Figure 2. The interaction between the promoter hairpin and the N4 vRNAP.
(A) P2 promoter DNA structure in the binary complex. The hairpin-stem promoter consists of a double-stranded stem (−5 to 9, and −17 to −13) and a 3-nt loop (−10 to −12). Template DNA contains bases from −4 to +2 with the transcription start site at +1.
(B) Promoter hairpin loop recognition. R119 and K114 interact with −11G (N7 and 6-keto) and −10G (N7), respectively. W129 participates in a stacking interaction with −11G. The Fingers residues K849 and K850 form salt-bridges with the phosphate backbone at −12 and −13, respectively. Hydrogen bonds and salt-bridges are depicted by red and orange dashed lines, respectively. Color code of the structure motifs is indicated.
(C) Promoter recognition by the specificity loop (cyan) and the β-intercalating hairpin (orange) in the P2_7a binary complex. D901 and R904 of the specificity loop recognize bases −9/−10 and −8, respectively, from the major grove. R902 interacts with the phosphate backbone at −7 and −6. Residues K267 and K268 in the β-intercalating hairpin face the DNA stem to separate the last 2 bp of the 7 bp stem yielding a 5 bp stem, and direct the template DNA toward the active site.
(D) Difference of −11 and R119/W129 interactions between P1 (blue) and P2 (pink) promoters in the binary complexes. Only residues R119 and W129 in the P2 binary complex are shown. The bifurcate hydrogen bonds between −11G (P2 promoter) and R119 are depicted by dashed red lines.