A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity

Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M, Communications Biology 4(1) (2021) DOI

SASDLS2 – PfMDH L-lactate dehydrogenase bound to inhibitor 6a

L-lactate dehydrogenase
MWexperimental 114 kDa
MWexpected 141 kDa
VPorod 223 nm3
log I(s) 4.46×100 4.46×10-1 4.46×10-2 4.46×10-3
L-lactate dehydrogenase small angle scattering data  s, nm-1
ln I(s)
L-lactate dehydrogenase Guinier plot ln 4.47×100 Rg: 3.6 nm 0 (3.6 nm)-2 s2
(sRg)2I(s)/I(0)
L-lactate dehydrogenase Kratky plot 1.104 0 √3 sRg
p(r)
L-lactate dehydrogenase pair distance distribution function Rg: 3.5 nm 0 Dmax: 11.4 nm

Data validation

Fits and models

log I(s)
 s, nm-1
L-lactate dehydrogenase DAMMIF model
SAXS data from solutions of PfMDH L-lactate dehydrogenase bound to inhibitor 6a in 100 mM Na-phosphate buffer, 400 mM NaCl, pH 7.4 were measured using a Xenocs Xeuss 2.0 instrument equipped with a Pilatus3 R 1M detector (Department of Macromolecular Physics, Adam Mickiewicz University, Poznań, Poland) at a wavelength of λ = 0.134 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.49 mg/ml was measured. Two successive 600 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.

Inhibitor 6a was added to 1 mM concentration. The model displayed is a bead-occupancy and volume-corrected spatial representation derived from an aligned individual model cohort (damfilt) and does not correspond to the fit to the SAXS data displayed in this entry. Experimental temperature: UNKNOWN.

L-lactate dehydrogenase (PfMDH)
Mol. type   Protein
Organism   Plasmodium falciparum
Olig. state   Tetramer
Mon. MW   35.3 kDa
 
UniProt   Q6VVP7 (1-313)
Sequence   FASTA