Tuesday, June 15, 2010

A possible mechanism for elongation factors--finally?

Like the last speculation, this one involves the ribosome. In particular, the two elongation factors that in bacteria are known as EF-Tu and EF-G. Like all GTPases, these proteins have a catalytic domain that resembles the Ras family of signaling molecules. Clearly, however, the details of the catalysis are distinct. In common with each other, both types of proteins have low catalytic activity on their own (though the quantitative meaning of "low" varies"), and need to be activated by binding to something else in order to achieve rapid catalysis.

In the case of Ras-like proteins, these partners are called GTPase-activating proteins, or GAPs, and they bind to a particular region of the proteins near the phosphates of the bound GTP. Their activity commonly (though not always) involves an arginine side chain that is inserted into the active site and presumably stabilizes the transition state. However, EF-Tu and EF-G are activated by interacting with a particular state of the ribosome. The sarcin-ricin loop, or SRL, of the large subunit occupies a position similar to GAPs in Ras-like GTPases, but in the available structures it makes few contacts to the protein. This is probably due to the fact that one part of the protein, the so-called Switch I segment, is disordered.

Some researchers have suggested that the disordering of this segment is what triggers catalysis, but I am very skeptical of that, largely for the simple reason that I've never seen another enzyme where catalysis is facilitated by decreasing the number or closeness of contacts to the substrate. In fact, the common scenario is the opposite, where loop or domain closures activate enzymes by making the contacts more extensive. I rather suspect that the disorder observed is due to the inability to actually form and trap the GTP-bound, activated form in the crystal. But in any case, the "arginine finger" mechanism, or similar, cannot operate, as there are no positively charged groups of any kind protruding from the SRL.

An intriguing (relatively) recent paper suggested that a GTPase involved in 30S ribosomal subunit assembly, YqeH, uses a potassium ion coordinated near the GTP phosphates to replace the arginine used by Ras. This was based on a previous structural demonstration that a related protein involved in tRNA modification uses this mechanism. Interestingly, both of these GTPases interact with folded RNA in one way or another, which raises the question of whether the elongation factors could similarly use a second metal ion (in addition to the Mg2+ common to all GTPases) to trigger catalysis upon interaction with the SRL. In fact, there is an acidic Asp residue in the P-loop region of both EFs near where this hypothetical cation would have to be.

However, a quick inspection of the structures of EF-Tu and EF-G bound to the ribosome shows that even at the modest resolution, a direct participation of the SRL in the coordination sphere of such an ion is essentially ruled out, at least in the approximate relative positioning of the molecules observed. Therefore, any role of the SRL in electrostatically recruiting a cation would need to be water-mediated. Alternatively, the Switch I region of GTP-bound EF-Tu contains a short helix whose dipole points very roughly toward the Asp in the P-loop, and realignment of this helix upon ribosome binding may provide a way to recruit a cation only upon proper juxtaposition of the two. As no structure exists of EF-G with the switch segments ordered, it is unknown whether this helix exists in that protein as well. It seems that even if a second cation is involved in the mechanism of elongation factors, it will be very difficult to obtain a structure with it present.

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