Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins.

Abstract

There is a structural similarity between the presumed DNA-binding regions of the Escherichia coli catabolite gene activator protein (CAP) and the cro repressor protein (cro) from bacteriophage .lambda.. The correspondence between the 2 proteins is particularly striking for a structural unit consisting of 2 consecutive .alpha.-helices. The 24 .alpha.-carbon atoms that constitute the 2-helical structural units in the 2 proteins can be superimposed with a root-mean-square disagreement of 1.1 .ANG.. This agreement is very unlikely to be due to a chance correspondence. For both CAP activator and cro repressor proteins it is the 2nd .alpha.-helix of the 2-helical unit that has been proposed to bind within the major groove of left-handed or right-handed B DNA, respectively. The structural correspondence between CAP and cro seen here, together with other recent evidence of sequence homologies between cro, CAP and other proteins that bind double-stranded DNA, suggests that the 2-helical unit is likely to be a common feature of many DNA-binding proteins. Some principles of specific protein-double-stranded DNA interaction may be general and include recognition via .alpha.-helices fitting into the major groove of the DNA.