Carbohydrate Binding Module Family 67

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• Author: ^^^Satoshi Kaneko^^^
• Responsible Curator: ^^^Harry Gilbert^^^

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CAZy DB link

https://www.cazy.org/CBM67.html

Ligand specificities

The sugar binding structure of a GH78 α-ʟ-rhamnosidase from Streptomyces avermitilis (SaRha78A) revealed a ʟ-rhamnose binding module CBM67 (SaCBM67) within the six-domain arrangement [1]. SaCBM67 bound ʟ-rhamnose and ʟ-mannose with a K_a of 7.2 × 10³ M⁻¹and 3.6 × 10³ M⁻¹, and free energy of binding ΔG of −5.3 kcal/mol and −4.8 kcal/mol, respectively, but did not bind to ʟ-rhamnose in the presence of 5 mM EDTA [1]. Similarly the D179A and N180A mutants of SaCBM67, in which removed calcium-mediated and direct hydrogen bonds with ʟ-rhamnose, abolish ligand binding, confirming the importance of calcium in the binding of SaCBM67 to its ligand [1]. No binding tol-galactose or ʟ-fucose was also observed [1].

Note: Here is an example of how to insert references in the text, together with the "biblio" section below: Please see these references for an essential introduction to the CAZy classification system: [2, 3]. CBMs, in particular, have been extensively reviewed [4, 5, 6, 7, 8].

Structural Features

Content in this section should include, in paragraph form, a description of:

• Fold: Structural fold (beta trefoil, beta sandwich, etc.)
• Type: Include here Type A, B, or C and properties
• Features of ligand binding: Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

Functionalities

Content in this section should include, in paragraph form, a description of:

• Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
• Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
• Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

Family Firsts

First Identified

SaCBM67 from the S. avermitilis α-ʟ-rhamnosidase SaRha78A was the first member of the family to be identified and characterized. [1].

First Structural Characterization

The first structure in CBM67 is a module involved in BsRhaB from Bacillus sp. GL1 [9], but the function of the module has not been demonstrated. The first structure-based characterization of a member of family CBM67 was SaCBM67 [1].

References

1. Fujimoto Z, Jackson A, Michikawa M, Maehara T, Momma M, Henrissat B, Gilbert HJ, and Kaneko S. (2013). The structure of a Streptomyces avermitilis α-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement. J Biol Chem. 2013;288(17):12376-85. DOI:10.1074/jbc.M113.460097 |

2. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. The Biochemist, vol. 30, no. 4., pp. 26-32. Download PDF version.

4. 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 |
5. 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 |
6. 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 |
7. 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 |
8. Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, and Rodríguez-Sanoja R. (2017). Advances in molecular engineering of carbohydrate-binding modules. Proteins. 2017;85(9):1602-1617. DOI:10.1002/prot.25327 |
9. Cui Z, Maruyama Y, Mikami B, Hashimoto W, and Murata K. (2007). Crystal structure of glycoside hydrolase family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1. J Mol Biol. 2007;374(2):384-98. DOI:10.1016/j.jmb.2007.09.003 |