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]. CBM6 modules are in general attached to bacterial or archeal polysaccharide degrading enzymes and can be found attached to xylanases, cellulases, agarases, laminarinases, etc [3]. 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 eukarotic CBM6 occurence. In the latter case, the β-1,3-glucan binding of the C-terminal tandem CBM6s has been demonstrated [4]. Those CBM6s having characterized binding activities 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. Remarkably, the characterization and 3D structure of a CBM6 from Cellvibrio mixtus revealed two distinct binding sites that displayed differential binding specificities [5, 6].

Note: Here is an example of how to insert references in the text, together with the "biblio" section below: Please see these references for an essential introduction to the CAZy classification system: [7, 8]. CBMs, in particular, have been extensively reviewed [9, 10, 11, 12].

Structural Features

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

• Fold: Likewise many other CBMs, the overall fold corresponds to a β-sandwich, but the first identified ligand binding site was not, as usual, located at a shallow cleft on the concave surface of the β-sheets (cleft B in CBM6). Alternatively, a binding site was found located within the connecting loops of the two β-sheets (cleft A in CBM6). Interestingly, some CBM6s display binding affinities for both binding sites,
• Type: Include here Type A, B, or C and properties
• Features of ligand binding: 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. 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 |
4. 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 |
5. 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 |
6. 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 |