CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39-A, Chandigarh 160036, India.
Sci Rep. 2017 Jan 12;7:40452. doi: 10.1038/srep40452.
3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg. Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg is still elusive. Therefore, mechanistic role played by Mg in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg have shown entry of Mg from bulk solvent into active site. Presence of Mg in active site has constrained conformations of Ru5P and has reduced flexibility of loop-2. Formation of hydrogen bonds among Thr-108 and residues - Gly-109, Val-110, Ser-111, and Asp-114 are found to be critical for entry of Mg into active site. Subsequent in silico mutations of residues, Thr-108 and Asp-114 have substantiated the importance of these interactions. Loop-4 of one monomer is being proposed to act as a "lid" covering the active site of other monomer. Further, the conserved nature of residues taking part in the transfer of Mg suggests the same mechanism being present in DHBPS of other microorganisms. Thus, this study provides insights into the functioning of DHBPS that can be used for the designing of inhibitors.
3,4-二羟基-2-丁酮-4-磷酸合酶（DHBPS）在 Mg 的存在下催化 D-核酮糖 5-磷酸（Ru5P）转化为 L-3,4-二羟基-2-丁酮-4-磷酸。尽管已经报道了 DHBPS 与 Ru5P 和非催化金属离子复合物的晶体结构，但仍难以获得与 Ru5P 以及 Mg 结合的结构。因此，Mg 在 DHBPS 结构中所扮演的机械作用机制还了解甚少。在这项研究中，对 DHBPS-Ru5P 复合物与 Mg 的分子动力学模拟表明，Mg 从主体溶剂进入活性位点。Mg 在活性位点的存在限制了 Ru5P 的构象，并降低了环 2 的灵活性。发现 Thr-108 与 Gly-109、Val-110、Ser-111 和 Asp-114 之间形成氢键对于 Mg 进入活性位点是至关重要的。随后对 Thr-108 和 Asp-114 残基进行的计算机模拟突变证实了这些相互作用的重要性。一个单体的环 4 被提议作为覆盖另一个单体活性位点的“盖子”。此外，参与 Mg 转移的残基的保守性质表明，相同的机制存在于其他微生物的 DHBPS 中。因此，这项研究提供了对 DHBPS 功能的深入了解，可用于抑制剂的设计。
