9CG8
CRYSTAL STRUCTURE OF THE P285S VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR FORREST
Summary for 9CG8
| Entry DOI | 10.2210/pdb9cg8/pdb |
| Related | 9CE6 |
| Descriptor | Serine hydroxymethyltransferase (2 entities in total) |
| Functional Keywords | enzyme, missense variant, transferase |
| Biological source | Glycine max (soybean) |
| Total number of polymer chains | 6 |
| Total formula weight | 326811.52 |
| Authors | Beamer, L.J.,Samarakoon, V.,Owuocha, L.F. (deposition date: 2024-06-28, release date: 2024-10-16, Last modification date: 2024-11-06) |
| Primary citation | Samarakoon, V.,Owuocha, L.F.,Hammond, J.,Mitchum, M.G.,Beamer, L.J. Key structural role of a conserved cis-proline revealed by the P285S variant of soybean serine hydroxymethyltransferase 8. Biochem.J., 481:1557-1568, 2024 Cited by PubMed Abstract: The enzyme serine hydroxymethyltransferase (SHMT) plays a key role in folate metabolism and is conserved in all kingdoms of life. SHMT is a pyridoxal 5'-phosphate (PLP) - dependent enzyme that catalyzes the conversion of L-serine and (6S)-tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. Crystal structures of multiple members of the SHMT family have shown that the enzyme has a single conserved cis proline, which is located near the active site. Here, we have characterized a Pro to Ser amino acid variant (P285S) that affects this conserved cis proline in soybean SHMT8. P285S was identified as one of a set of mutations that affect the resistance of soybean to the agricultural pathogen soybean cyst nematode. We find that replacement of Pro285 by serine eliminates PLP-mediated catalytic activity of SHMT8, reduces folate binding, decreases enzyme stability, and affects the dimer-tetramer ratio of the enzyme in solution. Crystal structures at 1.9 - 2.2 Å resolution reveal a local reordering of the polypeptide chain that extends an a-helix and shifts a turn region into the active site. This results in a dramatically perturbed PLP-binding pose, where the ring of the cofactor is flipped by ~180° with concomitant loss of conserved enzyme-PLP interactions. A nearby region of the polypeptide becomes disordered, evidenced by missing electron density for ~10 residues. These structural perturbations are consistent with the loss of enzyme activity and folate binding and underscore the important role of the Pro285 cis-peptide in SHMT structure and function. PubMed: 39373197DOI: 10.1042/BCJ20240338 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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