Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7

YdaT is a functional equivalent of the CII repressor in certain lambdoid phages and prophages. YdaT from the cryptic prophage CP-933P in the genome of Escherichia coli O157:H7 is functional as a DNA binding protein and recognizes a 5'-TTGATTN6AATCAA-3' inverted repeat. The DNA binding domain is a helix-turn-helix (HTH) containing POU domain and is followed by a long -helix (6) that forms an anti-parallel four-helix bundle, creating a tetramer. The loop between helix 2 and the recognition helix 3 in the HTH motif is unusually long compared to typical HTH motifs and is highly variable in sequence and length within the YdaT family. The POU domains have a large degree of freedom to move relative to the helix bundle in the free structure, but their orientation becomes fixed upon DNA binding.