Two structures of a lambda Cro variant highlight dimer flexibility but disfavor major dimer distortions upon specific binding of cognate DNA

Previously reported crystal structures of free and DNA-bound dimers of λ Cro differ strongly (about 4 Å backbone rmsd), suggesting both flexibility of the dimer interface and induced-fit protein structure changes caused by sequence-specific DNA binding. Here, we present two crystal structures, in space groups P3₂21 and C2 at 1.35 and 1.40 Å resolution, respectively, of a variant of λ Cro with three mutations in its recognition helix (Q27P/A29S/K32Q, or PSQ for short). One dimer structure (P3₂21; PSQ form 1) resembles the DNA-bound wild-type Cro dimer (1.0 Å backbone rmsd), while the other (C2; PSQ form 2) resembles neither unbound (3.6 Å) nor bound (2.4 Å) wild-type Cro. Both PSQ form 2 and unbound wild-type dimer crystals have a similar interdimer β-sheet interaction between the β1 strands at the edges of the dimer. In the former, an infinite, open β-structure along one crystal axis results, while in the latter, a closed tetrameric barrel is formed. Neither the DNA-bound wild-type structure nor PSQ form 1 contains these interdimer interactions. We propose that β-sheet superstructures resulting from crystal contact interactions distort Cro dimers from their preferred solution conformation, which actually resembles the DNA-bound structure. These results highlight the remarkable flexibility of λ Cro but also suggest that sequence-specific DNA binding may not induce large changes in the protein structure.