A new-specificity mutant of 434 repressor that defines an amino acid–base pair contact

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Abstract
The represser encoded by bacteriophage 434 binds to its operators by inserting a 'recognition' α-helix into the major groove of the DNA1,2. We have identified an amino acid–base pair contact that determines (in part) the DNA-binding specificity of 434 represser. The identification is based on the properties of a 'new-specificity' mutant, named Represser[Ala 28], which bears the substitution of Ala for Gln at the first residue of its recognition α-helix. Represser[Ala 28] binds with high affinity to a particular doubly mutant operator bearing the same substitution at position 1 in each half-site, but does not bind to either the wild-type operator or to other mutant operators. We describe molecular models of residue 28–base pair 1 interactions that account for the binding specificities of both the mutant and wild-type proteins.