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TitleFidaxomicin jams RNA polymerase motions needed for initiation via RbpA contacts.
Journal, issue, pagesElife, Vol. 7, Year 2018
Publish dateFeb 26, 2018
AuthorsHande Boyaci / James Chen / Mirjana Lilic / Margaret Palka / Rachel Anne Mooney / Robert Landick / Seth A Darst / Elizabeth A Campbell /
PubMed AbstractFidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against RNAP in vitro, but clinical use of Fdx is limited to treating intestinal infections due to poor ...Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against RNAP in vitro, but clinical use of Fdx is limited to treating intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on . Additional structures define conformational states of RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket.
External linksElife / PubMed:29480804 / PubMed Central
MethodsEM (single particle)
Resolution3.27 - 5.15 Å
Structure data

7319

6bzo

EMDB-7319, PDB-6bzo:
Mtb RNAP Holo/RbpA/Fidaxomicin/upstream fork DNA
Method: EM (single particle) / Resolution: 3.38 Å

7320

6c04

EMDB-7320, PDB-6c04:
Mtb RNAP Holo/RbpA/double fork DNA -closed clamp
Method: EM (single particle) / Resolution: 3.27 Å

7322

6c05

EMDB-7322, PDB-6c05:
Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state
Method: EM (single particle) / Resolution: 5.15 Å

7323

6c06

EMDB-7323, PDB-6c06:
Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin
Method: EM (single particle) / Resolution: 5.15 Å

Chemicals

ChemComp-FI8:
Fidaxomicin / antibiotic*YM

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • mycobacterium tuberculosis (bacteria)
Keywordstranscription/dna/antibiotic / RNA Polymerase / Antibiotic / Inhibitor / TRANSCRIPTION / transcription-dna-antibiotic complex / transcription/dna / initiation / transcription bubble / closed clamp / transcription-dna complex / transcription/antibiotic / switch region inhibitor / transcription-antibiotic complex

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