Dynamics is an essential process to drive an enzyme to perform a function. When a protein sequence encodes for its three-dimensional structure and hence its function, it essentially defines the intrinsic dynamics of the molecule. The static X-ray crystal structure was thought to shed little insight into the molecule’s dynamics until the recently available tool “Ensemble refinement” (ER). Here, we report the structure–function–dynamics of PanPL, an alginate-specific, endolytic, allosteric polysaccharide lyase belonging to the PL-5 family from Pandoraea apista. The crystal structures determined in apo and tetra-ManA bound forms reveal that the PanPL maintains a closed state with an N-terminal loop lid (N-loop-lid) arched over the active site. The B-factor analyses and ER congruently reveal how pH influences the functionally relevant atomic fluctuations at the N-loop-lid. The ER unveils enhanced fluctuations at the N-loop-lid upon substrate binding. The normal-mode analysis finds that the functional states are confined. The 1 μs simulation study suggests the existence of a hidden open state. The longer N-loop-lid selects a mechanism to adopt a closed state and undergo fluctuations to facilitate the substrate binding. Here, our work demonstrates the distinct modes of dynamics; both intrinsic and substrate-induced conformational changes are vital for enzyme functioning and allostery.

中文翻译：

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变构多糖裂解酶功能中隐藏结构动力学的不同模式

动力学是驱动酶执行功能的必要过程。当蛋白质序列编码其三维结构并因此编码其功能时，它基本上定义了分子的内在动力学。静态 X 射线晶体结构被认为无法深入了解分子的动力学，直到最近可用的工具“整体细化”（ER）。在这里，我们报告了 PanPL 的结构-功能-动力学，这是一种藻酸盐特异性、内溶性、变构多糖裂解酶，属于Pandoraea apista的 PL-5 家族. 以 apo 和 tetra-ManA 结合形式确定的晶体结构表明，PanPL 保持闭合状态，N 端环盖 (N-loop-lid) 在活性位点上方拱起。B 因子分析和 ER 一致地揭示了 pH 如何影响 N 环盖处功能相关的原子波动。ER 在底物结合时揭示了 N 环盖处增强的波动。正常模式分析发现功能状态受到限制。1 μs 模拟研究表明存在隐藏的开放状态。较长的 N-loop-lid 选择一种机制以采用闭合状态并经历波动以促进底物结合。在这里，我们的工作展示了不同的动力学模式；内在和底物诱导的构象变化对于酶的功能和变构至关重要。