Conformational transition of Sec machinery inferred from bacterial SecYE structures

Abstract

Over 30% of proteins are secreted across or integrated into membranes. Their newly synthesized forms contain either cleavable signal sequences or non-cleavable membrane anchor sequences, which direct them to the evolutionarily conserved Sec translocon (SecYEG in prokaryotes and Sec61, comprising α-, γ- and β-subunits, in eukaryotes). The translocon then functions as a protein-conducting channel1. These processes of protein localization occur either at or after translation. In bacteria, the SecA ATPase2,3 drives post-translational translocation. The only high-resolution structure of a translocon available so far is that for SecYEβ from the archaeon Methanococcus jannaschii4, which lacks SecA. Here we present the 3.2-Å-resolution crystal structure of the SecYE translocon from a SecA-containing organism, Thermus thermophilus. The structure, solved as a complex with an anti-SecY Fab fragment, revealed a ‘pre-open’ state of SecYE, in which several transmembrane helices are shifted, as compared to the previous SecYEβ structure4, to create a hydrophobic crack open to the cytoplasm. Fab and SecA bind to a common site at the tip of the cytoplasmic domain of SecY. Molecular dynamics and disulphide mapping analyses suggest that the pre-open state might represent a SecYE conformational transition that is inducible by SecA binding. Moreover, we identified a SecA–SecYE interface that comprises SecA residues originally buried inside the protein, indicating that both the channel and the motor components of the Sec machinery undergo cooperative conformational changes on formation of the functional complex.

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Figure 1: Overall structure of T. thermophilus SecYE.
Figure 2: Comparison of the T. thermophilus SecYE and M. jannaschii SecYEβ structures.
Figure 3: Contacting residues between T. thermophilus SecA and SecYE.
Figure 4: Multiple modes of SecA–SecY interactions.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The coordinates and structure factors have been deposited in the Protein Data Bank, under the accession codes 2ZJS for Fab–SecYE and 2ZQP for SecYE.

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Acknowledgements

We thank K. Inaba, Y. Akiyama and M. Hattori for useful suggestions about sample preparation and crystallization; T. Sakamoto and T. Saika for their assistance in the purification of T. thermophilus SecYE; K. Mochizuki, M. Sano, K. Yoshikaie, T. Adachi and Y. Echizen for technical support; and the beamline staff members at BL41XU of SPring-8 (Sayo, Japan) and NW12 of PF (Tsukuba, Japan) for technical help during data collection. We also thank I. Artsimovitch for critically reading the manuscript. This work was supported by a SORST program grant from JST (Japan Science and Technology) to O.N., by a CREST grant from JST to K.I. and N.D., by a BIRD grant from JST to H.M. and Y.S., by Global COE Program (Center of Education and Research for Advanced Genome-Based Medicine) and a grant for the National Project on Protein Structural and Functional Analyses from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) to O.N., by NIH grants to D.G.V., by grants from MEXT to H.M., S.F., R.I., K.I. and O.N., and by Mitsubishi Foundation grants to O.N.

Author Contributions T.T. carried out the structural determination and the biochemical experiments of T. thermophilus SecYE. H.M. carried out biochemical analyses of SecA–SecY interactions. A.P. and D.G.V. assisted with the crystallization and data collection of SecYE as well as with manuscript preparation. S.F., R.I. and O.N. assisted with the structural determination. T.M. and Y.S. performed the molecular dynamics simulation. N.D. performed disulphide-bond quantification and mass spectrometry. All authors discussed the results and commented on the manuscript. O.N. and K.I. supervised the work and wrote/edited the manuscript.

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Correspondence to Koreaki Ito or Osamu Nureki.

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Tsukazaki, T., Mori, H., Fukai, S. et al. Conformational transition of Sec machinery inferred from bacterial SecYE structures. Nature 455, 988–991 (2008). https://doi.org/10.1038/nature07421

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