A new class of bacterial RNA polymerase inhibitor affects nucleotide addition.
RNA polymerase (RNAP) is the central enzyme of gene expression. Despite availability of crystal structures, details of its nucleotide addition cycle remain obscure. We describe bacterial RNAP inhibitors (the CBR703 series) whose properties illuminate this mechanism. These compounds inhibit known catalytic activities of RNAP (nucleotide addition, pyrophosphorolysis, and Gre-stimulated transcript cleavage) but not translocation of RNA or DNA when translocation is uncoupled from catalysis. CBR703-resistance substitutions occur on an outside surface of RNAP opposite its internal active site. We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix.
Artsimovitch
Irina
I
Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
Chu
Clement
C
Lynch
A Simon
AS
Landick
Robert
R
D000578:Amidines / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism / Q000494:pharmacology*; D001665:Binding Sites; D002384:Catalysis; D004269:DNA, Bacterial / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D024881:Drug Resistance, Bacterial; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism / Q000494:pharmacology; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics; D005090:Exodeoxyribonucleases / Q000378:metabolism; D006898:Hydroxylamines / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism / Q000494:pharmacology*; D008958:Models, Molecular; D009154:Mutation; D009711:Nucleotides / Q000378:metabolism*; D010671:Phenylurea Compounds / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism / Q000494:pharmacology; D010879:Piperazines / Q000737:chemistry / Q000302:isolation & purification / Q000494:pharmacology; D011401:Promoter Regions, Genetic / Q000187:drug effects; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011720:Pyrazoles / Q000737:chemistry / Q000302:isolation & purification / Q000494:pharmacology; D012329:RNA, Bacterial / Q000096:biosynthesis*; D013698:Templates, Genetic; D014158:Transcription, Genetic / Q000187:drug effects*
D000578:Amidines; C478598:CBR 703; C478599:CBR 9379; C478600:CBR 9393; D004269:DNA, Bacterial; D004791:Enzyme Inhibitors; D006898:Hydroxylamines; D009711:Nucleotides; D010671:Phenylurea Compounds; D010879:Piperazines; D011720:Pyrazoles; D012329:RNA, Bacterial; D012321:DNA-Directed RNA Polymerases; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III