The crystal structure of yeast phenylalanine tRNA at 2.0 angstrom resolution: Cleavage by Mg2+ in 15-year old crystals

We have re-determined the crystal structure of yeast tRNA(Phe) to 2.0 Angst rom resolution using 15 year old crystals. The accuracy of the new structur e, due both to higher resolution data and formerly unavailable refinement m ethods, consolidates the previous structural information, but also reveals novel details. Ln particular, the water structure around the tightly bound Mg2+ is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecu les in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-aff inity Mg2+ binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the T Psi C arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have a lso found that two specific regions of the tRNA in the crystals are partial ly cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg2+. (C) 2000 Academic Press.