Independent Ligand-Induced Folding of the RNA-Binding Domain and Two Functionally Distinct Antitermination Regions in the Phage λ N Protein

Abstract

The transcriptional antitermination protein N of bacteriophage λ binds the boxB component of the RNA enhancer nut ( boxA + boxB) and the E. coli elongation factor NusA. Efficient antitermination by N requires an RNA-binding domain (amino acids 1–22) and two activating regions for antitermination: a newly identified NusA-binding region (amino acids 34–47) that suppresses NusA's enhancement of termination, and a carboxy-terminal region (amino acids 73–107) that interacts directly with RNA polymerase. Heteronuclear magnetic resonance experiments demonstrate that N is a disordered protein. Interaction with boxB RNA induces only the RNA-binding domain of N to adopt a folded conformation, while the activating regions of the protein remain disordered in the absence of their target proteins.