Figure 1. Generic structure–function map for members of the ⁷⁰ family. The protein sequence is represented as a bar from the N-terminus (left) to the C-terminus (right). The amino acid sequence is divided into four conserved regions. Regions 2 and 4 (blue) contain the key regions implicated in core-binding and promoter recognition and melting. Recognition of the –35 promoter element is mediated by a helix-turn-helix (HTH) unit in region 4, and amino acids from this region may also provide a contact point for some activator proteins. Amino acids important for both –10 region recognition and promoter melting are on an helix (helix 14), spanning regions 2.3 and 2.4.

Figure 2. A close-up view of interactions between E. coli ⁷⁰ and a consensus promoter element. The factor has two domains corresponding roughly to regions 2 and 4. Region 2 interacts with the –10 element. Conserved threonine (T) and glutamine (Q) residues are implicated in recognition of the start site distal thymine (T in the DNA). An adjacent cluster of aromatic amino acid side-chains (two tryptophan, W, and a tyrosine, Y) provide hydrophobic and stacking interactions (stippled bars) with the ssDNA formed during melting of the promoter DNA. Recognition of the –35 element by region 4 involves, in part, specific amino acid side-chain contacts from two arginine (R) residues with the edges of the base pairs.