Structural and functional defects of mitochondrial serine hydroxymethyltransferase genetic variants responsible for a novel neurodevelopmental syndrome

In 2020 seven genetic variants of the mitochondrial serine hydroxymethyl transferase (SHMT2) were linked to a novel brain and heart developmental syndrome. SHMT2 is a pyridoxal 5′-phosphate (PLP) binding enzyme involved in one-carbon metabolism and mitochondrial redox homeostasis, which also shows several moonlighting functions and protein-protein interactions that are related to its ability to change its oligomeric state. Molecular dynamics suggested that these genetic variants may cause a range of different structural defects ultimately affecting the conformation of the active site, cofactor affinity and the oligomerization state. Here we present a systematic biochemical and structural analysis of these variants. We expressed and purified the SHMT2 mutants and evaluated their oligomeric state, PLP binding affinity, thermal stability, and catalytic activities compared to the wild-type enzyme. The crystal structures of the less active mutants were then solved to pinpoint the structural determinants of the defects highlighted in solution. The results are discussed considering the multi-functional role of SHMT2 and expand our current understanding of the enzyme’s sophisticated conformational and allosteric dynamics.