Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Oligomeric defects in soybean serine hydroxymethyltransferase 8: tetramer destabilization by A149T and other variants associated with soybean cyst nematode resistance.
Journal, issue, pages	FEBS J, Year 2026
Publish date	Mar 31, 2026
Authors	Vindya Samarakoon / David P Buckley / Luckio F Owuocha / Clarissa L Durie / Melissa G Mitchum / Lesa J Beamer /
PubMed Abstract	Serine hydroxymethyltransferase (SHMT) is a conserved enzyme in folate-mediated one-carbon metabolism, where it contributes to nucleotide biosynthesis, methylation capacity, and cellular stress ...Serine hydroxymethyltransferase (SHMT) is a conserved enzyme in folate-mediated one-carbon metabolism, where it contributes to nucleotide biosynthesis, methylation capacity, and cellular stress responses. Amino acid polymorphisms of soybean SHMT8 are known to affect the resistance of soybean to its primary pathogen, the soybean cyst nematode (SCN). A set of SHMT8 variants from ethyl methanesulfonate (EMS)-mutagenized soybean populations has been identified with varying resistance phenotypes, but their biochemical consequences remain poorly understood. Here, we use biochemical and structural studies to assess the impacts of the A149T variant on soybean SHMT8. Despite the conservative nature of the substitution, A149T reduces folate binding, pyridoxal-5'-phosphate-dependent catalysis, and thermal stability. High-resolution crystal structures (1.9-2.3 Å resolution) reveal only very minor structural changes. However, while the usual tetrameric assembly of the enzyme is retained at the high protein concentration in crystals, multiple other methods including a 2.9 Å cryo-electron microscopy (cryo-EM) structure show that the A149T variant is predominantly a dimer. Significant structural changes in the dimer are consistent with the observed biochemical impacts of the variant and help explain the well-known reduction in activity associated with dimerization of SHMT in other systems. We also find destabilization of the tetrameric assembly in other SHMT8 variants associated with changes in SCN resistance, suggesting that weakened oligomerization may be a common consequence of such mutations. Together, these results highlight quaternary structure as a critical determinant of SHMT8 activity and stability and suggest a potential mechanistic link between enzyme biochemistry and soybean defense.
External links	FEBS J / PubMed:41914311
Methods	EM (single particle) / X-ray diffraction
Resolution	1.87 - 2.92 Å
Structure data	75307 10nm EMDB-75307, PDB-10nm: CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP Method: EM (single particle) / Resolution: 2.92 Å PDB-9y6b: CRYSTAL STRUCTURE OF A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP-GLYCINE Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9y6d: CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST IN COMPLEX WITH PLP-GLYCINE Method: X-RAY DIFFRACTION / Resolution: 2.25 Å PDB-9y7g: CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST IN COMPLEX WITH PLP Method: X-RAY DIFFRACTION / Resolution: 1.87 Å PDB-9ybz: CRYSTAL STRUCTURE OF THE A149T VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP Method: X-RAY DIFFRACTION / Resolution: 2.28 Å
Chemicals	ChemComp-PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] ChemComp-HOH: WATER
Source	glycine max (soybean)
Keywords	TRANSFERASE / enzyme / missense variant