A new kind of carbohydrate-binding protein, found in a soil-derived Bacteroidetes species, Chitinophaga pinensis, displays a high binding specificity for branched polysaccharides.

The biological function of the protein, provisionally named “F-protein”, is still unknown; however, two examples from this new protein family have already been partly characterised. The protein family seems to have the ability to specifically bind branched polysaccharide chains, and each protein can bind multiple polysaccharide chains as it has multiple binding sites. This enables cross-linking of polysaccharides to form hydrogel materials. In this project we have investigated the carbohydrate binding of two F-domains from the Cpin 2580 gene that also includes a glycoside hydrolase family 18 (GH18) chitinase domain and found them to primarily bind to 1-6 linked β-glucans. We have found the GH18 domain’s chitinase activity to be negatively impacted in its naturally occurring F-domain “sandwich” configuration, hinting at a biological non-catalytic role for this domain. We have discovered unexpected chitin binding for the full complex of two Fdomains together with GH18. We have successfully formed hydrogels from scleroglucan at low concentration, using four recombinant proteins containing either of the F-domains, and shown that gels form both with and without an appended GH18 domain. We have investigated the evolutionary context of the F-domain through PSI-BLAST of the full Cpin 2580 protein and the Fdomain sequence alone. We have found the F-domain to occur predominantly appended to a glycoside hydrolase catalytic subunit with and without a secretion domain targeting the protein to the type IX secretion system (T9SS). We have also found it to occur with an alginate lyase subunit, in this case without a T9SS tail. We have theorised a biological role for the Cpin 2580 gene as an adhesion lectin targeting potentially a fungal cell wall, and a biological micro environment dominated by decomposing microbial biomass as carbohydrate source. The sequence analyses presented here will hopefully guiding future efforts to explore for additional F-domain containing genes in nature.