Structural Snapshots of Proteus vulgaris Tryptophan Indole-Lyase Reveal Insights into the Catalytic Mechanism

Journal Article · Thu Jul 18 00:00:00 EDT 2024 · ACS Catalysis

DOI:https://doi.org/10.1021/acscatal.4c03232· OSTI ID:2470137

Phillips, Robert S. ^[1]; Brown, S. Meredith ^[1]; Patel, Ravi S. ^[1]

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1. University of Georgia, Athens, GA (United States)

Tryptophan indole lyase (TIL; [E.C. 4.1.99.1]) is a bacterial pyridoxal-5′-phosphate (PLP)-dependent enzyme that catalyzes reversible β-elimination of indole from L-tryptophan. The mechanism of elimination of indole from L-tryptophan starts with the formation of an external aldimine of the substrate and PLP, followed by deprotonation of the α-CH of the substrate, forming a resonance-stabilized quinonoid intermediate. Proton transfer to C3 of the indole ring and carbon–carbon bond cleavage of the quinonoid intermediate provide indole and aminoacrylate bound to PLP, which then releases indole, followed by iminopyruvate. We have now determined the X-ray crystal structures of TIL complexes with (3S)-dioxindolyl-l-alanine, an inhibitor, and with substrates L-tryptophan, 7-aza-L-tryptophan, and S-ethyl-l-cysteine (SEC) in the presence of benzimidazole (BZI), an isostere of the product indole. These structures show a mixture of gem-diamine, external aldimine, quinonoid, and aminoacrylate intermediates, in both open and closed active site conformations. In the closed conformations of L-tryptophan, (3S)-dioxindolyl-l-alanine, and 7-aza-L-tryptophan complexes, hydrogen bonds form between Asp-133 with N1 of the ligand heterocyclic ring and NE2 of His-458 in the small domain of TIL. This hydrogen bond also forms in the BZI complex with the aminoacrylate intermediates formed from both L-tryptophan and SEC. The closed quinonoid complex of 7-aza-L-tryptophan shows that the azaindole ring in the closed conformation is bent out of plane of the Cβ–C3 bond by about 40°, putting it in a geometry that leads toward the transition-state geometry. Thus, both conformational dynamics and substrate activation play critical roles in the reaction mechanism of the TIL.

• Research Organization: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
• Sponsoring Organization: National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)
• Grant/Contract Number: AC02-06CH11357; W-31-109-ENG-3
• OSTI ID: 2470137
• Journal Information: ACS Catalysis, Journal Name: ACS Catalysis Journal Issue: 15 Vol. 14; ISSN 2155-5435
• Publisher: American Chemical Society (ACS)
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Chemical structure
Chemistry
Conformation
Enzyme dynamics
Indoles
Noncovalent interactions
Proton transfer
Pyridoxal-5′-phosphate
Reaction mechanism
Reaction mechanisms
X-ray crystallography