X-ray crystal structure of the polymerase domain of the bacteriophage N4 virion RNA polymerase

Proc Natl Acad Sci U S A. 2008 Apr 1;105(13):5046-51. doi: 10.1073/pnas.0712325105. Epub 2008 Mar 24.

Abstract

Coliphage N4 virion RNA polymerase (vRNAP), which is injected into the host upon infection, transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. Here, we describe the 2.0-A resolution x-ray crystal structure of N4 mini-vRNAP, a member of the T7-like, single-unit RNAP family and the minimal component having all RNAP functions of the full-length vRNAP. The structure resembles a "fisted right hand" with Fingers, Palm and Thumb subdomains connected to an N-terminal domain. We established that the specificity loop extending from the Fingers along with W129 of the N-terminal domain play critical roles in hairpin-promoter recognition. A comparison with the structure of the T7 RNAP initiation complex reveals that the pathway of the DNA to the active site is blocked in the apo-form vRNAP, indicating that vRNAP must undergo a large-scale conformational change upon promoter DNA binding and explaining the highly restricted promoter specificity of vRNAP that is essential for phage early transcription.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacteriophage N4 / chemistry*
  • Bacteriophage N4 / genetics
  • Bacteriophage N4 / metabolism*
  • Crystallography, X-Ray
  • DNA / genetics
  • DNA-Directed RNA Polymerases / chemistry*
  • DNA-Directed RNA Polymerases / metabolism*
  • Models, Molecular
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Virion / chemistry*
  • Virion / genetics
  • Virion / metabolism*

Substances

  • DNA
  • DNA-Directed RNA Polymerases

Associated data

  • PDB/2PO4