@article{615f8f68bd984fa8b2e1f80e279b4561,
title = "Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3)",
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-{\AA} 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.",
author = "Wei Lin and Kalyan Das and David Degen and Abhishek Mazumder and Diego Duchi and Dongye Wang and Ebright, {Yon W.} and Ebright, {Richard Y.} and Elena Sineva and Matthew Gigliotti and Aashish Srivastava and Sukhendu Mandal and Yi Jiang and Yu Liu and Ruiheng Yin and Zhening Zhang and Eng, {Edward T.} and Dennis Thomas and Stefano Donadio and Haibo Zhang and Changsheng Zhang and Kapanidis, {Achillefs N.} and Ebright, {Richard H.}",
note = "Funding Information: This work was supported by a Rega Foundation award (to K.D.) and NIH grants GM041376 , AI104660 , and AI109713-01 (to R.H.E.). We thank W. Fenical, H. Irschik, R. Jansen, A. L. Sonenshein, and E. Steinbrecher for compounds; J. Mukhopadhyay, S. Rodrigue, and J. Swezey for strains and plasmids; A.P.S. at Argonne National Laboratory for beamline access; the Rutgers University cryo-EM facility and the National Resource for Automated Molecular Microscopy (supported by NIH grant GM103310 and Simons Foundation grant 349247 ) for cryo-EM access; and K. Callanan, B. Carragher, and C. Potter for discussion. Funding Information: This work was supported by a Rega Foundation award (to K.D.) and NIH grants GM041376, AI104660, and AI109713-01 (to R.H.E.). We thank W. Fenical, H. Irschik, R. Jansen, A. L. Sonenshein, and E. Steinbrecher for compounds; J. Mukhopadhyay, S. Rodrigue, and J. Swezey for strains and plasmids; A.P.S. at Argonne National Laboratory for beamline access; the Rutgers University cryo-EM facility and the National Resource for Automated Molecular Microscopy (supported by NIH grant GM103310 and Simons Foundation grant 349247) for cryo-EM access; and K. Callanan, B. Carragher, and C. Potter for discussion. Publisher Copyright: {\textcopyright} 2018 Elsevier Inc.",
year = "2018",
month = apr,
day = "5",
doi = "10.1016/j.molcel.2018.02.026",
language = "English (US)",
volume = "70",
pages = "60--71.e15",
journal = "Molecular Cell",
issn = "1097-2765",
publisher = "Cell Press",
number = "1",
}