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

被引：14

作者：

Kumar A. ^{[1
]}

Kumar S. ^{[2
]}

Kumar A. ^{[1
]}

Sharma N. ^{[4
]}

Sharma M. ^{[5
]}

Singh K.P. ^{[1
,6
]}

Rathore M. ^{[7
]}

Gajula M.N.V.P. ^{[8
]}

机构：

[1] Advance Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun

[2] Bioinformatics Centre, Biotech Park, Lucknow

[3] Plant Proteomics Lab, National Institute of Plant Genome Research (NIPGR), New Delhi

[4] Department of Health Research, Ministry of Health and Family Welfare, IRCS Building, New Delhi

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

[6] Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004, Haryana

[7] Department of Biotechnology, Mohan Lal Sukhadia University, Udaipur, Rajasthan

[8] Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Rajendra Nagar, Hyderabad

来源：

Proceedings of the National Academy of Sciences, India Section B: Biological Sciences | 2018年 / 88卷 / 4期

关键词：

Binding sites; Homology modeling; Molecular docking; Molecular dynamics; Protein 3D structure;

D O I：

10.1007/s40011-017-0898-0

中图分类号：

学科分类号：

摘要：

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. © 2017, The National Academy of Sciences, India.

引用

页码：1539 / 1548

页数：9

共 36 条

[11]

Balasubramanian A., Ponnuraj K., Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure, J Mol Biol, 400, pp. 274-283, (2010)

[12]

Kojima S., Bohner A., von Wiren N., Molecular mechanisms of urea transport in plants, J Membr Biol, 212, pp. 83-91, (2006)

[13]

Wang W.H., Kohler B., Cao F.Q., Liu L.H., Molecular and physiological aspects of urea transport in higher plants, Plant Sci, 175, pp. 467-477, (2008)

[14]

Cao F.Q., Werner A.K., Dahncke K., Romeis T., Liu L.H., Witte C.P., Identification and characterization of proteins involved in rice urea and arginine catabolism, Plant Physiol, 154, pp. 98-108, (2010)

[15]

Balasubramanian A., Durairajpandian V., Elumalai S., Mathivanan N., Munirajan A.K., Ponnuraj K., Structural and functional studies on urease from pigeon pea (Cajanus cajan), Int J Biol Macromol, 58, pp. 301-309, (2013)

[16]

Yata V.K., Thapa A., Mattaparthi V.S., Structural insight into the binding interactions of modeled structure of Arabidopsis thaliana urease with urea: an in silico study, J Biomol Struct Dyn, 33, pp. 845-851, (2015)

[17]

Filiz E., Vatansever R., Ozyigit I.I., Molecular docking of Glycine max and Medicago truncatula ureases with urea

[18]

bioinformatics approaches, Mol Biol Rep, 43, pp. 129-140, (2016)

[19]

Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A., Protein identification and analysis tools on the ExPASy server, The proteomics protocols handbook, pp. 571-607, (2005)

[20]

Geourjon C., Deleage G., SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments, Comput Appl Biosci, 11, pp. 681-684, (1995)

← 1 2 3 4 →