Structural basis for transcription elongation by bacterial RNA polymerase

Nature. 2007 Jul 12;448(7150):157-62. doi: 10.1038/nature05932. Epub 2007 Jun 20.

Abstract

The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-A resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the beta'-subunit 'lid' loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.

Publication types

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

MeSH terms

  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / metabolism
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / metabolism
  • Models, Molecular
  • Multiprotein Complexes / chemistry
  • Multiprotein Complexes / metabolism
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / metabolism
  • Thermus thermophilus / chemistry*
  • Thermus thermophilus / enzymology*
  • Thermus thermophilus / genetics
  • Thermus thermophilus / metabolism
  • Transcription, Genetic*

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Multiprotein Complexes
  • RNA, Bacterial
  • DNA-Directed RNA Polymerases

Associated data

  • PDB/2O5I