In silico structural and functional characterization and phylogenetic study of alkaline phosphatase in bacterium,Rhizobium leguminosarum (Frank 1879) |
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| Institution: | 1. COMSATS University Islamabad, Sahiwal campus, Pakistan instead of COMSATS Institute of Information Technology COMSATS, Institute of Information Technology GT Road COMSATS Road, 57000, Sahiwal, Pakistan;2. Bahauddin Zakariya University, Multan, Pakistan;1. São Carlos Institute of Physics, São Paulo University, São Carlos, SP 13563-120, Brazil;2. Brazilian Nanotechnology National Laboratory, LNNano/CNPEM, Campinas, SP 13083-970, Brazil;1. Department of Applied Chemistry, Zhejiang Gongshang University, Hangzhou 310018, China;2. Department of Chemistry, Zhejiang University, Hangzhou 310028, China;1. Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia;2. L.V. Kirensky Institute of Physics, 50 Akademgorodok, Krasnoyarsk 660036, Russia;3. Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea;4. National University of Science and Technology MISiS, 4 Leninskiy prospekt, Moscow 119049, Russia |
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| Abstract: | Phosphorus is one of the primary macronutrient of plants, which is present in soil. It is essential for normal growth and development of plants. Plants use inorganic form of phosphate but organic form can also be assimilated with the help of soil inhabiting bacteria. Alkaline phosphatase is an enzyme present in Rizobium bacteria. This enzyme is responsible for solubilization and mineralization of organic phosphate and makes it readily available for plants. In the present study, nine different strains of Rhizobium leguminosarum were selected for a detailed computational structural and functional characterization and phylogenetic studies of alkaline phosphatase. Amino acid sequences were retrieved from UniProt and saved in FASTA format for use in analysis. Phylogenetic analysis of these strains was done by using MEGA7. 3D structure prediction was performed by using online server I-Tasser. Galaxy Web and 3D Refine were used for structure refinement. The refined structures were evaluated using two validation servers, QMEAN and SAVES. Protein-protein interaction analysis was done by using STRING. For detailed functional characterization, Cofactor, Coach, RaptorX, PSORT and MEME were used. Overall quality of predicted protein models was above 80%. Refined and validated models were submitted into PMDB. Seven out of nine strains were closely related and other two were distantly related. Protein-Protein interaction showed no significant co-expression among the interaction partners. |
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| Keywords: | Alkaline phosphatase Solubilization and mineralization Soil fertility Phylogenetic analysis |
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