Functional annotation of the cda1 gene from bacillus thuringiensis: Through homology modeling and molecular docking

Insecticidal proteins from bacillus thuringiensis have been exploited to develop insect-resistance in crop plants. we are using b. thuringiensis serovar konkukian s4 as a model organism to elucidate the substrate utilization pathways in bacteria. functional annotation of the putative genes involved in recalcitrant substrate degradation is vital in this context. genome sequence analyses of the serovar konkukian have shown the presence of a probable chitin deacetylase/xylanase gene named as cda1. the protein sequence of the said gene was retrieved from uniprot database to describe its function using in silico tools. primary structure analyses show that the protein cda1 is hydrophobic in nature due to the high content of nonpolar amino acid residues. the instability (ii) and aliphatic indices are computed to be 23.73 and 93.6,respectively by expasy's protparam that classify the protein as stable for a wide range of temperatures. secondary structure analyses predicted that cda1 has predominantly α-helical structure. domain and motif prediction by pfam has shown the protein to contain one potential domain called polysaccharide deacetylase 1 and two potential motifs,respectively. the three dimensional structure of the cda1 was predicted using online available servers like phyre,swissmodel and ps2 followed by modeller 9.9 through homology modeling. to elucidate the function of the protein,molecular docking was performed by autodock vina using chitin and xylan oligomers as substrate. moreover,the protein was compared with several chitin deacetylases and xylanases through comparative phylogenic analyses. our results have demonstrated that cda1 is a chitin deacetylase. this is the very first report on this gene from b. thuringiensis.