Figure 5 - full size

 

Figure 5.
Figure 5. Frayed Nucleotides Overlap the NTP, Closed Trigger Loop, and the TFIIS Hairpin
(A) Frayed nucleotides overlap the NTP bound to the insertion site (green cyan, taken from bacterial Pol EC, PDB-code 2O5J [Vassylyev et al., 2007b]). Van der Waals radii are represented by colored dots. All structures were superimposed with their active site regions.
(B and C) Frayed nucleotides overlap the closed trigger loop (cyan) at residue F1084 (B, taken from the Pol II EC, PDB-code 2E2H [Wang et al., 2006]) and/or at residue H1242 (C, bacterial Pol EC, PDB-code 2O5J [Vassylyev et al., 2007b]).
(D) Frayed nucleotides overlap the tip of the hairpin of the cleavage-stimulatory factor TFIIS. The structures of EC III, EC IV, and the Pol II-TFIIS complex (PDB-code 1PQV, [Kettenberger et al., 2003]) were superimposed with their active center regions. TFIIS is shown in orange. The canonical side view is used.
(E) Detailed view of the superposition in (D) around the active site, revealing a potential clash of the TFIIS acidic hairpin with the frayed nucleotides.

The above figure is reprinted by permission from Cell Press: Mol Cell (2009, 34, 710-721) copyright 2009.