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. 2008 Oct 16;455(7215):936-43.
doi: 10.1038/nature07335.

Structure of a complex of the ATPase SecA and the protein-translocation channel

Jochen Zimmer  1 , Yunsun Nam, Tom A Rapoport
Affiliations

Structure of a complex of the ATPase SecA and the protein-translocation channel

Jochen Zimmer et al. Nature. .

Abstract

Most proteins are secreted from bacteria by the interaction of the cytoplasmic SecA ATPase with a membrane channel, formed by the heterotrimeric SecY complex. Here we report the crystal structure of SecA bound to the SecY complex, with a maximum resolution of 4.5 ångström (A), obtained for components from Thermotoga maritima. One copy of SecA in an intermediate state of ATP hydrolysis is bound to one molecule of the SecY complex. Both partners undergo important conformational changes on interaction. The polypeptide-cross-linking domain of SecA makes a large conformational change that could capture the translocation substrate in a 'clamp'. Polypeptide movement through the SecY channel could be achieved by the motion of a 'two-helix finger' of SecA inside the cytoplasmic funnel of SecY, and by the coordinated tightening and widening of SecA's clamp above the SecY pore. SecA binding generates a 'window' at the lateral gate of the SecY channel and it displaces the plug domain, preparing the channel for signal sequence binding and channel opening.

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Figures

Figure 1.
Figure 1.
Architecture of the T. maritima SecA–SecYEG complex. a, Stereo view of a σA-weighted, phase combined, NCS averaged, and B-factor sharpened 2Fo - Fc electron density map (contoured at 1σ). The view of the lateral gate of SecY is shown, with the Cα-trace of SecY in grey, SecE in red, SecG in green and SecA in blue. b, Cartoon of the complex viewed from the side. The lines indicate the membrane boundaries. c, As in b, but viewed from the cytoplasm. d, The two-helix finger of SecA inside the cytoplasmic funnel of SecY. TM2b and TM8, as well as the tip of the 6–7 loop, are shown as cartoons for clarity. Plug residues are coloured in orange. e, As in d, but shown from the back.
Figure 2.
Figure 2.
Conformational changes of SecA. a–c, Different orientations of the PPXD relative to the NBDs. The view is from the cytosol, as in Fig. 1c. The closed (a) and open (b) conformations refer to the B. subtilis SecA structures (PDB accessions 1M6N and 1TF2, respectively). The loop of the PPXD contacting NBD1 and NBD2 in the SecA–SecY complex is highlighted in red. The insertion in the T. maritima NBD1 is shown in purple. The conserved β-strands connecting NBD1 with the PPXD are shown in orange. d, Position of the NBDs in the ADP-bound state of B. subtilis SecA (grey) versus the ADP–BeF x bound state of T. maritima SecA (blue) when associated with SecY. The structures were aligned with respect to NBD1. The rotation axis indicated by a black circle is parallel to the plane of the membrane. The modelled ADP–BeF3-is shown as orange sticks.
Figure 3.
Figure 3.
Conformational changes of SecY. a, Comparison of the T. maritima SecA–SecYEG complex with the SecY channel from M. jannaschii (Mj). The alignment is on the basis of TM2b–TM5 of SecY. The view on the right corresponds to a slice through the SecY channel (the plane is indicated by the dashed line on the left). TMs are numbered, and loops are omitted, for clarity. Similarly positioned (root mean squared deviation (r.m.s.d.) ≤1.8 Å) and deviating TMs of T. maritima SecY are shown in grey and blue, respectively. Helix movements are indicated by red arrows. b, Semi-transparent surface of the SecY channel. The window in the lateral gate of SecY is indicated by a view on the back wall of the channel, formed by TM5 and TM10 (in yellow). TM2b, TM3, TM7 and TM8 are shown as black cartoons.
Figure 4.
Figure 4.
The polypeptide clamp of SecA. a, Surface representation of B. subtilis SecA (PDB accession 1TF2) with conserved amino acid residues colour coded (blue denotes the highest, and red denotes the lowest conservation). b, As in a, except that the conserved hydrophobic residues along the proposed polypeptide clamp of SecA are shown in orange. c, The T. maritima SecA–SecYEG complex with SecA shown in blue, and SecY, SecE and SecG shown in grey, red and green, respectively. The PPXD was removed for clarity. The residues that were labelled orange in b are shown as red sticks. The yellow circle indicates the translocation pore in SecY.
Figure 5.
Figure 5.
Model for SecA-mediated protein translocation. a, Proposed polypeptide translocation pathway through the SecA–SecYEG complex. The signal sequence of a hypothetical polypeptide (red trace) is intercalated into the lateral gate of SecY. The clamp of SecA is highlighted as a semi-transparent green torus, and the two-helix finger is shown as a brown cylinder. b, Upon ATP binding, the clamp of SecA would widen, allowing the two-helix finger to bind to the polypeptide and move it into the channel. After ATP hydrolysis, the clamp would tighten and the finger would reset. SecA probably adopts more than two conformational states during ATP hydrolysis. The structure might represent a situation in which the two-helix finger is in its ‘down-state’ and the clamp is already closed, although the conformation of the clamp may be different in the presence of a translocating polypeptide.
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References

    1. Rapoport TA Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 450, 663–669 (2007). - PubMed
    1. Neumann-Haefelin C, Schafer U, Muller M & Koch HG SRP-dependent co-translational targeting and SecA-dependent translocation analyzed as individual steps in the export of a bacterial protein. EMBO J 19, 6419–6426 (2000). - PMC - PubMed
    1. Qi HY & Bernstein HD SecA is required for the insertion of inner membrane proteins targeted by the Escherichia coli signal recognition particle. J Biol Chem 274, 8993–8997 (1999). - PubMed
    1. Duong F & Wickner W Sec-dependent membrane protein biogenesis: SecYEG, preprotein hydrophobicity and translocation kinetics control the stop-transfer function. Embo J 17, 696–705 (1998). - PMC - PubMed
    1. van den Berg B et al. X-ray structure of a protein-conducting channel. Nature 427, 36–44 (2004). - PubMed

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