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

PDB-id

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

Class

transcription-DNA

Method

cryo-EM (2.49 Å)

Summary

cryo-EM structure of e. coli rnap sigma32 complex

Reference

Lu Q, Chen T, Wang J, Wang F, Ye W, Ma L, Wu S (2023): "Structural Insight into the Mechanism of sigma 32-Mediated Transcription Initiation of Bacterial RNA Polymerase." Biomolecules, 13. doi: 10.3390/biom13050738.

Abstract

Bacterial RNA polymerases (RNAP) form distinct holoenzymes with different σ factors to initiate diverse gene expression programs. In this study, we report a cryo-EM structure at 2.49 Å of RNA polymerase transcription complex containing a temperature-sensitive bacterial σ factor, σ₃₂ (σ₃₂-RPo). The structure of σ₃₂-RPo reveals key interactions essential for the assembly of E. coli σ₃₂-RNAP holoenzyme and for promoter recognition and unwinding by σ₃₂. Specifically, a weak interaction between σ₃₂ and -35/-10 spacer is mediated by T128 and K130 in σ₃₂. A histidine in σ₃₂, rather than a tryptophan in σ₇₀, acts as a wedge to separate the base pair at the upstream junction of the transcription bubble, highlighting the differential promoter-melting capability of different residue combinations. Structure superimposition revealed relatively different orientations between βFTH and σ₄ from other σ-engaged RNAPs and biochemical data suggest that a biased σ₄-βFTH configuration may be adopted to modulate binding affinity to promoter so as to orchestrate the recognition and regulation of different promoters. Collectively, these unique structural features advance our understanding of the mechanism of transcription initiation mediated by different σ factors.