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In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata

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Abstract

The enzyme catalase breaks down H2O2, a potentially harmful oxidant, to H2O and O2. Besides oxidase activity, the enzyme also exhibits peroxidase activity. Therefore, it plays an important role in maintaining health and regulating pathophysiology of the organisms. However, 3D structure of this important enzyme in invertebrates particularly in crabs is not yet available. Therefore, an attempt has been made to predict the structure of the crab catalase and to envisage its catalytic interaction with H2O2. A three dimensional model of crab catalase was constructed using the NADPH binding site on Beef Liver catalase from Bos taurus (PDBID: 7CAT) as template by comparative modeling approach. Backbone conformation of the modeled structure by PROCHECK revealed that more than 98% of the residues fell in the allowed regions, ERRAT results confirmed good quality of modeled structure and VERIFY3D profile was satisfying. Molecular docking has been used to know the binding modes of hydrogen peroxide with the crab catalase protein. The receptor structures used for docking were derived from molecular dynamics (MD) simulations of homology modeled structure. The docking results showed that the three important determinant residues Arg68, Val70 and Arg108 in catalase were binding with H2O2 as they had strong hydrogen bonding contacts with the substrate. Our analysis provides insight into the structural properties of crab catalase and defines its active sites for binding with substrate. These data are important for further studies of catalase of invertebrates in general and that of crabs in particular.

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Author notes

  1. Gagan Bihari Nityananda Chainy

    Present address: Imgenex India Pvt. Ltd., E-5, Infocity, Bhubaneswar, 751024, India

Authors and Affiliations

  1. Department of Zoology, Utkal University, Bhubaneswar, 751004, India

    Biswaranjan Paital & Gagan Bihari Nityananda Chainy

  2. Bioinformatics Centre, Institute of Life Sciences, Nalco Square, Bhubaneswar, 751023, India

    Sunil Kumar

  3. Department of Computational Biology and Bioinformatics, Jacob School of Biotechnology and Bioengineering, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad, 211007, India

    Rohit Farmer

  4. Departments of Zoology, Berhampur University, Berhampur, 760007, India

    Niraj Kanti Tripathy

  5. Department of Biotechnology, Utkal University, Bhubaneswar, 751004, India

    Gagan Bihari Nityananda Chainy

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  1. Biswaranjan Paital
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Correspondence to Sunil Kumar.

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Paital, B., Kumar, S., Farmer, R. et al. In silico prediction and characterization of 3D structure and binding properties of catalase from the commercially important crab, Scylla serrata. Interdiscip Sci Comput Life Sci 3, 110–120 (2011). https://doi.org/10.1007/s12539-011-0071-z

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  • DOI: https://doi.org/10.1007/s12539-011-0071-z

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