The N-terminus is unstructured, but not dynamically disordered, in the complex between HK022 Nun protein and λ-phage BoxB RNA hairpin

Abstract

The Nun protein of lambdoid phage HK022 excludes λ-phage superinfection by blocking expression of genes downstream from the λ nut sequences. Heteronuclear NMR studies have been performed on a Nun peptide comprising residues 1–49 bound to the nutR BoxB RNA. The pattern of 13C chemical shifts indicates that the arginine-rich motif of Nun forms an induced α-helix, consisting of residues 23–43, when bound to BoxB RNA, consistent with the structure of a shorter (residues 22–44) Nun peptide/ BoxB RNA complex [Faber, C., Schärpf, M., Becker, T., Sticht, H. and Rösch (2001) J. Biol. Chem. 276, 32064–32070]. The N-terminal extension, residues 1–22, does not show chemical shifts or nuclear Overhauser effects characteristic of stable secondary structure. Nonetheless, 15N relaxation measurements indicate that this region is not completely disordered, as expected for a random coil peptide. Restriction of conformation flexibility in the N-terminal extension of Nun may be important for binding to other target molecules involved in transcription termination.