9LEW

The crystal structure of DinJ-YafQ complex from Vibrio cholerae

Summary for 9LEW

• Entry DOI: 10.2210/pdb9lew/pdb
• Descriptor: DNA-damage-inducible protein J, Type II toxin-antitoxin system YafQ family toxin, SULFATE ION, ... (5 entities in total)
• Functional Keywords: toxin-antitoxin complex, dna binding protein, toxin, antitoxin
• Biological source: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961); More
• Total number of polymer chains: 8
• Total formula weight: 87681.23

Authors

Mun, S.A.,Ha, J.H.,Jang, T.H.,Hong, E.,Bae, J.,Son, J. (deposition date: 2025-01-07, release date: 2025-07-30)

Primary citation

Mun, S.A.,Yeon, G.B.,Park, Y.H.,Yoon, H.,Ha, J.H.,Jang, T.H.,Hong, E.,Bae, J.,Son, J.
Novel oligomerization state of DinJ-YafQ complex from Vibrio cholerae-Structural and biochemical insights.
Int.J.Biol.Macromol., 320:145865-145865, 2025

PubMed Abstract: Toxin-antitoxin (TA) systems are widely distributed in archaeal and bacterial genomes and are crucial for maintaining the physiological functions required for cellular homeostasis. The DinJ-YafQ TA system belongs to the well-known RelBE family of Type II TA systems. Vibrio cholerae, the causative agent of cholera, infects humans through the consumption of contaminated, unpurified drinking water. Its genome contains a cassette of 19 TA system-related genes located on chromosome II, six of which are classified under the RelBE family. Herein, we determined the crystal structure of the V. cholerae DinJ (VcDinJ, antitoxin)-YafQ (VcYafQ, toxin) complex at 2.3 Å resolution. The unique orientation of the VcDinJ RHH motifs relative to the YafQ molecules promotes the formation of a highly oligomerized hetero-hexadecamer (16-mer) in a concentration-dependent manner. According to biochemical experiments, the VcDinJ-YafQ complex directly binds to the promoter region of its operon, suggesting its role as a transcriptional repressor. An autoregulatory mechanism in which DNA binding induces conformational changes is suggested based on structural modeling through DNA superposition. This finding supports the concentration-dependent and DNA-associated oligomerization of the VcDinJ-YafQ complex.

PubMed: 40639525
DOI: 10.1016/j.ijbiomac.2025.145865

Experimental method

X-RAY DIFFRACTION (2.3 Å)