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Difference between revisions of "Carbohydrate-binding modules"
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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: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed<cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>. | ||
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− | == | + | == 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 over 65 families based on amino acid sequence similarities. | ||
+ | |||
+ | === 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 | ||
Revision as of 08:10, 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 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 over 65 families based on amino acid sequence similarities.
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
-
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 |