SOLUTION STRUCTURE OF THE ANTICODON-BINDING DOMAIN OF ESCHERICHIA-COLI LYSYL-TRANSFER-RNA SYNTHETASE AND STUDIES OF ITS INTERACTION WITH TRNA(LYS)

A protein domain corresponding to residues 31 to 149 of the E. coli Ly syl-tRNA synthetase species corresponding to the lysS gene was express ed and N-15-labelled. H-1 and N-15 NMR resonance assignments for this domain were obtained by two-dimensional and three-dimensional homonucl ear and heteronuclear spectroscopy. Using distance geometry and simula ted annealing, a three-dimensional structure could be calculated using 701 NOE and 86 dihedral angle restraints. It is composed of a five-st randed antiparallel beta-barrel capped by three alpha-helices at its e nds. This structure closely resembles that of the N-terminal domain of the other E. coli lysyl-tRNA synthetase species expressed from the ly sU gene and is highly homologous to the fold observed for the correspo nding region of aspartyl-tRNA synthetase. It is shown that the isolate d N-terminal fragment of lysyl-tRNA synthetase can interact with tRNA( Lys) as well as with poly (U), which mimics the anticodon sequence. Am ino acid residues involved in these interactions were identified and, in the case of poly-U, a number of specific protein-RNA contacts were characterized. Specific recognition of tRNA(Lys) involves a cluster of four structurally well-defined aromatic residues, anchored on the bet a-strands, and basic residues located on the surrounding loops. This o rganization is reminiscent of other RNA binding proteins, such as the U1A small nuclear ribonucleoprotein. (C) 1995 Academic Press Limited