Structure-Based Gene Mining and Characterization of Pectin-Specific Carbohydrate-Binding Modules: Discovery of Novel CBM Families

Pectin is a biologically and commercially important polysaccharide with a variety of applications. Carbohydrate-binding modules (CBMs) are commonly used polysaccharide-binding proteins that facilitate research on both polysaccharides and carbohydrate-active enzymes. In this study, we conducted a structure-based approach to CBM gene mining and applied it to identify previously undiscovered CBMs in more than 10000 pectin lyase sequences. Six new CBMs targeting pectic polysaccharides were identified, with the <i>K</i>_a values ranging from ∼10⁵ M^-1 to ∼10⁶ M^-1. These six proteins demonstrate diverse binding capabilities toward diverse pectic polysaccharides. The sequence novelty and defined function of the six proteins reveal new CBM families. This represents the largest number of novel CBM families identified to date for a single type of polysaccharide. The novel CBMs enrich the toolbox of pectin-binding proteins, and this approach is a promising route for the future discovery of new CBM families.