Crystal structure of a complete threonyl tRNA synthetase: toggle clamp model?

Tran T, Fenwick M, Edwards T, Dranow D, Abendroth J, Shek R, Tillery L, Craig J, Van Voorhis W, Myler P, Biochemical and Biophysical Research Communications :152677 (2025) DOI

SASDXZ7 – SmThrRS model for open state based on PDB entry 6vu9

Stenotrophomonas maltophilia threonyl tRNA synthetase
MWexperimental 141 kDa
MWexpected 146 kDa
log I(s) 6.43×101 6.43×100 6.43×10-1 6.43×10-2
Stenotrophomonas maltophilia threonyl tRNA synthetase small angle scattering data  s, nm-1
ln I(s)
Stenotrophomonas maltophilia threonyl tRNA synthetase Guinier plot ln 6.44×101 Rg: 4.2 nm 0 (4.2 nm)-2 s2
(sRg)2I(s)/I(0)
Stenotrophomonas maltophilia threonyl tRNA synthetase Kratky plot 1.104 0 3 sRg
Dmax: 16.2 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Stenotrophomonas maltophilia threonyl tRNA synthetase PDB (PROTEIN DATA BANK) model

log I(s)
 s, nm-1
Stenotrophomonas maltophilia threonyl tRNA synthetase PDB (PROTEIN DATA BANK) model

Synchrotron SAXS data from solutions of SmThrRS model for open state based on PDB entry 6vu9 in 20 mM HEPES, 0.2 M NaCl, 1.5% v/v glycerol, and 1 mM TCEP, pH 7 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS) storage ring (Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.10 mg/ml was measured at 20°C. 660 successive 2 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

The trace was processed with Chromixs. The IFT was computed in BioXtas-RAW 2.3.0. The Dmax was set to 162 Angstroms. GNOM gives a similar Dmax at a qmax of 0.3 A^-1.

Stenotrophomonas maltophilia threonyl tRNA synthetase
Mol. type   Protein
Organism   Stenotrophomonas maltophilia (strain K279a) (522373)
Olig. state   Dimer
Mon. MW   72.9 kDa
 
UniProt   B2FN79
Sequence   FASTA
 
PDB ID   6VU9
 
PDB ID   6VU9