9GDA

RNAP-TopoI complex on duplex scaffold

Summary for 9GDA

• Entry DOI: 10.2210/pdb9gda/pdb
• EMDB information: 51259
• Descriptor: DNA-directed RNA polymerase subunit alpha, ZINC ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• Functional Keywords: rna polymerase, topoisomerase, dna topology, transcription
• Biological source: Escherichia coli; More
• Total number of polymer chains: 9
• Total formula weight: 520031.48

Authors

Vidmar, V.,Weixlbaumer, A.,Lamour, V. (deposition date: 2024-08-05, release date: 2025-11-05, Last modification date: 2025-12-17)

Primary citation

Vidmar, V.,Borde, C.,Bruno, L.,Miropolskaya, N.,Takacs, M.,Batisse, C.,Saint-Andre, C.,Zhu, C.,Espeli, O.,Lamour, V.,Weixlbaumer, A.
DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation.
Nat.Struct.Mol.Biol., 2025

PubMed Abstract: During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we elucidated how bacterial RNAP and DNA topoisomerase I (TopoI), which relaxes negative supercoils, operate in close spatial proximity. TopoI binds to relaxed DNA upstream of RNAP, and this involves a conformational switch in the TopoI functional domains. This suggests that TopoI exerts a sensing role before the formation of negative supercoils. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage and binds the complementary strand with an auxiliary domain. Transcriptomic and phenotypic analyses suggest that mutations affecting conformational changes in TopoI impact gene expression and operon polarity in bacteria. In summary, we propose a comprehensive model for DNA relaxation in the proximity of active bacterial transcription.

PubMed: 41326756
DOI: 10.1038/s41594-025-01703-5

Experimental method

ELECTRON MICROSCOPY (2.7 Å)