Molecular Modelling of a Thermostable Glycoside Hydrolase from Caldivirga maquilingensis and Its Substrate Docking Mechanism for Galactooligosaccharides Synthesis

Glycoside hydrolases (GHs) are very important enzymes that can catalyze the breakdown of the glycosidic bonds between carbohydrates and non-carbohydrates to synthesize GOS prebiotic sugars and hydrolyze lactose in the dairy industry. GOS can stimulate the growth of gut microbiota to have beneficial health effects in the host. The current work investigated molecular modelling and lactose substrate docking of a thermostable GH family 1 from Caldivirga maquilingensis strain IC-167 and determined its mechanism for GOS synthesis. The 3D model structure obtained from the Swiss model analysis tool revealed that GH 1 from Caldivirga maquilingensis was a tetramer with a catalytic pocket at the center of each monomer. The overall quality of the model was 93%. When lactose was docked in the catalytic site using AutoDock Vina software, the catalytic amino acid residues were identified to be Glu 387 and Glu 209 which acted as nucleophile and acid/base residues respectively. Other amino acid residues like His 153, Gln 19, Glu 432, Ala 266, Asn 267, Ser 268 and Trp 433 were also found to be surrounding the catalytic site and playing an essential role in ligand binding and recognition of the lactose substrate for GOS synthesis. These findings offer an understanding of how enzyme protein structure determines catalytic specificity, which serves as new knowledge basis to engineer GH 1 from C. maquilingensis for the biosynthesis of GOS with a broad or narrow degree of polymerization range