Use of “Loss-of-Contact” Substitutions to Identify Residues Involved in an Amino Acid-Base Pair Contact: Effect of Substitution of Gln18 of Lac Repressor by Gly, Ser, and Leu

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Abstract
A procedure to identify which base pair of lac operator (lacO) a suspected contacting amino acid of Lac repressor (LacR) interacts with is presented. The procedure is to eliminate the ability of the amino acid under study to contact DNA, and then to determine at which base pair—if any—specificity is eliminated. To implement this procedure, four sets of Escherichia coli K-12 strains have been constructed. These strains permit: (i) the substitution of a selected amino acid of LacR by, respectively, Gly, Ser, Leu, or Gln, and (ii) the analysis of the specificity of the resulting substituted LacR with respect to base pairs 5,6,7,8,9, and 10 of lacO. This procedure has been applied to Gln18 of LacR. The preliminary data indicate that LacR(Gln18⇒Gly) is unable to distinguish between the O+ base pair G:C and the Oc base pair T:A at position 7 of lacO (KDoc/KDO + = 0.93). In contrast, LacR(Glnl8⇒Gly) discriminates O+ from Oc by a factor of 13 to 23 at each other position. The same qualitative pattern of results was obtained with LacR(Glnl8⇒Ser) and LacR(Gln18⇒Leu). Therefore, I propose that Gln18 contacts base pair 7 of lacO. This proposal is consistent with the contact predicted in Ebright, R. in Protein Structure, Folding, and Design. D. Oxender ed., Alan R. Liss, New York (1985), in press.