Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2

• Published in: Molecular cell 2011-03, Vol.41 (6), p.693-703
• Main Authors: Chakrabarti, Sutapa, Jayachandran, Uma, Bonneau, Fabien, Fiorini, Francesca, Basquin, Claire, Domcke, Silvia, Le Hir, Hervé, Conti, Elena
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphatases - chemistry; Adenosine Triphosphatases - genetics; Adenosine Triphosphatases - metabolism; adenosinetriphosphatase; Animals; binding properties; Binding Sites; Biochemistry, Molecular Biology; catalytic activity; crystal structure; Crystallography, X-Ray; Humans; Life Sciences; messenger RNA; Models, Molecular; Molecular Sequence Data; monitoring; Multiprotein Complexes - metabolism; Nucleotides - metabolism; Protein Structure, Tertiary; Rec A Recombinases - chemistry; Rec A Recombinases - genetics; Rec A Recombinases - metabolism; RNA - genetics; RNA - metabolism; RNA Stability - genetics; stop codon; Trans-Activators - chemistry; Trans-Activators - genetics; Trans-Activators - metabolism; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2011.02.010

Upf1 is a crucial factor in nonsense-mediated mRNA decay, the eukaryotic surveillance pathway that degrades mRNAs containing premature stop codons. The essential RNA-dependent ATPase activity of Upf1 is triggered by the formation of the surveillance complex with Upf2-Upf3. We report crystal structures of Upf1 in the presence and absence of the CH domain, captured in the transition state with ADP:AlF 4 − and RNA. In isolation, Upf1 clamps onto the RNA, enclosing it in a channel formed by both the catalytic and regulatory domains. Upon binding to Upf2, the regulatory CH domain of Upf1 undergoes a large conformational change, causing the catalytic helicase domain to bind RNA less extensively and triggering its helicase activity. Formation of the surveillance complex thus modifies the RNA binding properties and the catalytic activity of Upf1, causing it to switch from an RNA-clamping mode to an RNA-unwinding mode. ► Upf1 binds RNA at an extended channel with nanomolar affinity ► The Upf1 CH domain promotes RNA binding allosterically via conformational changes ► Binding of Upf2 reduces the extent of RNA binding by Upf1 ► In the absence of the CH domain, RNA binding is decreased and unwinding is enhanced