The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization

Roche J, Girard E, Mas C, Madern D, Journal of Structural Biology (2019) DOI

SASDF93 – Ignicoccus islandicus malate dehydrogenase

Malate dehydrogenase

MW^experimental	119	kDa
MW^expected	134	kDa
V^Porod	198	nm³

log I(s) 1.09×10² 1.09×10¹ 1.09×10⁰ 1.09×10^-1

Malate dehydrogenase small angle scattering data

s, nm^-1

Log plot Log-Log plot

ln I(s)

ln 1.09×10² R_g: 3.3 nm 0 (3.3 nm)^-2 s²

(sR_g)²I(s)/I(0)

1.104 0 √3 sR_g

p(r)	R_g: 3.2 nm 0 D_max: 9.0 nm

Data validation

Experimental data range

p(r) fit to data

Metric

Value

s_min D_max / π

0.3

N_Shannon

Worse

Better

Metric

Value

p_cormap

χ²

0.534
0.994

Worse

Better

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

Malate dehydrogenase PDB (PROTEIN DATA BANK) model

Synchrotron SAXS data from solutions of I. islandicus malate dehydrogenase in 50 mM Tris-HCl 50 mM NaCl, pH 7.4 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.125 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.4 and 9.3 mg/ml were measured at 20°C. 10 successive 1 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.

Malate dehydrogenase
Mol. type		Protein
Organism		Ignicoccus islandicus DSM 13165
Olig. state		Tetramer
Mon. MW		33.6 kDa

UniProt		A0A0U3FQH7
Sequence		FASTA

PDB ID		6QSS