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Konas D, Cho S, Thomas OD, Bhatti MM, Leon Hernandez K, Moran C, Booter H, Candela T, Lacap J, McFadden P, van den Berg S, Welter AM, Peralta A, Janson CA, Catalano J, Goodey NM. Investigating the Roles of Active Site Residues in Mycobacterium tuberculosis Indole-3-glycerol Phosphate Synthase, a Potential Target for Antitubercular Agents. ACS BIO & MED CHEM AU 2023; 3:438-447. [PMID: 37876495 PMCID: PMC10591298 DOI: 10.1021/acsbiomedchemau.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 10/26/2023]
Abstract
Mycobacterium tuberculosis drug resistance is emerging and new drug targets are needed. Tryptophan biosynthesis is necessary for M. tuberculosis replication and virulence. Indole-3-glycerol phosphate synthase (IGPS) catalyzes a step in M. tuberculosis tryptophan biosynthesis and has been suggested as a potential anti-infective target, but our understanding of this enzyme is limited. To aid in inhibitor design and gain a greater mechanistic picture of this enzyme, there is a need to understand the roles of active site amino acids in ligand binding and catalysis. In this work, we explored the roles of conserved active site amino acids Glu57, Lys59, Lys119, Glu168, and Glu219. Mutation of each to Ala results in loss of all detectable activity. The Glu57Gln, Lys59Arg, Lys119Arg, Glu168Gln, and Glu219Asp mutations result in large activity losses, while Glu219Gln has enhanced activity. Analysis of the enzymatic data yields the following main conclusions: (A) Lys119 is the likely catalytic acid in the CdRP ring closure step. (B) Glu168 stabilizes a charged reaction intermediate and may also be the catalytic base. (C) Glu57, Glu219, and Lys119 form a closely arranged triad in which Glu57 and Glu219 modulate the pKa of Lys119, and thus overall activity. This increased understanding of inter- and intramolecular interactions and demonstration of the highly coordinated nature of the M. tuberculosis IGPS active site provide new mechanistic information and guidance for future work with this potential new drug target.
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Affiliation(s)
- David
W. Konas
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Sarah Cho
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Oshane D. Thomas
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Maryum M. Bhatti
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Katherine Leon Hernandez
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Cinthya Moran
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Hedda Booter
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Thomas Candela
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Joseph Lacap
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Paige McFadden
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Savannah van den Berg
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Alyssa M. Welter
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Ashley Peralta
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Cheryl A. Janson
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Jaclyn Catalano
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Nina M. Goodey
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
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Esposito N, Konas DW, Goodey NM. Indole-3-Glycerol Phosphate Synthase From Mycobacterium tuberculosis: A Potential New Drug Target. Chembiochem 2022; 23:e202100314. [PMID: 34383995 PMCID: PMC9041893 DOI: 10.1002/cbic.202100314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/29/2021] [Indexed: 01/21/2023]
Abstract
Tuberculosis (TB), caused by the pathogen Mycobacterium tuberculosis, affects millions of people worldwide. Several TB drugs have lost efficacy due to emerging drug resistance and new anti-TB targets are needed. Recent research suggests that indole-3-glycerol phosphate synthase (IGPS) in M. tuberculosis (MtIGPS) could be such a target. IGPS is a (β/α)8 -barrel enzyme that catalyzes the conversion of 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate (CdRP) into indole-glycerol-phosphate (IGP) in the bacterial tryptophan biosynthetic pathway. M. tuberculosis over expresses the tryptophan pathway genes during an immune response and inhibition of MtIGPS allows CD4 T-cells to more effectively fight against M. tuberculosis. Here we review the published data on MtIGPS expression, kinetics, mechanism, and inhibition. We also discuss MtIGPS crystal structures and compare them to other IGPS structures to reveal potential structure-function relationships of interest for the purposes of drug design and biocatalyst engineering.
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Affiliation(s)
- Nikolas Esposito
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - David W. Konas
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Nina M. Goodey
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
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3
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Söderholm A, Newton MS, Patrick WM, Selmer M. Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa: Decarboxylation is not essential for indole formation. J Biol Chem 2020; 295:15948-15956. [PMID: 32928960 PMCID: PMC7681013 DOI: 10.1074/jbc.ra120.014936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/11/2020] [Indexed: 11/27/2022] Open
Abstract
In tryptophan biosynthesis, the reaction catalyzed by the enzyme indole-3-glycerol phosphate synthase (IGPS) starts with a condensation step in which the substrate's carboxylated phenyl group makes a nucleophilic attack to form the pyrrole ring of the indole, followed by a decarboxylation that restores the aromaticity of the phenyl. IGPS from Pseudomonas aeruginosa has the highest turnover number of all characterized IGPS enzymes, providing an excellent model system to test the necessity of the decarboxylation step. Since the 1960s, this step has been considered to be mechanistically essential based on studies of the IGPS–phosphoribosylanthranilate isomerase fusion protein from Escherichia coli. Here, we present the crystal structure of P. aeruginosa IGPS in complex with reduced CdRP, a nonreactive substrate analog, and using a sensitive discontinuous assay, we demonstrate weak promiscuous activity on the decarboxylated substrate 1-(phenylamino)-1-deoxyribulose-5-phosphate, with an ∼1000× lower rate of IGP formation than from the native substrate. We also show that E. coli IGPS, at an even lower rate, can produce IGP from decarboxylated substrate. Our structure of P. aeruginosa IGPS has eight molecules in the asymmetric unit, of which seven contain ligand and one displays a previously unobserved conformation closer to the reactive state. One of the few nonconserved active-site residues, Phe201 in P. aeruginosa IGPS, is by mutagenesis demonstrated to be important for the higher turnover of this enzyme on both substrates. Our results demonstrate that despite IGPS's classification as a carboxy-lyase (i.e. decarboxylase), decarboxylation is not a completely essential step in its catalysis.
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Affiliation(s)
- Annika Söderholm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
| | - Matilda S Newton
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
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O'Rourke KF, Sahu D, Bosken YK, D'Amico RN, Chang CEA, Boehr DD. Coordinated Network Changes across the Catalytic Cycle of Alpha Tryptophan Synthase. Structure 2019; 27:1405-1415.e5. [PMID: 31257109 DOI: 10.1016/j.str.2019.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 03/22/2019] [Accepted: 05/30/2019] [Indexed: 12/23/2022]
Abstract
Networks of noncovalent interactions are important for protein structural dynamics. We used nuclear magnetic resonance chemical shift covariance analyses on an inactive variant of the alpha subunit of tryptophan synthase to map amino acid interaction networks across its catalytic cycle. Although some network connections were common to every enzyme state, many of the network connections strengthened or weakened over the catalytic cycle; these changes were highly coordinated. These results suggest a higher level of network organization. Our analyses identified periodic, second-order networks that show highly coordinated interaction changes across the catalytic cycle. These periodic networks may help synchronize the sequence of structural transitions necessary for enzyme function. Molecular dynamics simulations identified interaction changes across the catalytic cycle, including those involving the catalytic residue Glu49, which may help drive other interaction changes throughout the enzyme structure. Similar periodic networks may direct structural transitions and allosteric interactions in other proteins.
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Affiliation(s)
- Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yuliana K Bosken
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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Zaccardi MJ, Yezdimer EM, Boehr DD. Functional identification of the general acid and base in the dehydration step of indole-3-glycerol phosphate synthase catalysis. J Biol Chem 2013; 288:26350-6. [PMID: 23900843 DOI: 10.1074/jbc.m113.487447] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase is a proposed target for new antimicrobials and is a favored starting framework in enzyme engineering studies. Forty years ago, Parry proposed that the enzyme mechanism proceeds through two intermediates in a series of condensation, decarboxylation, and dehydration steps. X-ray crystal structures have suggested that Lys-110 (numbering according to the Sulfolobus solfataricus enzyme) behaves as a general acid both in the condensation and dehydration steps, but did not reveal an efficient pathway for the reprotonation of this critical residue. Our mutagenesis and kinetic experiments suggest an alternative mechanism whereby Lys-110 acts as a general acid in the condensation step, but another invariant residue, Lys-53, acts as the general acid in the dehydration step. These studies also indicate that the conserved residue Glu-51 acts as the general base in the dehydration step. The revised mechanism effectively divides the active site into discrete regions where the catalytic surfaces containing Lys-110 and Lys-53/Glu-51 catalyze the ring closure (i.e. condensation and decarboxylation) and dehydration steps, respectively. These results can be leveraged toward the development of novel inhibitors against this validated antimicrobial target and toward the rational engineering of the enzyme to produce indole derivatives that are highly prized by the pharmaceutical and agricultural industries.
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Affiliation(s)
- Margot J Zaccardi
- From the Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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Czekster CM, Neto BAD, Lapis AAM, Dupont J, Santos DS, Basso LA. Steady-state kinetics of indole-3-glycerol phosphate synthase from Mycobacterium tuberculosis. Arch Biochem Biophys 2009; 486:19-26. [PMID: 19364491 DOI: 10.1016/j.abb.2009.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/13/2009] [Accepted: 04/07/2009] [Indexed: 11/24/2022]
Abstract
Indole-3-glycerol phosphate synthase (IGPS) catalyzes the irreversible ring closure of 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate (CdRP), through decarboxylation and dehydration steps, releasing indole-3-glycerol phosphate (IGP), the fourth step in the biosynthesis of tryptophan. This pathway is essential for Mycobacterium tuberculosis virulence. Here we describe the cloning, expression, purification, and kinetic characterization of IGPS from M. tuberculosis. To perform kinetic studies, CdRP was chemically synthesized, purified, and spectroscopically and spectrometrically characterized. CdRP fluorescence was pH-dependent, probably owing to excited-state intramolecular proton transfer. The activation energy was calculated, and solvent isotope effects and proton inventory studies were performed. pH-rate profiles were carried out to probe for acid/base catalysis, showing that a deprotonated residue is necessary for CdRP binding and conversion to IGP. A model to describe a steady-state kinetic sequence for MtIGPS-catalized chemical reaction is proposed.
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Affiliation(s)
- Clarissa M Czekster
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, 6681/92A Ipiranga Av., 90619-900 Porto Alegre, RS, Brazil
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