The structure of the coliphage HK022 Nun protein-lambda-phage boxB RNA complex. Implications for the mechanism of transcription termination

J Biol Chem. 2001 Aug 24;276(34):32064-70. doi: 10.1074/jbc.M102975200. Epub 2001 May 16.


Nun protein from coliphage HK022 binds to phage boxB RNA and functions, in contrast to phage lambda N protein, as a transcriptional terminator. The basic Nun-(10-44) peptide contains the boxB RNA binding arginine rich motif, ARM. The peptide binds boxB RNA and competes with the phage lambda ARM peptide N-(1-36) as indicated by nuclear magnetic resonance (NMR) spectroscopy titrations. In two-dimensional nuclear Overhauser enhancement spectroscopy experiments boxB RNA in complex with Nun-(20-44) exhibits the same pattern of resonances as it does in complex with N peptides containing the ARM, and we could show that Nun-(20-44) forms a bent alpha-helix upon binding to the boxB RNA. The structure of the boxB RNA-bound Nun-(20-44) was determined on the basis of 191 intra- and 30 intermolecular distance restraints. Ser-24 is anchored to the lower RNA stem, and stacking of Tyr-39 and A7 is clearly experimentally indicated. Arg-28 shows numerous contacts to the RNA stem. Leu-22, Ile-30, Trp-33, Ile-37, and Leu-41 form a hydrophobic surface, which could be a recognition site for additional host factors such as NusG. Such a hydrophobic surface area is not present in N-(1-36) bound to boxB RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacteriophage lambda / chemistry*
  • Base Sequence
  • Coliphages / chemistry*
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Nuclear Magnetic Resonance, Biomolecular
  • RNA, Viral / chemistry*
  • Sequence Homology, Amino Acid
  • Templates, Genetic
  • Transcription Factors / chemistry*
  • Transcription, Genetic*
  • Viral Proteins / chemistry*


  • Nun protein, Enterobacteria phage HK022
  • RNA, Viral
  • Transcription Factors
  • Viral Proteins