The active site, found in the PLP-binding domain, consists of the PLP cofactor bound to a lysine residue in the form of a Schiff base.

The protonated nitrogen on the PLP aromatic ring is hydrogen bonded to a carboxylate on an aspartic side chain.

The mechanism of arginine decarboxylase is analogous to other deaminating and decarboxylating PLP enzymes in its use of a Schiff base intermediate.

[7] Initially, Lys386 residue is displaced in a transamination reaction by the L-arginine substrate, forming an arginine Schiff base with the PLP cofactor.

[8] Decarboxylation of arginine carboxylate group then occurs, where it is hypothesized that the C-C bond broken is perpendicular to the PLP pyridine ring.

Protonation of the amino acid leads to the formation of a new Schiff base that subsequently undergoes a transamination reaction by the lysine reside of arginine decarboxylase, regenerating the catalytically active PLP and releasing agmantine as a product.

[12] This particular assembling strategy used by E. coli arginine decarboxylase is also commonly used by other acidophilic organisms to cope with acidic growth conditions.