Insights into the Solution Structure and Oligomeric State of Fructose-1,6-bisphosphate Aldolase and Pyruvate Kinase from Nakaseomyces glabratus by Small-Angle X-ray Scattering (SAXS) and AlphaFold Prediction

Cuéllar-Cruz M, Siliqi D Moreno A, ACS Omega (2026) DOI

SASDYV6 – Candida glabrata Pyruvate Kinase (Pk)

Pyruvate Kinase
MWexperimental 53 kDa
MWexpected 55 kDa
VPorod 88 nm3
log I(s) 3.71×10-3 3.71×10-4 3.71×10-5 3.71×10-6
Pyruvate Kinase small angle scattering data  s, nm-1
ln I(s)
Pyruvate Kinase Guinier plot ln 3.72×10-3 Rg: 4 nm 0 (4 nm)-2 s2
(sRg)2I(s)/I(0)
Pyruvate Kinase Kratky plot 1.104 0 √3 sRg
p(r)
Pyruvate Kinase pair distance distribution function Rg: 4.4 nm 0 Dmax: 17.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Pyruvate Kinase GASBOR model
log I(s)
 s, nm-1
Pyruvate Kinase ALPHAFOLD model
Synchrotron SAXS data from solutions of Candida glabrata Pyruvate Kinase (Pk) in 20 mM Tris-HCl pH, 300 mM NaCl, pH 8 were collected on the B21 beam line at the Diamond Light Source storage ring (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.09464 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 40.00 μl sample at 5 mg/ml was injected at a 0.08 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 15°C. 600 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.

Synchrotron SAXS data from solutions of Pyruvate Kinase (Pk)e enzyme in 50 mM sodium phosphate, 500 mM NaCl, 500 mM imidazole, and 1 mM phenylmethylsulfonyl fluoride (PMSF) at pH 8.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.094 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 40.00 μl sample at 5 mg/ml was injected at a 0.07 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 15°C. 620 successive 3 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.

Pyruvate Kinase (Pk)
Mol. type   Protein
Organism   Nakaseomyces glabratus
Olig. state   Monomer
Mon. MW   55 kDa
 
UniProt   Q6FIS9
Sequence   FASTA