Carbohydrate Binding Module Family 106

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• Author: Wenwen Tao
• Responsible Curator: Yaoguang Chang

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CAZy DB link

https://www.cazy.org/CBM106.html

Ligand specificities

VbCBM106 represents the first characterized member of the CBM106 family, which is appended to a PL6 potential alginate lyase found in the marine bacteria Vibrio breoganii. The CBM showed the favorable specificity to alginate, while it could not bind to other polyuronic acids, such as hyaluronic acid, chondroitin sulfates, dermatan sulfate, and pectin, as well as other polysaccharides from brown algae including laminarin and fucoidan [1].

Structural Features

Figure 1. Crystal structure of VbCBM106. The strand, helix, and loop were colored in cyan, yellow, and white respectively. The sequential order of these strands and helices was depicted from P4 through to G200.

The crystal structure (1.55 Å) of VbCBM106 exhibits a typical β-sandwich fold, which is composed of two antiparallel β-sheets formed by 11 β-strands and 4 helixes (Fig.1). Site-directed mutagenesis assays demonstrated that the residues R59, R61, K63, K139, and R190 play critical roles in the ligand binding of VbCBM106 [1].

Functionalities

VbCBM106 and some of its homologous sequences are linked to the catalytic modules of the PL6 family or its subfamily PL6_1. In the natural environments, VbCBM106 might could enhance the catalytic efficiency of its appended enzymes by increasing the contact between adjacent catalytic domains and alginate [1].

Family Firsts

First Identified

The first member VbCBM106 is a component of a potential PL6 alginate lyase from a marine bacterium Vibrio breoganii [1].

First Structural Characterization

VbCBM106 (PDB 8zqf) is the first and currently only member of the CBM106 family with the structural information [1].

References

1. Mei X, Tao W, Sun H, Liu G, Chen G, Zhang Y, Xue C, and Chang Y. (2024). Characterization and structural identification of a novel alginate-specific carbohydrate-binding module (CBM): The founding member of a new CBM family. Int J Biol Macromol. 2024;277(Pt 3):134221. DOI:10.1016/j.ijbiomac.2024.134221 |