Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin.
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 A 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.
Skordalakes
Emmanuel
E
Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
Brogan
Andrew P
AP
Park
Boon Saeng
BS
Kohn
Harold
H
Berger
James M
JM
D000251:Adenosine Triphosphatases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000037:antagonists & inhibitors; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001665:Binding Sites; D019086:Bridged Bicyclo Compounds, Heterocyclic / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D015394:Molecular Structure; D009154:Mutation; D011485:Protein Binding; D012234:Rho Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013059:Spectrum Analysis, Raman; D013329:Structure-Activity Relationship; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic
D000900:Anti-Bacterial Agents; D019086:Bridged Bicyclo Compounds, Heterocyclic; D012234:Rho Factor; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases; C024504:bicozamycin