Structural and functional investigation of tRNA guanine transglycosylase

Katharina Sievers, University of Göttingen Dissertation - (2023) URL

SASDRC8 – Human tRNA guanine transglycosylase bound to aspartate transfer RNA (tRNA-Asp)

Queuine tRNA-ribosyltransferase catalytic subunit 1
Queuine tRNA-ribosyltransferase accessory subunit 2
transfer RNA (Aspartate)
MWexperimental 101 kDa
MWexpected 116 kDa
VPorod 160 nm3
log I(s) 4.39×10-2 4.39×10-3 4.39×10-4 4.39×10-5
Queuine tRNA-ribosyltransferase catalytic subunit 1 Queuine tRNA-ribosyltransferase accessory subunit 2 transfer RNA (Aspartate) small angle scattering data  s, nm-1
ln I(s)
Queuine tRNA-ribosyltransferase catalytic subunit 1 Queuine tRNA-ribosyltransferase accessory subunit 2 transfer RNA (Aspartate) Guinier plot ln 4.39×10-2 Rg: 3.5 nm 0 (3.5 nm)-2 s2
(sRg)2I(s)/I(0)
Queuine tRNA-ribosyltransferase catalytic subunit 1 Queuine tRNA-ribosyltransferase accessory subunit 2 transfer RNA (Aspartate) Kratky plot 1.104 0 3 sRg
p(r)
Queuine tRNA-ribosyltransferase catalytic subunit 1 Queuine tRNA-ribosyltransferase accessory subunit 2 transfer RNA (Aspartate) pair distance distribution function Rg: 3.5 nm 0 Dmax: 10.9 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Human tRNA guanine transglycosylase bound to aspartate transfer RNA (tRNA-Asp) Rg histogram Rg, nm
Queuine tRNA-ribosyltransferase catalytic subunit 1 Queuine tRNA-ribosyltransferase accessory subunit 2 transfer RNA (Aspartate) EOM/RANCH model
Queuine tRNA-ribosyltransferase catalytic subunit 1 Queuine tRNA-ribosyltransferase accessory subunit 2 transfer RNA (Aspartate) EOM/RANCH model
Queuine tRNA-ribosyltransferase catalytic subunit 1 Queuine tRNA-ribosyltransferase accessory subunit 2 transfer RNA (Aspartate) EOM/RANCH model

Synchrotron SAXS data from solutions of tRNA guanine transglycosylase bound to aspartate transfer RNA in 20 mM HEPES, 100 mM NaCl, 3% (w/v) glycerol, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 75.00 μl sample at 4.5 mg/ml was injected at a 0.70 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 2160 successive 1 second frames were collected through the SEC elution. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Queuine tRNA-ribosyltransferase catalytic subunit 1
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   44.2 kDa
 
UniProt   Q9BXR0 (1-403)
Sequence   FASTA
 
Queuine tRNA-ribosyltransferase accessory subunit 2
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   46.7 kDa
 
UniProt   Q9H974 (1-415)
Sequence   FASTA
 
transfer RNA (Aspartate) (tRNAAsp)
Mol. type   RNA
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   25.2 kDa
Sequence   FASTA