The conformational gymnastics of the Escherichia coli SecA molecular machine and its interactions with signal sequences

Protein secretion is a selective and regulated process that is essential in all organisms. In bacteria the preprotein translocase SecA, either free in the cytosol or associated with the SecYEG translocon, recognizes and binds most post-translational secretory proteins containing an N-terminal signal sequence. In Gram-negative bacteria, the molecular chaperone SecB binds many of the preproteins to keep them in a translocation-competent state. Subsequently, SecB delivers the preproteins to the translocon-associated SecA, which binds the signal sequence and also interacts with mature regions of the preprotein. After the preprotein/SecA/SecYEG complex has formed, the energy derived from ATP hydrolysis by SecA coupled with the proton motive force drives the insertion of the preprotein through the translocon pore. During the translocation reaction, the conformation of SecA dramatically changes from an inactive closed form (c-SecA) to one more active and open states. The various crystal structures of SecA have provided many structural details about c-SecA. The recent low resolution crystal structure of a fragment of SecA bound to SecYEG (Zimmer et al., 2008) has provided a starting point for structural analysis of the active and open conformation of SecA. Previous work in our laboratory demonstrated that an N-terminal proteolytic fragment of SecA, SecA64, is an activated form of SecA that with higher affinity signal peptides better than c-SecA (Triplett et al., 2001). To correlate the SecA64 results with full-length SecA, we determined that SecA in the presence of low concentrations of urea has an enhanced ATPase activity similar to translocation level, which is comparable to what was observed with SecA64. Analysis by CD and Trp fluorescence indicates the presence of an intermediate at 2.2 M urea at 22°C (termed u-SecA). Using limited proteolysis, we determined that u-SecA is in an protease-sensitive conformation that mimics the translocation-active form of SecA. These structural rearrangements occur primarily in the C-terminal one-third of the protein. Next, we sought to understand the signal sequence interactions with c-SecA and translocation-active u-SecA. Using a photoactivatable cross-linking approach along with limited proteolysis, two-dimensional gels, and domain mapping with region-specific antibodies, the signal sequence-binding site was mapped to the interface of NBF II, PPXD, and HSD. The site is the same in both forms of SecA but in our data suggests u-SecA that the binding groove as expanded