A conserved structural element is a kinetic modulator of nucleotide exchange in the EF-Tu

A recent publication [1] reports that the P-loop, a conserved structural element in the catalytic domain of many different NTP-ases, might participate in modulating the nucleotide exchange rates for a broad class of NTP-ases.

The study was performed in detail on the EF-Tu protein, which catalyzes the GTP/GDP hydrolysis. Results show that the internal dynamics of the P-loop does not affect the nucleotide exchange rates, but rather P-loop forms a P-loop anchor via hydrogen bonds with another structural element of the protein, helix C. The P-loop anchor contributes to the activation entropy of the nucleotide exchange,  and consequently modulates the nucleotide-binding kinetics. 

Presently, two classes of P-anchors have been identified, depending on the nature of stabilization of the anchor, one class is hydrogen-bond stabilized, while the other is stabilized by the hydrophobic effect. The finding is consistent with the natural mechanism of the nucleotide exchange on the EF-Tu, where the nucleotide is exchanged upon the binding of another protein (EF-Ts) that disrupts the stability of the P-anchor, making the P-loop more flexible. The larger flexbility of the P-loop increases the entropic contribution to the activation free energy, resulting in faster nucleotide dissociation.

[1] Mercier E., Girodat D., Wieden H.-J., A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu, JA  - Sci. Rep., 2015.