6CA0

Cryo-EM structure of E. coli RNAP sigma70 open complex

Summary for 6CA0

• Entry DOI: 10.2210/pdb6ca0/pdb
• EMDB information: 7438 7439
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, ZINC ION, ... (11 entities in total)
• Functional Keywords: escherichia coli, rna polymerase, transcription, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 10
• Total formula weight: 491425.18

Authors

Narayanan, A.,Vago, F.,Li, K.,Qayyum, M.Z.,Yernool, D.,Jiang, W.,Murakami, K.S. (deposition date: 2018-01-29, release date: 2018-02-28, Last modification date: 2024-03-13)

Primary citation

Narayanan, A.,Vago, F.S.,Li, K.,Qayyum, M.Z.,Yernool, D.,Jiang, W.,Murakami, K.S.
Cryo-EM structure ofEscherichia colisigma70RNA polymerase and promoter DNA complex revealed a role of sigma non-conserved region during the open complex formation.
J. Biol. Chem., 293:7367-7375, 2018

PubMed Abstract: First step of gene expression is transcribing the genetic information stored in DNA to RNA by the transcription machinery including RNA polymerase (RNAP). In , a primary σ factor forms the RNAP holoenzyme to express housekeeping genes. The σ contains a large insertion between the conserved regions 1.2 and 2.1, the σ non-conserved region (σ), but its function remains to be elucidated. In this study, we determined the cryo-EM structures of the RNAP σ holoenzyme and its complex with promoter DNA (open complex, RPo) at 4.2 and 5.75 Å resolutions, respectively, to reveal native conformations of RNAP and DNA. The RPo structure presented here found an interaction between the σ and promoter DNA just upstream of the -10 element, which was not observed in a previously determined RNAP transcription initiation complex (RPo plus short RNA) structure by X-ray crystallography because of restraint of crystal packing effects. Disruption of the σ and DNA interaction by the amino acid substitutions (R157A/R157E) influences the DNA opening around the transcription start site and therefore decreases the transcription activity of RNAP. We propose that the σ and DNA interaction is conserved in proteobacteria, and RNAP in other bacteria replaces its role with a transcription factor.

PubMed: 29581236
DOI: 10.1074/jbc.RA118.002161

Experimental method

ELECTRON MICROSCOPY (5.75 Å)