Architecture of RNA Polymerase II and Implications for the Transcription Mechanism

TLDR

Yeast RNA polymerase II subunits are highly homologous to human proteins, with nine of ten conserved across eukaryotic RNA polymerases I, II, and III. The model reveals jaws formed by Rpb1, Rpb5, and Rpb9 that grip downstream DNA, a clamp composed of Rpb1, Rpb2, and Rpb6 that can be locked by RNA, and a pore beneath the active center that permits substrate entry and transcript exit during proofreading and pausing. The study presents a 3‑Å resolution backbone model of yeast RNA polymerase II and identifies a clamp that is locked in a closed state by RNA, explaining the stability of transcribing complexes.

Abstract

A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.