RNA polymerase inhibitors reveal active-site motions essential for the nucleotide addition cycle

• 成果类型: Article
• 署名作者: Dhingra, Yukti; Landick, Robert; Campbell, Elizabeth A.; Darst, Seth A.
• 署名单位: Rockefeller University; University of Wisconsin System; University of Wisconsin Madison; University of Wisconsin System; University of Wisconsin Madison; Rockefeller University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2609228123
• 发表日期: 2026-07-07
• 页码: e2609228123
• 关键词: allosteric inhibition; antibiotic mechanism; cryo-electron microscopy; nucleotide addition; RNA polymerase; TRIGGER LOOP FUNCTIONS; structural basis; TRANSCRIPTION INHIBITION; F LOOP; HAIRPIN; catalysis; mechanism; mediate; lacking; roles

摘要

The nucleotide addition cycle (NAC) of multisubunit DNA-dependent RNA polymerases (RNAPs) involves coordinated conformational changes in conserved active-site structural elements, including the trigger loop (TL). The TL is open (unfolded) in most RNAP structures but can close (fold) in substrate-bound (post- or pretranslocated) states of the RNAP, promoting catalysis. TL closure has been associated with closure of another conserved structural element, the Rim-Helices/F-loop (RH-FL), but the role of the RH-FL in the NAC is unclear. Antibiotic leads CBR9379 and AAP-SO2 inhibit the Escherichia coli and Mycobacterium tuberculosis RNAPs, respectively, by binding in a pocket formed by the bridge helix and RH-FL. The precise mechanism of action for these inhibitors is yet to be defined. We present cryoelectron microscopy structures showing that both compounds inhibit the RNAP NAC by preventing RH-FL closure, thereby allosterically destabilizing the closed TL. This work reveals a conserved mechanistic principle of RNAP catalysis across all domains of life and provides insight for antibiotic design.