimer molecule [2,4,5,24,25,28]; the same applies for AMPK’s yeast homologue SNF1 [12]. A C-terminal position is also found for CBM48 in FLO6, a protein involved in starch biosynthesis [34]. With regard to sequence/structure relationships and the way of carbohydrate binding, the modules from the family GH48 are most closely related to those from the family CBM20 [31] and, in a wider sense, also to those from families CBM21, CBM53 [35,36] and the recently established family CBM69 [37]      .
+The CBM48 in amylolytic enzymes from the family [[GH13]] precedes the catalytic TIM-barrel. This is the case of isoamylase <cite>Katsuya1998 Sim2014</cite>, maltooligosyltrehalohydrolase <cite>Feese2000 Timmis2005 Leiros2006</cite>, branching enzyme <cite>Chaen2012 Abad2002 Pal2010 Noguchi2011 Palomo2009</cite>, debranching enzyme <cite>Woo2008 Song2010</cite>, pullulanase <cite>Mikami2006 Gourlay2009 Turkenburg2009 Xu2014</cite>, limit dextrinase <cite>Vester-Christensen2010 Moeller2012 Moeller2015a Moeller2015b</cite> and a bifunctional α-amylase/cyclomaltodextrinase <cite>Park2013</cite>. In the non-amylolytic SEX4 proteins from plants and green algae, the module is positioned C-terminally with respect to the catalytic glucan phosphatase domain <cite>Meekins2014 Vander-Kooi2010 Gentry2009</cite>. A special case is represented by mammalian AMPKs that possess the CBM48 within the β-subunits of its αβγ heterotrimer molecule <cite>Koay2010 Polekhina2005 Mobbs2015 Xiao2013 Calabrese2014 Li2015</cite>; the same applies for AMPK’s yeast homologue SNF1 <cite>Amodeo2007</cite>. A C-terminal position is also found for CBM48 in FLO6, a protein involved in starch biosynthesis <cite>Peng2014a</cite>. With regard to sequence/structure relationships and the way of carbohydrate binding, the modules from the family CBM48 are most closely related to those from the family [[CBM20]] <cite>Janecek2011</cite> and, in a wider sense, also to those from families [[CBM21]], [[CBM53]] <cite>Machovic2006a Christiansen2009</cite> and the recently established family [[CBM69]] <cite>Peng2014b</cite>.
 == Family Firsts ==
 ;First Identified
- The family CBM48 was first referred to as (CBM20+CBM21)-related groups based on the in silico analysis of various proteins and taxa [35] and then defined within the CAZy database as an independent CBM family [38,39]      .
+The family CBM48 was first referred to as (CBM20+CBM21)-related groups based on the in silico analysis of various proteins and taxa <cite>Machovic2006a</cite> and then defined within the CAZy database as an independent CBM family <cite>Machovic2008 Cantarel2009</cite>.
 ;First Structural Characterization
- Based on current knowledge [31,38,39], the first CBM48 structure without any carbohydrate bound was solved as the N-terminal domain of the isoamylase from Pseudomonas amyloderamosa [6]. The first CBM48 structure confirming its carbohydrate binding ability (a complex with β-cyclodextrin) was determined for the β1 subunit of the rat AMPK [4], but it is of note that at that time the family CBM48 was not established [40].      .
+Based on current knowledge <cite>Janecek2011 Machovic2008 Cantarel2009</cite>, the first CBM48 structure without any carbohydrate bound was solved as the N-terminal domain of the isoamylase from Pseudomonas amyloderamosa <cite>Katsuya1998</cite>. The first CBM48 structure confirming its carbohydrate binding ability (a complex with β-cyclodextrin) was determined for the β1 subunit of the rat AMPK <cite>Polekhina2005</cite>, but it is of note that at that time the family CBM48 was not established <cite>Machovic2006b</cite>.
 == References ==
 <biblio>
-x600
 #Chaen2012 pmid=22771800
 #Koay2010 pmid=20637197
 #Meekins2014 pmid=24799671
 #Polekhina2005 pmid=16216577
 #Mobbs2015 pmid=25774984
 #Katsuya1998 pmid=9719642
 #Feese2000 pmid=10926520
 #Abad2002 pmid=12196524
 #Timmis2005 pmid=15784255
 #Leiros2006 pmid=16421442
 #Mikami2006 pmid=16650854
 #Amodeo2007 pmid=17851534
 #Woo2008 pmid=18703518
 #Gourlay2009 pmid=19329633
 #Turkenburg2009 pmid=19382205
 #Pal2010 pmid=20444687
 #Song2010 pmid=20187119
+#Vander-Kooi2010 pmid=20679247
-#Vander Kooi2010 pmid=20679247
 #Vester-Christensen2010 pmid=20863834
 #Noguchi2011 pmid=21493662
 #Moeller2012 pmid=22949184
 #Okazaki2012 pmid=22334583
 #Park2013 pmid=22902546
 #Xiao2013 pmid=24352254
 #Calabrese2014 pmid=25066137
 #Sim2014 pmid=24993830
 #Xu2014 pmid=24375572
 #Li2015 pmid=25412657
 #Moeller2015a pmid=25792743
 #Moeller2015b pmid=25562209
 #Janecek2011 pmid=22112614
 #Palomo2009 pmid=19139240
 #Gentry2009 pmid=19818631
 #Peng2014a pmid=24456533
 #Machovic2006a pmid=17084392
 #Christiansen2009 pmid=19682075
 #Peng2014b pmid=24613924
 #Machovic2008 Machovic M, and Janecek S. “Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48.” Biologia 2008; 63: 1057-68. ([http://dx.doi.org/10.2478/s11756-008-0162-4 DOI: 10.2478/s11756-008-0162-4])
 #Cantarel2009 pmid=18838391
 #Machovic2006b pmid=17013558
 </biblio>
 [[Category:Carbohydrate Binding Module Families|CBM048]]