Low phytate soybeans are desirable both from a nutritional and economic standpoint. Inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinase (IPK1), optimizes the metabolic flux of phytate generation in soybean and thus shows much promise as a likely candidate for pathway regulation. In the present study, the differential spatial and temporal expression profiling of GmIpk1 and its two homologs Glyma06g03310 and Glyma04g03310 were carried out in Glycine max L. var Pusa 9712 revealing the early stages of seed development to be the potential target for gene manipulation. NCBI databank was screened using BLASTp to retrieve 32 plant IPK1 sequences showing high homology to GmIPK1 and its homologs. Bio-computational tools were employed to predict the protein’s properties, conserved domains, and secondary structures. Using state-of-the-art in silico physicochemical approach, the three-dimensional (3D) GmIPK1 protein model (PMD ID—PM0079931), was developed based on Arabidopsis thaliana (PDB ID: 4AQK). Superimposition of 4AQK and best model of GmIPK1 revealed that the GmIPK1 aligned well and shows a sequence identity score of 54.32% with 4AQK and a low RMSD of 0.163 nm and almost similar structural features. The modeled structure was further refined considering the stereochemical geometry, energy and packing environment between the model and the template along with validation of its intrinsic dynamics. Molecular dynamics simulation studies of GmIPK1 were carried out to obtain structural insights and to understand the interactive behavior of this enzyme with ligands ADP and IP₆. The results of this study provide some fundamental knowledge on the distinct mechanistic step performed by the key residues to elucidate the structure–function relationship of GmIPK1, as an initiative towards engineering “low phytate soybean”.

从营养和经济的角度来看，低植酸大豆都是理想的。肌醇1，3，4，5，6 -戊KIS磷酸2-激酶（IPK1），优化植酸代大豆的代谢通量，从而示出了很大希望作为通路调节的一个可能的候选。在本研究中，GmIpk1及其两个同源物Glyma06g03310和Glyma04g03310的时空差异表达谱在Glycine max L. var Pusa 9712中进行，揭示了种子发育的早期阶段是基因操纵的潜在目标。使用BLASTp筛选NCBI数据库，检索32个与Gm具有高度同源性的植物IPK1序列IPK1及其同源物。使用生物计算工具来预测蛋白质的特性，保守结构域和二级结构。使用最新的计算机硅物理化学方法，基于拟南芥（PDB ID：4AQK）开发了三维（3D）Gm IPK1蛋白模型（PMD ID- PM0079931）。4AQK和Gm IPK1的最佳模型的叠加表明GmIPK1排列良好，显示4AQK的序列同一性得分为54.32％，RMSD低至0.163 nm，结构特征几乎相似。考虑到模型和模板之间的立体化学几何形状，能量和填充环境以及其内在动力学的验证，对模型结构进行了进一步的完善。进行了分子动力学模拟研究Gm IPK1以获得结构上的见解，并了解该酶与配体ADP和IP ₆的相互作用。这项研究的结果为关键残基为阐明Gm IPK1的结构与功能关系所采取的独特机理步骤提供了一些基础知识，以此作为工程化“低植酸大豆”的一项举措。