Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase
Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase
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DOI：
10.1002/prot.25296
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发表时间：
2017-07-01
影响因子：
2.9
通讯作者：
Papageorgiou, Anastassios C.
中科院分区：
文献类型：
--
作者：
Kellici, Tahsin F.;Mavromoustakos, Thomas;Papageorgiou, Anastassios C.
在PhaZ 7 Y105 E突变体的两个高分辨率晶体结构中鉴定了PhaZ 7细胞外聚（3-羟基丁酸酯）解聚酶的表面环的开放和闭合构象。分子动力学（MD）模拟揭示了281-295环的高均方根波动（RMSF），特别是在残基Asp 289（RMSF 7.62埃）。3-羟基丁酸三聚体和催化残基Ser 136之间的共价对接表明，底物的结合能在开环构象中比在闭环构象中明显更有利。与apo（无底物）形式相比，底物共价结合的MD模拟描绘了残基281-295的1埃RMSF高值。此外，活性位点中底物的存在增强了环采用闭合形式的能力。综上所述，分析表明，PhaZ 7解聚酶的柔性环281-295可以充当盖结构域以控制底物接近酶的活性位点。蛋白质2017; 85：1351-1361。(c)2017 Wiley Periodicals，Inc.
An open and a closed conformation of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase were identified in two high-resolution crystal structures of a PhaZ7 Y105E mutant. Molecular dynamics (MD) simulations revealed high root mean square fluctuations (RMSF) of the 281-295 loop, in particular at residue Asp289 (RMSF 7.62 angstrom). Covalent docking between a 3-hydroxybutyric acid trimer and the catalytic residue Ser136 showed that the binding energy of the substrate is significantly more favorable in the open loop conformation compared to that in the closed loop conformation. MD simulations with the substrate covalently bound depicted 1 angstrom RMSF higher values for the residues 281-295 in comparison to the apo (substrate-free) form. In addition, the presence of the substrate in the active site enhanced the ability of the loop to adopt a closed form. Taken together, the analysis suggests that the flexible loop 281-295 of PhaZ7 depolymerase can act as a lid domain to control substrate access to the active site of the enzyme. Proteins 2017; 85:1351-1361. (c) 2017 Wiley Periodicals, Inc.