CRYSTAL-STRUCTURE OF UNMODIFIED TRNA(GLN) COMPLEXED WITH GLUTAMINYL-TRANSFER-RNA SYNTHETASE AND ATP SUGGESTS A POSSIBLE ROLE FOR PSEUDO-URIDINES IN STABILIZATION OF RNA STRUCTURE

tRNA(2)(Gln) made in vitro by transcription with T7 RNA polymerase doe s not contain the pseudouridines at positions 38, 39, and 55, the 4-th iouridine at position 8, or any of the methylated bases found in the t RNA(2)(Gln) made in vivo. Cocrystals of unmodified tRNA(2)(Gln) comple xed with glutaminyl-tRNA synthetase from Escherichia coli are isomorph ous with those of the complex with modified tRNA(2)(Gln). A difference electron density map between the complexes with modified and unmodifi ed tRNAs calculated at 2.5-Angstrom resolution shows no differences in the protein or tRNA structures, except for some very small shifts in atoms contacting the thiol at the 4 position of uridine 8 that are req uired to accommodate the smaller oxygen in the unmodified tRNA. Perhap s the most functionally significant change in the unmodified tRNA is t he absence of the specifically bound water molecules that are observed to cross-link the N5 of the pseudo-uridines to their 5' phosphate. Th is suggests a possible role for pseudouridinylation in stabilization o f the tRNA through water-mediated linking of these modified bases to t he backbone, which is consistent with the lower thermal stability of t he unmodified tRNA. An identical water-bridging structure is possible at four of the five other psuedo-uridines in known tRNA structures.