Molecular modeling and in-silico characterization of Glycine max Inositol (1, 3, 4) tris 5/6 kinase-1(Gmitpk1) - a potential candidate gene for developing low phytate transgenics

摘要

Inositol (1, 3, 4) tris 5/6 kinase (Itpk) is a key player in lipid-independent pathway of phytate biosynthesis. In this study, the full length coding sequence of Gmitpk1 was cloned and blasted to retrieve the available inositol phosphate kinases (ipks) from the public domain. Sequence analysis of the selected 18 plant kinases revealed a consensus ‘ATP-grasp’ domain. Secondary structure predictions showed high alpha helix content (80.02%) which justified the structural flexibility as well as the versatility of these kinases. Homology modelling of the Gmitpk1 performed using the template crystal structure of inositol tetrakisphosphate-1-kinase (2q7d.1.A) from Homo sapiens revealed the presence of N and C-terminal domains with a mixed α/β topology having an active site located in the deep cleft between the domains. The model was further refined using intrinsic dynamic tools like ProSA, Verify3D, WEBnm and ElNemo. This study has enabled the elucidation of the 3Dstructure of Gmitpk1and the data has been submitted to protein model data base (PMD) - PM0079572 (first report). Ligand binding residues and energy computations have revealed Mg2+, ATP and ADP as the most likely ligands for Gmitpk1. The study throws light on some novel insights into the structural features of Gmitpk1, a potential candidate for developing low phytate transgenic soybean.