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Mol Cell. 2018 Apr 5;70(1):60-71.e15. doi: 10.1016/j.molcel.2018.02.026. Epub 2018 Mar 29.

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).

Author information

1
Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA.
2
Rega Institute and Department of Microbiology and Immunology, KU Leuven, 3000 Leuven, Belgium. Electronic address: kalyan.das@kuleuven.be.
3
Department of Physics, University of Oxford, Oxford OX1 3PU, UK.
4
The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York NY 10027, USA.
5
Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA.
6
NAICONS Srl., 20139 Milan, Italy.
7
South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
8
Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA. Electronic address: ebright@waksman.rutgers.edu.

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.

KEYWORDS:

Mycobacterium tuberculosis; RNA polymerase; RNA polymerase clamp; RNA polymerase inhibitor; RNA polymerase switch region; antibiotic; cryo-electron microscopy; fidaxomicin; lipiarmycin; single-molecule fluorescence resonance energy transfer

PMID:
29606590
PMCID:
PMC6205224
[Available on 2019-04-05]
DOI:
10.1016/j.molcel.2018.02.026
[Indexed for MEDLINE]

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