7VWZ

Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation

Summary for 7VWZ

• Entry DOI: 10.2210/pdb7vwz/pdb
• EMDB information: 32166
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, DNA-directed RNA polymerase subunit beta, ... (10 entities in total)
• Functional Keywords: bacterial rna polymerase, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 10
• Total formula weight: 569742.46

Authors

Lin, W.,Feng, Y.,Shi, J. (deposition date: 2021-11-12, release date: 2022-06-08, Last modification date: 2024-06-26)

Primary citation

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.
Structural basis of transcription activation by Rob, a pleiotropic AraC/XylS family regulator.
Nucleic Acids Res., 50:5974-5987, 2022

PubMed 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.

PubMed: 35641097
DOI: 10.1093/nar/gkac433

Experimental method

ELECTRON MICROSCOPY (4 Å)