Structural and biophysical characterization of a multidomain xylanase Xyl

Abstract

The depletion of fossil fuels, associated pollution, and resulting health hazards are of concern worldwide. Woody biomass provides an alternative source of cleaner and renewable energy by being converted into biofuels through processes like fermentation and saccharification. The efficient use of woody biomass relies on effective xylan depolymerization. Xylans, heteropolysaccharides with 1,4-linked β-D-xylopyranose units, form the main constituent of hemicellulose, the second most abundant wood component. However, their complex structure impedes enzymatic breakdown, elevating biomass recalcitrance and hindering biofuel production efficiency. Successful xylan depolymerization is essential for optimizing the utilization of woody biomass as a sustainable and efficient energy source. Xylan depolymerization involves hemicellulolytic xylanases from glycoside hydrolase (GH) families 5, 8, 10, 11, 30, 43, 62, and 98 in the CAZy database, with xylanases playing a key but not exclusive role in this enzymatic process. We analysed a multidomain xylanase (Xyl) from the hindgut metagenome of the snouted harvester termite Trinervitermes trinervoides that releases xylobiose and xylotriose from beech and birch xylan and wheat arabinoxylan. The four domains of Xyl include an N-terminal GH11 xylanase domain, two family 36-like carbohydrate-binding domains Xyl-CBM36-1 and 2, and a C-terminal CE4 acetylxylan esterase domain. This study aimed to explore the structure, function, and biophysical properties of the multidomain xylanase Xyl, examining both individual domains and their combinations. Various molecular biology methods to include gene cloning, protein production and purification and biochemical and crystallography methods were employed. The crystal structures of Xyl-GH11, Xyl-CBM36-1 and Xyl-CE4 domains were solved alongside the crystal structure of the two-domain construct, GH11-CBM36-1. The two-domain crystal structure revealed extensive similarity to known GH11 domain structures, however, there was no electron density corresponding to the Xyl-CBM36 1 domain, suggesting a random orientation of the Xyl-CBM36-1 domain relative to the Xyl-GH11 domain. Isothermal titration calorimetry (ITC) experiments similarly did not reveal specific interactions between the individual Xyl domains, implying a “beads-on-a-string” model for Xyl and its domains.