Proc. Natl. Acad. Sci. USA 10.1073/pnas.1406156111

Credit: SATISH NAIR

Human gut commensal bacteria are required for digestion of carbohydrates such as xylan, but the specific enzymes involved in these processes are not fully characterized. To gain insights into xylan degradation, Zhang et al. examined two Bacterioides strains that are particularly enriched in genes that encode carbohydrate-active enzymes. Transcriptional analysis of bacterial cells exposed to xylan demonstrated that the genes encoding the putative proteins BiXyn10A and BACOVA_04390 from the glycoside hydrolase 10 (GH10) family were the most upregulated in the two strains; biochemical analysis of purified BiXyn10A showed that it degrades two common xylan substrates. Bioinformatics analysis identified an unusual 250-amino-acid insertion within the GH10 sequence of BiXyn10A that was suspected to encode tandem carbohydrate-binding modules (CBMs), though it had low homology to known CBMs. Isothermal titration calorimetry of the two isolated CBMs demonstrated that they bind wheat arabinoxylan and related substrates with slightly different specificity, and mutational analysis confirmed the importance of these modules for xylan degradation by the GH10 enzyme. Biochemical characterization of additional homologs of the tandem CBMs from BiXyn10A homologs confirmed binding to xylohexaose. A co-crystal structure of this interaction suggests that these new CBMs are specific for xylan because of the unusual orthogonal placement of aromatic residues within the binding site that pinch the xylan substrate, inducing a kink in the backbone.