DNA Binding of PhoB and its Interaction with RNA Polymerase

We have identified the DNA-binding domain (DBD) of an Escherichia coliactivator protein PhoB as its C-terminal 91 residues. Four amino acid positions in the PhoB DBD are found important for interaction with the RNA polymerase holoenzyme that contains the σ 70subunit. Assuming that the PhoB DBD is structurally similar to the histone H5 DBD, the four positions are placed around the turn region that connects two putative helices, 2 and 3 (helix 3 is likely to be the recognition helix). The binding sites of PhoB, three with the sequence TGTCA and one of TTACA, are identified in the pstSpromoter. The pstSpromoter has intrinsic bending (or bendability), which is much enhanced upon binding PhoB. On the basis of the above, some aspects of the PhoB-DNA-RNA polymerase interaction are discussed.