EMD-41856

Single-particle
3.23 Å
EMD-41856 Deposition: 07/09/2023
Map released: 17/01/2024
Last modified: 21/02/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
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EMD-41856

Cryo-EM structure of E. coli NarL-transcription activation complex at 3.2A

EMD-41856

Single-particle
3.23 Å
EMD-41856 Deposition: 07/09/2023
Map released: 17/01/2024
Last modified: 21/02/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Escherichia coli
Sample: E. coli NarL transcription activation complex on the yeaR promoter
Fitted models: 8u3b (Avg. Q-score: 0.454)

Deposition Authors: Liu B , Kompaniiets D, Wang D
Structural basis for transcription activation by the nitrate-responsive regulator NarL.
Kompaniiets D, He L, Wang D, Zhou W , Yang Y, Hu Y , Liu B
(2024) Nucleic Acids Res , 52 , 1471 - 1482
PUBMED: 38197271
DOI: doi:10.1093/nar/gkad1231
ISSN: 1362-4962
ASTM: NARHAD
Abstract:
Transcription activation is a crucial step of regulation during transcription initiation and a classic check point in response to different stimuli and stress factors. The Escherichia coli NarL is a nitrate-responsive global transcription factor that controls the expression of nearly 100 genes. However, the molecular mechanism of NarL-mediated transcription activation is not well defined. Here we present a cryo-EM structure of NarL-dependent transcription activation complex (TAC) assembled on the yeaR promoter at 3.2 Å resolution. Our structure shows that the NarL dimer binds at the -43.5 site of the promoter DNA with its C-terminal domain (CTD) not only binding to the DNA but also making interactions with RNA polymerase subunit alpha CTD (αCTD). The key role of these NarL-mediated interactions in transcription activation was further confirmed by in vivo and in vitro transcription assays. Additionally, the NarL dimer binds DNA in a different plane from that observed in the structure of class II TACs. Unlike the canonical class II activation mechanism, NarL does not interact with σ4, while RNAP αCTD is bound to DNA on the opposite side of NarL. Our findings provide a structural basis for detailed mechanistic understanding of NarL-dependent transcription activation on yeaR promoter and reveal a potentially novel mechanism of transcription activation.