Recent structural studies of carbohydrate-binding modules

Abstract

Carbohydrate-binding modules (CBMs) are found in many carbohydrate-active enzymes. CBMs bind to a range of polysaccharides, their primary function being to increase the catalytic efficiency of the carbohydrate-active enzymes against soluble and/or insoluble substrates. CBMs bind to their target ligands with high specificities and affinities. Thus, CBM systems are excellent models to study the mechanism of protein-carbohydrate interaction. To date, CBMs have been classified into 45 different families and many structural and functional studies have been reported. At present, three-dimensional structures of CBMs from 31 different families have been determined. These structures demonstrate that the fold most commonly found in CBMs is the beta-sandwich. In the past few years, about 10 new structures from different families have been reported. These enable detailed classification of CBM structures. This article reviews recent structural and functional studies of CBMs and discusses the sub-classification of beta-sandwich CBMs.

Domain evolution in the GH13 pullulanase subfamily with focus on the carbohydrate-binding module family 48

“…2). It is well known that a CBM in general can be characterized by a typical secondary structure composed of β-strands forming the core of the motif (Boraston et al 2004;Hashimoto 2006). This applies for the CBM20 (Penninga et al 1996;Sorimachi et al 1997) and CBM21 ) as well as for the known structures of CBM48 modules (Fig.…”

“…Thus the SBDs and/or GBDs can be found in the families CBM20, CBM21, CBM25, CBM26, CBM34, CBM41, CBM45 and recently also in CBM48 (Machovic & Janecek 2006a). Except for the family CBM45 (Mikkelsen et al 2006), three-dimensional structures are known for at least one representative from each of the seven families (Coutinho & Henrissat 1999a); interestingly these SBDs all adopt a β-sandwich motif with an immunoglobulin fold (Boraston et al 2004;Rodriguez-Sanoja et al 2005;Hashimoto 2006;Machovic & Janecek 2006a). From the evolutionary point of view, based on a detailed bioinformatics study the families CBM20 and CBM21 have already been proposed to be classified into a CBM clan (Machovic et al 2005).…”

Substrate binding by a bacterial ABC transporter involved in polysaccharide export

“…CBMs are currently divided into 49 families based on sequence similarity (www.cazy.org). Available structures indicate that a ␤-sandwich fold is the most common fold seen in CMBs and at least seven CBM families (CBM 9,20,25,26,31,33,and 34) have an Ig-like topology (13). Specific recognition of the terminal sugars of polysaccharides has been demonstrated in CBMs, resembling the situation in C-Wzt O9a .…”

Recombinant Laforin for Structural Studies

“…Laforin is the only human DSP known to have a carbohydrate binding module (CBM) responsible for targeting the phosphatase towards glycogen (Wang et al, 2002). CBMs are typically found in glucosyl hydrolases and glucotransferases in bacterial, fungal or plant genomes (Boraston et al, 2000;Boraston et al, 2004;Gentry & Pace, 2009;Hashimoto, 2006;Shoseyov et al, 2006). The vast majority of enzymes containing CBMs utilize the domain to bind a specific glucan and enzymatically act on the sugar, as in the case of -amylase (Boraston et al, 2004).…”

“…While laforin and SEX4 bind similar types of glucans, they utilize distinct CBMs (Boraston et al, 2004). CBMs are classified into 62 evolutionarily distinct families, based on their primary sequence, secondary and tertiary structure predictions, and crystal structures (Boraston et al, 2004;Hashimoto, 2006;Shoseyov et al, 2006). In 2004, laforin was included in the CBM20 family, formerly known as the starch-binding domain of family 4 -SBD4 (CAZy database -http://www.cazy.org/Carbohydrate-BindingModules.html) (Coutinho & Henrissat, 1999).…”