SNAP output for PDB entry 8x6g [SNAP web server]

PDB-id

8x6g; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription

Method

cryo-EM (3.3 Å)

Summary

cryo-EM structure of staphylococcus aureus sigb-dependent rnap-promoter open complex

Reference

Yuan L, Liu Q, Xu L, Wu B, Feng Y (2024): "Structural basis of promoter recognition by Staphylococcus aureus RNA polymerase." Nat Commun, 15, 4850. doi: 10.1038/s41467-024-49229-6.

Abstract

Bacterial RNAP needs to form holoenzyme with σ factors to initiate transcription. While Staphylococcus aureus σ_A controls housekeeping functions, S. aureus σ_B regulates virulence, biofilm formation, persistence, cell internalization, membrane transport, and antimicrobial resistance. Besides the sequence difference, the spacers between the -35 element and -10 element of σ_B regulated promoters are shorter than those of σ_A regulated promoters. Therefore, how σ_B recognizes and initiates transcription from target promoters can not be inferred from that of the well studied σ. Here, we report the cryo-EM structures of S. aureus RNAP-promoter open complexes comprising σ_A and σ_B, respectively. Structural analyses, in combination with biochemical experiments, reveal the structural basis for the promoter specificity of S. aureus transcription. Although the -10 element of σ_A regulated promoters is recognized by domain σ_A2 as single-stranded DNA, the -10 element of σ_B regulated promoters is co-recognized by domains σ_B2 and σ_B3 as double-stranded DNA, accounting for the short spacers of σ_B regulated promoters. S. aureus RNAP is a validated target of antibiotics, and our structures pave the way for rational drug design targeting S. aureus RNAP.