Three-dimensional structure of the E. coli DNA-binding protein FIS

The factor for inversion stimulation, FIS, is involved in several cellular processes, including site-specific recombination and transcriptional activation. In the reactions catalysed by the DNA invertases Gin, Hin and Cin, FIS stimulates recombination by binding to an enhancer sequence. Within the enhancer, two FIS dimers (each 2 x 98 amino acids) bind to two 15-base-pair consensus sequences and induce bending of the DNA. Current models propose that the enhancer-FIS complex organizes a specific synapse, either through direct interactions with Gin, or by modelling the substrate into a configuration suitable for recombination. Using X-ray analysis at 2.0 A resolution, we now show that FIS is composed of four alpha helices tightly intertwined to form a globular dimer with two protruding helix-turn-helix motifs. The 24 N-terminal amino acids are so poorly defined in the electron density map as to make interpretation doubtful, indicating that they might act as 'feelers' suitable for DNA or protein (invertase) recognition. We infer from model building that DNA has to bend for tight binding to FIS.