Comparison of the structures of Cro and λ repressor proteins from bacteriophage λ

The three-dimensional structures of cro repressor protein and of the amino-terminal domain of λ repressor protein, both from bacteriophage λ, are compared. The second and third α-helices, α₂ and α₃, are shown to have essentially identical conformations in the two proteins, confirming the significance of the amino acid sequence homology previously noted between these and other DNA binding proteins in the region corresponding to these helices. The correspondence between the two-helical units in cro and λ repressor protein is better than the striking agreement noted previously between two-helical units in cro and catabolite gene-activator protein. Parts of the first α-helices of repressor and cro show a structural correspondence that suggests a revised sequence homology between the two proteins in their extreme amino-terminal regions. In particular, there is a short loop between the α₁ and α₂ helices of λ repressor that is missing from cro. This structural difference may account for the observed differences found with different cros and repressors in the pattern of phosphates whose ethylation prevents the binding of these proteins to their specific recognition sites. Although the two proteins have strikingly similar α₂-α₃ helical units that are presumed to bind to DNA in an essentially similar manner, stereochemical restrictions prevent the α₂-α₃ units of the respective proteins aligning on the DNA in exactly the same way.