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

SASDX28 – SmThrRS model for closed state based on PDB entry 1qf6

Stenotrophomonas maltophilia threonyl tRNA synthetase
MWexperimental 146 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
p(r)
Stenotrophomonas maltophilia threonyl tRNA synthetase pair distance distribution function Rg: 4.3 nm 0 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 closed state based on PDB entry 1qf6 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 using DENSS. 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   1QF6
 
PDB ID   1QF6