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RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle

Abstract

The signal recognition particle (SRP) targets nascent proteins to cellular membranes for insertion or secretion by recognizing polypeptides containing an N-terminal signal sequence as they emerge from the ribosome. GTP-dependent binding of SRP to its receptor protein leads to controlled release of the nascent chain into a membrane-spanning translocon pore. Here we show that the association of the SRP with its receptor triggers a marked conformational change in the complex, localizing the SRP RNA and the adjacent signal peptide–binding site at the SRP-receptor heterodimer interface. The orientation of the RNA suggests how peptide binding and GTP hydrolysis can be coupled through direct structural contact during cycles of SRP-directed protein translocation.

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Figure 1: Hydroxyl radical probing of the 4.5S RNA by Ffh in the E. coli SRP–FtsY (residues 197–498) complex.
Figure 2: Hydroxyl radical probing of the 4.5S RNA by FtsY (residues 197–498) in the E. coli SRP–FtsY complex.
Figure 3: Molecular model of the E. coli SRP–FtsY complex.
Figure 4: FtsY (residues 197–498) is required for the observed SRP conformational rearrangement, and the 4.5S RNA tetraloop affects the heterodimer GTPase activity.

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Acknowledgements

We thank I.J. MacRae for helpful discussions on the BABE-Fe modification sites of Ffh and FtsY and K. Karbstein, W. Gilbert, C.S. Fraser, N.H. Chmiel, J.W. Hershey and H.F. Noller for review of the manuscript. The work was supported by grant GM22778 from the US National Institutes of Health.

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Correspondence to Jennifer A Doudna.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Fluorescence assay to monitor BABE-Fe conjugation of Ffh and FtsY. (PDF 54 kb)

Supplementary Fig. 2

Gel mobility shift assay of BABE-Fe–modified Ffh and FtsY. (PDF 193 kb)

Supplementary Fig. 3

Ffh M- and G-domain cleavage quantification. (PDF 641 kb)

Supplementary Fig. 4

View of the Ffh-FtsY heterodime.r (PDF 288 kb)

Supplementary Fig. 5

FtsY cleavage data quantification. (PDF 180 kb)

Supplementary Fig. 6

Molecular models of the SRP-FtsY complex. (PDF 193 kb)

Supplementary Fig. 7

Quantification of cleavage data produced by Ffh. (PDF 31 kb)

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Spanggord, R., Siu, F., Ke, A. et al. RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle. Nat Struct Mol Biol 12, 1116–1122 (2005). https://doi.org/10.1038/nsmb1025

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