Figure 2

Structural characteristics of E. coli σ⁷⁰. (a) The protein sequence has been divided into four regions on the basis of sequence conservation with other members of the σ⁷⁰ family. Residues in the carboxy-terminal part of region 4 (subregion 4.2) form a helix-turn-helix motif that contacts the -35 element of the promoter. Residues from conserved regions 2 and 3 cooperate to mediate recognition of the -10 region and melting of the DNA. A residue in the amino-terminal part of region 3 (3.0) contacts the conserved TG motif in the extended -10 element of certain promoters that do not require a -35 region. Residues from an α helix in region 2 that corresponds to the conserved subregions 2.3 and 2.4 interact intimately with the -10 element. Subregion 2.3 is thought to interact primarily with single-stranded DNA in the open complex (dashed arrow). The three domains of the σ factor observed by X-ray crystallography (σ₂, σ₃ and σ₄) are indicated underneath the linear structure. Note that the protein domains correspond closely (although not precisely) with the regions assigned by sequence comparisons. (b) A model for the interaction of RNA polymerase holoenzyme (containing, β,β ', two α, and ω one subunit in addition to the σ factor) with promoter DNA. The model is based on crystallographic analyses of σ domains, holoenzyme, and holoenzyme-model DNA complexes [10,14,15,25]. The major functional domains of the σ factor are shown in dark grey. The bold arrow indicates the direction of transcription. Although the template strand in the transcription bubble passes underneath the β unit and the σ₂ domain, the path of the DNA is shown throughout its length. Adapted from [21].