Structural mimicry in the phage phi21 N peptide-boxB RNA complex.
We determined the solution structure of a 22-amino-acid peptide from the amino-terminal domain of the bacteriophage phi21 N protein in complex with its cognate 24-mer boxB RNA hairpin using heteronuclear magnetic resonance spectroscopy. The N peptide binds as an alpha-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 phi21 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 phi21 boxB loop, in complex with the N peptide, is strikingly similar to the GNRA tetraloop-like folds of the related lambda 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.
Cilley
Christopher D
CD
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
Williamson
James R
JR
D000595:Amino Acid Sequence; D017100:Bacteriophage P22 / Q000737:chemistry; D001435:Bacteriophages / Q000737:chemistry*; D001665:Binding Sites; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D008958:Models, Molecular; D018716:Molecular Mimicry; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D055672:Static Electricity; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000378:metabolism
D046911:Macromolecular Substances; C059417:N protein, Bacteriophage lambda; D010455:Peptides; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D054334:Viral Regulatory and Accessory Proteins