6OUL image
Deposition Date 2019-05-04
Release Date 2020-02-26
Last Version Date 2024-03-20
Entry Detail
PDB ID:
6OUL
Keywords:
Title:
Cryo-EM structure of Escherichia coli RNAP polymerase bound to rpsTP2 promoter DNA
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Chain IDs:A (auth: G), B (auth: H), I (auth: R)
Chain Length:329
Number of Molecules:3
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Chain IDs:C (auth: I)
Chain Length:1342
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Chain IDs:D (auth: J)
Chain Length:1430
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Chain IDs:E (auth: K)
Chain Length:91
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:RNA polymerase sigma factor RpoD
Chain IDs:F (auth: L)
Chain Length:616
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template strand of rpsTP2 DNA promoter
Chain IDs:G (auth: P)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polydeoxyribonucleotide
Molecule:Template strand of rpsTP2 DNA promoter
Chain IDs:H (auth: Q)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli K-12
Primary Citation
E. coliTraR allosterically regulates transcription initiation by altering RNA polymerase conformation.
Elife 8 ? ? (2019)
PMID: 31841111 DOI: 10.7554/eLife.49375

Abstact

TraR and its homolog DksA are bacterial proteins that regulate transcription initiation by binding directly to RNA polymerase (RNAP) rather than to promoter DNA. Effects of TraR mimic the combined effects of DksA and its cofactor ppGpp, but the structural basis for regulation by these factors remains unclear. Here, we use cryo-electron microscopy to determine structures of Escherichia coli RNAP, with or without TraR, and of an RNAP-promoter complex. TraR binding induced RNAP conformational changes not seen in previous crystallographic analyses, and a quantitative analysis revealed TraR-induced changes in RNAP conformational heterogeneity. These changes involve mobile regions of RNAP affecting promoter DNA interactions, including the βlobe, the clamp, the bridge helix, and several lineage-specific insertions. Using mutational approaches, we show that these structural changes, as well as effects on σ70 region 1.1, are critical for transcription activation or inhibition, depending on the kinetic features of regulated promoters.

Legend

Protein

Chemical

Disease

Primary Citation of related structures