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Online Journal of Bioinformatics ©
Volume 14 (3): 274-281, 2013
Homology Modelling of Laccase from White-rot Fungus, Schizophyllum commune.
G Vidyasagar Reddy1, Ch Vijaya2 and K Venkateswarlu1*
Department of Biotechnology1/Marine Biology2, Vikrama Simhapuri University, Nellore 524001, India
Reddy GV, Vijaya CH, Venkateswarlu K., Homology Modelling of Laccase from White-rot Fungus, Schizophyllum commune, Onl J Bioinform., Volume 14 (3): 274-281, 2013. Laccases are oxidoreductases belonging to the multinuclear copper-containing oxidases that have high industrial demand. Laccase from Schizophyllum commune is acidic, hydrophilic and stable, containing 518 amino acids with a molecular weight of 55868.8. Homology modelling was done through Modeller9v7 software using PDB: 2HRG_A as a template. Energy minimization was done using GROMOS 96 force field. The predicted 3D structure has 11 helices and 29 strands. Pymol was used to establish the final 3D structure. Ramachandran Plot revealed 93.8% of the residues in most favored regions. Prosa Z–Scores of the template protein and laccase from S. commune are -7.86 and -7.48, respectively, suggesting similarity between the two structures. ERRAT value of 82.897 indicated validation of the predicted structure. Proknow functional annotation revealed new possibilities of the enzyme’s usage in industrial processes. This modeled structure can be used to predict active sites, and to identify the substrates and cofactor, if any, and regulation in the synthesis and function of the enzyme through docking studies.
Key words: Laccase, Lignolytic enzyme, White-rot fungi, Homology modelling, Functional annotation