Distinctive features and structural significance of the Homo sapiens ethylmalonic encephalopathy protein iron binding site

Al Kikhney, Marco Salomone-Stagni.

SASDAF7 – Metal-bound hETHE1

Persulfide dioxygenase ETHE1, mitochondrial
MWexperimental 42 kDa
MWexpected 56 kDa
VPorod 70 nm3
log I(s) 9.99×101 9.99×100 9.99×10-1 9.99×10-2
Persulfide dioxygenase ETHE1, mitochondrial small angle scattering data  s, nm-1
ln I(s)
Persulfide dioxygenase ETHE1, mitochondrial Guinier plot ln 10.00×101 Rg: 2.5 nm 0 (2.5 nm)-2 s2
(sRg)2I(s)/I(0)
Persulfide dioxygenase ETHE1, mitochondrial Kratky plot 1.104 0 3 sRg
p(r)
Persulfide dioxygenase ETHE1, mitochondrial pair distance distribution function Rg: 2.4 nm 0 Dmax: 7.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Persulfide dioxygenase ETHE1, mitochondrial PDB (PROTEIN DATA BANK) model

log I(s)
 s, nm-1
Persulfide dioxygenase ETHE1, mitochondrial DAMMIN model

Synchrotron SAXS data from solutions of Metal-bound hETHE1 in 50 mM Tris 150 mM NaCl 2 mM TCEP, pH 8 were collected on the EMBL X33 beam line at the DORIS III, DESY storage ring (Hamburg, Germany) using a Pilatus 1M-W detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.15 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 2 and 5 mg/ml were measured at 9°C. Four successive 30 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 low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.

Metal-bound hETHE1 was shown by SAXS to be a globular protein compatible with a dimeric hETHE1 in solution. The calculated scattering pattern from a high resolution model of dimeric ETHE1 is in a very good agreement (χ2 value of 1.5) with the experimental data from hETHE1. The low resolution shape of metal-bound hETHE1 was reconstructed ab initio using DAMMIN with P2 symmetry imposed. The ab initio model fits the experimental data with a discrepancy χ2 = 1.3 and is in a good agreement with the high resolution ETHE1 structure.

Tags: X33
Persulfide dioxygenase ETHE1, mitochondrial (hETHE1)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   27.9 kDa
 
UniProt   O95571
PDB ID   4CHL