9R35

Crystal structure of the Pseudomonas putida Xre-RES toxin-antitoxin complex bound to promoter DNA

Summary for 9R35

• Entry DOI: 10.2210/pdb9r35/pdb
• Descriptor: Toxin Res, XRE anti-toxin, DNA reverse (30-mer), ... (5 entities in total)
• Functional Keywords: protein-dna complex, res toxin, xre antitoxin, gene regulation
• Biological source: Pseudomonas putida KT2440; More
• Total number of polymer chains: 32
• Total formula weight: 485632.75

Authors

Henriksen, F.O.G.,Brodersen, D.E. (deposition date: 2025-05-02, release date: 2025-08-20, Last modification date: 2025-09-03)

Primary citation

Henriksen, F.O.G.,Van, L.B.,Brodersen, D.E.,Skjerning, R.B.
Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.
Plos Genet., 21:e1011749-e1011749, 2025

PubMed Abstract: Transcriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechanistic and structural insights into this phenomenon remain limited. The Pseudomonas putida toxin-antitoxin (TA) system Xre-RES has an unusual 4:2 stoichiometry including two potential DNA-binding sites, compatible with a complex mechanism of transcriptional autoregulation. Here, we show that the Xre-RES complex interacts specifically with a palindromic DNA repeat in the promoter in a 1:1 molar ratio, leading to transcriptional repression. We determine the 2.7 Å crystal structure of the protein-DNA complex, revealing an unexpected asymmetry in the interaction and suggesting the presence of a secondary binding site, which is supported by structural prediction of the binding to the intact promoter region. Additionally, we show that the antitoxin can be partially dislodged from the Xre-RES complex, resulting in Xre monomers and a 2:2 Xre-RES complex, neither of which repress transcription. These findings highlight a dynamic, concentration-dependent model of transcriptional autoregulation, in which the Xre-RES complex transitions between a non-binding (2:2) and a DNA-binding (4:2) form.

PubMed: 40577318
DOI: 10.1371/journal.pgen.1011749

Experimental method

X-RAY DIFFRACTION (2.7 Å)