Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome
Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome
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DOI：
10.1073/pnas.1604790113
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发表时间：
2016-07-05
影响因子：
11.1
通讯作者：
Wilson, Daniel N.
中科院分区：
文献类型：
--
作者：
Arenz, Stefan;Juette, Manuel F.;Wilson, Daniel N.
核糖体是治疗性抗生素的主要靶标之一。然而，多重耐药性的增加对我们现有武器库的利用构成了越来越大的威胁。正霉素类抗生素依尼米星 (EVN) 和阿维拉霉素 (AVI) 以核糖体为靶点，与任何其他类别的抗生素不表现出交叉耐药性，这表明它们与核糖体上的独特位点结合，因此可能代表了开发新抗菌药物的一种途径。在这里，我们展示了 EVN 和 AVI 与大肠杆菌核糖体复合物的冷冻电镜结构，分辨率为 3.6 至 3.9 埃。这些结构表明，EVN 和 AVI 与大亚基上的单个位点结合，该位点与核糖体上其他已知的抗生素结合位点不同。两种抗生素均采用延伸构象，跨越 23S rRNA 螺旋 89 和 91 的小沟，并与核糖体蛋白 L16 的精氨酸残基相互作用。该结合位点与 A 位点结合 tRNA 的肘区重叠。与这一发现一致，单分子 FRET (smFRET) 实验表明，两种抗生素都会干扰调节过程的后期步骤，其中氨酰基-tRNA 进入大核糖体亚基的肽基转移酶中心。这些数据为这些抗生素如何抑制蛋白质合成的延伸阶段提供了结构和机制原理。
The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-angstrom resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis.