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SRP RNA controls a conformational switch regulating the SRP–SRP receptor interaction

Nature Structural & Molecular Biology volume 15, pages 916–923 (2008)Cite this article

Abstract

The interaction of the signal-recognition particle (SRP) with its receptor (SR) mediates co-translational protein targeting to the membrane. SRP and SR interact via their homologous core GTPase domains and N-terminal four-helix bundles (N domains). SRP–SR complex formation is slow unless catalyzed by SRP's essential RNA component. We show that truncation of the first helix of the N domain (helix N1) of both proteins dramatically accelerates their interaction. SRP and SR with helix N1 truncations interact at nearly the RNA-catalyzed rate in the absence of RNA. NMR spectroscopy and analysis of GTPase activity show that helix N1 truncation in SR mimics the conformational switch caused by complex formation. These results demonstrate that the N-terminal helices of SRP and SR are autoinhibitory for complex formation in the absence of SRP RNA, suggesting a mechanism for RNA-mediated coordination of the SRP–SR interaction.

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Figure 1: Structural and schematic representations of the FtsY and Ffh constructs used in this study.
Figure 2: The N-terminal helices of Ffh and FtsY inhibit Ffh–FtsY association in the absence of 4.5S RNA.
Figure 3: The N-terminal helices of Ffh and FtsY stimulate Ffh–FtsY complex dissociation in the presence of 4.5S RNA.
Figure 4: The N-terminal helix of FtsY represses its basal GTPase activity.
Figure 5: FtsYΔN1 assumes an 'Ffh-bound' conformation in the presence of GppNHp.
Figure 6: Binding of Ffh to FtsY exposes the N-terminal helix of FtsY.
Figure 7: Model for Ffh–FtsY structural rearrangement upon complex formation.
Figure 8: Thermodynamic model describing the mechanism of SRP RNA control of the interaction of the SRP and SR.

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Acknowledgements

The authors would like to thank C. Guthrie, P. Egea and members of the Walter laboratory for insightful comments and careful reading of the manuscript. This work was supported by funding to P.W. from the US National Institutes of Health and the Howard Hughes Medical Institute. The Jane Coffin Childs Memorial Fund supports S.B.N. N.B. was supported by a predoctoral fellowship from the US National Science Foundation. J.D.G. and S.N.F. were supported by the Sandler Family Foundation for Basic Sciences. S.N.F. was supported in part by the Achievement Awards for College Scientists (ARCS) Foundation.

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Author notes

  1. Saskia B Neher and Niels Bradshaw: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute, University of California at San Francisco, 600 16th Street, San Francisco, 94158, California, USA

    Saskia B Neher, Niels Bradshaw & Peter Walter

  2. Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, 94158, California, USA

    Saskia B Neher, Niels Bradshaw & Peter Walter

  3. Department of Pharmaceutical Chemistry, University of California at San Francisco, 600 16th Street, San Francisco, 94158, California, USA

    Stephen N Floor & John D Gross

  4. Graduate Group in Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, 94158, California, USA

    Stephen N Floor

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Contributions

S.B.N. and N.B. prepared reagents and performed Ffh–FtsY association and dissociation assays; N.B. carried out GTPase experiments; N.B., S.N.F. and J.D.G. designed, executed and interpreted the NMR experiments; S.B.N. performed partial proteolysis assays; S.B.N., N.B. and P.W. wrote the article.

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Correspondence to Peter Walter.

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Neher, S., Bradshaw, N., Floor, S. et al. SRP RNA controls a conformational switch regulating the SRP–SRP receptor interaction. Nat Struct Mol Biol 15, 916–923 (2008). https://doi.org/10.1038/nsmb.1467

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