A noncanonical PLP-dependent enzyme catalyzes β-serine biosynthesis in the edeine antibiotic pathway

Abstract PLP-dependent enzymes constitute one of the largest and most versatile enzyme families, yet few pathways for β-amino acid biosynthesis have been defined. Here we identify and characterize EdeM, a noncanonical PLP-dependent enzyme in the edeine biosynthetic pathway that generates enantiomerically pure D-β-serine through an unprecedented intramolecular rearrangement. We present crystal structures of EdeM alongside isotopic labeling and computational studies that reveal a migration of the α-carbon to the β-position. Unlike canonical aminotransferase mechanisms, which proceed through a hydrolysis-dependent step, reactions in H 2 18 O exclude hydrolysis, and experiments with ¹³CO 2 show that the carboxyl group derived from L-serine is retained without exchange with bulk CO 2 . Deuterium labeling further identifies the hydrogen transfers involved. Together, these data support a 1,2-migration mechanism consistent with all experimental observations, revealing a previously unrecognized PLP-dependent rearrangement pathway. EdeM thus expands the catalytic repertoire of PLP enzymes and provides the first enzymatic route to D-β-serine.