Carbohydrate Binding Module Family 6

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• Author: ^^^Mirjam Czjzek^^^
• Responsible Curator: ^^^Mirjam Czjzek^^^

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CAZy DB link

https://www.cazy.org/CBM6.html

Ligand specificities

The ligand specificity of the first characterized CBM6, originating from a multimodular xylanase from Clostridium thermocellum, was determined to be xylan [1], although the results showed that this CBM6 was also able to bind to avicel and acid-swollen cellulose. This was also the first CBM6 for which a 3D structure was determined [2], and multiple sequence alignments, analyzed in the light of the first 3D structure, already gave clear indications that large diversity in specificity was to be expected among CBM6 modules [2]. Remarkably, the characterization and 3D structure of a CBM6 from Cellvibrio mixtus revealed two distinct binding sites that displayed differential binding specificities [3, 4]. CBM6 modules are in general attached to bacterial or archeal polysaccharide degrading enzymes and can be found attached to xylanases, cellulases, agarases, laminarinases, etc [5]. Interestingly, modules assigned to the CBM6 family have also been found associated to fungal enzymes and to the α-subunit of the coagulation factor G in horseshoe crabs (see the eukarotic CBM6 occurence). In the latter case, the β-1,3-glucan binding of the C-terminal tandem CBM6s has been demonstrated [6]. Those CBM6s having characterized binding specificities cover : both linear and branched/decorated xylan, β-1,4-glucan (or cellulose), mixed-linked β-1,3-1,4-glucan (or lichenan), agarose, β-1,3-glucan (or laminarin) and chitin. Based on phylogenetic analyses of all reported CBM6 sequences in 2009 (a total of 167), four subfamilies have been defined that coincide with classes of substrate binding specificity as follows : subfamily 6a, hemicellulose; subfamily 6b, xylan; subfamily 6c, β-glucans with a variety of linkages; and subfamily 6d, agarose [7].

Structural Features

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• Fold: Likewise many other CBMs the CBM6 modules, roughly containing 120 amino acids, display the overall fold of a β-sandwich, predominantly consisting of five antiparallel β-strands on one face and four antiparallel β-strands on the other face, connected by loops with variable lengths. Within the hierarchal CATH classification the modules belong to the jelly-roll superfamily 2.60.120.260 called "galactose-binding domain-like" that contains 515 unique domains.
• Type: Due to the existance of the dual binding sites in CBM6s, both Type B and C binding properties have been observed for individual CBM6s.
• Features of ligand binding: The first identified ligand binding site was not, as usual, located at a shallow cleft on the concave surface of the β-sheets (binding site II, formerly called cleft B in CBM6). Alternatively, a binding site was found located at the apex, within the connecting loops of the two β-sheets (binding site I, formerly cleft A in CBM6) (PDB 1gmm). Interestingly, some CBM6s display binding affinities for both binding sites (PDB 1uyy), either with distinct specificities for each site (PDB 1uy0 and PDB 1uyz) or synergistic binding involving both sites at the same time [4], while binding properties of other CBM6s make use of only one binding site, which is in general site I at the apex (i.e. PDB 1uxx;PDB 1nae;PDB 1w9w). The apex site I is made up of two important, highly conserved aromatic residues (mostly W and Y) that "sandwich" a sugar monomer [2, 7]. These conserved residues are neighboured by a much more variable loop (defined as zone E in Abbott et al. [7]) that make up the diversity in binding specificity. Consistantly, a variable number of sugar-binding subites have been observed for site I, ranging from one (end binder) up to five binding subsites. The precise structural and energetic contributions of four of the binding subsites have been dissected, for the first time, in detail by combining crystallography and ITC in the case of the Clostridium stercorarium CsCBM6-1 [8]. To date, only one CBM6 has been structuraly and biochemically characterized that makes use of binding site II, which is the CBM6 from Cellvibrio mixtus [3, 4] (PDB 1uxz)

Functionalities

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• Functional role of CBM: The predominant functional role to date described for CBM6 modules is carbohydrate binding and targeting. It has been shown that this type of module synergistically enhances the activity of the adjacent catalytic domain on insoluble substrates.
• Most Common Associated Modules: 1. xylanases, lichenases, β-agarases, laminarinases, deacetylases; 2. dockerins and coagulation factors.
• Novel Applications: The CBM6 from Clostridium thermocellum has been used to label plant tissues [9].

Family Firsts

First Identified

The xylose binding CBM6 from a multi-modular xylanase/actetyl-esterase from Clostridium thermocellum (CtCBM6) was the first to be identified and biochemically characterized. To a lesser extent the module was also able to bind to avicel and acid-swollen cellulose [1].

First Structural Characterization

The same xylose binding CBM6 from Clostridium thermocellum (PDB 1gmm) was also the first structuraly characterized CBM6. The 3D structure revealed that the location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence was not conserved [2].

References

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