X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme

J Biol Chem. 2013 Mar 29;288(13):9126-34. doi: 10.1074/jbc.M112.430900. Epub 2013 Feb 6.

Abstract

Escherichia coli RNA polymerase (RNAP) is the most studied bacterial RNAP and has been used as the model RNAP for screening and evaluating potential RNAP-targeting antibiotics. However, the x-ray crystal structure of E. coli RNAP has been limited to individual domains. Here, I report the x-ray structure of the E. coli RNAP σ(70) holoenzyme, which shows σ region 1.1 (σ1.1) and the α subunit C-terminal domain for the first time in the context of an intact RNAP. σ1.1 is positioned at the RNAP DNA-binding channel and completely blocks DNA entry to the RNAP active site. The structure reveals that σ1.1 contains a basic patch on its surface, which may play an important role in DNA interaction to facilitate open promoter complex formation. The α subunit C-terminal domain is positioned next to σ domain 4 with a fully stretched linker between the N- and C-terminal domains. E. coli RNAP crystals can be prepared from a convenient overexpression system, allowing further structural studies of bacterial RNAP mutants, including functionally deficient and antibiotic-resistant RNAPs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Crystallography, X-Ray / methods
  • DNA / chemistry
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / enzymology*
  • Holoenzymes / chemistry*
  • Models, Molecular
  • Molecular Conformation
  • Mutation
  • Plasmids / metabolism
  • Promoter Regions, Genetic
  • Protein Conformation
  • Protein Structure, Tertiary
  • Sigma Factor / chemistry*
  • Sigma Factor / metabolism
  • Thermus / enzymology
  • Transcription, Genetic

Substances

  • Holoenzymes
  • Sigma Factor
  • DNA
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases