Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
BioAnalysis, LLC, 1135 Dunton Street, Unit 2, Philadelphia, PA, 19123, USA.
Nat Commun. 2020 Aug 7;11(1):3969. doi: 10.1038/s41467-020-17733-0.
Mevalonate diphosphate decarboxylases (MDDs) catalyze the ATP-dependent-Mg-decarboxylation of mevalonate-5-diphosphate (MVAPP) to produce isopentenyl diphosphate (IPP), which is essential in both eukaryotes and prokaryotes for polyisoprenoid synthesis. The substrates, MVAPP and ATP, have been shown to bind sequentially to MDD. Here we report crystals in which the enzyme remains active, allowing the visualization of conformational changes in Enterococcus faecalis MDD that describe sequential steps in an induced fit enzymatic reaction. Initial binding of MVAPP modulates the ATP binding pocket with a large loop movement. Upon ATP binding, a phosphate binding loop bends over the active site to recognize ATP and bring the molecules to their catalytically favored configuration. Positioned substrates then can chelate two Mg ions for the two steps of the reaction. Closure of the active site entrance brings a conserved lysine to trigger dissociative phosphoryl transfer of γ-phosphate from ATP to MVAPP, followed by the production of IPP.
甲羟戊酸二磷酸脱羧酶（MDDs）催化 ATP 依赖性 Mg 脱羧基化甲羟戊酸-5-二磷酸（MVAPP）产生异戊烯二磷酸（IPP），这在真核生物和原核生物中对于多异戊二烯合成都是必不可少的。已证明底物 MVAPP 和 ATP 依次结合到 MDD 上。在此，我们报告了酶仍然保持活性的晶体，从而可以观察到粪肠球菌 MDD 中的构象变化，这些变化描述了诱导契合酶反应中的连续步骤。MVAPP 的初始结合调节 ATP 结合口袋，导致大环运动。在 ATP 结合后，磷酸结合环弯曲到活性位点以识别 ATP，并使分子处于其催化有利的构象。然后定位的底物可以螯合两个 Mg 离子，以完成反应的两个步骤。活性位点入口的关闭使保守的赖氨酸触发从 ATP 到 MVAPP 的 γ-磷酸的去磷酸化转移，随后产生 IPP。
