Come one, come all, and witness the molecular MACHINE

Last week was a big one for the Rapoport lab.

Throughout my years here, I've come to realy apreciate how structure biology can realy lead to insight. In the latest issue of Nature, two papers describe how proteins are pumped out of cells by the SecA secretory protein.

Background:
You can divide proteins into three classes, those that stay inside the cell, those that are pumped out of the cell and those that must be incorporated into the membrane. The problem with the last two classes of proteins is that they must cross a membrane. This is accomplished by the translocon, a protein conducting channel that is conserved throughout life. In bacteria it is refered to as SecY and in eukaryotes (that wuld be us), Sec61. Secreted proteins completly traverse the channel while membrane bound proteins enter the chanel and exit sideways through a lateral gate.

So how are secreted and membrane bound proteins translocated through the translocon?

There are two mechanisms. In the first, called co-translational insertion, the ribosome sits ontop of the channel and forces the newly synthesized protein into the pore. The energy necessary for translocation is generated by the protein synthesis machinery. In addition bacteria have a second method to translocates pre-synthesized proteins, and this requires the SecA pump. So how does SecA work?

Well in the latest issue of Nature the machine has been unveiled - and it looks cool. From the structure of the SecA-SecY complex, and the accompaning biochemistry paper, it becomes clear how a molecular pump could work. The part of SecA that holds on to the peptide becomes obvious and acts like a "clamp", in previous structures the clamp was open (an not obvious), but oin the complex the clamp closes. Just like a tightening fist, the SecA clamp has a cleft that is continuous with the chanel's pore. In addition SecA and SecY both have a lateral opening to allow membrane bound proteins to exit sideways and thus partition into the membrane, and yes both lateral exits are contiguous. Finally the SecY pore was seen to be plugged by a short alpha-helix - but when SecA binds to the translocon, the SecY's configuration changes so that the plug moves (although not enough to allow a clear passage across the chanel) and the chanel widens. But there's more, SecA plunges two of it's alpha-helices into the chanel itself to help open the pore. These two helices (or helix finger) resemble peptide pushing loops present in many polypeptide pumps such as the 19S subunit of the proteasome and ClpX.

So how does the machine work? It's most likely a three step process that will resemble the following:

Step one, the substrate is engaged to an opened SecA-SecY. Step two the substrate is shoved into the chanel by the helix finger. Step three, the clamp holds onto the partially translocated substrate, meanwhile the helix finger is pulled back and reset. Go back to step one.

This cycle will continue untill the substrate is translocated fully through the pore. Each step is hooked up to a distinct step of ATP hydrolysis. Because the cycle of ATP hydrolysis proceeds in one direction,

ATP => ATP trasitional state => ADP+P => noATP (or Apo form)

the corresponding machine can only go around the cycle in one direction as well

Open => Shove helix finger in => Hold with clamp => Reset helix finger

But more work will need to be done on each of the ATP hydrolysis steps inorder to fully understand how the machine really works.

Ref:
Jochen Zimmer, Yunsun Nam & Tom A. Rapoport
Structure of a complex of the ATPase SecA and the protein-translocation channel
Nature (08) 455:936

Karl J. Erlandson, Stephanie B. M. Miller, Yunsun Nam, Andrew R. Osborne, Jochen Zimmer & Tom A. Rapoport
A role for the two-helix finger of the SecA ATPase in protein translocation
Nature (08) 455:984