EMD-32166
Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation
EMD-32166
Single-particle4.0 Å
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Map released: 08/06/2022
Last modified: 26/06/2024
Sample Organism:
Escherichia coli K-12,
Escherichia coli
Sample: Rob-dependent transcription activation complex
Fitted models: 7vwz (Avg. Q-score: 0.345)
Deposition Authors: Lin W
,
Feng Y
Sample: Rob-dependent transcription activation complex
Fitted models: 7vwz (Avg. Q-score: 0.345)
Deposition Authors: Lin W
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Structural basis of transcription activation by Rob, a pleiotropic AraC/XylS family regulator.
Shi J,
Wang F,
Li F,
Wang L,
Xiong Y,
Wen A,
Jin Y,
Jin S,
Gao F,
Feng Z,
Li J,
Zhang Y,
Shang Z
,
Wang S
,
Feng Y
,
Lin W
(2022) Nucleic Acids Res , 50 , 5974 - 5987
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(2022) Nucleic Acids Res , 50 , 5974 - 5987
Abstract:
Rob, which serves as a paradigm of the large AraC/XylS family transcription activators, regulates diverse subsets of genes involved in multidrug resistance and stress response. However, the underlying mechanism of how it engages bacterial RNA polymerase and promoter DNA to finely respond to environmental stimuli is still elusive. Here, we present two cryo-EM structures of Rob-dependent transcription activation complex (Rob-TAC) comprising of Escherichia coli RNA polymerase (RNAP), Rob-regulated promoter and Rob in alternative conformations. The structures show that a single Rob engages RNAP by interacting with RNAP αCTD and σ70R4, revealing their generally important regulatory roles. Notably, by occluding σ70R4 from binding to -35 element, Rob specifically binds to the conserved Rob binding box through its consensus HTH motifs, and retains DNA bending by aid of the accessory acidic loop. More strikingly, our ligand docking and biochemical analysis demonstrate that the large Rob C-terminal domain (Rob CTD) shares great structural similarity with the global Gyrl-like domains in effector binding and allosteric regulation, and coordinately promotes formation of competent Rob-TAC. Altogether, our structural and biochemical data highlight the detailed molecular mechanism of Rob-dependent transcription activation, and provide favorable evidences for understanding the physiological roles of the other AraC/XylS-family transcription factors.
Rob, which serves as a paradigm of the large AraC/XylS family transcription activators, regulates diverse subsets of genes involved in multidrug resistance and stress response. However, the underlying mechanism of how it engages bacterial RNA polymerase and promoter DNA to finely respond to environmental stimuli is still elusive. Here, we present two cryo-EM structures of Rob-dependent transcription activation complex (Rob-TAC) comprising of Escherichia coli RNA polymerase (RNAP), Rob-regulated promoter and Rob in alternative conformations. The structures show that a single Rob engages RNAP by interacting with RNAP αCTD and σ70R4, revealing their generally important regulatory roles. Notably, by occluding σ70R4 from binding to -35 element, Rob specifically binds to the conserved Rob binding box through its consensus HTH motifs, and retains DNA bending by aid of the accessory acidic loop. More strikingly, our ligand docking and biochemical analysis demonstrate that the large Rob C-terminal domain (Rob CTD) shares great structural similarity with the global Gyrl-like domains in effector binding and allosteric regulation, and coordinately promotes formation of competent Rob-TAC. Altogether, our structural and biochemical data highlight the detailed molecular mechanism of Rob-dependent transcription activation, and provide favorable evidences for understanding the physiological roles of the other AraC/XylS-family transcription factors.