Racemization of the substrate and product by serine palmitoyltransferase from Sphingobacterium multivorum yields two enantiomers of the product from D-serine.

Serine palmitoyltransferase (SPT) catalyzes the pyridoxal-5'-phosphate (PLP)-dependent decarboxylative condensation of L-serine and palmitoyl-CoA to form 3-ketodihydrosphingosine (KDS). Although SPT was shown to synthesize corresponding products from amino acids other than L-serine, it is still arguable whether SPT catalyzes the reaction with D-serine, which is a question of biological importance. Using high substrate and enzyme concentrations, KDS was detected after the incubation of SPT from Sphingobacterium multivorum with D-serine and palmitoyl-CoA. Furthermore, the KDS comprised equal amounts of 2S- and 2R-isomers. 1 H-NMR study showed a slow hydrogen-deuterium exchange at Cα of serine mediated by SPT. We further confirmed that SPT catalyzed the racemization of serine. The rate of the KDS formation from D-serine was comparable to those for the α-hydrogen exchange and the racemization reaction. The structure of the D-serine-soaked crystal (1.65 Å resolution) showed a distinct electron density of the PLP-L-serine aldimine, interpreted as the racemized product trapped in the active site. The structure of the α-methyl-D-serine-soaked crystal (1.70 Å resolution) showed the PLP-α-methyl-D-serine aldimine, mimicking the D-serine-SPT complex prior to racemization. Based on these enzymological and structural analyses, the synthesis of KDS from D-serine was explained as the result of the slow racemization to L-serine followed by the reaction with palmitoyl-CoA, and SPT would not catalyze the direct condensation between D-serine and palmitoyl-CoA. It was also shown that the S. multivorum SPT catalyzed the racemization of the product KDS, which would explain the presence of (2R)-KDS in the reaction products.