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Recognition of a signal peptide by the signal recognition particle

Abstract

Targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (SRP) when nascent polypeptide chains emerge from the ribosome. The SRP–ribosome nascent chain complex is then targeted through its GTP-dependent interaction with SRP receptor to the protein-conducting channel on endoplasmic reticulum membrane in eukaryotes or plasma membrane in bacteria. A universally conserved component of SRP (refs 1, 2), SRP54 or its bacterial homologue, fifty-four homologue (Ffh), binds the signal peptides, which have a highly divergent sequence divisible into a positively charged n-region, an h-region commonly containing 8–20 hydrophobic residues and a polar c-region3,4,5. No structure has been reported that exemplifies SRP54 binding of any signal sequence. Here we have produced a fusion protein between Sulfolobus solfataricus SRP54 (Ffh) and a signal peptide connected via a flexible linker. This fusion protein oligomerizes in solution through interaction between the SRP54 and signal peptide moieties belonging to different chains, and it is functional, as demonstrated by its ability to bind SRP RNA and SRP receptor FtsY. We present the crystal structure at 3.5 Å resolution of an SRP54–signal peptide complex in the dimer, which reveals how a signal sequence is recognized by SRP54.

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Figure 1: Structure of SRP54 in complex with a signal sequence.
Figure 2: Interaction of the M domain with a signal peptide.
Figure 3: Structural change of SRP54 upon signal sequence binding.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for SRP54* have been deposited in the Protein Data Bank under accession number 3KL4.

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Acknowledgements

We thank members of the Nagai group for assisting with data collection, O. Daumke for help with the GTP binding and GTPase assays, and J. Kavran for discussion. This project was supported by the Medical Research Council of the UK. C.Y.J. was supported by a HFSP grant.

Author information

Authors and Affiliations

Authors

Contributions

The project was conceived and designed by C.Y.J. and K.N. All experiments were executed by C.Y.J. with the help of K.N. (cloning), C.O. and J.L. (crystallography), and H.H. and C.V.R. (mass spectrometry). The refinement was carried out by C.Y.J. and J.L., and the paper was written by C.Y.J., J.L. and K.N., with important input from others.

Corresponding author

Correspondence to Kiyoshi Nagai.

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The authors declare no competing financial interests.

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This file contains Supplementary Figures S1-S9 with legends and Supplementary Tables S1-S2. (PDF 10185 kb)

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Janda, C., Li, J., Oubridge, C. et al. Recognition of a signal peptide by the signal recognition particle. Nature 465, 507–510 (2010). https://doi.org/10.1038/nature08870

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