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 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.
Faber
C
C
Lehrstuhl für Biopolymere, Universität Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany.
Schärpf
M
M
Becker
T
T
Sticht
H
H
Rösch
P
P
D000595:Amino Acid Sequence; D010582:Bacteriophage lambda / Q000737:chemistry*; D001483:Base Sequence; D003090:Coliphages / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D012367:RNA, Viral / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D013698:Templates, Genetic; D014157:Transcription Factors / Q000737:chemistry*; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000737:chemistry*
C073501:Nun protein, Enterobacteria phage HK022; D012367:RNA, Viral; D014157:Transcription Factors; D014764:Viral Proteins