Molecular modelling and docking studies of an α-1,4-amylase from endophytic Bacillus amyloliquefaciens

alpha-1,4-Amylase is one of the most important industrial enzymes and there is enormous interest in isolating alpha-1,4-amylase with better properties. The alpha-1,4-amylase producing endophytic Bacillus amyloliquefaciens was isolated and characterized from Hevea brasiliensis. The alpha-1,4-amylase gene after cloning and sequencing contained 1542 base pairs. A homology model of the alpha-1,4-amylase enzyme was built from the deduced amino acid sequence. The modelled and template alpha-1,4-amylase enzyme (PDB ID:3bh4) showed 97.7% sequence identity with similar secondary and tertiary structures. Computer aided docking studies of the substrate (maltotetraose) with the modelled as well as the template enzymes showed that although the binding energies were almost the same in both the complexes, the number of hydrogen bonds and van der Waals interactions in the active sites of the two enzymes were different. These variations might be due to the change in the amino acid residues of the active site regions of two enzymes. The mutated polar amino acids in the active site of modelled alpha-1,4-amylase favoured more hydrogen bond formation with the substrate. The difference in the active site interactions may improve the specificity of the enzyme and affect the catalytic potential of alpha-1,4-amylase.