Structural basis for -35 element recognition by σ chimera proteins and their interactions with PmrA response regulator.

In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of σ factors (σ ) to activate transcription. However, σ of σ appears to be poorly folded on its own. Here, by fusing σ with the RNA polymerase β-flap-tip-helix, we constructed two σ chimera proteins, one from σ and another from σ of Klebsiella pneumoniae. The two chimera proteins well folded into a monomeric form with strong binding affinities for -35 element DNA. Determining the crystal structure of in complex with -35 element DNA revealed that adopts a similar structure as σ in the Escherichia coli RNA polymerase σ holoenzyme and recognizes -35 element DNA specifically by several conserved residues from the helix-turn-helix motif. By using nuclear magnetic resonance (NMR), was demonstrated to recognize -35 element DNA similar to . Carr-Purcell-Meiboom-Gill relaxation dispersion analyses showed that the N-terminal helix and the β-flap-tip-helix of have a concurrent transient α-helical structure and DNA binding reduced the slow dynamics on . Finally, only was shown to interact with the response regulator PmrA and its promoter DNA. The chimera proteins are capable of -35 element DNA recognition and can be used for study with transcription factors or other factors that interact with domain 4 of σ factors.