Crystal structure of the P2 C-repressor: a binder of non-palindromic direct DNA repeats

Abstract

As opposed to the vast majority of prokaryotic repressors, the immunity repressor of temperate Escherichia coli phage P2 (C) recognizes non-palindromic direct repeats of DNA rather than inverted repeats. We have determined the crystal structure of P2 C at 1.8 Å. This constitutes the first structure solved from the family of C proteins from P2-like bacteriophages. The structure reveals that the P2 C protein forms a symmetric dimer oriented to bind the major groove of two consecutive turns of the DNA. Surprisingly, P2 C has great similarities to binders of palindromic sequences. Nevertheless, the two identical DNA-binding helixes of the symmetric P2 C dimer have to bind different DNA sequences. Helix 3 is identified as the DNA-recognition motif in P2 C by alanine scanning and the importance for the individual residues in DNA recognition is defined. A truncation mutant shows that the disordered C-terminus is dispensable for repressor function. The short distance between the DNA-binding helices together with a possible interaction between two P2 C dimers are proposed to be responsible for extensive bending of the DNA. The structure provides insight into the mechanisms behind the mutants of P2 C causing dimer disruption, temperature sensitivity and insensitivity to the P4 antirepressor.

Bacteriophage P2

“…9 Dimers of C protein bind 2 direct repeats, separated by 2 helical turns, which span the ¡10 region of the early promoter P e to repress transcription of cox and the replication genes. 10 The Cox protein binds to and represses the P c promoter, which is needed for transcription of the C and int genes. 11,12 Cox is a winged HTH protein that oligomerizes as a helical filament and wraps DNA around its outside.…”

Bacteriophage Protein–Protein Interactions

“…GpC acts as a symmetric dimer, and its three-dimensional structure has been determined (Eriksson et al ., 2000; Massad et al ., 2010). Cox is multifunctional and acts as a repressor, as well as an excisionase, thereby coupling the transcriptional switch that controls lytic growth versus formation of lysogeny with the integration/excision of the phage genome in or out of the host chromosome.…”

The three‐dimensional structure of TrmB, a transcriptional regulator of dual function in the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose

“…The P2 C repressor structure was determined in absence of DNA . It is a dimer containing two HTH domains.…”