title: 2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site.
abstract: The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) was solved at 2.9 A using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5'AMP complex (TAM; Doublié S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17-31). In agreement with small-angle solution X-ray scattering experiments, unliganded TrpRS has a conformation in which both monomers open, leaving only the tryptophan-binding regions of their active sites intact. The amino terminal alphaA-helix, TIGN, and KMSKS signature sequences, and the distal 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 and 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 between the other two. These domain rearrangements provide a new structural paradigm 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 associated with the two catalytic signature sequences to the helical domain containing the presumptive anticodon-binding site provides a mechanism to coordinate active-site chemistry with relocation of the major tRNA binding determinants.
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill 27514, USA.
authors.forename: V A
authors.initials: VA
authors.lastname: Ilyin
authors.forename: B
authors.initials: B
authors.lastname: Temple
authors.forename: M
authors.initials: M
authors.lastname: Hu
authors.forename: G
authors.initials: G
authors.lastname: Li
authors.forename: Y
authors.initials: Y
authors.lastname: Yin
authors.forename: P
authors.initials: P
authors.lastname: Vachette
authors.forename: C W
authors.initials: CW
authors.lastname: Carter
mesh_terms: D000227:Adenine Nucleotides / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D019281:Dimerization; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D013816:Thermodynamics; D014369:Tryptophan-tRNA Ligase / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000227:Adenine Nucleotides; D008024:Ligands; D014369:Tryptophan-tRNA Ligase