Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin

Emmanuel Skordalakes, Andrew P. Brogan, Boon Saeng Park, Harold Kohn, James M. Berger

Research output: Contribution to journalArticlepeer-review

Abstract

Rho is a hexameric RNA/DNA helicase/translocase that terminates transcription of select genes in bacteria. The naturally occurring antibiotic, bicyclomycin (BCM), acts as a noncompetitive inhibitor of ATP turnover to disrupt this process. We have determined three independent X-ray crystal structures of Rho complexed with BCM and two semisynthetic derivatives, 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB) and 5a-formylbicyclomycin (FB) to 3.15, 3.05, and 3.15 Å resolution, respectively. The structures show that BCM and its derivatives are nonnucleotide inhibitors that interact with Rho at a pocket adjacent to the ATP and RNA binding sites in the C-terminal half of the protein. BCM association prevents ATP turnover by an unexpected mechanism, occluding the binding of the nucleophilic water molecule required for ATP hydrolysis. Our data explain why only certain elements of BCM have been amenable to modification and serve as a template for the design of new inhibitors.

Original languageEnglish (US)
Pages (from-to)99-109
Number of pages11
JournalStructure
Volume13
Issue number1
DOIs
StatePublished - Jan 2005
Externally publishedYes

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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