FIGURE 3. The RNA-binding channel.
From the following article:
Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover
Anastasia J. Callaghan, Maria Jose Marcaida, Jonathan A. Stead, Kenneth J. McDowall, William G. Scott and Ben F. Luisi
Nature 437, 1187-1191 (20 October 2005)
doi: 10.1038/nature04084
a, The principal dimer viewed along the twofold symmetry axis. The RNA is contacted by the S1, 5' sensor, RNase H-like and different parts of the DNase I-like subdomains of protomers A and B. b, The proposed catalytic site of RNase E. The magnesium ion (magenta) interacts with a phosphate of the RNA (green), and Asp 346 and Asp 303 of protomer A (red). The 2Fo - Fc-style electron density map (black) is at 2.5
. c, The 5' sensing pocket. RNA (green) and 5' sensor residues (gold) are shown. The terminal phosphate of the RNA (purple) is engaged by a semicircular ring of hydrogen-bond donors, Thr 170 and Arg 169. d, A 'mouse-trap' model for communication between the 5' sensing pocket and the site of catalysis. On binding the 5' phosphate, the 5' sensor (gold) induces the S1 domain (blue) to clamp down on the RNA (green) near the scissile phosphate (green P). This orients the RNA for cleavage at the Mg ion (magenta) in the DNase I domain (red). The proposed movement of the S1 domain is exaggerated for illustrative purposes.
