8T0L

E. coli Sw2/Snf2 ATPase RapA bound to both ADP-AlF3 and reconstituted E. coli RNA polymerase post-termination complex on negatively-supercoiled DNA

Summary for 8T0L

• Entry DOI: 10.2210/pdb8t0l/pdb
• EMDB information: 40943
• Descriptor: DNA-directed RNA polymerase subunit alpha, ADENOSINE-5'-DIPHOSPHATE, ALUMINUM FLUORIDE, ... (11 entities in total)
• Functional Keywords: rna polymerase, negatively supercoiled dna, sigma-independent transcription, rapa, rnap recycling, sw2/snf2 atpase, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 484284.91

Authors

Brewer, J.J.,Darst, S.A.,Campbell, E.A. (deposition date: 2023-06-01, release date: 2025-04-02)

Primary citation

Brewer, J.J.,Inlow, K.,Mooney, R.A.,Bosch, B.,Olinares, P.D.B.,Marcelino, L.P.,Chait, B.T.,Landick, R.,Gelles, J.,Campbell, E.A.,Darst, S.A.
RapA opens the RNA polymerase clamp to disrupt post-termination complexes and prevent cytotoxic R-loop formation.
Nat.Struct.Mol.Biol., 2025

PubMed Abstract: Following transcript release during intrinsic termination, Escherichia coli RNA polymerase (RNAP) often remains associated with DNA in a post-termination complex (PTC). RNAPs in PTCs are removed from the DNA by the SWI2/SNF2 adenosine triphosphatase (ATPase) RapA. Here we determined PTC structures on negatively supercoiled DNA and with RapA engaged to dislodge the PTC. We found that core RNAP in the PTC can unwind DNA and initiate RNA synthesis but is prone to producing R-loops. Nucleotide binding to RapA triggers a conformational change that opens the RNAP clamp, allowing DNA in the RNAP cleft to reanneal and dissociate. We show that RapA helps to control cytotoxic R-loop formation in vivo, likely by disrupting PTCs. We suggest that analogous ATPases acting on PTCs to suppress transcriptional noise and R-loop formation may be widespread. These results hold importance for the bacterial transcription cycle and highlight a role for RapA in maintaining genome stability.

PubMed: 39779919
DOI: 10.1038/s41594-024-01447-8

Experimental method

ELECTRON MICROSCOPY (3.62 Å)