Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions.
Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions.
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ClpC1 的 N 端结构域与抗结核天然产物 ecumicin 复合物的结构揭示了独特的结合相互作用。
DOI：
10.1107/s2059798320004027
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Abad-Zapatero,Celerino
中科院分区：
文献类型：
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作者：
Wolf,NinaM;Lee,Hyun;Zagal,Daniel;Nam,JooWon;Oh,DongChan;Lee,Hanki;Suh,JooWon;Pauli,GuidoF;Cho,Sanghyun;Abad-Zapatero,Celerino
结核的病原结核分枝杆菌中与蛋白质稳态相关的生物学过程最近被确定为治疗干预的关键途径。特别感兴趣的蛋白质是ClpC1和ClpC1 - clpp1 - clpp2蛋白酶体复合物。本文介绍了一种有效的抗结核大环沉积肽ecumicin与ClpC1 n端结构域（ClpC1- ntd）络合的结构。ClpC1-NTD-ecumicin复合物的晶体为单斜晶（单位细胞参数a = 80.0, b = 130.0, c = 112.0 Å， β = 90.07°；空间群P21；每个不对称单元12个配合物），衍射分辨率为2.5 Å。利用自旋函数解决空间群歧义，采用分子置换法求解结构。新结构的ecumicin复合物具有独特的1:2（目标：配体）化学计量，利用了目标n端结构域α-螺旋折叠中的分子内二元结构。ecumicin复合物的结构揭示了在独特延伸的n端上广泛的相互作用，n端是已知环肽复合物的关键结合位点。与先前报道的rufoomycin I复合物相比，该结构揭示了可能与理解这些潜在抗结核药物先导物的作用机制相关的独特特征。将ecumicin复合物和ClpC1-NTD-L92S/L96P双突变结构与rufomycin I和cycloomarin A复合物的可用结构进行比较，揭示了该小n端螺旋结构域的一系列构象变化以及参与抗生素耐药机制的微小螺旋改变。不同的结合模式和结构改变可能与不同的作用模式有关。
The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1–ClpP1–ClpP2 proteasome complex. The structure of the potent antituberculosis macrocyclic depsipeptide ecumicin complexed with the N-terminal domain of ClpC1 (ClpC1-NTD) is presented here. Crystals of the ClpC1-NTD–ecumicin complex were monoclinic (unit-cell parameters a = 80.0, b = 130.0, c = 112.0 Å, β = 90.07°; space group P21; 12 complexes per asymmetric unit) and diffracted to 2.5 Å resolution. The structure was solved by molecular replacement using the self-rotation function to resolve space-group ambiguities. The new structure of the ecumicin complex showed a unique 1:2 (target:ligand) stoichiometry exploiting the intramolecular dyad in the α-helical fold of the target N-terminal domain. The structure of the ecumicin complex unveiled extensive interactions in the uniquely extended N-terminus, a critical binding site for the known cyclopeptide complexes. This structure, in comparison with the previously reported rufomycin I complex, revealed unique features that could be relevant for understanding the mechanism of action of these potential antituberculosis drug leads. Comparison of the ecumicin complex and the ClpC1-NTD-L92S/L96P double-mutant structure with the available structures of rufomycin I and cyclomarin A complexes revealed a range of conformational changes available to this small N-terminal helical domain and the minor helical alterations involved in the antibiotic-resistance mechanism. The different modes of binding and structural alterations could be related to distinct modes of action.