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Serotonin N‐acetyltransferase (SNAT) is the key rate‐limiting enzyme in melatonin biosynthesis. It mediates melatonin biosynthesis in plants by using serotonin and 5‐methoxytryptamine (5‐MT), but little is known of its underlying mechanisms. Herein, we present a detailed reaction mechanism of a SNAT from Oryza sativa through combined structural and molecular dynamics (MD) analysis. We report the crystal structures of plant SNAT in the apo and binary/ternary complex forms with acetyl‐CoA (AcCoA), serotonin, and 5‐MT. OsSNAT exhibits a unique enzymatically active dimeric fold not found in the known structures of arylalkylamine N‐acetyltransferase (AANAT) family. The key residues W188, D189, D226, N220, and Y233 located around the active pocket are important in catalysis, confirmed by site‐directed mutagenesis. Combined with MD simulations, we hypothesize a novel plausible catalytic mechanism in which D226 and Y233 function as catalytic base and acid during the acetyl‐transfer reaction.

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