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Difference between revisions of "Carbohydrate Binding Module Family 48"
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== Functionalities ==
== Functionalities ==
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>
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>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 ==
== Family Firsts ==
Revision as of 05:29, 7 July 2015
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Authors: ^^^Stefan Janecek^^^ and ^^^Birte Svensson^^^
- Responsible Curators: ^^^Stefan Janecek^^^ and ^^^Birte Svensson^^^
|CAZy DB link|
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 , maltooligosaccharides , maltoheptaose , β-cyclodextrin , single α-1,6-branched glucosyl, maltosyl and maltoteatraosyl maltoheptaose  and single α-1,6-branched glucosyl β-cyclodextrin .
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 . The structure is a typical β-sandwich with one well-defined binding site . As seen in the β1 subunit of the rat AMP-activated protein kinase (AMPK) , 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  and starch excess4 (SEX4) protein  both from plants. Notably, in complexes of the rice starch branching enzyme  and the SEX4 protein  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 , but of these only the CBM48 from rice starch branching enzyme has been solved in complex with carbohydrate ligands .
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 . 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 . A C-terminal position is also found for CBM48 in FLO6, a protein involved in starch biosynthesis . 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  and, in a wider sense, also to those from families CBM21, CBM53 [35, 36] and the recently established family CBM69 .
- 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  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 . The first CBM48 structure confirming its carbohydrate binding ability (a complex with β-cyclodextrin) was determined for the β1 subunit of the rat AMPK , but it is of note that at that time the family CBM48 was not established .
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