Structural mimicry in the phage [phis]21 N peptide–boxB RNA complex

Abstract

We determined the solution structure of a 22-amino-acid peptide from the amino-terminal domain of the bacteriophage [phis]21 N protein in complex with its cognate 24-mer boxB RNA hairpin using heteronuclear magnetic resonance spectroscopy. The N peptide binds as an α-helix and interacts predominately with the major groove side of the 5′ half of the boxB RNA stem-loop. This binding interface is defined by surface complementarity of polar and nonpolar interactions, and little sequence-specific recognition. The [phis]21 boxB loop (CUAACC) has hydrogen bond and backbone torsions typical of the “U-turn” motif, as well as base stacking of the last 4 nt, and a hydrogen bonded C:C pair closing the loop. The exposed face of the [phis]21 boxB loop, in complex with the N peptide, is strikingly similar to the GNRA tetraloop-like folds of the related λ and P22 bacteriophage N peptide–boxB RNA complexes. The N peptide–boxB complexes of the various phage, while individually distinct, provide similar structural features for interactions with the Escherichia coli host factors to enable antitermination.

Keywords

• Transcription antitermination
• bacteriophage N protein
• NMR spectroscopy
• U-turn
• protein/RNA interactions