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Difference between revisions of "Carbohydrate-binding modules"
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== Overview == | == Overview == | ||
| − | Carbohydrate-binding modules (CBMs) are defined as a stretch of amino acid sequence which folds into | + | Carbohydrate-binding modules (CBMs) are defined as a stretch of amino acid sequence which folds into a discreet and 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. |
| Line 18: | Line 18: | ||
== Classification == | == Classification == | ||
=== Sequence-based classification === | === Sequence-based classification === | ||
| − | Carbohydrate-binding modules | + | 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 === | === Types === | ||
| + | CBMs are classified into three "Types" depending on the shape and degree of polymerization of the interacting carbohydrate ligand: | ||
A: polycrystalline surface binding | A: polycrystalline surface binding | ||
| Line 36: | Line 37: | ||
2. Demonstrate binding to carbohydrate ligand. | 2. Demonstrate binding to carbohydrate ligand. | ||
| − | 3. Additional family members are then determined based on amino acid sequence similarity | + | 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 demonstrate 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), 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== | ==Mechanism== | ||
Revision as of 13:18, 19 May 2013
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: ^^^Alicia Lammerts van Bueren^^^
- Responsible Curator: ^^^Al Boraston^^^ and ^^^Spencer Williams^^^
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 a discreet and 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 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 demonstrate 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), 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
-
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
- 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 |
- 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 |
- 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 |
- 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 |
- 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 |