CAZypedia needs your help!
We have many unassigned pages in need of Authors and Responsible Curators. See a page that's out-of-date and just needs a touch-up? - You are also welcome to become a CAZypedian. Here's how.
Scientists at all career stages, including students, are welcome to contribute.
Learn more about CAZypedia's misson here and in this article.
Totally new to the CAZy classification? Read this first.

Difference between revisions of "Carbohydrate-binding modules"

From CAZypedia
Jump to navigation Jump to search
Line 9: Line 9:
  
 
== Overview ==
 
== 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.
+
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 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.)
+
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 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).
+
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

Under construction icon-blue-48px.png

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.


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

  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

    [DaviesSinnott2008]
  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 | PubMed ID:18838391 [Cantarel2009]
  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 | PubMed ID:15214846 [Boraston2004]
  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 | PubMed ID:17131061 [Hashimoto2006]
  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 | PubMed ID:16760304 [Shoseyov2006]
  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 | PubMed ID:19908036 [Guillen2010]

All Medline abstracts: PubMed