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

Phillips, Robert S.; Brown, S. Meredith; Patel, Ravi S.

doi:10.1021/acscatal.4c03232

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

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

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)

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)Copyright Statement

Country of Publication:: United States

Language:: English

References (60)

Fermentative Production of Halogenated Tryptophan Derivatives with Corynebacterium glutamicum Overexpressing Tryptophanase or Decarboxylase Genes Kerbs, Anastasia; Burgardt, Arthur; Veldmann, Kareen H. ChemBioChem, Vol. 23, Issue 9 https://doi.org/10.1002/cbic.202200007	journal	March 2022
SEQCROW : A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems Schaefer, Anthony J.; Ingman, Victoria M.; Wheeler, Steven E. Journal of Computational Chemistry, Vol. 42, Issue 24 https://doi.org/10.1002/jcc.26700	journal	June 2021
Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data Casañal, Ana; Lohkamp, Bernhard; Emsley, Paul Protein Science, Vol. 29, Issue 4 https://doi.org/10.1002/pro.3791	journal	March 2020
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
Direct spectrophotometric assay of tryptophanase Suelter, C. H. FEBS Letters, Vol. 66, Issue 2 https://doi.org/10.1016/0014-5793(76)80510-8	journal	July 1976
The mechanism of Escherichia coli tryptophan indole-lyase: substituent effects on steady-state and pre-steady-state kinetic parameters for aryl-substituted tryptophan derivatives Lee, Minsu; Phillips, Robert S. Bioorganic & Medicinal Chemistry, Vol. 3, Issue 2 https://doi.org/10.1016/0968-0896(95)00016-A	journal	February 1995
Stereochemistry and mechanism of reactions catalyzed by tryptophanase Escherichia coli Vederas, J. C.; Schleicher, E.; Tsai, M. D. Journal of Biological Chemistry, Vol. 253, Issue 15 https://doi.org/10.1016/S0021-9258(17)30377-0	journal	August 1978
Differential inhibition of tryptophan synthase and of tryptophanase by the two diastereoisomers of 2,3-dihydro-L-tryptophan. Implications for the stereochemistry of the reaction intermediates. Phillips, R. S.; Miles, E. W.; Cohen, L. A. Journal of Biological Chemistry, Vol. 260, Issue 27 https://doi.org/10.1016/S0021-9258(17)38622-2	journal	November 1985
Characterization of the tryptophanase operon of Proteus vulgaris. Cloning, nucleotide sequence, amino acid homology, and in vitro synthesis of the leader peptide and regulatory analysis. Kamath, A. V.; Yanofsky, C. Journal of Biological Chemistry, Vol. 267, Issue 28 https://doi.org/10.1016/S0021-9258(19)88653-2	journal	October 1992
A theoretical study of the structure, charge distribution and gas-phase basicity of azaindoles Catalán, J.; Mó, O.; Pérez, P. Tetrahedron, Vol. 39, Issue 17 https://doi.org/10.1016/S0040-4020(01)82458-3	journal	January 1983
Enzymatic synthesis of aza-l-tryptophans: The preparation of 5- and 6-Aza-l-tryptophan Sloan, Milton J.; Phillips, Robert S. Bioorganic & Medicinal Chemistry Letters, Vol. 2, Issue 9 https://doi.org/10.1016/S0960-894X(00)80617-4	journal	September 1992
Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate Graboski, Amanda L.; Kowalewski, Mark E.; Simpson, Joshua B. Cell Chemical Biology, Vol. 30, Issue 11 https://doi.org/10.1016/j.chembiol.2023.07.015	journal	November 2023
Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism Phillips, Robert S.; Craig, Steven Biochemistry, Vol. 57, Issue 43 https://doi.org/10.1021/acs.biochem.8b00724	journal	September 2018
Ground-State Destabilization by Phe-448 and Phe-449 Contributes to Tyrosine Phenol-Lyase Catalysis Phillips, Robert S.; Vita, Andrew; Spivey, J. Blaine ACS Catalysis, Vol. 6, Issue 10 https://doi.org/10.1021/acscatal.6b01495	journal	September 2016
Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics Phillips, Robert S.; Craig, Steven; Kovalevsky, Andrey ACS Catalysis, Vol. 10, Issue 3 https://doi.org/10.1021/acscatal.9b03967	journal	December 2019
A View at the Millennium: the Efficiency of Enzymatic Catalysis Bruice, Thomas C. Accounts of Chemical Research, Vol. 35, Issue 3 https://doi.org/10.1021/ar0001665	journal	March 2002
Analysis of ground-state and transition-state effects in enzyme catalysis Menger, F. M. Biochemistry, Vol. 31, Issue 23 https://doi.org/10.1021/bi00138a018	journal	July 1992
Reaction of indole and analogs with amino acid complexes of Escherichia coli tryptophan indole-lyase: detection of a new reaction intermediate by rapid-scanning stopped-flow spectrophotometry Phillips, Robert S. Biochemistry, Vol. 30, Issue 24 https://doi.org/10.1021/bi00238a017	journal	June 1991
Interactions of tryptophan synthase, tryptophanase, and pyridoxal phosphate with oxindolyl-L-alanine and 2,3-dihydro-L-tryptophan: support for an indolenine intermediate in tryptophan metabolism Phillips, Robert S.; Miles, Edith Wilson; Cohen, Louis A. Biochemistry, Vol. 23, Issue 25 https://doi.org/10.1021/bi00320a052	journal	December 1984
Mechanistic deductions from multiple kinetic and solvent deuterium isotope effects and pH studies of pyridoxal phosphate dependent carbon-carbon lyases: Escherichia coli tryptophan indole-lyase Kiick, Dennis M.; Phillips, Robert S. Biochemistry, Vol. 27, Issue 19 https://doi.org/10.1021/bi00419a024	journal	September 1988
Formation of an intermediate and its rate of conversion to pyruvate during the tryptophanase-catalyzed degradation of S-o-nitrophenyl-L-cysteine Hillebrand, Greg G.; Dye, James L.; Suelter, Clarence H. Biochemistry, Vol. 18, Issue 9 https://doi.org/10.1021/bi00576a018	journal	May 1979
Formation in Vitro of Hybrid Dimers of H463F and Y74F Mutant Escherichia coli Tryptophan Indole-lyase Rescues Activity with l -Tryptophan ^† Phillips, Robert S.; Johnson, Nancy; Kamath, Ajith V. Biochemistry, Vol. 41, Issue 12 https://doi.org/10.1021/bi015838t	journal	March 2002
Role of Aspartate-133 and Histidine-458 in the Mechanism of Tryptophan Indole-Lyase from Proteus vulgaris ^† Demidkina, Tatyana V.; Zakomirdina, Lyudmila N.; Kulikova, Vitalia V. Biochemistry, Vol. 42, Issue 38 https://doi.org/10.1021/bi034348t	journal	September 2003
Differential Effects of Temperature and Hydrostatic Pressure on the Formation of Quinonoid Intermediates from l -Trp and l -Met by H463F Mutant Escherichia coli Tryptophan Indole-lyase ^† Phillips, Robert S.; Holtermann, Georg Biochemistry, Vol. 44, Issue 43 https://doi.org/10.1021/bi051062a	journal	November 2005
Evidence of Preorganization in Quinonoid Intermediate Formation from l -Trp in H463F Mutant Escherichia coli Tryptophan Indole-lyase from Effects of Pressure and pH Phillips, Robert S.; Kalu, Ukoha; Hay, Sam Biochemistry, Vol. 51, Issue 33 https://doi.org/10.1021/bi300632k	journal	August 2012
Effects of α-Deuteration and of Aza and Thia Analogs of l-Tryptophan on Formation of Intermediates in the Reaction of Escherichia coli Tryptophan Indole-lyase Sloan, Milton J.; Phillips, Robert S. Biochemistry, Vol. 35, Issue 50 https://doi.org/10.1021/bi961211c	journal	January 1996
Molecular Architecture and Biological Reactions: Answers to many basic problems of biology—nature of growth, mechanism of duplication of viruses and genes, action of enzymes, mechanism, of physiological activity of drugs, hormones, and vitamins, structure and action of nerve and brain tissue—may lie in knowledge of molecular structure and intermolecular reactions Pauling, Linus Chemical & Engineering News, Vol. 24, Issue 10 https://doi.org/10.1021/cen-v024n010.p1375	journal	May 1946
Mechanism of tryptophan indole-lyase: insights from pre-steady-state kinetics and substrate and solvent isotope effects Phillips, Robert S. Journal of the American Chemical Society, Vol. 111, Issue 2 https://doi.org/10.1021/ja00184a051	journal	January 1989
The Protonation of Indoles. Basicity Studies. The Dependence of Acidity Functions on Indicator Structure Hinman, R. L.; Lang, J. Journal of the American Chemical Society, Vol. 86, Issue 18 https://doi.org/10.1021/ja01072a040	journal	September 1964
Crystallographic Snapshots of Tyrosine Phenol-lyase Show That Substrate Strain Plays a Role in C–C Bond Cleavage Milić, Dalibor; Demidkina, Tatyana V.; Faleev, Nicolai G. Journal of the American Chemical Society, Vol. 133, Issue 41 https://doi.org/10.1021/ja203361g	journal	October 2011
Ground-State Electronic Destabilization via Hyperconjugation in Aspartate Aminotransferase Griswold, Wait R.; Castro, Joan Nieto; Fisher, Andrew J. Journal of the American Chemical Society, Vol. 134, Issue 20 https://doi.org/10.1021/ja302809e	journal	May 2012
Proton Transfer and Carbon−Carbon Bond Cleavage in the Elimination of Indole Catalyzed by Escherichia coli Tryptophan Indole-Lyase Phillips, Robert S.; Sundararaju, Bakthavatsalam; Faleev, Nicolai G. Journal of the American Chemical Society, Vol. 122, Issue 6 https://doi.org/10.1021/ja991647q	journal	February 2000
Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase Vladimirova, Anna; Patskovsky, Yury; Fedorov, Alexander A. Journal of the American Chemical Society, Vol. 138, Issue 3 https://doi.org/10.1021/jacs.5b08251	journal	January 2016
Preparative separation of the diastereoisomers of dioxindolyl-L-alanine and assignment of stereochemistry at C-3 Labroo, Rita B.; Cohen, Louis A. The Journal of Organic Chemistry, Vol. 55, Issue 16 https://doi.org/10.1021/jo00303a027	journal	August 1990
Sub-ångström-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate Lüdtke, Stefan; Neumann, Piotr; Erixon, Karl M. Nature Chemistry, Vol. 5, Issue 9 https://doi.org/10.1038/nchem.1728	journal	August 2013
Cleavage of Escherichia coli tryptophan indole‐lyase by trypsin at Lys406 affects the transmission of conformational changes associated with monovalent cation activation Phillips, Robert S.; Doshi, Kokila J. European Journal of Biochemistry, Vol. 255, Issue 2 https://doi.org/10.1046/j.1432-1327.1998.2550508.x	journal	July 1998
The ORCA quantum chemistry program package Neese, Frank; Wennmohs, Frank; Becker, Ute The Journal of Chemical Physics, Vol. 152, Issue 22 https://doi.org/10.1063/5.0004608	journal	June 2020
Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance Vega, Nicole M.; Allison, Kyle R.; Samuels, Amanda N. Proceedings of the National Academy of Sciences, Vol. 110, Issue 35 https://doi.org/10.1073/pnas.1308085110	journal	August 2013
Indoles from commensal bacteria extend healthspan Sonowal, Robert; Swimm, Alyson; Sahoo, Anusmita Proceedings of the National Academy of Sciences, Vol. 114, Issue 36 https://doi.org/10.1073/pnas.1706464114	journal	August 2017
The mechanism of tryptophan induction of tryptophanase operon expression: Tryptophan inhibits release factor-mediated cleavage of TnaC-peptidyl-tRNA ^Pro Gong, Feng; Ito, Koichi; Nakamura, Yoshikazu Proceedings of the National Academy of Sciences, Vol. 98, Issue 16 https://doi.org/10.1073/pnas.171299298	journal	July 2001
Reversibility of the Tryptophanase Reaction: Synthesis of Tryptophan from Indole, Pyruvate, and Ammonia Watanabe, T.; Snell, E. E. Proceedings of the National Academy of Sciences, Vol. 69, Issue 5 https://doi.org/10.1073/pnas.69.5.1086	journal	May 1972
Crystals of Tryptophan Indole-Lyase and Tyrosine Phenol-Lyase Form Stable Quinonoid Complexes Phillips, Robert S.; Demidkina, Tatyana V.; Zakomirdina, Lyudmila N. Journal of Biological Chemistry, Vol. 277, Issue 24 https://doi.org/10.1074/jbc.M200216200	journal	April 2002
Indole signaling decreases biofilm formation and related virulence of Listeria monocytogenes Rattanaphan, Paramaporn; Mittraparp-Arthorn, Pimonsri; Srinoun, Kanitta FEMS Microbiology Letters, Vol. 367, Issue 14 https://doi.org/10.1093/femsle/fnaa116	journal	July 2020
Robust indexing for automatic data collection Sauter, Nicholas K.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 37, Issue 3 https://doi.org/10.1107/S0021889804005874	journal	May 2004
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Advances in automated data analysis and processing within autoPROC , combined with improved characterisation, mitigation and visualisation of the anisotropy of diffraction limits using STARANISO Vonrhein, Clemens; Tickle, Ian J.; Flensburg, Claus Acta Crystallographica Section A Foundations and Advances, Vol. 74, Issue a1 https://doi.org/10.1107/S010876731809640X	journal	July 2018
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation Moriarty, Nigel W.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10 https://doi.org/10.1107/S0907444909029436	journal	September 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
The crystal structure ofProteus vulgaristryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism Phillips, Robert S.; Buisman, Adriaan A.; Choi, Sarah Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 8 https://doi.org/10.1107/S2059798318003352	journal	July 2018
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Indole signalling contributes to the stable maintenance of Escherichia coli multicopy plasmids Chant, Eleanor L.; Summers, David K. Molecular Microbiology, Vol. 63, Issue 1 https://doi.org/10.1111/j.1365-2958.2006.05481.x	journal	January 2007
Hunting the eagle killer: A cyanobacterial neurotoxin causes vacuolar myelinopathy Breinlinger, Steffen; Phillips, Tabitha J.; Haram, Brigette N. Science, Vol. 371, Issue 6536 https://doi.org/10.1126/science.aax9050	journal	March 2021
The Tryptophanase Gene Cluster of Haemophilus influenzae Type b: Evidence for Horizontal Gene Transfer Martin, Kimberly; Morlin, Gregory; Smith, Arnold Journal of Bacteriology, Vol. 180, Issue 1 https://doi.org/10.1128/JB.180.1.107-118.1998	journal	January 1998
Tryptophanase in Diverse Bacterial Species DeMoss, R. D.; Moser, K. Journal of Bacteriology, Vol. 98, Issue 1 https://doi.org/10.1128/jb.98.1.167-171.1969	journal	April 1969
Bacterial Indole as a Multifunctional Regulator of Klebsiella oxytoca Complex Enterotoxicity Ledala, Nagender; Malik, Mishika; Rezaul, Karim mBio, Vol. 13, Issue 1 https://doi.org/10.1128/mbio.03752-21	journal	February 2022
Indole can act as an extracellular signal to regulate biofilm formation of Escherichia coli and other indole-producing bacteria Di Martino, P.; Fursy, R.; Bret, L. Canadian Journal of Microbiology, Vol. 49, Issue 7 https://doi.org/10.1139/w03-056	journal	July 2003
The RNA Chaperone Hfq Impacts Growth, Metabolism and Production of Virulence Factors in Yersinia enterocolitica Kakoschke, Tamara; Kakoschke, Sara; Magistro, Giuseppe PLoS ONE, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pone.0086113	journal	January 2014

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
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Indoles
Noncovalent interactions
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Pyridoxal-5′-phosphate
Reaction mechanism
Reaction mechanisms
X-ray crystallography

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

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