Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Tokyo 113-0032, Japan.
J Phys Chem B. 2012 Oct 4;116(39):11798-808. doi: 10.1021/jp303198u. Epub 2012 Sep 24.
Autotaxin (ATX) is a secreted lysophospholipase D that produces lysophosphatidic acid, a lipid mediator that activates G protein-coupled receptors to evoke various cellular responses. The nuclease-like domain of ATX and the Asn524-linked glycan are reportedly critical for the catalytic activity. Recently, the crystal structures of ATX were determined, but the means by which the nuclease-like domain and the N-glycosylation participate in the catalytic activity still remain undetermined. To address this question, we conducted molecular dynamics simulations of ATX. The simulation trajectories starting from the full-length structure and from structures lacking the nuclease-like domain and/or the glycan were compared. The results suggested that an allosteric interaction pathway, formed by the catalytic domain, including the two insertion regions, the essential glycan modification, and the nuclease-like domain, may stabilize the proper location of the catalytic threonine residue. The results complement those from previous biochemical experiments.
自分泌酶（ATX）是一种分泌型溶脂酶 D，能够产生溶血磷脂酸，这是一种脂质介质，可激活 G 蛋白偶联受体，引发各种细胞反应。据报道，ATX 的核酸酶样结构域和 Asn524 连接的聚糖对于其催化活性至关重要。最近，已经确定了 ATX 的晶体结构，但核酸酶样结构域和 N-糖基化如何参与催化活性仍未确定。为了解决这个问题，我们对 ATX 进行了分子动力学模拟。比较了从全长结构以及缺少核酸酶样结构域和/或聚糖的结构开始的模拟轨迹。结果表明，由催化结构域形成的变构相互作用途径，包括两个插入区、必需的糖基化修饰和核酸酶样结构域，可能稳定催化苏氨酸残基的适当位置。这些结果与以前的生化实验结果相补充。
