Structural basis of DNA recognition by the alternative sigma-factor, sigma54

J Mol Biol. 2007 Jun 15;369(4):1070-8. doi: 10.1016/j.jmb.2007.04.019. Epub 2007 Apr 12.

Abstract

The sigma subunit of bacterial RNA polymerase (RNAP) regulates gene expression by directing RNAP to specific promoters. Unlike sigma(70)-type proteins, the alternative sigma factor, sigma(54), requires interaction with an ATPase to open DNA. We present the solution structure of the C-terminal domain of sigma(54) bound to the -24 promoter element, in which the conserved RpoN box motif inserts into the major groove of the DNA. This structure elucidates the basis for sequence specific recognition of the -24 element, orients sigma(54) on the promoter, and suggests how the C-terminal domain of sigma(54) interacts with RNAP.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • DNA* / chemistry
  • DNA* / metabolism
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Gene Expression Regulation, Bacterial
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Conformation
  • RNA Polymerase Sigma 54 / chemistry*
  • RNA Polymerase Sigma 54 / genetics
  • RNA Polymerase Sigma 54 / metabolism*
  • Sequence Alignment

Substances

  • Bacterial Proteins
  • Macromolecular Substances
  • DNA
  • DNA-Directed RNA Polymerases
  • RNA Polymerase Sigma 54

Associated data

  • GENBANK/AAC06814
  • PDB/2O8K
  • PDB/2O9L