Solution structure of the ribosome recycling factor from Aquifex aeolicus

The solution structure of ribosome recycling factor (RRF) from hyperthermop hilic bacterium, Aquifex aeolicus, was determined by heteronuclear multidim ensional NMR spectroscopy. Fifteen structures were calculated using restrai nts derived from NOE. J-coupling, and T-1/T-2 anisotropies. The resulting s tructure has an overall L-shaped conformation with two domains and is simil ar to that of a tRNA molecule. The domain I (corresponding to the anticodon stem of tRNA) is a rigid three alpha -helix bundle. Being slightly differe nt from usual coiled-coil arrangements, each helix of domain I is not twist ed but straight and parallel to the main axis. The domain II (corresponding to the portion with the CCA end of tRNA) is an alpha/beta domain with an a lpha -helix and two beta -sheets, that has some flexible regions. The backb one atomic root-mean-square deviation (rmsd) values of both domains were 0. 7 Angstrom when calculated separately, which is smaller than that of the mo lecule as a whole (1.4 A). Measurement of N-15-{H-1} NOE values show that t he residues in the corner of the L-shaped molecule are undergoing fast inte rnal motion. These results indicate that the joint region between two domai ns contributes to the fluctuation in the orientation of two domains. Thus, it was shown that RRF remains the tRNA mimicry in solution where it functio ns.