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Homology Modeling, Molecular Docking and Molecular Dynamics Based Functional Insights into Rice Urease Bound to Urea

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Proceedings of the National Academy of Sciences, India Section B: Biological Sciences Aims and scope Submit manuscript

Abstract

Urease (EC 3.5.1.5) is an important member of most popular amidohydrolases superfamily that is well known for catalyzes the hydrolysis of urea into ammonia and carbon dioxide. Urease protein exclusively found in a wide range of living organisms including plant, algae, bacteria, fungi and some invertebrates. In plants, urease play an important role of recapturing the nitrogen from urea. Despite its critical interplay in plants the structural and functional aspects of urease in O. sativa are still unresolved. In the present study, a three-dimensional structure of rice urease was deduced by using homology modelling based approach. Molecular dynamics simulations were performed to gain further insight into the molecular mechanism and mode of action of urease of rice. Further, the possible binding interactions of modeled structure of urease with urea were assessed by using a geometry-based molecular docking algorithm. The study reveals the role of Ser324, Ala329 and Val385 of rice urease enzyme in binding with the substrate urea. In conclusion, this study presents a 3D model of rice urease and helps understanding the molecular basis for the mechanism of urease interaction with substrate urea at atomic level.

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Acknowledgements

This work was supported by SERB, Department of Science and Technology, India through Ramanujan Fellowship SR/S2/RJN-22/2011. The authors thank Dr. Prashanth Suravajhala for useful comments and Bioclues.org for proofreading the manuscript. They also extend sincere thanks to Dr. E. A. Siddiq, Professor Emeritus, and Dr. C. Cheralu, Director of Institute of Biotechnology, PJTSAU for their extended support. They highly acknowledge ‘C-DAC, India’ for providing the computational facilities.

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Authors and Affiliations

  1. Advance Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, 248007, India

    Anuj Kumar & Krishan Pal Singh

  2. Bioinformatics Centre, Biotech Park, Lucknow, 226018, India

    Sanjay Kumar

  3. Plant Proteomics Lab, National Institute of Plant Genome Research (NIPGR), New Delhi, India

    Amit Kumar

  4. Department of Health Research, Ministry of Health and Family Welfare, IRCS Building, New Delhi, 110001, India

    Naveen Sharma

  5. Bioinformatics Lab, National Institute of Cancer Prevention and Research (NICPR), I-7, Sector - 39, Noida, Uttar Pradesh, 201301, India

    Mansi Sharma

  6. Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125004, India

    Krishan Pal Singh

  7. Department of Biotechnology, Mohan Lal Sukhadia University, Udaipur, Rajasthan, India

    Madhu Rathore

  8. Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendra Nagar, Hyderabad, 500030, India

    M. N. V. Prasad Gajula

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  1. Anuj Kumar
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  2. Sanjay Kumar
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  3. Amit Kumar
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  8. M. N. V. Prasad Gajula
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Correspondence to M. N. V. Prasad Gajula.

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Significance Statement

The structural insights (3D structure) of O. sativa urease has been deduced followed by identification of its interacting residues during N-recapturing and molecular dynamics. The authors predicted the regulatory partners of urease including nitrate transporters, synthetase, etc. first time in model cereal crop rice boosting the biofortification program leading to crop improvement.

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Kumar, A., Kumar, S., Kumar, A. et al. Homology Modeling, Molecular Docking and Molecular Dynamics Based Functional Insights into Rice Urease Bound to Urea. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 88, 1539–1548 (2018). https://doi.org/10.1007/s40011-017-0898-0

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  • DOI: https://doi.org/10.1007/s40011-017-0898-0

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