Bacterial transcription relies on a multisubunit DNA-dependent RNA polymerase holoenzyme core composed of two alpha, one beta encoded by rpoB, one beta-prime encoded by rpoC and one omega subunit plus sigma factor for promoter recognition. Rifampin belonging to rifamycin ansamycin class fits snugly into a deep hydrophobic pocket within the beta subunit located inside the main DNA-RNA channel but more than 12 angstroms away from the catalytic Mg2+ center that coordinates nucleotide addition. By occupying this pocket, the drug sterically obstructs the path for nascent RNA chains longer than two to three nucleotides, preventing productive elongation after initiation. The RNA-DNA hybrid cannot extend beyond short abortive transcripts, full-length mRNA synthesis collapses and transcription aborts. Mammalian RNA polymerases I, II, III lack this conserved pocket, giving exquisite selective toxicity. Single point mutations in rpoB at cluster I, especially S531L and H526Y, alter pocket geometry and confer high-level resistance well documented in Mycobacterium tuberculosis surveillance, which underlies rifampin use as first-line antitubercular and as molecular marker of multidrug resistance.
Ref:
Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: Bacterial RNA Polymerase and Rifampin Mechanism.
