Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.
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.
Laowanapiban
Poramaet
P
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
Kapustina
Maryna
M
Vonrhein
Clemens
C
Delarue
Marc
M
Koehl
Patrice
P
Carter
Charles W
CW
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*
D011756:Diphosphates; D008024:Ligands; D000249:Adenosine Monophosphate; D014364:Tryptophan; D014369:Tryptophan-tRNA Ligase