Download MendeleyStructural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
Lin, G., Barnes, C.O., Weiss, S., Dutagaci, B., Qiu, C., Feig, M., Song, J., Lyubimov, A., Cohen, A.E., Kaplan, C.D., Calero, G.(2024) Proc Natl Acad Sci U S A 121: e2318527121-e2318527121
- PubMed: 39190355
- DOI: https://doi.org/10.1073/pnas.2318527121
- Primary Citation of Related Structures:
8U9R, 8U9X, 9BVT, 9BW0 - PubMed Abstract:
Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
Organizational Affiliation:
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261.
