title: Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.
abstract: Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamics trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: Poramaet
authors.initials: P
authors.lastname: Laowanapiban
authors.forename: Maryna
authors.initials: M
authors.lastname: Kapustina
authors.forename: Clemens
authors.initials: C
authors.lastname: Vonrhein
authors.forename: Marc
authors.initials: M
authors.lastname: Delarue
authors.forename: Patrice
authors.initials: P
authors.lastname: Koehl
authors.forename: Charles W
authors.initials: CW
authors.lastname: Carter
mesh_terms: D000249:Adenosine Monophosphate; D001665:Binding Sites; D018360:Crystallography, X-Ray; D011756:Diphosphates; D001411:Geobacillus stearothermophilus / Q000201:enzymology*; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D014364:Tryptophan; D014369:Tryptophan-tRNA Ligase / Q000737:chemistry*
chemical_list: D011756:Diphosphates; D008024:Ligands; D000249:Adenosine Monophosphate; D014364:Tryptophan; D014369:Tryptophan-tRNA Ligase