Molecular Mechanism of GTPase Activation at the Signal Recognition Particle (SRP) RNA Distal End

• Published in: The Journal of biological chemistry Vol. 288; no. 51; pp. 36385 - 36397
• Main Authors: Shen, Kuang, Wang, Yaqiang, Hwang Fu, Yu-Hsien, Zhang, Qi, Feigon, Juli, Shan, Shu-ou
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 20.12.2013; American Society for Biochemistry and Molecular Biology
• Subjects: Amino Acid Sequence; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Base Sequence; Escherichia coli - chemistry; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; G Proteins; GTP Phosphohydrolases - chemistry; GTP Phosphohydrolases - metabolism; Molecular Docking Simulation; Molecular Sequence Data; Mutation; Nuclear Magnetic Resonance; Nucleic Acid Conformation; Protein Binding; Protein Targeting; Protein-Nucleic Acid Interaction; Receptors, Cytoplasmic and Nuclear - chemistry; Receptors, Cytoplasmic and Nuclear - metabolism; RNA; RNA, Small Cytoplasmic - chemistry; RNA, Small Cytoplasmic - metabolism; Signal Recognition Particle - chemistry; Signal Recognition Particle - genetics; Signal Recognition Particle - metabolism; Single Molecule Biophysics; Single Molecule Biophysics; Nuclear Magnetic Resonance; Protein-Nucleic Acid Interaction; RNA; G Proteins; Protein Targeting
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M113.513614

The signal recognition particle (SRP) RNA is a universally conserved and essential component of the SRP that mediates the co-translational targeting of proteins to the correct cellular membrane. During the targeting reaction, two functional ends in the SRP RNA mediate distinct functions. Whereas the RNA tetraloop facilitates initial assembly of two GTPases between the SRP and SRP receptor, this GTPase complex subsequently relocalizes ∼100 Å to the 5′,3′-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover. Here we combined biochemical, single molecule, and NMR studies to investigate the molecular mechanism of this large scale conformational change. We show that two independent sites contribute to the interaction of the GTPase complex with the SRP RNA distal end. Loop E plays a crucial role in the precise positioning of the GTPase complex on these two sites by inducing a defined bend in the RNA helix and thus generating a preorganized recognition surface. GTPase docking can be uncoupled from its subsequent activation, which is mediated by conserved bases in the next internal loop. These results, combined with recent structural work, elucidate how the SRP RNA induces GTPase relocalization and activation at the end of the protein targeting reaction. Background: A large GTPase movement on the signal recognition particle (SRP) RNA activates GTP hydrolysis to complete protein targeting. Results: GTPase activation requires distinct primary and secondary docking sites and catalytic bases, optimally positioned on the SRP RNA. Conclusion: The SRP RNA forms a preorganized surface to mediate specific GTPase activation. Significance: Study of the SRP RNA broadens our understanding of RNA-protein recognition and protein targeting.