9CU3

Allosteric mechanism of DriD transcription activator

Summary for 9CU3

• Entry DOI: 10.2210/pdb9cu3/pdb
• Descriptor: WYL domain-containing protein, GLYCEROL, SULFATE ION, ... (4 entities in total)
• Functional Keywords: transcription, activation, dna binding protein
• Biological source: Caulobacter vibrioides CB15
• Total number of polymer chains: 2
• Total formula weight: 59951.74

Authors

Cannistraci, E.G.,Schumacher, M.A. (deposition date: 2024-07-25, release date: 2025-04-23, Last modification date: 2025-11-05)

Primary citation

Cannistraci, E.,Srinivasu, B.Y.,Chavez Orozco Jr., J.,Gozzi, K.,Wales, T.E.,Schumacher, M.A.
Allosteric activation mechanism of DriD, a WYL-domain containing transcription regulator.
Commun Biol, 8:679-679, 2025

PubMed Abstract: WYL-domain containing transcription factors regulate fundamental processes in bacterial physiology, yet how these proteins sense cellular cues to elicit an allosteric response is not well understood. Here we describe the allosteric activation mechanism of DriD, a Caulobacter crescentus homodimeric WYL-domain containing transcription regulator that activates a non-canonical DNA damage pathway. DriD senses ssDNA, produced upon DNA damage via interaction with its WYL domain. This stimulates DriD target DNA binding. However, its DNA-binding domains (DNABDs) are 50 Å from the WYL-domains and linked by a three-helix bundle domain (3HB). Using a combination of crystallography, biochemistry, and HDX-MS we unveil an allosteric mechanism whereby an inhibitory interaction, formed between the DriD DNABD and 3HB in the apo form, is freed upon ssDNA binding, allowing target DNA binding. These findings may serve as a model for understanding activation by the large family of homodimeric WYL activators, including those in pathogenic bacteria.

PubMed: 40301632
DOI: 10.1038/s42003-025-08111-x

Experimental method

X-RAY DIFFRACTION (1.9 Å)