Shared operator recognition specificity between Trp repressor and the repressors of bacteriophage 434

Trp repressor is the only DNA-binding regulatory protein having a helix-turn-helix motif that has been reported to engage its operator target by a mechanism termed indirect readout: the Trp repressor-DNA interface is replete with hydrogen bonds between amino acid residues and non-esterified oxygen atoms of the sugar-phosphate backbone, and contains numerous specifically positioned water molecules. In Escherichia coli mutants deleted for trpR, the immunity repressor of phage 434 led to an eightfold reduction in trp promoter utilization. The Cro434 repressor also inhibited transcription from the trp promoter. The 434 repressors, considered to interact directly with operator targets, carry recognition helices positioned near the N terminus of each protein. The DNA-recognizing elements of Trp repressor lie toward the C terminus. The trp operator thus appears to possess significant plasticity in terms of its ability to assume conformational states that allow complex formation with more than one class of regulatory protein.