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

Molecular cell (2018-04-03)
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 Zhang, Changsheng Zhang, Achillefs N Kapanidis, Richard H Ebright
RESUMO

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.

MATERIAIS
Número do produto
Marca
Descrição do produto

Sigma-Aldrich
(±)-6-Hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid, 97%
Sigma-Aldrich
Chloramphenicol, ≥98% (HPLC)
Sigma-Aldrich
L-(+)-Arabinose, ≥99%
Sigma-Aldrich
Ampicillin sodium salt, powder or crystals, BioReagent, suitable for cell culture
Sigma-Aldrich
Benzyl bromide, reagent grade, 98%
Sigma-Aldrich
Kanamycin sulfate from Streptomyces kanamyceticus, Animal Component-free
Sigma-Aldrich
Sodium acrylate, 97%