FIG. 1.

Structures of eukaryotic and prokaryotic RNAPs. (A) Structure of S. cerevisiae RNAP II bound to nucleic acids (PDB accession number 1Y1W). (Left panel) The various subunits and the DNA-RNA hybrid are shown (see color code). Some main domains of the enzyme are circled in black and gray. (Right panel) Structure of T. aquaticus RNAP (PDB accession number 1I6V). The various subunits are shown (see color code), as well as the positions of the cleft, pore, and RNA exit channel. (B) Structural elements of RNAP II in the region of the DNA-RNA hybrid. The rudder, switch 2, funnel, bridge helix, trigger loop, lid, switch 1, and switch 5 features of Rpb1 and the fork loop 1, fork loop 2, switch 3, and switch 4 features of Rpb2 are indicated. The positions of metals A and B and the residues coordinating them are shown. (C) Mechanism of ribonucleotide addition to the RNA chain. Residues known to coordinate the two Mg²⁺ ions (pink spheres) are shown and coordination bonds are in green dotted lines. DNA and RNA are shown in gray and white, respectively. Black arrows show the nucleophilic attack.