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 within a larger encoded protein sequence and folds into a discreet and independent module, forming part of 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

History of CBMs

CBMs were initially characterized as cellulose binding domains in cellobiohydrolases CBHI and CBHII from Trichoderma reesei [7, 8] and cellulases CenA and CexA from Cellulomonas fimi [9]. Limited proteolysis experiments of 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 "cellulose binding domains" are critical for targeting the enzymes onto its substrate and enhancing their hydrolytic activity.

Classification

Sequence-based classification

Carbohydrate-binding modules are currently classified into 67 families based on amino acid sequence similarities (May 2013), which are 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, others...)

Types

CBMs are classified into three "Types" depending on the shape and degree of polymerization of the interacting carbohydrate ligand:

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. To be defined as a true CBM, it must form part of a larger amino acid sequence encoding a putative CAZyme (or enzyme with demonstrated activity on a carbohydrate-containing substrate and the CBM enhances the catalytic efficiency of the enzyme by binding with or in close proximity of the substrate).

Amino acid sequence-based classification of a CBM family may lead to the incorporation of other carbohydrate binding proteins within a given family, including lectins (such as ricin (CBM13), tachycitin (CBM14), wheat germ agglutinin (CBM18), fucolectin (CBM47), and malectin (CBM57)) and periplasmic solute binding proteins (such as CBM32). However to meet the true definition of a CBM, all of the above three mentioned criteria must be met.

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 |

7. Van Tilbeurgh, H., Tomme P., Claeyssens M., Bhikhabhai R., Pettersson G.(1986) Limited proteolysis of the cellobiohydrolase I from Trichoderma reesei. FEBS Lett. 204,223–227. [1]

8. Tomme P, Van Tilbeurgh H, Pettersson G, Van Damme J, Vandekerckhove J, Knowles J, Teeri T, and Claeyssens M. (1988). Studies of the cellulolytic system of Trichoderma reesei QM 9414. Analysis of domain function in two cellobiohydrolases by limited proteolysis. Eur J Biochem. 1988;170(3):575-81. DOI:10.1111/j.1432-1033.1988.tb13736.x |
9. Gilkes NR, Warren RA, Miller RC Jr, and Kilburn DG. (1988). Precise excision of the cellulose binding domains from two Cellulomonas fimi cellulases by a homologous protease and the effect on catalysis. J Biol Chem. 1988;263(21):10401-7. | Google Books | Open Library