9CE6

Key structural role for the conserved cis-proline of soybean serine hydroxymethyltransferase

Summary for 9CE6

• Entry DOI: 10.2210/pdb9ce6/pdb
• Descriptor: Serine hydroxymethyltransferase (2 entities in total)
• Functional Keywords: enzyme, transferase, missense mutation, ligand complex
• Biological source: Glycine max (soybean)
• Total number of polymer chains: 2
• Total formula weight: 108718.88

Authors

Beamer, L.J.,Samarakoon, V. (deposition date: 2024-06-26, 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

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 α-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: 39373197
DOI: 10.1042/BCJ20240338

Experimental method

X-RAY DIFFRACTION (2.25 Å)