SNAP output for PDB entry 8f1j [SNAP web server]

PDB-id

8f1j; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA

Method

cryo-EM (2.6 Å)

Summary

Sign RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsu36mm2 (-12a)

Reference

Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA (2023): "A general mechanism for transcription bubble nucleation in bacteria." Proc.Natl.Acad.Sci.USA, 120, e2220874120. doi: 10.1073/pnas.2220874120.

Abstract

Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ₇₀, nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ₇₀. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ_N-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ_N, like σ₇₀, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.