Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?

Leth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M, J Biol Chem (2019) Europe PMC

SASDFB2 – Urokinase plasminogen activator surface receptor, uPAR, K50C-V70C

Urokinase plasminogen activator surface receptor
MWI(0) 41 kDa
MWexpected 37 kDa
VPorod 66 nm3
log I(s) 3.20×10-2 3.20×10-3 3.20×10-4 3.20×10-5
Urokinase plasminogen activator surface receptor small angle scattering data  s, nm-1
ln I(s)
Urokinase plasminogen activator surface receptor Guinier plot ln 3.20×10-2 Rg: 2.5 nm 0 (2.5 nm)-2 s2
(sRg)2I(s)/I(0)
Urokinase plasminogen activator surface receptor Kratky plot 1.104 0 √3 sRg
p(r)
Urokinase plasminogen activator surface receptor pair distance distribution function Rg: 2.7 nm 0 Dmax: 9.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Urokinase plasminogen activator surface receptor DAMMIN model
Synchrotron SAXS data from solutions of uPAR K50C-V70C in 20 mM PBS, 5 %(v/v) glycerol, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2.8 mg/ml were measured at 10°C. 20 successive 0.050 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.

Introduced disulfide in the first LU domain, DI, of uPAR (K50C-V70C).

Urokinase plasminogen activator surface receptor (uPAR)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   37.0 kDa
 
UniProt   Q03405
Sequence   FASTA