Carbohydrate-binding modules

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• Author: Alicia Lammerts van Bueren and Elizabeth Ficko-Blean
• Responsible Curator: Al Boraston and Spencer Williams

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Overview

Figure 1. An example of modularity in a CBM-containing glycoside hydrolase. Sialidase from Micromonospora viridifaciens contains an N-terminal CBM32 (red) X20 linker (yellow) and a C-terminal catalytic GH33 module (green) [1]. Graphical representation of modularity in amino acid sequence (top) and 3D crystal structure (bottom) PDB ID 1eut.

Carbohydrate-binding modules (CBMs) [2, 3, 4, 5, 6, 7] are a class of sugar-binding proteins that comprise amino acid sequences within a larger encoded protein sequence that fold into a structurally discrete module, typically forming part of a larger multi-modular enzyme [8] (Figure 1). The conventional role of a CBM is to bind to carbohydrate ligand and direct the catalytic machinery onto its substrate, thus enhancing the catalytic efficiency of the multimodular carbohydrate-active enzyme; however, there are several key exceptions of divergent evolution in the functions of CBMs [9] which are discussed below. The individual CBMs are themselves devoid of any catalytic activity and are most commonly associated with Glycoside Hydrolases but have also been identified in Polysaccharide Lyases, polysaccharide oxidases, Glycosyltransferases, plant cell wall-binding expansins [10] and in some lectins [9].

CBMs themselves do not undergo any conformational changes when binding ligand. Rather, the topography of the carbohydrate-binding site is preformed to be complementary to the shape of the target ligand (see Types). This is achieved by the presence of amino acid side chains present on the CBM binding surface or within the CBM binding cleft or pocket. Multimodular enzymes that include CBMs may as a whole be quite flexible and undergo significant conformational changes when binding substrate. Flexible Ser-Thr-Pro sequences often link adjacent modules and can allow for shifts in the orientation and direction of the catalytic module with respect to the CBM on the target substrate. In other enzymes the linking regions may be quite rigid, such as the 5-helical bundle linker module linking a CBM32 to a GH84 module [11].

History of CBMs

CBMs were initially characterized as cellulose binding domains (CBDs) in cellobiohydrolases CBHI and CBHII from Trichoderma reesei [12, 13] and cellulases CenA and CexA from Cellulomonas fimi [14]. Limited proteolysis experiments on these enzymes yielded truncated enzyme products that showed a reduced or complete loss in their ability to hydrolyze cellulose substrates. The reduction in enzymatic activity was attributed to the loss of ~100 amino acid C-terminal domains which prevented the adsorbption of the enzymes onto cellulose substrate. Thus it was proposed that these independent "domains" are critical for targeting the enzymes onto its substrate and enhancing their hydrolytic activity. It rapidly became evident that CBDs were not only appended to cellulases but were also found in a range of other plant cell wall degrading enzymes [15, 16, 17].

Initially, CBDs were categorized into 13 Types based on amino acid sequence similarities [18]. This classification system became complicated when similar functional domains from non-cellulolytic carbohydrate-active enzymes were discovered that did not bind cellulose but met all of the criteria of a CBD (for example see [19]). The term carbohydrate-binding module was proposed to solve this problem to be inclusive of all ancillary modules with non-catalytic carbohydrate-binding function (for a review see [2]). Since this time, CBMs have been found appended to enzymes that interact with almost all characterized carbohydrate materials found on Earth (Table 1).

Table 1: List of Carbohydrates and Interacting CBM Familiesa
Cellulose	CBM1, CBM2, CBM3, CBM4, CBM6, CBM8, CBM9, CBM10, CBM16, CBM17, CBM28, CBM30, CBM37, CBM44, CBM46, CBM49, CBM59, CBM63, CBM64
Xylan	CBM2, CBM4, CBM6, CBM9, CBM13, CBM15, CBM22, CBM31, CBM35, CBM36, CBM37, CBM44, CBM54, CBM59, CBM60
Plant Cell Wall - Other (eg: beta-glucans, pectins, mannans, gluco- and galacturonans)	CBM4, CBM6, CBM11, CBM13, CBM16, CBM22, CBM23, CBM27, CBM28, CBM29, CBM32, CBM35, CBM39, CBM42, CBM43, CBM52, CBM56, CBM59, CBM61, CBM62, CBM65, CBM67
Chitin	CBM1, CBM2, CBM3, CBM5, CBM12, CBM14, CBM18, CBM19, CBM37, CBM50, CBM54, CBM55
Alpha-glucans (starch/glycogen, mutan)	CBM20, CBM21, CBM24, CBM25, CBM26, CBM34, CBM41, CBM45, CBM48, CBM53, CBM58
Mammalian Glycans	CBM32, CBM40, CBM47, CBM51, CBM57b
Algal (seaweed) Saccharides (e.g. porphyran, agarose, carrageenan, alginate, laminarin)	CBM6, CBM16
Other	Bacterial cell wall sugars: CBM35, CBM39, CBM50 Fructans: CBM38, CBM66 Yeast cell wall glucans: CBM54
aBased on the Carbohydrate Active enZyme database. CBM7 is a deleted entry and CBM33 is now reclassified as Auxiliary Activities family AA10. bonly human lectin malectin has been characterized, however a search based on amino acid sequence similarities found that similar modules are appended to many uncharacterized glycoside hydrolases [20].

Classification

Sequence Based Classification

Carbohydrate-binding modules are classified into many tens of families based on amino acid sequence similarities (a continually updated list is available in the Carbohydrate Active enZyme database). These families often cluster modules with similar structural folds and carbohydrate-binding function. However, there are several families that exhibit diversity in the carbohydrate ligands they target (Table 1).

Fold

Figure 2. Classical CBM beta-sandwich fold. C-terminal family CBM27 from Thermotoga maritima mannanase, a Type B CBM (A)(side and front view, PDB ID 1OF4) [21] and C-terminal family CBM6 from Clostridium stercorarium xylanase (B) (PDB ID 1NAE) [22] showing binding sites on the face (A) and loop region (B) of the beta sandwich fold respectively.

CBMs fall into one of 7 fold families [2]. The most common fold exhibited by CBMs is the beta-sandwich fold comprised of two overlapping beta-sheets each consisting of three to six antiparallel beta strands (Figure 2). The ligand binding site may be located on one face of the beta-sheet (Figure 2A) or may be positioned within the variable loop region of the beta-sheet (Figure 2B). There are examples of CBMs in the beta-sandwich fold family exhibiting dual binding sites such as CBM6 [23] and dual starch-binding sites in CBM20 [24]. Other fold families include the beta-trefoil fold, cystine knot, OB fold, the hevein and hevein-like and unique folds [2]. CBMs of the beta-trefoil fold family (CBM13, CBM42) present multivalent sugar-binding sites, as demonstrated for their interaction with xylan and arabinoxylan respectively [25].

Types

Figure 3. CBM Types. (A) Schematic of different CBM Types binding with different regions of a polysaccharide substrate. (B) Type A CBM2b from Pyrococcus furiosis GH18 chitinase(PDB ID 2CRW) [26]. Aromatic side chains of Type A CBMs form the planar binding surface.

CBMs are classified into three main Types defined by the shape and degree of polymerization of their target ligand (Figure 3A). The architecture of the binding site determines what region within a saccharide macromolecule the enzyme will target. The classification of CBM Types is as follows [2, 6, 7]:

• Type A: bind to crystalline surfaces of the polysaccharides cellulose and chitin (example families CBM1, CBM2, CBM3, CBM5, CBM10). Their binding sites are planar and rich in aromatic amino acid residues creating a flat platform to bind to the planar polycrystalline chitin/cellulose surface (Figure 3B). Type A CBMs are unique and differ significantly from Type B or C.
• Type B: bind internal glycan chains (endo-type). Type B are the most abundant form of CBMs reported to date. Type B binding sites appear as extended grooves or clefts comprised of binding subsites to generally accommodate longer sugar chains with four or more monosaccharide units (see Figure 2A for an example). There are some examples of CBMs, in families CBM6, CBM13, CBM20, CBM36 and CBM60, that contain two subsites.
• Type C: bind termini of glycans (reducing/non-reducing ends, exo-type). Type C binding sites are short pockets for recognizing short sugar ligands containing one to three monosaccharide units (example families CBM9, CBM13, CBM32, CBM47, CBM66, CBM67). Families containing Type C CBMs are considered 'lectin-like' and may include lectins and CBMs with no appended catalytic modules as members.

Properties of CBM Carbohydrate Binding Interactions

Functional Roles of CBMs

CBMs carry out four main functional roles:

• Targeting Effect: CBMs target the enzyme to distinct regions on a saccharide substrate (reducing end, non-reducing end, internal polysaccharide chains), depending on the architecture of its binding site (see Types).

• Proximity Effect: CBMs increase the concentration of enzyme in close proximity to its saccharide substrate. This leads to more rapid and efficient substrate degradation.

An excellent example demonstrating targeting and proximity effects of plant cell wall specific CBMs is available [27].

• Disruptive Effect: Some CBMs have been shown to disrupt the surface of tightly packed polysaccharides, such as cellulose fibres and starch granules, causing the substrate to loosen and become more exposed to the catalytic module for more efficient degradation. Disruptive roles have been described for cellulose binding CBM2a [28] and CBM44 [29]. Dual starch-binding domains of family CBM20 from Aspergillus niger glucoamylase have been shown to disrupt the surface of starch [30] while dual-associated CBM41 modules may have a disruptive role in degrading glycogen granules [31]. CBM33 was thought to have a disruptive effect on chitin, however these have now been reclassified as copper-dependent lytic polysaccharide monooxygenases [32] and are found in CAZy Auxiliary Activity Family 10.

• Adhesion: CBMs have been shown to adhere enzymes onto the surface of bacterial cell wall components while exhibiting catalytic activity on an external neighboring carbohydrate substrate. For example, CBM35 modules have been shown to interact with the surface glucuronic acid containing sugars in the cell wall of Amycolatopsis orientalis while the catalytic module is active on external chitosan likely originating from the cell wall of competing soil fungal species [33]. Streptococcus pneumoniae uses a CBM71 as an adhesin, to mediate adherence to host cell surfaces displaying lactose or N-acetyllactosamine [34].

There are examples in the literature of CBMs extending the active site sub-sites of their appended glycosidase modules. The glycogen-degrading pneumococcal virulence factor SpuA has its active site extended by one of two tandem CBM41s [35]. The glucan starch phosphatase Starch Excess4 has its active site extended by a CBM48 [36].

Several lectins are classified as CBMs even though they are not on the same polypeptide chain as a carbohydrate-active enzyme. See Blurred Lines: CBMs, Lectins and Outliers for a more complete discussion.

Driving Forces of CBM-Carbohydrate Interactions

There are two key features that drive CBM-carbohydrate interactions. Extensive hydrogen bonding occurs between the hydroxyl groups of carbohydrate ligands and polar amino acid residues within the binding site. Additional water-mediated hydrogen bonding networks between these groups can also be found in the binding site. By far the most important characteristic driving force mediating protein-carbohydrate interactions is the position and orientation of aromatic amino acid residues (Try, Tyr and sometimes Phe) within the binding site. These essential planar residues provide a hydrophobic platform for the planar face of sugar rings, an interaction resembling hydrophobic stacking interactions. Weak intermolecular electrostatic interactions occur between C-H and pi electrons in the planar ring systems and contribute 1.5 - 2.5 kcal/mol energy to the binding reaction [37]. CBMs may also use coordinated metal ions within the binding site to directly interact with their target ligand. For example, families CBM36 [38] and CBM60 [39] exhibit calcium-dependent binding to xylooligosaccharides.

CBM-carbohydrate interactions in general are quite weak (K_a affinities in mM^-1 to uM^-1 range) making the interaction easily reversible. This feature allows for "recycling" of the appended enzyme to bind to a new region on the substrate once catalysis has been completed at a given site. Some CBMs that bind crystalline ligands, typified by CBM2a, bind with apparent irreversibility (they do not desorb when free CBM is diluted), displaying surface mobility and exchanging with free CBM [40, 41]. Multivalent effects (more than one saccharide-binding site or multiple CBMs within the polypeptide) may act to increase the overall affinity relative to a single binding site interaction.

CBM Promiscuity

Because of the diversity of carbohydrate structures and motifs found in plant and mammalian glycans, some CBMs have evolved to recognize more than one type of monosaccharide or glycosidic bond linkage within the binding pocket, a feature called CBM promiscuity. For example a family CBM32 from Clostridium perfringens NagH binds N-acetyl-glucosamine in the primary subsite but can accommodate N-acetyl-galactosamine or mannose in the secondary site [42]. There are several examples of ligand promiscuity within family CBM32. In plant cell wall recognizing CBMs, they are often able to accommodate both cellulose and hemicelluloses. For example, several family CBM6 members interact with cellulose, xylose or laminarin [22, 43]. Family CBM41 appended to a GH13 pullulanase can accommodate both alpha-1,4- and alpha-1,6-linked glucose found in amylopectin (from starch/glycogen) [44]. The flexibility in carbohydrate recognition by CBMs contributes to the targeting efficiency of carbohydrate-active enzymes in environments where there is diverse range of saccharides present (such as the plant cell wall or mammalian tissues).

CBMs and Multivalency

Multivalency is the collective strength of several interactions with a given ligand. Because CBM-carbohydrate interactions are relatively weak, some carbohydrate-active enzymes, mainly glycoside hydrolases, have developed ways to increase their interaction with substrate via a multivalent effect. Individually, some CBMs may contain multiple binding sites to form a multivalent interaction with their target ligand, although this form of multivalency is quite rare (for example CBM6, CBM13 and CBM20). More commonly, glycoside hydrolases may contain more than one CBM within their modular architecture, either arranged in tandem or at opposing N and C terminal ends of the protein sequence, or both. These CBMs may target the same carbohydrate ligand, different regions within the same ligand, or different ligands in a complex saccharide amalgam. A multivalent interaction enhances the overall affinity of an enzyme for its substrate. Furthermore, tandem CBMs may cooperatively target the enzyme towards specific saccharide regions based on their ligand specificity and the orientation and position of the binding sites with respect to one another.

Blurred Lines: CBMs, Lectins and Outliers

While CBMs are generally considered to be discrete entities within a polypeptide chain, there are some exceptions. The glycogen-degrading pneumococcal virulence factor SpuA has its active site extended by one of two tandem CBM41s [35] and the glucan starch phosphatase Starch Excess4 has its active site extended by a CBM48 [36]. Thus, the full biological contribution to carbohydrate-binding within the polypeptide is contributed by a multivalent interaction as an extension of the catalytic module's carbohydrate-binding properties. The PA14 domain is found in bacterial toxins, enzymes, adhesins and signaling molecules [45]. It has been described as appended to the polypeptide sequence of some glycoside hydrolase enzymes (for example some GH31s) and the crystal structure of a GH31 reveals the PA14 domain is closely associated with the catalytic module, on the side of the substrate-binding cleft, potentially facilitating the binding of longer oligosaccharides [46]. It has also been described as a domain integrated into the core of some GH3 glycoside hydrolase modules. In one example, the GH3 integrated PA14 domain demonstrates carbohydrate-binding function and acts to block the active site cleft, thus conferring substrate specificity for disaccharide substrates [47]. Similarly, in a GH2 mannosidase, the PA14 domain determines exo- rather than endo-activity for the catalytic module [48]. Evidently, more research needs to go into the structure and function of these domains as they are found in a wide variety of polypeptide sequences and the functions of the PA14 domains may be diverse. They have not yet been classified into the CAZy classification system, though they are mentioned here as the domains have been referred to as CBMs in the literature [9].

Unrelated sugar-binding proteins have converged on similar biochemical mechanisms of saccharide recognition [9]. The direct interaction of Ca²⁺ ions with saccharides in sugar binding sites was first described in C-type animal lectins [49], named thusly because of their sugar-binding requirement for Ca²⁺. Other sugar-binding proteins that also require Ca²⁺ for binding, include yeast flocculation proteins [50] and other yeast adhesins [51, 52], and two CBM families, CBM36 and CBM60 [39].

Several lectins [53, 54] are classified as CBMs in the Carbohydrate Active enZyme database as they share amino acid sequence similarity, exhibit similar folds and display similar carbohydrate binding properties. For example, ricin toxin B chain from Ricinus communis resides in family CBM13, while wheat germ agglutinin (WGA) can be found in family CBM18. The human lectin malectin is classified as family CBM57 and plays a role in N-linked glycan processing of polypeptides in the endoplasmic reticulum [20, 55]. CBMs may also share properties with lectins that are not (yet) incorporated in the Carbohydrate Active enZyme database. For example, the fucose-specific Anquila anguila lectin AAA was described as similar to Type C CBMs found in family CBM6 and CBM32 [22] and is now classified as a CBM47 [56]. Lectins which are classified as CBMs are incorporated into a family because they were found to share amino acid sequence identity with a known CBM appended to a carbohydrate-active enzyme. A brief historical overview of the discovery and characterization of lectins is available [53] as is a review describing the convergent and divergent mechanisms of sugar recognition across the kingdoms of life [9].

The biological reaction of agglutination is when particles that are suspended in a liquid collect into clumps, such as that occuring as a serologic response to a specific antibody. The most prominent feature that is genarally considered to separate CBMs from lectins is the involvement of lectins in agglutination of sugar-containing molecules or glycoconjugates. Lectins exploit multivalency, often forming quaternary structures as homodimers, trimers or tetramers with several binding sites which then agglutinate the target glycocongugate [53, 54]. Few studies have been done on the agglutinating effects of CBMs or CBM tandems; however, a CBM26/CBM25 pair from Bacillus halodurans is described as strongly agglutinating on soluble amylopectin (and pullulan), suggesting multivalent binding of the individual CBMs to sites on separate glucan chains [56]. CBMs individually are not known to be directly involved in the formation of quaternary structures and are not known to have agglutinating properties - in common with sugar-recognition modules of all glycan-binding proteins, including lectins [9]. Other examples of CBMs participating in quaternary structures but not directly implicated in quaternary structure formation are found in cellulosome complexes [57, 58, 59] and in some secreted pathogenic bacterial enzymes complexes [11, 60] where complex formation is mediated through specific cohesin-dockerin module interactions.

Amino acid sequence-based classification of a CBM family may lead to the incorporation of other non-catalytic-associated CBMs within a given family. Some examples of families containing CBMs without appended catalytic modules include those with lectins (such as tachycitin (CBM14), wheat germ agglutinin (CBM18), fucolectin (CBM47), and malectin (CBM57)), and those with periplasmic solute binding proteins (CBM32). Interestingly, the lectin ricin B chain (CBM13), while not on the same polypeptide chain, is covalently linked through a disulfide bond to the ricin A chain with its N-glycosidase activity [61]. The ricin A chain N-glycosidase cleaves a specific adenine from the pentose ribose in ribosomal RNA [62]. Finally, CBM29 is a family with only two members, which have no appended catalytic modules; however, the function of these CBMs is to target the catalytic cellulosome machinery to substrate [57].

Studying CBM-ligand Interactions

A review on approaches to studying the binding function of carbohydrate-binding modules is available [63]. Typically, molecular biology techniques are used to overproduce a CBM protein in a host strain such as Escherichia coli which is then isolated and purified. Initial screening for carbohydrate binding interactions can be performed using techniques such as microarrays [31] or fluorescence microscopy [27, 31, 64]. Several approaches can be taken to verify and quantify CBM-polysaccharide interaction, including affinity gel electrophoresis, UV difference and fluorescence spectroscopy, solid state depletion assay, and isothermal titration calorimetry [65]. Demonstration of carbohydrate binding function by CBMs is essential to understanding the biological role of these non-catalytic modules.

Biotechnological applications of CBMs

CBMs and their carbohydrate-binding properties are used for many different biological applications. Below is a non-exhaustive list of several examples:

• Features of CBMs are currently being exploited to create designer CAZymes with enhanced or modified carbohydrate recognition functions [66, 67, 68, 69].

• Family CBM9 can be used as an affinity tag to purify tagged proteins on a cellulose-based affinity column [70].

• CBMs are used as molecular probes to detect presence of specific carbohydrate motifs in plant [27, 64] and mammalian tissues [44, 56].

• CBMs are used in fibre modification. Engineered CBMs have been shown to increase the strength of cellulose pulp in paper-making processes [71, 72], in crosslinking polysaccharide fibres for biomaterials [73] and cotton fibre modification [74].

• There are several examples of CBMs being used to immobilize whole cells onto carbohydrate surfaces [75, 76, 77].

• CBMs are used to enhance bioprocessing enzymes for industrial uses in pulp processing and biofuel production [29, 78, 79].

• Starch binding CBMs added onto transglucosylating enzyme CGTase from GH13 created a fusion enzyme with more efficient transglucosylating activity with soluble starch, important for industrial biotransformation processes [80].

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