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

Content in this section should include, in paragraph form, a description of:

• Fold: Likewise many other CBMs, the 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 the "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 , either with distinct specificities for each site or synergistic involving both at the same time, while binding properties of other CBM6s make only us of one binding site, which is in general site I, at the apex. 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 (non-reducing end binder) up to five binding subsites. and Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

Functionalities

Content in this section should include, in paragraph form, a description of:

• Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
• Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
• Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

Family Firsts

First Identified

Insert archetype here, possibly including very brief synopsis.

First Structural Characterization

Insert archetype here, possibly including very brief synopsis.

References

1. Fernandes AC, Fontes CM, Gilbert HJ, Hazlewood GP, Fernandes TH, and Ferreira LM. (1999). Homologous xylanases from Clostridium thermocellum: evidence for bi-functional activity, synergism between xylanase catalytic modules and the presence of xylan-binding domains in enzyme complexes. Biochem J. 1999;342 ( Pt 1)(Pt 1):105-10. | Google Books | Open Library
2. Czjzek M, Bolam DN, Mosbah A, Allouch J, Fontes CM, Ferreira LM, Bornet O, Zamboni V, Darbon H, Smith NL, Black GW, Henrissat B, and Gilbert HJ. (2001). The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved. J Biol Chem. 2001;276(51):48580-7. DOI:10.1074/jbc.M109142200 |
3. Henshaw JL, Bolam DN, Pires VM, Czjzek M, Henrissat B, Ferreira LM, Fontes CM, and Gilbert HJ. (2004). The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities. J Biol Chem. 2004;279(20):21552-9. DOI:10.1074/jbc.M401620200 |
4. Pires VM, Henshaw JL, Prates JA, Bolam DN, Ferreira LM, Fontes CM, Henrissat B, Planas A, Gilbert HJ, and Czjzek M. (2004). The crystal structure of the family 6 carbohydrate binding module from Cellvibrio mixtus endoglucanase 5a in complex with oligosaccharides reveals two distinct binding sites with different ligand specificities. J Biol Chem. 2004;279(20):21560-8. DOI:10.1074/jbc.M401599200 |
5. Michel G, Barbeyron T, Kloareg B, and Czjzek M. (2009). The family 6 carbohydrate-binding modules have coevolved with their appended catalytic modules toward similar substrate specificity. Glycobiology. 2009;19(6):615-23. DOI:10.1093/glycob/cwp028 |
6. Takaki Y, Seki N, Kawabata Si S, Iwanaga S, and Muta T. (2002). Duplicated binding sites for (1-->3)-beta-D-glucan in the horseshoe crab coagulation factor G: implications for a molecular basis of the pattern recognition in innate immunity. J Biol Chem. 2002;277(16):14281-7. DOI:10.1074/jbc.M200177200 |
7. Abbott DW, Ficko-Blean E, van Bueren AL, Rogowski A, Cartmell A, Coutinho PM, Henrissat B, Gilbert HJ, and Boraston AB. (2009). Analysis of the structural and functional diversity of plant cell wall specific family 6 carbohydrate binding modules. Biochemistry. 2009;48(43):10395-404. DOI:10.1021/bi9013424 |