Fig. 1: Salmonella typhimurium tryptophan synthase structure and reaction mechanism.

a The TS αββα tetramer ribbon model (α in green and β in cyan and orange) with indole-3-glycerol (IGP) phosphate bound in the α-active site and pyridoxal 5′-phosphate bound as the internal aldimine in the β-active site (PDB 1BKS and 1QOQ). The cleavage of IGP in the α-reaction releases indole, which travels down a 25 Å hydrophobic channel (dashed line, residues lining the channel shown in black) to the β-active site and couples to a PLP-activated serine (aminoacrylate). The monovalent cation site (occupied by Na⁺ shown as a purple sphere) is involved in coordinating the two reactions. Motion in the communication (Comm) domain (orange) of the β-subunit defines the open and closed conformations of the enzyme. b PLP activation of L-Ser in the TS β-active site initiates with the binding of L-Ser as a Michaelis complex that is likely coupled to the presence of indole in the hydrophobic channel. Numbering of the PLP ring is depicted in the internal aldimine Schiff base structure. The unprotonated α-amino group of L-Ser links to the internal aldimine protonated Schiff base replacing the catalytic lysine (Lys 87) to form the external aldimine. Lys 87 then acts as a general base to abstract a proton from the substrate Cα to form the transient carbanionic intermediate, which proceeds through β-elimination to release water and form the reactive aminoacrylate intermediate. Question marks denote atoms where the protonation state is of particular interest. Question marks were omitted from the internal aldimine structure for simplicity.