SNAP output for PDB entry 6kj6 [SNAP web server]

PDB-id

6kj6; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription

Method

cryo-EM (3.8 Å)

Summary

cryo-EM structure of escherichia coli crl transcription activation complex

Reference

Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao G, Feng Y, Yang B, Zhang Y (2019): "Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor." Elife, 8. doi: 10.7554/eLife.50928.

Abstract

σ_S is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses including antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σ_S-mediated transcription requires a σ_S-specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an Escherichia coli transcription activation complex (E. coli Crl-TAC) comprising E. coli σ_S-RNA polymerase (σ_S-RNAP) holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with domain 2 of σ_S (σ_S2) and the RNAP core enzyme, but does not contact promoter DNA. Results from subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicate that Crl stabilizes key structural motifs within σ_S2 to promote the assembly of the σ_S-RNAP holoenzyme and also to facilitate formation of an RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.