Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design.

Shaw GX, Fan L, Cherry S, Shi G, Tropea JE, Ji X, Curr Res Struct Biol 5:100095 (2023) Europe PMC

SASDWA7 – Dihydroneopterin aldolase from H.pylori (HpDHNA:Pterin)

Dihydroneopterin aldolase
MWexperimental 53 kDa
MWexpected 55 kDa
VPorod 77 nm3
log I(s) 1.85×10-2 1.85×10-3 1.85×10-4 1.85×10-5
Dihydroneopterin aldolase small angle scattering data  s, nm-1
ln I(s)
Dihydroneopterin aldolase Guinier plot ln 1.85×10-2 Rg: 2.5 nm 0 (2.5 nm)-2 s2
(sRg)2I(s)/I(0)
Dihydroneopterin aldolase Kratky plot 1.104 0 √3 sRg
p(r)
Dihydroneopterin aldolase pair distance distribution function Rg: 2.5 nm 0 Dmax: 7.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Dihydroneopterin aldolase DAMMIN model
Synchrotron SAXS data from solutions of Dihydroneopterin aldolase from H.pylori (HpDHNA:Pterin) in 25 mM Tris-HCl pH 7.5 and 150 mM NaCl, pH 7.5 were collected on the 12-ID-B SAXS/WAXS beam line at the Advanced Photon Source (APS), Argonne National Laboratory storage ring (Lemont, IL, USA) using a Pilatus 2M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.0932 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 4 mg/ml were measured at 20°C. 45 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 concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.

Molecular weight based on Vc method is 55.3KDa Molecular weight based on apparent volume method is 53.4KDa

Dihydroneopterin aldolase (DHNA)
Mol. type   Protein
Organism   Helicobacter pylori (strain G27)
Olig. state   Tetramer
Mon. MW   13.8 kDa
 
UniProt   B5Z9C8 (1-117)
Sequence   FASTA