Swing-gate model of nucleotide entry into the RNA polymerase active center

Abstract

Each elementary step of transcription involves translocation of the 3′ terminus of RNA in the RNA polymerase active center, followed by the entry of a nucleoside triphosphate. The structural basis of these transitions was studied using RNA-protein crosslinks. The contacts were mapped and projected onto the crystal structure, in which the "F bridge" helix in the β′ subunit is either bent or relaxed. Bending/relaxation of the F bridge correlates with lateral movements of the RNA 3′ terminus. The bent conformation is sterically incompatable with the occupancy of the nucleotide site, suggesting that the switch regulates both the entry of substrates and the translocation of the transcript. The switch occurs as part of a cooperative transition of a larger structural domain that consists of the F helix and the supporting G loop.