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 α -helix ( α 6) that forms an antiparallel four-helix bundle, creating a tetramer. The loop between helix α 2 and the recognition helix α 3 in the HTH motif is unusually long compared with 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.

Source: Acta Crystallographica Section D - February 27, 2023 Category: Biochemistry Authors: Proli č -Kalin š ek, M. Volkov, A.N. Had ž i, S. Van Dyck, J. Bervoets, I. Charlier, D. Loris, R. Tags: CII repressors DNA binding YdaT transcription regulation toxin – antitoxin research papers Source Type: research