Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

• Published in: bioRxiv
• Main Authors: Holmes, Jacob B, Liu, Viktoriia, Caulkins, Bethany G, Hilario, Eduardo, Ghosh, Rittik K, Drago, Victoria N, Young, Robert P, Romero, Jennifer, Gill, Adam D, Bogie, Paul M, Paulino, Joana, Wang, Xiaoling, Riviere, Gwladys, Bosken, Yuliana K, Struppe, Jochem, Hassan, Alia, Guidoulianov, Jevgeni, Perrone, Barbara, Chang, Chia-En A, Frederic Mentink- Vigier, Long, Joanna R, Hooley, Richard J, Mueser, Timothy C, Dunn, Michael F, Mueller, Leonard J
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 15.05.2021
• Subjects: Benzimidazoles; Computer applications; Crystallography; Indoles; Intermediates; NMR; Nuclear magnetic resonance; Serine; Structure-function relationships; Tryptophan; Tryptophan synthase; X-ray crystallography
• DOI: 10.1101/2021.05.12.443852

NMR-assisted crystallography – the synergistic combination of solid-state NMR, X-ray crystallography, and first-principles computational chemistry – holds remarkable promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in the enzyme active site – including hydrogen atom locations and tautomeric equilibria – it offers insight into structure, dynamics, and function. Here, we make use of this combined approach to characterize the α-aminoacrylate intermediate in tryptophan synthase, a defining species for pyridoxal-5'-phosphate-dependent enzymes on the β-elimination and replacement pathway. By uniquely identifying the protonation states of ionizable sites on the cofactor, substrates, and catalytic side chains, as well as the location and orientation of structural waters in the active site, a remarkably clear picture of structure and reactivity emerges. Most incredibly, this intermediate appears to be mere tenths of angstroms away from the preceding transition state in which the β-hydroxyl of the serine substrate is lost. The position and orientation of the structural water immediately adjacent to the substrate β-carbon suggests not only the fate of the hydroxyl group, but also the pathway back to the transition state and the identity of the active site acid-base catalytic residue. Reaction of this intermediate with benzimidazole (BZI), an isostere of the natural substrate, indole, shows BZI bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the BZI position, indole is positioned with C3 in contact with the α-aminoacrylate Cβ and aligned for nucleophilic attack. Competing Interest Statement The authors have declared no competing interest.