Carbohydrate Binding Module Family 15

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: ^^^Harry Gilbert^^^
• Responsible Curator: ^^^Harry Gilbert^^^

---

CAZy DB link

https://www.cazy.org/CBM15.html

Ligand specificities

The three family 15 CBMs (CBM15s) are all derived from the Cellvibrio bacterial genus. The one fully characterized CBM15 from Cellvibrio japonicus Xyl10C [1] bound to different forms of xylan with a preference for oat spelt xylan (KA of ~1.4 x 104 M-1). The CBM also bound to xylooligosacchrides exhibiting affinities for xylohexaose and xylopentaose that were similar to oat spelt xylan, and significantly weaker affinity for xylotetraose and xylotriose. The protein displayed weak but measurable affinity (KA of ~2 x 103 M-1) for barley beta1,3-beta1,4-mixed linked glucan and cellohexaose. The CBM15 did not bind to insoluble xylan or amorphous cellulose. Isothermal titration calorimetry showed that binding to xylan and glucan ligands was driven by enthalpic forces with changes in entropy have a negative impact on affinity [1]. The stoichiometry of binding to soluble xylans was consistent with an endo binding mode, demonstrating that the family 15 module is a type B CBM.

Structural Features

CBM15s comprise ~150 amino acids. The crystal structure of the protein module from the ‘’C. japonicus’’ GH10 xylanase Xyn10C was determined in complex with xylohexaose [1]. The structure of CBM15 forms a classic beta-jelly roll, predominantly consisting of five major anti-parallel beta-strands on the two faces CBM15 contains a deep cleft that runs along the concave face of the b-sheet, 20–25 Å long, which forms the binding site for the target ligands. The protein was crystallized in the presence of xylohexaose, and the structure reveals five well-ordered xylose rings (defined as Xyl1 to Xyl5 from the reducing to non-reducing end). Two solvent-exposed tryptophan residues, Trp176 and Trp181, lie in the binding groove and make hydrophobic stacking interactions with Xyl2 and Xyl4, respectively. The indole rings of the two tryptophans were perpendicular to each other and their position is consistent with binding n and n+2 xylose residues in the 3-fold helix structure of xylan. The conformation of these aromatic residues are very similar to the pair of tryptophans that interact with xylan in the CBM2s in Cellulomonas fimi Xyn11A [2]. Only Xyl 2 and Xyl3 of the bound xylopentaose made direct interactions with the CBM. It was argued that the paucity of polar interactions enabled the CBM to bind to highly decorated xylans. Mutagenesis studies showed that the two surface trypotphans were essential for xylan recognition. Mutation of the polar residues that had a direct or indirect interaction with xylans or xylopentaose reduced affinity by 100- and 10-fold, respectively [3].

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

4. 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 |

5. 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.

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