Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U596, Université de Strasbourg, Illkirch, France.
BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, UMR7178, Université de Strasbourg, France.
FEBS J. 2017 Jan;284(1):77-96. doi: 10.1111/febs.13953. Epub 2016 Nov 23.
PRMT2 is the less-characterized member of the protein arginine methyltransferase family in terms of structure, activity, and cellular functions. PRMT2 is a modular protein containing a catalytic Ado-Met-binding domain and unique Src homology 3 domain that binds proteins with proline-rich motifs. PRMT2 is involved in a variety of cellular processes and has diverse roles in transcriptional regulation through different mechanisms depending on its binding partners. PRMT2 has been demonstrated to have weak methyltransferase activity on a histone H4 substrate, but its optimal substrates have not yet been identified. To obtain insights into the function and activity of PRMT2, we solve several crystal structures of PRMT2 from two homologs (zebrafish and mouse) in complex with either the methylation product S-adenosyl-L-homocysteine or other compounds including the first synthetic PRMT2 inhibitor (Cp1) studied so far. We reveal that the N-terminal-containing SH3 module is disordered in the full-length crystal structures, and highlights idiosyncratic features of the PRMT2 active site. We identify a new nonhistone protein substrate belonging to the serine-/arginine-rich protein family which interacts with PRMT2 and we characterize six methylation sites by mass spectrometry. To better understand structural basis for Cp1 binding, we also solve the structure of the complex PRMT4:Cp1. We compare the inhibitor-protein interactions occurring in the PRMT2 and PRMT4 complex crystal structures and show that this compound inhibits efficiently PRMT2. These results are a first step toward a better understanding of PRMT2 substrate recognition and may accelerate the development of structure-based drug design of PRMT2 inhibitors.
All coordinates and structure factors have been deposited in the Protein Data Bank: zPRMT2 -SFG = 5g02; zPRMT2 -SAH = 5fub; mPRMT2 -SAH = 5ful; mPRMT2 -Cp1 = 5fwa, mCARM1 -Cp1 = 5k8v.
PRMT2 是蛋白精氨酸甲基转移酶家族中结构、活性和细胞功能研究较少的成员。PRMT2 是一种模块化蛋白质，包含一个催化 Ado-Met 结合结构域和独特的Src 同源 3 结构域，该结构域与富含脯氨酸的模体结合。PRMT2 参与多种细胞过程，并通过不同的机制在转录调控中发挥不同的作用，具体取决于其结合伙伴。已经证明 PRMT2 在组蛋白 H4 底物上具有较弱的甲基转移酶活性，但尚未确定其最佳底物。为了深入了解 PRMT2 的功能和活性，我们解析了来自两种同源物（斑马鱼和小鼠）的 PRMT2 与甲基化产物 S-腺苷-L-同型半胱氨酸或其他化合物（包括迄今为止研究的第一个合成 PRMT2 抑制剂 Cp1）复合物的几个晶体结构。我们揭示了全长晶体结构中包含 N 端的 SH3 模块是无序的，并突出了 PRMT2 活性位点的独特特征。我们鉴定了一种新的非组蛋白蛋白底物，属于丝氨酸/精氨酸丰富蛋白家族，与 PRMT2 相互作用，并通过质谱法对六个甲基化位点进行了表征。为了更好地理解 Cp1 结合的结构基础，我们还解析了 PRMT4：Cp1 复合物的结构。我们比较了 PRMT2 和 PRMT4 复合物晶体结构中发生的抑制剂-蛋白相互作用，并表明该化合物能有效抑制 PRMT2。这些结果是深入了解 PRMT2 底物识别的第一步，可能会加速基于结构的 PRMT2 抑制剂药物设计的发展。
所有坐标和结构因子都已被存入蛋白数据库：zPRMT2-SFG = 5g02；zPRMT2-SAH = 5fub；mPRMT2-SAH = 5ful；mPRMT2-Cp1 = 5fwa，mCARM1-Cp1 = 5k8v。
