chapter  3
20 Pages

Study of α-Amylase Based on their Compositional Parameters of Its Gene Along with Its Protein Structure

WithSunil Kanti Mondal, Satadruta Das, Madhab Kumar Sen

The hydrolysis of the glycosidic bonds in starch to yield small sugars is carried out by α-amylases, which contain the domain α-amylase superfamily and also posses the domains like: DUF1937, DUF1966, Malt amylase according to their host lineage. These domains content pattern is clearly reflected in the phylogenetic tree obtained using protein sequences of α-amylase mainly from Aspergillus and Bacillus. The GC% at different position of the codon and the overall GC% are significantly low in Bacillus than Aspergillus and this has proper reflection in codon usage and biasness with few exceptions like CCG, ACG. Statistical analysis also indicates that the genes from Bacillus are under biasness but the same case is not for Aspergillus but all the genes from both are under mutational pressure. The distributions of the nucleotides as well as the codons are uneven especially among the sites that are functionally constrained. This can be considered as an important factor for the most of the variance in both codons and amino acids. Furthermore, directional mutation can be held responsible for most of these neutral changes. Structure of alpha amylases have Ca2+ and Na+ binding site which are mostly occupied by the negatively charged amino acids might serve multiple structural roles to facilitate biological reaction. Binding site of Ca2+ lies between domain A and B making an extensive loop over the probable active site. The structural alignment of alpha amylase from Aspergillus and Bacillus shows non-significant difference between them though the host organisms belong from distantly related lineages.