SNAP output for PDB entry 7khe [SNAP web server]

PDB-id

7khe; SNAP-derived features in text and JSON formats; DNAproDB

Class

transcription-DNA

Method

cryo-EM (3.58 Å)

Summary

Escherichia coli RNA polymerase and rrnbp1 promoter pre-open complex with dksa-ppgpp

Reference

Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS (2021): "Structural basis of ribosomal RNA transcription regulation." Nat Commun, 12, 528. doi: 10.1038/s41467-020-20776-y.

Abstract

Ribosomal RNA (rRNA) is most highly expressed in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. Here, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ₇₀ holoenzyme during rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element using dimerized α subunit carboxyl-terminal domains and scrunches the template DNA with the σ finger and β' lid to select the transcription start site favorable for rapid promoter escape. Promoter binding induces conformational change of σ domain 2 that opens a gate for DNA loading and ejects σ_1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding also opens the DNA loading gate, which is not coupled to σ_1.1 ejection and impedes open complex formation. These results provide a molecular basis for the exceptionally active rRNA transcription and its vulnerability to DksA/ppGpp.