Carbohydrate Binding Module Family 79

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• Author: ^^^Immacolata Venditto^^^
• Responsible Curator: ^^^Harry Gilbert^^^

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CAZy DB link

https://www.cazy.org/CBM79.html

Ligand specificities

CBM79 is a family identified in the Ruminococcus flavefaciens cellulosome, an anaerobic, cellulolytic bacterium that plays an important role in the ruminal digestion of plant cell walls [1]. Two CBM79s (CBM79-1_RfGH9 and CBM79-2_RfGH9) were identified in an enzyme that contains a catalytic module derived from GH9 with endo-β1,4-glucanases activity. Both CBM79s bind to a range of β-1,4- and mixed linked β-1,3-1,4-glucans [2]. The ligand binding of CBM79-1_RfGH9 was quantified by isothermal titration calorimetry and semi-quantitatively using microarrays [2]. CBM79-1_RfGH9 binds barley β-glucan and hydroxyethylcellulose (HEC) with similar affinities. The small increase in KA from cellotetraose to cellohexaose suggests that ligand recognition is dominated by four sugar binding sites. The binding to xyloglucan is weaker than the other β-glucans, indicating that the protein cannot recognize the xylose side chains. CBM79-1_RfGH9 binds regenerated (noncrystalline) insoluble cellulose (RC) with a K_A of 4.8 x 10⁴ M^-1 .

Structural Features

The structure of CBM79-1_RfGH9 was solved using single-wavelength anomalous diffraction (SAD) methods and selenomethionyl protein to a resolution of 1.8 Å. CBM79-1_RfGH9 has a β-sandwich fold and contains two β-sheets, 1 and 2, respectively (Figure 1) [2]. β-sheet 2 forms a cleft in which aromatic residues are a dominant feature. Tyr563, Trp564, Tyr597, Trp606 and Trp607 in CBM79-1RfGH9 form a twisted hydrophobic platform. In CBM79-1_RfGH9, the concave surface forms an unusually solvent exposed cleft or planar surface, with loops connecting β-strands 1 and 2 and β-strands 4 and 5 strongly contributing to the curved topology of β-sheet 2. Two tryptophan residues (Trp564 and Trp606) play a key role in ligand recognition, adopting a planar orientation in CBM79-1_RfGH9.

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

Insert archetype here, possibly including very brief synopsis.

First Structural Characterization

Insert archetype here, possibly including very brief synopsis.

References

3. 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 |

4. 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.

5. 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 |
6. 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 |
7. 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 |
8. 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 |
9. 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 |