Catalyzes the condensation of L-serine with palmitoyl-CoA (hexadecanoyl-CoA) to produce 3-oxosphinganine. H(+) + hexadecanoyl-CoA + L-serine = 3-oxosphinganine + CO2 + CoA Significantly inhibited by palmitoyl-CoA concentrations greater than 100 uM. kcat is 0.03 sec(-1) (in the presence of 100 uM of palmitoyl-CoA). Optimum pH is 7.0 to 8.0. Lipid metabolism; sphingolipid metabolism. Homodimer. Predominantly concentrated in a limited region near the inner membrane or organelle-like multilayered membrane structure. Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.