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

Nun protein from coliphage HK022 binds to phage boxB RNA and functions, in contrast to phage lambda N protein, as a transcriptional termination The ba sic 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 pept ide 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 a-helix upon binding to the bo xB RNA. The structure of the boxB RNA-bound Nun-(20-44) was determined on t he 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 e xperimentally indicated. Arg-28 shows numerous contacts to the RNA stem. Le u-22, IIe30, Trp-33, IIe-37, and Leu-41 form a hydrophobic surface, which c ould 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.