Crystal structure of plant PLDα1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D
Crystal structure of plant PLDα1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D
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植物PLDα1的晶体结构揭示了真核磷脂酶D的催化和调节机制。
DOI：
10.1038/s41422-019-0244-6
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发表时间：
2020-01-01
期刊：
影响因子：
44.1
通讯作者：
Zhang, Peng
中科院分区：
文献类型：
--
作者：
Li, Jianxu;Yu, Fang;Zhang, Peng
磷脂酶D（PLD）水解甘油磷脂的磷酸二酯键并产生磷脂酸（PA），其在许多生物体中充当第二信使。在真核生物中已经鉴定出大量的PLD，并且被视为药物设计的有希望的靶标，因为已知这些酶受到严格调控并且在许多人类疾病的病理生理学中起作用。然而，真核生物PLD的催化和调控的潜在分子机制仍然难以捉摸。在这里，我们确定了全长植物PLD α 1的晶体结构中的载脂蛋白状态，并在复杂的PA。结构表明，N-末端C2结构域与具有两个HKD基序的C-末端催化结构域疏水相互作用。我们的分析揭示了催化位点，底物结合机制，和一个新的钙离子结合位点，这是激活PLD所需的。此外，我们测试了几个有效的小分子抑制剂对PLD α 1，并提出了一个可能的竞争性抑制机制，根据基于结构的对接分析。这项研究解释了许多关于PLD的长期问题，并为PLD靶向抑制剂/药物设计提供了结构见解。
Phospholipase D (PLD) hydrolyzes the phosphodiester bond of glycerophospholipids and produces phosphatidic acid (PA), which acts as a second messenger in many living organisms. A large number of PLDs have been identified in eukaryotes, and are viewed as promising targets for drug design because these enzymes are known to be tightly regulated and to function in the pathophysiology of many human diseases. However, the underlying molecular mechanisms of catalysis and regulation of eukaryotic PLD remain elusive. Here, we determined the crystal structure of full-length plant PLD alpha 1 in the apo state and in complex with PA. The structure shows that the N-terminal C2 domain hydrophobically interacts with the C-terminal catalytic domain that features two HKD motifs. Our analysis reveals the catalytic site, substrate-binding mechanism, and a new Ca2+-binding site that is required for the activation of PLD. In addition, we tested several efficient small-molecule inhibitors against PLD alpha 1, and suggested a possible competitive inhibition mechanism according to structure-based docking analysis. This study explains many long-standing questions about PLDs and provides structural insights into PLD-targeted inhibitor/drug design.