Crystal Structure and Conformational Dynamics of N─N Bond‐Forming Piperazate Synthase

l ‐Piperazic acid ( l ‐Piz) is a noncanonical, α ‐hydrazino acid characterized by a 1,2‐diazinane heterocycle containing an N─N bond. It occurs in numerous natural products with potent biological activities and represents a key pharmaceutical building block. In nature, l ‐Piz is biosynthesized from l ‐ornithine via the intermediate N 5 ‐hydroxy‐ l ‐ornithine in a two‐enzyme cascade comprising a flavin adenine dinucleotide (FAD)‐dependent N ‐hydroxylating monooxygenase (NMO) and a heme‐dependent piperazate synthase (PZS). The NMO selectively hydroxylates the δ ‐amino group of l ‐ornithine, while PZS catalyzes intramolecular N─N bond formation to generate the six‐membered cyclic hydrazine scaffold of l ‐Piz. Here, we report the crystal structure, Piz‐forming activity, and molecular dynamics (MD) analysis of SbPZS, a representative PZS from Streptomyces sp. B93. High‐resolution structural analysis enabled a detailed comparison with previously characterized PZS homologs. To further delineate the molecular basis of catalysis, we performed MD simulations in combination with sequence‐based bioinformatic analyses. These studies provide insight into protein–substrate interactions, conformational dynamics, and the residues that contribute to active‐site organization. Moreover, we identify candidate hotspots for engineering to modulate substrate scope and catalytic efficiency. Collectively, our results establish a structural framework for understanding enzymatic N─N bond formation in Piz biosynthesis and lay the groundwork for future biocatalytic applications of PZSs.