The Bridge Helix of RNA Polymerase Acts as a Central Nanomechanical Switchboard for Coordinating Catalysis and Substrate Movement
Figure 1
Structural aspects of the Bridge Helix. (a) Overall position of the Bridge Helix within RNAP. The Bridge Helix is shown as a green cartoon structure. Also shown are the DNA template strand (light blue) and the nascent transcript (pink). The remainder of the enzyme is shown as a transparent outline. Based on PDB# 2E2H [17] and visualized with PyMol [18]. (b) Detailed view of the Bridge Helix. The Bridge Helix is shown as a green cartoon structure, and the positions of the two molecular hinges are highlighted in red (BH-HN) and blue (BH-HC). Adjacent domains are shown in purple (Link Domain) or grey (F-Loop). The nucleic acid substrates are shown as stick models (DNA template strand, light blue; nascent transcript, pink; rNTP in insertion site, dark pink). The two grey spheres represent the magnesium ions (Metal-A and Metal-B) which represent the catalytic site. Based on PDB# 2E2H [17] and visualized with PyMol [18]. (c) Alignment of Bridge Helix sequences from eukaryotes (Homo sapiens; Saccharomyces cerevisiae), archaea (Methanocaldococcus jannaschii (euryarchaeota); Sulfolobus solfataricus (crenarchaeota)), and bacteria (Escherichia coli, Thermus aquaticus, and Thermus thermophilus). Residues that are identical to the reference organism used in the author’s laboratory (M. jannaschii) are shown in red. The numbers flanking the sequences show the position of the Bridge Helix within the intact open reading frame of the subunits. The approximate locations of the two molecular hinge regions, BH-HN and BH-HC, are indicated by arrows.
