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Conformational transition of Sec machinery inferred from bacterial SecYE structures

Nature 455, 988-991 (2008)
Tomoya Tsukazaki1,7, Hiroyuki Mori2,7, Shuya Fukai1,8, Ryuichiro Ishitani3, Takaharu Mori4, Naoshi Dohmae5, Anna Perederina6, Yuji Sugita4, Dmitry G. Vassylyev6, Koreaki Ito2 & Osamu Nureki1,3
1. Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan 2. Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan 3. Division of Structural Biology, Department of Basic Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan 4. Advanced Science Institute, 5. Biomolecular Characterization Team and CREST/JST, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 6. Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA 7. These authors contributed equally to this work. 8. Present address: Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization, The University of Tokyo, 211 General Research Building, Institute of Molecular and Cellular Biosciences, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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 jannaschii 4, 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.