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LuxS is commonly found in various bacterial species, like A. hydrophila which causes infection in fish, shrimps, and prawns and is a great threat to aquaculture industry as well as public health. It is an essential enzyme and highly conserved in various bacterial species, and has a wide range of functions such as involved in quorum sensing (QS), sporulation, virulence and synthesis of biofilm. This study focused on the prediction of 3D-sturcture of LuxS by template similarity and its ligand binding sites analysis to define its structure-function relationship. Primary structure analysis of LuxS examined that about 42% of residues content are alpha-helix, which makes it stable for three-dimensional structure homology. For the con struction of homology modeling of LuxS, crystal structure (5e68.1.A) has been used as a template and Swiss model as a work space. The validation of model by ProSA, SAVES, PROCHECK, PROSAII and RMSD. All results analysis shows that refined model is reliable and it has78.11% amino acids sequence similarity with the template,0.4Åas RMSD, and Z-score is -6.21 and Ramachandran plot analysis shows that 83.4% of residues found in the most favored regions where only 0.4% falls into the disallowed regions. Zinc ion ligand was predicted with highest MAMMOTH score and its binding residues His-54, His-58 and Cys-128 were analyzed by COACH-Meta server. LuxS phylogeny was constructed by sequences and structures of the most similar sequences were analyzed. In silico, the information has been generated in this work expects to be the first step towards the structure determination of LuxS in A. hydrophila. |
