2.9 angstrom Crystal structure ligand-free tryptophanyl-tRNA synthetase: Domain movements fragment the adenine nucleotide binding site

The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) w as solved at 2.9 Angstrom using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, R-f ree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5'AMP comp lex (TAM; Doublie S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17-31). In agreement with small-angle solution X-ray scattering experimen ts, unliganded TrpRS has a conformation in which both monomers open, leavin g only the tryptophan-binding regions of their active sites intact. The ami no terminal alpha A-helix, TIGN, and KMSKS signature sequences, and the dis tal helical domain rotate as a single rigid body away from the dinucleotide -binding fold domain, opening the AMP binding site, seen in the TAM complex , into two halves. Comparison of side-chain packing in ligand-free TrpRS an d the TAM complex, using identification of nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189-1195), shows that significant repacking occurs between three relatively stable core regions, one of which acts as a bearing betwee n the other two. These domain rearrangements provide a new structural parad igm that is consistent in detail with the "induced-fit" mechanism proposed for TyrRS by Fersht et al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G , 1988, Biochemistry 27:1581-1587). Coupling of ATP binding determinants as sociated with the two catalytic signature sequences to the helical domain c ontaining the presumptive anticodon-binding site provides a mechanism to co ordinate active-site chemistry with relocation of the major tRNA binding de terminants.