9Q97

CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2

9Q97 の概要

• エントリーDOI: 10.2210/pdb9q97/pdb
• EMDBエントリー: 52947
• 分子名称: RNA polymerase sigma-54 factor, ALUMINUM FLUORIDE, MAGNESIUM ION, ... (11 entities in total)
• 機能のキーワード: sigma factor, transcription, complex, aaa+, dna-binding protein
• 由来する生物種: Klebsiella pneumoniae; 詳細
• タンパク質・核酸の鎖数: 14
• 化学式量合計: 643476.07

構造登録者

Gao, F.,Zhang, X. (登録日: 2025-02-26, 公開日: 2025-03-26, 最終更新日: 2025-07-02)

主引用文献

Gao, F.,Ye, F.,Buck, M.,Zhang, X.
Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling.
Proc.Natl.Acad.Sci.USA, 122:e2425868122-e2425868122, 2025

PubMed Abstract: Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need to be transcribed, with 60% bacteria containing at least one specialized σ factor, σ. σ recruits RNAP to promoters of genes associated with stress responses and forms a stable closed complex that does not spontaneously isomerize to the open state where promoter DNA is melted out and competent for transcription. The σ-mediated open complex formation requires specific AAA+ proteins (TPases ssociated with diverse cellular ctivities) known as bacterial enhancer-binding proteins (bEBPs). We have now obtained structures of new intermediate states of bEBP-bound complexes during transcription initiation, which elucidate the mechanism of DNA melting driven by ATPase activity of bEBPs and suggest a mechanistic model that couples the Adenosine triphosphate (ATP) hydrolysis cycle within the bEBP hexamer with σ unfolding. Our data reveal that bEBP forms a nonplanar hexamer with the hydrolysis-ready subunit located at the furthest/highest point of the spiral hexamer relative to the RNAP. ATP hydrolysis induces conformational changes in bEBP that drives a vectoral transiting of the regulatory N terminus of σ into the bEBP hexamer central pore causing the partial unfolding of σ, while forming specific bEBP contacts with promoter DNA. Furthermore, our data suggest a mechanism of the bEBP AAA+ protein that is distinct from the hand-over-hand mechanism proposed for many other AAA+ proteins, highlighting the versatile mechanisms utilized by the large protein family.

PubMed: 40273105
DOI: 10.1073/pnas.2425868122

実験手法

ELECTRON MICROSCOPY (4.6 Å)