Carbohydrate-binding modules

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• Author: ^^^Alicia Lammerts van Bueren^^^
• Responsible Curator: ^^^Al Boraston^^^ and ^^^Spencer Williams^^^

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This page is under construction. In the meantime, please see these references for an essential introduction to the CAZy classification system: [1, 2]. CBMs, in particular, have been extensively reviewed[3, 4, 5, 6].

Overview

Carbohydrate-binding modules (CBMs) are defined as a stretch of amino acid sequence which folds into an independent module within a larger multi-modular protein. Most commonly associated with glycoside hydrolases (but also polysaccharide lyases, polysaccharide oxidases, glycosyltransferases and expansins), their role 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. CBMs are themselves devoid of any catalytic activity.

Insert here a classical example demonstrating "modularity" of a CAZyme with CBMs

Classification

Sequence-based classification

Carbohydrate-binding modules have been classified into 67 families based on amino acid sequence similarities, which is available through the Carbohydrate Active enZyme database. Sequence-based relationships often cluster together modules with similar structural folds and carbohydrate-binding function. While this is true for most CBM families, there are several families that exhibit diversity in the carbohydrate ligands they target (examples include CBM6, CBM32, several others.)

Types

A: polycrystalline surface binding

B: oligosaccharides with DP>4 (mainly endo, within polysaccharide chains)

C: lectin-like mono/di/tri saccharides (mainly exo, reducing/non-reducing end)

Defining a new CBM family

In order to define a new CBM family, one must:

1. Demonstrate an independent module as part of a larger carbohydrate-active enzyme.

2. Demonstrate binding to carbohydrate ligand.

3. Additional family members are then determined based on amino acid sequence similarity and must be part of a larger amino acid sequence encoding a putative enzyme (CAZyme or otherwise, as long as the CBM is presumed to participate in enhancing the catalytic efficiency of the enzyme by binding with or in close proximity of the substrate).

Mechanism

Carbohydrate Binding Properties

Here describe CH-pi interactions, hydrogen bonding, VDW interactions

Roles of CBMs include:

Targeting

Proximity

Cell Wall anchoring

Disruptive* CBM33 was thought to have a disruptive effect on chitin, however these have now been reclassified as lytic oxygenases (expand) leaving the disruptive properties of CBMs questionable.

Structural Properties of CBMs

Fold

References

1. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). DOI: 10.1042/BJ20080382

2. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |
3. Boraston AB, Bolam DN, Gilbert HJ, and Davies GJ. (2004). Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J. 2004;382(Pt 3):769-81. DOI:10.1042/BJ20040892 |
4. Hashimoto H (2006). Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci. 2006;63(24):2954-67. DOI:10.1007/s00018-006-6195-3 |
5. Shoseyov O, Shani Z, and Levy I. (2006). Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev. 2006;70(2):283-95. DOI:10.1128/MMBR.00028-05 |
6. Guillén D, Sánchez S, and Rodríguez-Sanoja R. (2010). Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 2010;85(5):1241-9. DOI:10.1007/s00253-009-2331-y |