ISSN: 1314-6246 Kale & Deshmukh J. BioSci. Biotechnol. 2016, 5(1): 1-11. RESEARCH ARTICLE http://www.jbb.uni-plovdiv.bg 1 Swapnil K. Kale Amit G. Deshmukh 3D structure prediction of lignolytic enzymes lignin peroxidase and manganese peroxidase based on homology modelling Authors’ address: Nagarjun Medicinal Plants Garden, Dr. Panjabrao Deshmukh Agricultural University, Akola-444 104, India. Correspondence: Amit G. Deshmukh Nagarjun Medicinal Plants Garden, Dr. Panjabrao Deshmukh Agricultural University, Akola-444 104, India. Tel.: +91-9765013121 e-mail: agd4in@yahoo.com Article info: Received: 12 August 2015 Accepted: 19 October 2015 ABSTRACT Lignolytic enzymes have great biotechnological value in biopulping, biobleaching, and bioremediation. Manganese peroxidase (EC 1:11:1:13) and lignin peroxidase (EC 1:11:1:14) are extracellular and hem-containing peroxidases that catalyze H 2 O 2 -dependent oxidation of lignin. Because of their ability to catalyse oxidation of a wide range of organic compounds and even some inorganic compounds, they got tremendous industrial importance. In this study, 3D structure of lignin and manganese peroxidase has been predicted on the basis of homology modeling using Swiss PDB workspace. The physicochemical properties like molecular weight, isoelectric point, Grand average of hydropathy, instability and aliphatic index of the target enzymes were performed using Protparam. The predicted secondary structure of MnP has 18 helices and 6 strands, while LiP has 20 helices and 4 strands. Generated 3D structure was visualized in Pymol. The generated model for MnP and LiP has Z-score Qmean of 0.01 and -0.71, respectively. The predicted models were validated through Ramachandran Plot, which indicated that 96.1 and 95.5% of the residues are in most favored regions for MnP and LiP respectively. The quality of predicted models were assessed and confirmed by VERIFY 3D, PROCHECK and ERRAT. The modeled structure of MnP and LiP were submitted to the Protein Model Database. Key words: 3D structure, homology, lignin peroxidases, manganese peroxidases Introduction Lignin-degrading enzymes from white-rot fungi have been intensively studied for potential biotechnological applications such as biopulping, biobleaching, and bioremediation (Breen & Singleton, 1999; Hatakka, 2001). Lignin-degrading enzyme system consists of laccases, lignin peroxidases, manganese peroxidases, and manganese- independent peroxidases, and H 2 O 2 -generating oxidases (Hatakka, 1994). Manganese peroxidase (MnP; EC 1:11:1:13) and lignin peroxidase (LiP; EC 1:11:1:14) were firstly reported in Phanerochaete chrysosporium (Tien & Kirk, 1983; Glenn et al., 1983). MnP and LiP are extracellular and hem-containing peroxidases that catalyze H 2 O 2 -dependent oxidation of lignin (Glenn et al., 1983; Schoemaker, 1990) and related compounds (Kirk et al., 1986; Higuchi, 1985). Manganese peroxidase is considered one of the key enzymes involved in the lignin degradation caused by white rot fungi. Contribution of the Mn 2+ /Mn 3+ redox system as mediator of substrate oxidation is the main feature of catalytic cycle of MnP (Glenn et al., 1987). The Mn 3+ formed diffuses away from the active site of MnP (Wariishi et al., 1989) and takes part in the oxidation of organic substrates as a redox mediator (Pasczynski et al., 1986). The reducing substrate of MnP and LiP are different (Mn 2+ and nonphenolic aromatic), even though MnP shows a high sequence resemblance to LiP. LiP characterized by its ability to oxidize veratryl alcohol to veratryl aldehyde in presence of H 2 O 2 . On the other side, the MnP is unable to oxidize veratryl