Structure analysis of a putative exo-rhamnogalacturonan lyase of the polysaccharide lyase family 26 from Bacteroides thetaiotaomicron by computational methods

Pectinolytic enzymes are necessary to efficiently produce biofuels from plant biomass, as pectin reduces the accessibility of other cell wall-degrading enzymes. There are limited reports on enzymes degrading RG-I backbone of pectin. The first putative exo-rhamnogalacturonan lyase, BtPL26 from Bacteroides thetaiotaomicron belonging to polysaccharide lyase 26 family (PL26), was structurally analysed by computational methods. The modelled three-dimensional structure of BtPL26 showed (α/α)₆ barrel fold, characteristic of the PL26 family. Ramachandran plot exhibited 99.7% of amino acid residues in the allowed regions and only 0.3% residues (Asn117, Asn168 and Asn762) in the disallowed region, validating the modelled structure of BtPL26. Multiple sequence alignment of BtPL26 with PcRGLX from Penicillium chrysogenum 31B and YetA from Bacillus Subtilis revealed Tyr636, Arg811 and Arg825 as active-site residues. The secondary structure analysis of BtPL26 showed the presence of 24.4% α-helices, 32.1% β-sheets and the rest random coils. Molecular docking analysis showed that the active-site of BtPL26 can accommodate rhamnogalacturonan-I oligosaccharides of degrees of polymerization up to 5, i.e. RG-I pentasaccharide, but the favourable binding was with RG-I trisaccharide (− 3.89 kcal/mol) and RG-I disaccharide (− 3.71 kcal/mol). It also confirmed the involvement of catalytic residues, Tyr636, Arg811 and Arg825, in the ligand binding. The binding analysis of RG-I trisaccharide with BtPL26 by PyMOL v2.5 revealed that BtPL26 would cleave it between − 1 and + 1 subsites. MD simulation study of modelled protein structure and ligand-bound complex confirmed their stability and compactness.