Insights into the structural properties of d-serine dehydratase from Saccharomyces cerevisiae: An FT-IR spectroscopic and in silico approach

d-serine dehydratase (Dsd) from baker’s yeast is a recently discovered enzyme catalyzing the oxidation of d-serine to pyruvate and ammonia. The reaction depends on the cofactors pyridoxal-5′-phosphate (PLP) and Zn2+, featuring a very high selectivity towards the d-enantiomer of the amino acid serine. In humans, altered levels of d-serine in the cerebrospinal fluid (CSF) and blood correlate with the onset and evolution of a number of neurodegenerative diseases. Up to date very little is known on the structure of Dsd. Hence, we have investigated the structure of this enzyme by means of Fourier Transform infrared (FT-IR) spectroscopy and used the structural data derived thereof to validate a homology model of Dsd. In this model, Dsd adopts a fold that is characteristic of type III pyridoxal-dependent enzymes. This consists of an α/β (TIM) barrel and a β-sandwich domain at the N- and C-termini, respectively. Analysis of the Amide I and Amide III infrared bands revealed that the amounts of α (24%), β (29%) and unordered structures (47%) correlate well with those derived from the model (25%, 29% and 46% respectively), suggesting reliability of the latter. In addition, the model of Dsd was further refined by recreating the PLP- and zinc-restored active site based on a PLP- and zinc-dependent bacterial amino acid racemase recently crystallized, allowing us to identify the potential cofactor and metal binding residues of Dsd. ► d-serine dehydratase stability and structure. ► It shows the highest stability in the presence of the cofactors both at pH or p2H 8.0. ► It is prone to aggregation. ► It displays enhanced aggregation in deuterated buffers. ► FT-IR spectroscopy and bioinformatic tools provided information on Dsd's structure.