In silico structural and mechanistic sights into the N-glycosidase mechanism of Shiga toxin

Shiga toxin is the leading cause of food poisoning in the world. It is structurally similar to the plant type II ribosome-inactivating proteins (RIPs) and retains N-glycosidase activity. It acts specifically by depurinating the specific adenine A4605 of human 28S rRNA, ultimately inhibiting translation. Recent outbreaks and increasing demands for lab-scale meat assert the necessity for producing toxoids. In the current study, we have carried out the comparative structural and functional analysis of Shiga with ricin for N-glycosidase activity. Primary structural analysis indicates that Shiga is more flexible than ricin and one active site residue Gly121 (ricin), has been mutated to Ser (Shiga). Tertiary structure analysis confirms the conserved active site residue confirmation. Further, molecular dynamic studies indicate that the mutated Ser residue of Shiga imparts flexibility besides interacting with the conserved GAGA loop of 28s rRNA and contributes free energy of -5.39 kcal/mol. We have observed a decreasing trend line of average free binding energy with an average of -23 kcal/mol. The residue interaction network indicates that Arg is the key residue that protonates and initiates the N-glycosidase activity. Overall, these structural studies provide molecular insights into the N-glycosidase mechanism and serve as a prospect for the development of toxoids.