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

• Published in: Microbial Fermentation and Enzyme Technology pp. 41 - 60
• Main Authors: Mondal, Sunil Kanti, Das, Satadruta, Sen, Madhab Kumar
• Format: Book Chapter
• Language: English
• Published: CRC Press 2020
• Edition: 1
• Subjects: Amino Acid Frequencies; Lignin Peroxidase; Codon Usage; Bacillus Licheniformis; Animal Kingdoms; NCBI BLASTP; PERL; Acetyl Xylan Esterase; Glycoside Hydrolases; GC1; RSCU; Soy Proteins; Tannase; Maltogenic Amylase; GH Family; Synonymous Codon; TIM; Ethanol Fermentation; Codon Usage Bias
• ISBN: 0367183846; 9780367183844
• DOI: 10.1201/9780429061257-3

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. The hydrolysis of the glycosidic bonds in starch to yield small sugars is carried out by a-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. Enzymes are proteinaceous in nature and are known to accelerate the rate of biological reaction by lowering the activation energy. The enzyme α-amylase possesses catalytic activity, alpha-amylase activity, calcium ion binding site, hydrolase activity along with metal ion binding sites. The α-amylase of Bacillus licheniformis is widely studied due to its high thermostability and industrial importance. Average and standard deviation of relative synonymous codon usage of the codon of a-amylase encoding gene and amino acid frequencies for the proteins are encoded by the genes in different groups of microorganisms and for the entire selected organisms.