Crystal Structure of a Bacterial RNA Polymerase Holoenzyme at 2.6 A Resolution

Nature. 2002 Jun 13;417(6890):712-9. doi: 10.1038/nature752. Epub 2002 May 8.


In bacteria, the binding of a single protein, the initiation factor sigma, to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we report the crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 A resolution. In the structure, two amino-terminal domains of the sigma subunit form a V-shaped structure near the opening of the upstream DNA-binding channel of the active site cleft. The carboxy-terminal domain of sigma is near the outlet of the RNA-exit channel, about 57 A from the N-terminal domains. The extended linker domain forms a hairpin protruding into the active site cleft, then stretching through the RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / metabolism
  • Holoenzymes / chemistry
  • Holoenzymes / metabolism
  • Magnesium / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic / genetics
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Sigma Factor / chemistry
  • Sigma Factor / metabolism
  • Thermus thermophilus / enzymology*
  • Zinc Fingers


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

Associated data

  • PDB/1IW7