Introduction - This script shows the structure of the complex between the DNA-binding protein PurR and its target DNA. PurR acts a repressor for several genes that make purines. [Based on 2pugf.pdb - M.A.Schumaker, K.Y.Choi, H.Zalkin, R.G.Brennan, Science 266 763 (1994)].
Here we see PurR bound to DNA. The dimeric protein (MAGENTA and GREEN) binds to DNA via the N-terminal domain. The large C-terminal domain is responsible for dimer formation. The co-repressor, hypoxanthine (YELLOW spacefill) stablizes dimer formation.
The repressor binds to the major groove of the DNA through a helix-turn-helix motif (spacefill).
In addition, another helix from each monomer (CYAN) binds to the minor groove.
The interaction with the minor groove causes the minor groove to unwind, as shown by the space in the center of the groove.
The DNA is also severely bent around the minor groove, as shown here. These structural changes are somehow responsible for silencing gene expression.