Homology Modelling,Bioinformatics Analysis and Insilico Functional Annotation of an Antitoxin Protein from Streptomyces coelicolor A3 (2)
Journal of Proteomics & Computational Biology
Streptomyces coelicolor A3 (2) is a soil-dwelling, filamentous bacteria and a reservoir of a wide range of natural antibiotics. A hypothetical protein SCO2235 of this bacterium, comprising of 87 residues was selected for in silico analysis. Numerous bioinformatics tools were used to predict the structure and function of this protein. Subcellular localization of the targeted protein was also predicted. Multiple sequence alignment (MSA) was used to locate the conserved residues and for the
... ry structure analysis. Sequence homology was assessed against the protein data bank and non-redundant database by using BLASTP program of NCBI, which that revealed the targeted protein have similarity with different antitoxin protein. Homology model was obtained and PDB ID: 3D55: A served as a template having 71% homology with the protein SCO2235. The three-dimensional structure was predicted through Modeller. Validation of the three-dimensional structure was obtained through PROCHECK and QMEAN6 programs. Root Mean Squared Deviation (RMSD) calculation was used to detect super imposition of query and template structure associated with Z score. To get understandings about the physical and functional association of the targeted protein with others, STRING network analysis was implemented. Finally, the CASTp server was used to predict the active site of the protein. That is usually specific for toxin binding and DNA binding. To end, whole results hinted the biological function of the target protein to be an antitoxin. As the sequence is more unstable than the structure, here we tried to get some insights about the protein's (SCO2235) function, through predicting the secondary and three-dimensional structure as well as the comparative proteomics and catalytic sites.