Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach
Figure 3
Sequence and structure of Eco RNAP βflap-βi9.
(A) Sequence alignment comparing the sequence context of Eco RNAP βi9 with the corresponding region of Taq (which lacks βi9). Shaded residues are identical between the two sequences. The secondary structure for Eco is indicated directly above the sequence; filled rectangles denote α-helices, open rectangles denote β-strands. The number scale above the Eco secondary structure corresponds to the Eco β subunit sequence. Above the number scale, black lines denote the sequence regions common to all bacterial RNAPs [3]. Gaps in the βi9 sequence with numbers above denote the location and residue length of insertions in an alignment of 307 non-redundant βi9 sequences (see Supporting Information). The extent of the common βflap domain (thick cyan line) and the lineage-specific insert βi9 (thick orange line) is indicated at the top. (B) Two orthogonal views of Eco βflap-βi9 (βflap, cyan; βi9, orange). The views correspond to the reference views of Taq core RNAP (left, bottom view; right, front view), shown as a backbone worm and color-coded as follows: αI, αII, ω, gray; β', light pink; β, light cyan, except the βflap domain is colored cyan and labeled.