SNAP output for PDB entry 1hji [SNAP web server]

PDB-id

1hji; SNAP-derived features in text and JSON formats; DNAproDB

Class

bacteriophage hk022

Method

NMR

Summary

Bacteriophage hk022 nun-protein-nutboxb-RNA complex

Reference

Faber C, Schaerpf M, Becker T, Sticht H, Roesch P (2001): "The Structure of the Coliphage Hk022 Nun Protein-Lambda-Phage Boxb RNA Complex. Implications for the Mechanism of Transcription Termination." J.Biol.Chem., 276, 32064. doi: 10.1074/JBC.M102975200.

Abstract

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.