Crystal structure of Pseudomonas aeruginosa transcriptional regulator PA2196 bound to its operator DNA

Pseudomonas aeruginosa is a major opportunistic human pathogen. PA2196 from P. aeruginosa is a member of TetR family of transcriptional repressors, which is involved in adaptation to environmental changes as well as bacterial antibiotic resistance. PA2196 consists of nine α-helical bundles divided into two separate domains. The N-terminal domain, called the DNA-binding domain, is composed of helices α1-α3 and has a helix-turn-helix motif. The C-terminal domain, called the ligand-binding domain, has a hydrophobic pocket for ligand binding. Here, PA2196 was shown to bind to a 25 bp semi-palindromic dsDNA located in the upstream region of its own gene. The crystal structure of the PA2196-25mer dsDNA complex determined at a resolution of 2.9 Å revealed that two dimers of PA2196 bound to one dsDNA, with each monomer interacting with the major groove of DNA. Especially, residues in helix α3, including Lys41, Gly42, Ser43, and Tyr45, interacted mainly with the base and phosphate backbone of dsDNA. PA2196 underwent large conformational changes upon DNA binding, as the distances between DNA-binding domains measured between two G42s in subunits A and B decreased from 41.7 Å to 36.8 Å. Our crystal structure of PA2196-25mer dsDNA complex revealed that PA2196 is similar to QacR in that two dimers bound to one dsDNA through specific interactions.