Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3)

Wei Lin, Kalyan Das, David Degen, Abhishek Mazumder, Diego Duchi, Dongye Wang, Yon W. Ebright, Richard Y. Ebright, Elena Sineva, Matthew Gigliotti, Aashish Srivastava, Sukhendu Mandal, Yi Jiang, Yu Liu, Ruiheng Yin, Zhening Zhang, Edward T. Eng, Dennis Thomas, Stefano Donadio, Haibo ZhangChangsheng Zhang, Achillefs N. Kapanidis, Richard H. Ebright

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Abstract

Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution. The structure shows that Lpm binds at the base of the RNAP “clamp.” The structure exhibits an open conformation of the RNAP clamp, suggesting that Lpm traps an open-clamp state. Single-molecule fluorescence resonance energy transfer experiments confirm that Lpm traps an open-clamp state and define effects of Lpm on clamp dynamics. We suggest that Lpm inhibits transcription by trapping an open-clamp state, preventing simultaneous interaction with promoter −10 and −35 elements. The results account for the absence of cross-resistance between Lpm and other RNAP inhibitors, account for structure-activity relationships of Lpm derivatives, and enable structure-based design of improved Lpm derivatives. Lin et al. report cryo-EM and single-molecule spectroscopic analyses of the antibacterial drug fidaxomicin bound to its molecular target, RNA polymerase. The results define the structure of the drug-target complex, show that fidaxomicin traps the RNA polymerase clamp in an open conformational state, and enable structure-based design of improved fidaxomicin analogs.

Original languageEnglish (US)
Pages (from-to)60-71.e15
JournalMolecular cell
Volume70
Issue number1
DOIs
StatePublished - Apr 5 2018

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All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Cell Biology

Cite this

Lin, W., Das, K., Degen, D., Mazumder, A., Duchi, D., Wang, D., Ebright, Y. W., Ebright, R. Y., Sineva, E., Gigliotti, M., Srivastava, A., Mandal, S., Jiang, Y., Liu, Y., Yin, R., Zhang, Z., Eng, E. T., Thomas, D., Donadio, S., ... Ebright, R. H. (2018). Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular cell, 70(1), 60-71.e15. https://doi.org/10.1016/j.molcel.2018.02.026