Crystal Structure of the Isocitrate Dehydrogenase 2 from Acinetobacter baumannii (AbIDH2) Reveals a Novel Dimeric Structure with Two Monomeric-IDH-Like Subunits.
Crystal Structure of the Isocitrate Dehydrogenase 2 from Acinetobacter baumannii (AbIDH2) Reveals a Novel Dimeric Structure with Two Monomeric-IDH-Like Subunits.
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DOI：
10.3390/ijms19041131
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发表时间：
2018-04-10
影响因子：
5.6
通讯作者：
Zhu G
中科院分区：
文献类型：
--
作者：
Wang P;Wu Y;Liu J;Song P;Li S;Zhou X;Zhu G
单体异柠檬酸脱氢酶（IDH）具有大小约85 kDa的单个多肽。来自条件致病菌鲍曼不动杆菌（Acinetobacter baumannii，AbIDH 2）的IDH 2具有83 kDa的分子量，以前被认为是典型的单体IDH。然而，尺寸排阻色谱和分析超离心分析表明，AbIDH 2在溶液中以同源二聚体存在。无底物/辅酶的AbIDH 2的晶体学研究给出了二聚体结构，并且每个亚基包含结构域I和结构域II。二聚体组装主要通过来自二聚体界面平台的疏水相互作用（16个氢键和11个盐桥）来稳定，该界面平台以三个平行螺旋（α4，α12和α17）和来自结构域II的一个环为中心。动力学分析表明，与典型的单体IDH（~15 μM − 1·s − 1）相比，二聚体AbIDH 2显示出低得多的催化效率（0.39 μM − 1·s − 1）。同时改变对二聚体形成至关重要的关键残基以产生突变体mAbIDH 2。疏水力的破坏使二聚体AbIDH 2解离，使mAbIDH 2成为单体酶。mAbIDH 2的持续比活性（21.9 ± 2 U/mg）与AbIDH 2（25.4 ± 0.7 U/mg）相当。但mAbIDH 2是一种不耐热酶，表明热稳定的二聚体AbIDH 2可能对A.鲍曼不动杆菌。系统发育分析表明，存在许多AbIDH 2同源蛋白，从而扩大了单体IDH蛋白家族。
Monomeric isocitrate dehydrogenases (IDHs) have a single polypeptide sizing around 85 kDa. The IDH2 from the opportunistic bacterium Acinetobacter baumannii (AbIDH2) with a mass of 83 kDa was formerly recognized as a typical monomeric IDH. However, both size exclusion chromatography and analytical ultracentrifugation analysis indicated that AbIDH2 exists as a homodimer in solution. The crystallographic study of the substrate/coenzyme-free AbIDH2 gave a dimeric structure and each subunit contained a domain I and a domain II. The dimeric assembly is mainly stabilized by hydrophobic interactions (16 hydrogen bonds and 11 salt bridges) from the dimer’s interface platform, which centered around the three parallel helices (α4, α12, and α17) and one loop from the domain II. Kinetic analysis showed that the dimeric AbIDH2 showed much lower catalytic efficiency (0.39 μM−1·s−1) as compared to the typical monomeric IDHs (~15 μM−1·s−1). Key residues crucial for dimer formation were simultaneously changed to generate the mutant mAbIDH2. The disruption of the hydrophobic forces disassociated the dimeric AbIDH2, making mAbIDH2 a monomeric enzyme. mAbIDH2 sustained specific activity (21.9 ± 2 U/mg) comparable to AbIDH2 (25.4 ± 0.7 U/mg). However, mAbIDH2 proved to be a thermolabile enzyme, indicating that the thermostable dimeric AbIDH2 may have a physiological significance for the growth and pathogenesis of A. baumannii. Phylogenetic analysis demonstrated the existence of numerous AbIDH2 homologous proteins, thus expanding the monomeric IDH protein family.
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