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

Abstract

α-1,4-Amylase is one of the most important industrial enzymes and there is enormous interest in isolating α-1,4-amylase with better properties. The α-1,4-amylase producing endophytic Bacillus amyloliquefaciens was isolated and characterized from Hevea brasiliensis. The α-1,4-amylase gene after cloning and sequencing contained 1542 base pairs. A homology model of the α-1,4-amylase enzyme was built from the deduced amino acid sequence. The modelled and template α-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 α-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 α-1,4-amylase.

Amplification of Thermostable Neutral Protease Open Reading Frame from Geobacillus sp. DS3 Isolated from Sikidang Crater, Dieng Plateau, Central Java, Indonesia

“…The 3D structure of the enzyme must also be determined to understand its functions at the molecular level. The availability of DNA sequence from a novel microbial gene and its comparison with homologous enzymes permit us to identify the molecular determinants and amino acid residues involved in the desired features [13].…”