6ASG image
Entry Detail
PDB ID:
6ASG
Keywords:
Title:
Crystal structure of Thermus thermophilus RNA polymerase core enzyme
Biological Source:
PDB Version:
Deposition Date:
2017-08-24
Release Date:
2018-04-11
Method Details:
Experimental Method:
Resolution:
3.80 Å
R-Value Free:
0.27
R-Value Work:
0.22
R-Value Observed:
0.23
Space Group:
H 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit alpha
Chain IDs:C (auth: A), D (auth: B)
Chain Length:315
Number of Molecules:2
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit beta
Chain IDs:A (auth: C)
Chain Length:1119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit beta'
Chain IDs:B (auth: D)
Chain Length:1524
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase subunit omega
Chain IDs:E
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Primary Citation
Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).
Mol. Cell 70 60 71.e15 (2018)
PMID: 29606590 DOI: 10.1016/j.molcel.2018.02.026

Abstact

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.

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