Yata Vinod Kumar, Thapa Arun, Mattaparthi Venkata Satish Kumar
a Department of Biotechnology , Dr B.R. Ambedkar National Institute of Technology Jalandhar , Jalandhar 144 011 , India.
J Biomol Struct Dyn. 2015;33(4):845-51. doi: 10.1080/07391102.2014.915765. Epub 2014 May 15.
Urease (EC 3.5.1.5., urea amidohydrolase) catalyzes the hydrolysis of urea to ammonia and carbon dioxide. Urease is present to a greater abundance in plants and plays significant role related to nitrogen recycling from urea. But little is known about the structure and function of the urease derived from the Arabidopsis thaliana, the model system of choice for research in plant biology. In this study, a three-dimensional structural model of A. thaliana urease was constructed using computer-aided molecular modeling technique. The characteristic structural features of the modeled structure were then studied using atomistic molecular dynamics simulation. It was observed that the modeled structure was stable and regions between residues index (50-80, 500-700) to be significantly flexible. From the docking studies, we detected the possible binding interactions of modeled urease with urea. Ala399, Ile675, Thr398, and Thr679 residues of A. thaliana urease were observed to be significantly involved in binding with the substrate urea. We also compared the docking studies of ureases from other sources such as Canavalia ensiformis, Helicobacter pylori, and Bacillus pasteurii. In addition, we carried out mutation analysis to find the highly mutable amino acid residues of modeled A. thaliana urease. In this particular study, we observed Met485, Tyr510, Ser786, Val426, and Lys765 to be highly mutable amino acids. These results are significant for the mutagenesis analysis. As a whole, this study expounds the salient structural features as well the binding interactions of the modeled structure of A. thaliana urease.
脲酶（EC 3.5.1.5.，尿素酰胺水解酶）催化尿素水解为氨和二氧化碳。脲酶在植物中含量更为丰富，在尿素氮循环中发挥着重要作用。但对于拟南芥（植物生物学研究的首选模式系统）来源的脲酶的结构和功能却知之甚少。在本研究中，利用计算机辅助分子建模技术构建了拟南芥脲酶的三维结构模型。然后使用原子分子动力学模拟研究了该模型结构的特征性结构特点。观察到该模型结构是稳定的，并且残基索引（50 - 80，500 - 700）之间的区域具有明显的灵活性。通过对接研究，我们检测了模型脲酶与尿素可能的结合相互作用。观察到拟南芥脲酶的Ala399、Ile675、Thr398和Thr679残基与底物尿素的结合中发挥着重要作用。我们还比较了来自其他来源如刀豆、幽门螺杆菌和巴氏芽孢杆菌的脲酶的对接研究。此外，我们进行了突变分析以找出模型拟南芥脲酶的高变氨基酸残基。在这项具体研究中，我们观察到Met485、Tyr510、Ser786、Val426和Lys765是高变氨基酸。这些结果对于诱变分析具有重要意义。总体而言，本研究阐述了拟南芥脲酶模型结构的显著结构特点以及结合相互作用。
