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Figure 2.
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 green 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.
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