3FHJ

Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations

Summary for 3FHJ

• Entry DOI: 10.2210/pdb3fhj/pdb
• Related: 1D2R 1I6K 1I6L 1I6M 1M83 1MAU 1MB2 2OV4 3FI0
• Descriptor: Tryptophanyl-tRNA synthetase, TRYPTOPHAN, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: ligand-dependent domain rearrangement, mechanistic pathway, molecular simulations, aminoacyl-trna synthetase, atp-binding, cytoplasm, ligase, nucleotide-binding, protein biosynthesis, translation
• Biological source: Bacillus stearothermophilus
• Total number of polymer chains: 6
• Total formula weight: 227232.53

Authors

Laowanapiban, P.,Kapustina, M.,Vonrhein, C.,Delarue, M.,Koehl, P.,Carter Jr., C.W. (deposition date: 2008-12-09, release date: 2009-02-03, Last modification date: 2023-09-06)

Primary citation

Laowanapiban, P.,Kapustina, M.,Vonrhein, C.,Delarue, M.,Koehl, P.,Carter, C.W.
Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations.
Proc.Natl.Acad.Sci.Usa, 106:1790-1795, 2009

PubMed 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.

PubMed: 19174517
DOI: 10.1073/pnas.0812752106

Experimental method

X-RAY DIFFRACTION (2.65 Å)