8U3B

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

Summary for 8U3B

• Entry DOI: 10.2210/pdb8u3b/pdb
• EMDB information: 41856
• Descriptor: DNA-directed RNA polymerase subunit alpha, ZINC ION, MAGNESIUM ION, ... (11 entities in total)
• Functional Keywords: transcription, rna polymerase, transcription activation, narl, nitrate-responsive regulator, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 11
• Total formula weight: 523313.91

Authors

Liu, B.,Kompaniiets, D.,Wang, D. (deposition date: 2023-09-07, release date: 2024-01-17, Last modification date: 2024-02-21)

Primary citation

Kompaniiets, D.,He, L.,Wang, D.,Zhou, W.,Yang, Y.,Hu, Y.,Liu, B.
Structural basis for transcription activation by the nitrate-responsive regulator NarL.
Nucleic Acids Res., 52:1471-1482, 2024

PubMed 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.

PubMed: 38197271
DOI: 10.1093/nar/gkad1231

Experimental method

ELECTRON MICROSCOPY (3.23 Å)