1
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Tang Q, Tillmann M, Cohen JD. Analytical methods for stable isotope labeling to elucidate rapid auxin kinetics in Arabidopsis thaliana. PLoS One 2024; 19:e0303992. [PMID: 38776314 PMCID: PMC11111016 DOI: 10.1371/journal.pone.0303992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024] Open
Abstract
The phytohormone auxin plays a critical role in plant growth and development. Despite significant progress in elucidating metabolic pathways of the primary bioactive auxin, indole-3-acetic acid (IAA), over the past few decades, key components such as intermediates and enzymes have not been fully characterized, and the dynamic regulation of IAA metabolism in response to environmental signals has not been completely revealed. In this study, we established a protocol employing a highly sensitive liquid chromatography-mass spectrometry (LC-MS) instrumentation and a rapid stable isotope labeling approach. We treated Arabidopsis seedlings with two stable isotope labeled precursors ([13C6]anthranilate and [13C8, 15N1]indole) and monitored the label incorporation into proposed indolic compounds involved in IAA biosynthetic pathways. This Stable Isotope Labeled Kinetics (SILK) method allowed us to trace the turnover rates of IAA pathway precursors and product concurrently with a time scale of seconds to minutes. By measuring the entire pathways over time and using different isotopic tracer techniques, we demonstrated that these methods offer more detailed information about this complex interacting network of IAA biosynthesis, and should prove to be useful for studying auxin metabolic network in vivo in a variety of plant tissues and under different environmental conditions.
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Affiliation(s)
- Qian Tang
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Tillmann
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jerry D. Cohen
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
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2
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Ito S, Yagi K, Sugita Y. Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. J Chem Phys 2023; 158:115101. [PMID: 36948822 DOI: 10.1063/5.0134117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α- and β-subunits that catalyzes the last two steps of L-tryptophan (L-Trp) biosynthesis. The first stage of the reaction at the β-subunit is called β-reaction stage I, which converts the β-ligand from an internal aldimine [E(Ain)] to an α-aminoacrylate [E(A-A)] intermediate. The activity is known to increase 3-10-fold upon the binding of 3-indole-D-glycerol-3'-phosphate (IGP) at the α-subunit. The effect of α-ligand binding on β-reaction stage I at the distal β-active site is not well understood despite the abundant structural information available for TRPS. Here, we investigate the β-reaction stage I by carrying out minimum-energy pathway searches based on a hybrid quantum mechanics/molecular mechanics (QM/MM) model. The free-energy differences along the pathway are also examined using QM/MM umbrella sampling simulations with QM calculations at the B3LYP-D3/aug-cc-pVDZ level of theory. Our simulations suggest that the sidechain orientation of βD305 near the β-ligand likely plays an essential role in the allosteric regulation: a hydrogen bond is formed between βD305 and the β-ligand in the absence of the α-ligand, prohibiting a smooth rotation of the hydroxyl group in the quinonoid intermediate, whereas the dihedral angle rotates smoothly after the hydrogen bond is switched from βD305-β-ligand to βD305-βR141. This switch could occur upon the IGP-binding at the α-subunit, as evidenced by the existing TRPS crystal structures.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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3
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Ghosh RK, Hilario E, Chang CEA, Mueller LJ, Dunn MF. Allosteric regulation of substrate channeling: Salmonella typhimurium tryptophan synthase. Front Mol Biosci 2022; 9:923042. [PMID: 36172042 PMCID: PMC9512447 DOI: 10.3389/fmolb.2022.923042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The regulation of the synthesis of L-tryptophan (L-Trp) in enteric bacteria begins at the level of gene expression where the cellular concentration of L-Trp tightly controls expression of the five enzymes of the Trp operon responsible for the synthesis of L-Trp. Two of these enzymes, trpA and trpB, form an αββα bienzyme complex, designated as tryptophan synthase (TS). TS carries out the last two enzymatic processes comprising the synthesis of L-Trp. The TS α-subunits catalyze the cleavage of 3-indole D-glyceraldehyde 3′-phosphate to indole and D-glyceraldehyde 3-phosphate; the pyridoxal phosphate-requiring β-subunits catalyze a nine-step reaction sequence to replace the L-Ser hydroxyl by indole giving L-Trp and a water molecule. Within αβ dimeric units of the αββα bienzyme complex, the common intermediate indole is channeled from the α site to the β site via an interconnecting 25 Å-long tunnel. The TS system provides an unusual example of allosteric control wherein the structures of the nine different covalent intermediates along the β-reaction catalytic path and substrate binding to the α-site provide the allosteric triggers for switching the αββα system between the open (T) and closed (R) allosteric states. This triggering provides a linkage that couples the allosteric conformational coordinate to the covalent chemical reaction coordinates at the α- and β-sites. This coupling drives the α- and β-sites between T and R conformations to achieve regulation of substrate binding and/or product release, modulation of the α- and β-site catalytic activities, prevention of indole escape from the confines of the active sites and the interconnecting tunnel, and synchronization of the α- and β-site catalytic activities. Here we review recent advances in the understanding of the relationships between structure, function, and allosteric regulation of the complex found in Salmonella typhimurium.
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Affiliation(s)
- Rittik K. Ghosh
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Eduardo Hilario
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Leonard J. Mueller
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Leonard J. Mueller, ; Michael F. Dunn,
| | - Michael F. Dunn
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Leonard J. Mueller, ; Michael F. Dunn,
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4
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Ito S, Yagi K, Sugita Y. Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure. J Phys Chem B 2022; 126:3300-3308. [PMID: 35446577 PMCID: PMC9083551 DOI: 10.1021/acs.jpcb.2c01556] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α and β-subunits and catalyzes the last two steps of l-tryptophan (L-Trp) biosynthesis, namely, cleavage of 3-indole-d-glycerol-3'-phosphate (IGP) into indole and glyceraldehyde-3-phosphate (G3P) in the α-subunit, and a pyridoxal phosphate (PLP)-dependent reaction of indole and l-serine (L-Ser) to produce L-Trp in the β-subunit. Importantly, the IGP binding at the α-subunit affects the β-subunit conformation and its ligand-binding affinity, which, in turn, enhances the enzymatic reaction at the α-subunit. The intersubunit communications in TRPS have been investigated extensively for decades because of the fundamental and pharmaceutical importance, while it is still difficult to answer how TRPS allostery is regulated at the atomic detail. Here, we investigate the allosteric regulation of TRPS by all-atom classical molecular dynamics (MD) simulations and analyze the potential of mean-force (PMF) along conformational changes of the α- and β-subunits. The present simulation has revealed a widely opened conformation of the β-subunit, which provides a pathway for L-Ser to enter into the β-active site. The IGP binding closes the α-subunit and induces a wide opening of the β-subunit, thereby enhancing the binding affinity of L-Ser to the β-subunit. Structural analyses have identified critical hydrogen bonds (HBs) at the interface of the two subunits (αG181-βS178, αP57-βR175, etc.) and HBs between the β-subunit (βT110 - βH115) and a complex of PLP and L-Ser (an α-aminoacrylate intermediate). The former HBs regulate the allosteric, β-subunit opening, whereas the latter HBs are essential for closing the β-subunit in a later step. The proposed mechanism for how the interdomain communication in TRPS is realized with ligand bindings is consistent with the previous experimental data, giving a general idea to interpret the allosteric regulations in multidomain proteins.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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5
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Bosken YK, Ai R, Hilario E, Ghosh RK, Dunn MF, Kan S, Niks D, Zhou H, Ma W, Mueller LJ, Fan L, Chang CA. Discovery of antimicrobial agent targeting tryptophan synthase. Protein Sci 2022; 31:432-442. [PMID: 34767267 PMCID: PMC8820114 DOI: 10.1002/pro.4236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
Antibiotic resistance is a continually growing challenge in the treatment of various bacterial infections worldwide. New drugs and new drug targets are necessary to curb the threat of infectious diseases caused by multidrug-resistant pathogens. The tryptophan biosynthesis pathway is essential for bacterial growth but is absent in higher animals and humans. Drugs that can inhibit the bacterial biosynthesis of tryptophan offer a new class of antibiotics. In this work, we combined a structure-based strategy using in silico docking screening and molecular dynamics (MD) simulations to identify compounds targeting the α subunit of tryptophan synthase with experimental methods involving the whole-cell minimum inhibitory concentration (MIC) test, solution state NMR, and crystallography to confirm the inhibition of L-tryptophan biosynthesis. Screening 1,800 compounds from the National Cancer Institute Diversity Set I against α subunit revealed 28 compounds for experimental validation; four of the 28 hit compounds showed promising activity in MIC testing. We performed solution state NMR experiments to demonstrate that a one successful inhibitor, 3-amino-3-imino-2-phenyldiazenylpropanamide (Compound 1) binds to the α subunit. We also report a crystal structure of Salmonella enterica serotype Typhimurium tryptophan synthase in complex with Compound 1 which revealed a binding site at the αβ interface of the dimeric enzyme. MD simulations were carried out to examine two binding sites for the compound. Our results show that this small molecule inhibitor could be a promising lead for future drug development.
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Affiliation(s)
- Yuliana K. Bosken
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Rizi Ai
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Eduardo Hilario
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Rittik K. Ghosh
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Michael F. Dunn
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Shih‐Hsin Kan
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia,Present address:
CHOC Research InstituteOrangeCalifornia
| | - Dimitri Niks
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Huanbin Zhou
- Department of Microbiology and Plant PathologyUniversity of California at RiversideRiversideCalifornia,Present address:
Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Wenbo Ma
- Department of Microbiology and Plant PathologyUniversity of California at RiversideRiversideCalifornia,Present address:
The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Leonard J. Mueller
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Li Fan
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Chia‐En A. Chang
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
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6
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Schafer JW, Chen X, Schwartz SD. Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects. ACS Catal 2022; 12:913-922. [PMID: 35719741 PMCID: PMC9202816 DOI: 10.1021/acscatal.1c03913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Creating efficient and stable enzymes for catalysis in pharmaceutical and industrial laboratories is an important research goal. Arnold et al. used directed evolution to engineer a natural tryptophan synthase to create a mutant that is operable under laboratory conditions without the need for a natural allosteric effector. The use of directed evolution allows researchers to improve enzymes without understanding the structure-activity relationship. Here, we present a transition path sampling study of a key chemical transformation in the tryptophan synthase catalytic cycle. We observed that while directed evolution does mimic the natural allosteric effect from a stability perspective, fast protein dynamics associated with chemistry has been dramatically altered. This work provides further evidence of the role of protein dynamics in catalysis and clearly demonstrates the multifaceted complexity of mutations associated with protein engineering. This study also demonstrates a fascinating contrast between allosteric and stand-alone functions at the femtosecond time scale.
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Affiliation(s)
- Joseph W. Schafer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Xi Chen
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Steven D. Schwartz
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
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7
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Holmes JB, Liu V, Caulkins BG, Hilario E, Ghosh RK, Drago VN, Young RP, Romero JA, Gill AD, Bogie PM, Paulino J, Wang X, Riviere G, Bosken YK, Struppe J, Hassan A, Guidoulianov J, Perrone B, Mentink-Vigier F, Chang CEA, Long JR, Hooley RJ, Mueser TC, Dunn MF, Mueller LJ. Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate. Proc Natl Acad Sci U S A 2022; 119:e2109235119. [PMID: 34996869 PMCID: PMC8764694 DOI: 10.1073/pnas.2109235119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 02/07/2023] Open
Abstract
NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate Cβ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.
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Affiliation(s)
- Jacob B Holmes
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Bethany G Caulkins
- Department of Chemistry, University of California, Riverside, CA 92521
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711
| | - Eduardo Hilario
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rittik K Ghosh
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Victoria N Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606
| | - Robert P Young
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Jennifer A Romero
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Adam D Gill
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Paul M Bogie
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Joana Paulino
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310
| | - Xiaoling Wang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310
| | - Gwladys Riviere
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, National High Magnetic Field Laboratory, University of Florida, Gainesville, FL 32610
| | - Yuliana K Bosken
- Department of Biochemistry, University of California, Riverside, CA 92521
| | | | - Alia Hassan
- Bruker Switzerland AG 8117 Fällanden, Switzerland
| | | | | | | | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, National High Magnetic Field Laboratory, University of Florida, Gainesville, FL 32610
| | - Richard J Hooley
- Department of Chemistry, University of California, Riverside, CA 92521
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, CA 92521;
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521;
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8
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Ghosh RK, Hilario E, Liu V, Wang Y, Niks D, Holmes JB, Sakhrani VV, Mueller LJ, Dunn MF. Mutation of βGln114 to Ala Alters the Stabilities of Allosteric States in Tryptophan Synthase Catalysis. Biochemistry 2021; 60:3173-3186. [PMID: 34595921 DOI: 10.1021/acs.biochem.1c00383] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tryptophan synthase (TS) bienzyme complexes found in bacteria, yeasts, and molds are pyridoxal 5'-phosphate (PLP)-requiring enzymes that synthesize l-Trp. In the TS catalytic cycle, switching between the open and closed states of the α- and β-subunits via allosteric interactions is key to the efficient conversion of 3-indole-d-glycerol-3'-phosphate and l-Ser to l-Trp. In this process, the roles played by β-site residues proximal to the PLP cofactor have not yet been fully established. βGln114 is one such residue. To explore the roles played by βQ114, we conducted a detailed investigation of the βQ114A mutation on the structure and function of tryptophan synthase. Initial steady-state kinetic and static ultraviolet-visible spectroscopic analyses showed the Q to A mutation impairs catalytic activity and alters the stabilities of intermediates in the β-reaction. Therefore, we conducted X-ray structural and solid-state nuclear magnetic resonance spectroscopic studies to compare the wild-type and βQ114A mutant enzymes. These comparisons establish that the protein structural changes are limited to the Gln to Ala replacement, the loss of hydrogen bonds among the side chains of βGln114, βAsn145, and βArg148, and the inclusion of waters in the cavity created by substitution of the smaller Ala side chain. Because the conformations of the open and closed allosteric states are not changed by the mutation, we hypothesize that the altered properties arise from the lost hydrogen bonds that alter the relative stabilities of the open (βT state) and closed (βR state) conformations of the β-subunit and consequently alter the distribution of intermediates along the β-subunit catalytic path.
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Affiliation(s)
- Rittik K Ghosh
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Eduardo Hilario
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yangyang Wang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Jacob B Holmes
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Varun V Sakhrani
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, California 92521, United States
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9
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Michalska K, Wellington S, Maltseva N, Jedrzejczak R, Selem-Mojica N, Rosas-Becerra LR, Barona-Gómez F, Hung DT, Joachimiak A. Catalytically impaired TrpA subunit of tryptophan synthase from Chlamydia trachomatis is an allosteric regulator of TrpB. Protein Sci 2021; 30:1904-1918. [PMID: 34107106 PMCID: PMC8376405 DOI: 10.1002/pro.4143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/10/2022]
Abstract
Intracellular growth and pathogenesis of Chlamydia species is controlled by the availability of tryptophan, yet the complete biosynthetic pathway for l‐Trp is absent among members of the genus. Some representatives, however, preserve genes encoding tryptophan synthase, TrpAB – a bifunctional enzyme catalyzing the last two steps in l‐Trp synthesis. TrpA (subunit α) converts indole‐3‐glycerol phosphate into indole and glyceraldehyde‐3‐phosphate (α reaction). The former compound is subsequently used by TrpB (subunit β) to produce l‐Trp in the presence of l‐Ser and a pyridoxal 5′‐phosphate cofactor (β reaction). Previous studies have indicated that in Chlamydia, TrpA has lost its catalytic activity yet remains associated with TrpB to support the β reaction. Here, we provide detailed analysis of the TrpAB from C. trachomatis D/UW‐3/CX, confirming that accumulation of mutations in the active site of TrpA renders it enzymatically inactive, despite the conservation of the catalytic residues. We also show that TrpA remains a functional component of the TrpAB complex, increasing the activity of TrpB by four‐fold. The side chain of non‐conserved βArg267 functions as cation effector, potentially rendering the enzyme less susceptible to the solvent ion composition. The observed structural and functional changes detected herein were placed in a broader evolutionary and genomic context, allowing identification of these mutations in relation to their trp gene contexts in which they occur. Moreover, in agreement with the in vitro data, partial relaxation of purifying selection for TrpA, but not for TrpB, was detected, reinforcing a partial loss of TrpA functions during the course of evolution. PDB Code(s): 6V82;
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Affiliation(s)
- Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Samantha Wellington
- Department of Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA
| | - Nelly Selem-Mojica
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Mexico
| | - L Rodrigo Rosas-Becerra
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Mexico
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Mexico
| | - Deborah T Hung
- Department of Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, Illinois, USA.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA
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10
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D'Amico RN, Bosken YK, O'Rourke KF, Murray AM, Admasu W, Chang CEA, Boehr DD. Substitution of a Surface-Exposed Residue Involved in an Allosteric Network Enhances Tryptophan Synthase Function in Cells. Front Mol Biosci 2021; 8:679915. [PMID: 34124159 PMCID: PMC8187860 DOI: 10.3389/fmolb.2021.679915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Networks of noncovalent amino acid interactions propagate allosteric signals throughout proteins. Tryptophan synthase (TS) is an allosterically controlled bienzyme in which the indole product of the alpha subunit (αTS) is transferred through a 25 Å hydrophobic tunnel to the active site of the beta subunit (βTS). Previous nuclear magnetic resonance and molecular dynamics simulations identified allosteric networks in αTS important for its function. We show here that substitution of a distant, surface-exposed network residue in αTS enhances tryptophan production, not by activating αTS function, but through dynamically controlling the opening of the indole channel and stimulating βTS activity. While stimulation is modest, the substitution also enhances cell growth in a tryptophan-auxotrophic strain of Escherichia coli compared to complementation with wild-type αTS, emphasizing the biological importance of the network. Surface-exposed networks provide new opportunities in allosteric drug design and protein engineering, and hint at potential information conduits through which the functions of a metabolon or even larger proteome might be coordinated and regulated.
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Affiliation(s)
- Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Yuliana K Bosken
- Department of Chemistry, The University of California Riverside, Riverside, CA, United States
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Alec M Murray
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Woudasie Admasu
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Chia-En A Chang
- Department of Chemistry, The University of California Riverside, Riverside, CA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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11
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Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. mBio 2021; 12:mBio.00605-21. [PMID: 33975934 PMCID: PMC8262981 DOI: 10.1128/mbio.00605-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted infections and blindness globally. To date, Ct urogenital strains are considered tryptophan prototrophs, utilizing indole for tryptophan synthesis within a closed-conformation tetramer comprised of two α (TrpA)- and two β (TrpB)-subunits. In contrast, ocular strains are auxotrophs due to mutations in TrpA, relying on host tryptophan pools for survival. It has been speculated that there is strong selective pressure for urogenital strains to maintain a functional operon. Here, we performed genetic, phylogenetic, and novel functional modeling analyses of 595 geographically diverse Ct ocular, urethral, vaginal, and rectal strains with complete operon sequences. We found that ocular and urogenital, but not lymphogranuloma venereum, TrpA-coding sequences were under positive selection. However, vaginal and urethral strains exhibited greater nucleotide diversity and a higher ratio of nonsynonymous to synonymous substitutions [Pi(a)/Pi(s)] than ocular strains, suggesting a more rapid evolution of beneficial mutations. We also identified nonsynonymous amino acid changes for an ocular isolate with a urogenital backbone in the intergenic region between TrpR and TrpB at the exact binding site for YtgR-the only known iron-dependent transcription factor in Chlamydia-indicating that selective pressure has disabled the response to fluctuating iron levels. In silico effects on protein stability, ligand-binding affinity, and tryptophan repressor (TrpR) affinity for single-stranded DNA (ssDNA) measured by calculating free energy changes (ΔΔG) between Ct reference and mutant tryptophan operon proteins were also analyzed. We found that tryptophan synthase function was likely suboptimal compared to other bacterial tryptophan prototrophs and that a diversity of urogenital strain mutations rendered the synthase nonfunctional or inefficient. The novel mutations identified here affected active sites in an orthosteric manner but also hindered α- and β-subunit allosteric interactions from distant sites, reducing efficiency of the tryptophan synthase. Importantly, strains with mutant proteins were inclined toward energy conservation by exhibiting an altered affinity for their respective ligands compared to reference strains, indicating greater fitness. This is not surprising as l-tryptophan is one of the most energetically costly amino acids to synthesize. Mutations in the tryptophan repressor gene (trpR) among urogenital strains were similarly detrimental to function. Our findings indicate that urogenital strains are evolving more rapidly than previously recognized with mutations that impact tryptophan operon function in a manner that is energetically beneficial, providing a novel host-pathogen evolutionary mechanism for intracellular survival.IMPORTANCE Chlamydia trachomatis (Ct) is a major global public health concern causing sexually transmitted and ocular infections affecting over 130 million and 260 million people, respectively. Sequelae include infertility, preterm birth, ectopic pregnancy, and blindness. Ct relies on available host tryptophan pools and/or substrates to synthesize tryptophan to survive. Urogenital strains synthesize tryptophan from indole using their intact tryptophan synthase (TS). Ocular strains contain a trpA frameshift mutation that encodes a truncated TrpA with loss of TS function. We found that TS function is likely suboptimal compared to other tryptophan prototrophs and that urogenital stains contain diverse mutations that render TS nonfunctional/inefficient, evolve more rapidly than previously recognized, and impact operon function in a manner that is energetically beneficial, providing an alternative host-pathogen evolutionary mechanism for intracellular survival. Our research has broad scientific appeal since our approach can be applied to other bacteria that may explain evolution/survival in host-pathogen interactions.
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12
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Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021; 49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Allostery, in which binding of ligands to remote sites causes a functional change in the active sites, is a fascinating phenomenon observed in enzymes. Allostery can occur either with or without significant conformational changes in the enzymes, and the molecular basis of its mechanism can be difficult to decipher using only experimental techniques. Computational tools for analyzing enzyme sequences, structures, and dynamics can provide insights into the allosteric mechanism at the atomic level. Combining computational and experimental methods offers a powerful strategy for the study of enzyme allostery. The aromatic amino acid biosynthesis pathway is essential in microorganisms and plants. Multiple enzymes involved in this pathway are sensitive to feedback regulation by pathway end products and are known to use allostery to control their activities. To date, four enzymes in the aromatic amino acid biosynthesis pathway have been computationally investigated for their allosteric mechanisms, including 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, anthranilate synthase, chorismate mutase, and tryptophan synthase. Here we review the computational studies and findings on the allosteric mechanisms of these four enzymes. Results from these studies demonstrate the capability of computational tools and encourage future computational investigations of allostery in other enzymes of this pathway.
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13
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Simeth NA, Kinateder T, Rajendran C, Nazet J, Merkl R, Sterner R, König B, Kneuttinger AC. Towards Photochromic Azobenzene-Based Inhibitors for Tryptophan Synthase. Chemistry 2021; 27:2439-2451. [PMID: 33078454 PMCID: PMC7898615 DOI: 10.1002/chem.202004061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/16/2020] [Indexed: 01/25/2023]
Abstract
Light regulation of drug molecules has gained growing interest in biochemical and pharmacological research in recent years. In addition, a serious need for novel molecular targets of antibiotics has emerged presently. Herein, the development of a photocontrollable, azobenzene-based antibiotic precursor towards tryptophan synthase (TS), an essential metabolic multienzyme complex in bacteria, is presented. The compound exhibited moderately strong inhibition of TS in its E configuration and five times lower inhibition strength in its Z configuration. A combination of biochemical, crystallographic, and computational analyses was used to characterize the inhibition mode of this compound. Remarkably, binding of the inhibitor to a hitherto-unconsidered cavity results in an unproductive conformation of TS leading to noncompetitive inhibition of tryptophan production. In conclusion, we created a promising lead compound for combatting bacterial diseases, which targets an essential metabolic enzyme, and whose inhibition strength can be controlled with light.
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Affiliation(s)
- Nadja A. Simeth
- Institute for Organic ChemistryDepartment of Chemistry and PharmacyUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
- Stratingh Institute for ChemistryFaculty of Science and EngineeringUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Thomas Kinateder
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Chitra Rajendran
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Julian Nazet
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Rainer Merkl
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Reinhard Sterner
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Burkhard König
- Institute for Organic ChemistryDepartment of Chemistry and PharmacyUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Andrea C. Kneuttinger
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
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14
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Watkins-Dulaney E, Straathof S, Arnold F. Tryptophan Synthase: Biocatalyst Extraordinaire. Chembiochem 2021; 22:5-16. [PMID: 32677310 PMCID: PMC7935429 DOI: 10.1002/cbic.202000379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/15/2020] [Indexed: 12/23/2022]
Abstract
Tryptophan synthase (TrpS) has emerged as a paragon of noncanonical amino acid (ncAA) synthesis and is an ideal biocatalyst for synthetic and biological applications. TrpS catalyzes an irreversible, C-C bond-forming reaction between indole and serine to make l-tryptophan; native TrpS complexes possess fairly broad specificity for indole analogues, but are difficult to engineer to extend substrate scope or to confer other useful properties due to allosteric constraints and their heterodimeric structure. Directed evolution freed the catalytically relevant TrpS β-subunit (TrpB) from allosteric regulation by its TrpA partner and has enabled dramatic expansion of the enzyme's substrate scope. This review examines the long and storied career of TrpS from the perspective of its application in ncAA synthesis and biocatalytic cascades.
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Affiliation(s)
- Ella Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Frances Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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15
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Sakhrani VV, Hilario E, Caulkins BG, Hatcher-Skeers ME, Fan L, Dunn MF, Mueller LJ. Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR. JOURNAL OF BIOMOLECULAR NMR 2020; 74:341-354. [PMID: 32415580 PMCID: PMC7451264 DOI: 10.1007/s10858-020-00320-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Backbone assignments for the isolated α-subunit of Salmonella typhimurium tryptophan synthase (TS) are reported based on triple resonance solution-state NMR experiments on a uniformly 2H,13C,15N-labeled sample. From the backbone chemical shifts, secondary structure and random coil index order parameters (RCI-S2) are predicted. Titration with the 3-indole-D-glycerol 3'-phosphate analog, N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), leads to chemical shift perturbations indicative of conformational changes from which an estimate of the dissociation constant is obtained. Comparisons of the backbone chemical-shifts, RCI-S2 values, and site-specific relaxation times with and without F9 reveal allosteric changes including modulation in secondary structures and loop rigidity induced upon ligand binding. A comparison is made to the X-ray crystal structure of the α-subunit in the full TS αββα bi-enzyme complex and to two new X-ray crystal structures of the isolated TS α-subunit reported in this work.
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Affiliation(s)
- Varun V Sakhrani
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Eduardo Hilario
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Bethany G Caulkins
- Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Mary E Hatcher-Skeers
- Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Li Fan
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Michael F Dunn
- Department of Biochemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Leonard J Mueller
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA.
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16
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Michalska K, Chang C, Maltseva NI, Jedrzejczak R, Robertson GT, Gusovsky F, McCarren P, Schreiber SL, Nag PP, Joachimiak A. Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase. Protein Sci 2020; 29:779-788. [PMID: 31930594 PMCID: PMC7020977 DOI: 10.1002/pro.3825] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Global dispersion of multidrug resistant bacteria is very common and evolution of antibiotic-resistance is occurring at an alarming rate, presenting a formidable challenge for humanity. The development of new therapeuthics with novel molecular targets is urgently needed. Current drugs primarily affect protein, nucleic acid, and cell wall synthesis. Metabolic pathways, including those involved in amino acid biosynthesis, have recently sparked interest in the drug discovery community as potential reservoirs of such novel targets. Tryptophan biosynthesis, utilized by bacteria but absent in humans, represents one of the currently studied processes with a therapeutic focus. It has been shown that tryptophan synthase (TrpAB) is required for survival of Mycobacterium tuberculosis in macrophages and for evading host defense, and therefore is a promising drug target. Here we present crystal structures of TrpAB with two allosteric inhibitors of M. tuberculosis tryptophan synthase that belong to sulfolane and indole-5-sulfonamide chemical scaffolds. We compare our results with previously reported structural and biochemical studies of another, azetidine-containing M. tuberculosis tryptophan synthase inhibitor. This work shows how structurally distinct ligands can occupy the same allosteric site and make specific interactions. It also highlights the potential benefit of targeting more variable allosteric sites of important metabolic enzymes.
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Affiliation(s)
- Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Changsoo Chang
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Gregory T. Robertson
- Colorado State UniversityMycobacteria Research Laboratories, Department of Microbiology, Immunology and PathologyFort CollinsColorado
| | | | | | | | - Partha P. Nag
- Broad Institute of MIT and HarvardCambridgeMassachusetts
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
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17
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Norris A, Busch F, Schupfner M, Sterner R, Wysocki VH. Quaternary Structure of the Tryptophan Synthase α-Subunit Homolog BX1 from Zea mays. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:227-233. [PMID: 31933363 PMCID: PMC7313238 DOI: 10.1021/jasms.9b00068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
BX1 from Zea mays (zmBX1) is an enzyme of plant secondary metabolism that generates indole for the synthesis of plant defensins. It is a homologue of the tryptophan synthase α-subunit, TrpA. Whereas TrpA itself is a monomer in solution, zmBX1 is dimeric, confirmed in our work by native MS. Using cross-linking and mutagenesis, we identified the physiological dimerization interface of zmBX1. We found that homodimerization has only minor effects on catalysis and stability. A comparison of the zmBX1-zmBX1 homodimer and zmTrpA-zmTrpB heterodimer interfaces suggest that homodimerization in zmBX1 might, at an early point in evolution, have served as a mechanism to exclude the interaction with the tryptophan synthase β-subunit (zmTrpB), marking its transition from primary to secondary metabolism.
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Affiliation(s)
- Andrew Norris
- The Ohio State University , Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology , Columbus , Ohio 43210 , United States
| | - Florian Busch
- The Ohio State University , Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology , Columbus , Ohio 43210 , United States
| | - Michael Schupfner
- University of Regensburg , Institute for Biophysics and Physical Biochemistry , Regensburg D-93053 , Germany
| | - Reinhard Sterner
- University of Regensburg , Institute for Biophysics and Physical Biochemistry , Regensburg D-93053 , Germany
| | - Vicki H Wysocki
- The Ohio State University , Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology , Columbus , Ohio 43210 , United States
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18
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Phillips RS, Craig S, Kovalevsky A, Gerlits O, Weiss K, Iorgu AI, Heyes DJ, Hay S. Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert S. Phillips
- Department of Chemistry, University of Georgia, Athens, Georgia 30602 United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Steven Craig
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
| | - Oksana Gerlits
- Tennessee Wesleyan University, Athens, Tennessee 37303, United States
| | - Kevin Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
| | - Andreea I. Iorgu
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M17DN, U.K
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M17DN, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester M17DN, U.K
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19
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Zhang D, Lazim R. Exploring indole channeling in tryptophan synthase using steered molecular dynamics simulation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Teixeira CSS, Ramos MJ, Sousa SF, Cerqueira NMFSA. Solving the Catalytic Mechanism of Tryptophan Synthase: an Emergent Drug Target in the Treatment of Tuberculosis. ChemCatChem 2019. [DOI: 10.1002/cctc.201901505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carla S. Silva Teixeira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTEDepartamento de Química e BioquímicaFaculdade de CiênciasUniversidade do Porto Porto 4169-007 Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO@REQUIMTEBioSIMDepartamento de BiomedicinaFaculdade de MedicinaUniversidade do Porto Porto 4200-319 Portugal
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21
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Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D. Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon. mBio 2019; 10:e01464-19. [PMID: 31311884 PMCID: PMC6635532 DOI: 10.1128/mbio.01464-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 02/03/2023] Open
Abstract
Clinical persistence of Chlamydia trachomatis (Ct) sexually transmitted infections (STIs) is a major public health concern. In vitro persistence is known to develop through interferon gamma (IFN-γ) induction of indoleamine 2,3-dioxygenase (IDO), which catabolizes tryptophan, an essential amino acid for Ct replication. The organism can recover from persistence by synthesizing tryptophan from indole, a substrate for the enzyme tryptophan synthase. The majority of Ct strains, except for reference strain B/TW-5/OT, contain an operon comprised of α and β subunits that encode TrpA and TrpB, respectively, and form a functional αββα tetramer. However, trpA mutations in ocular Ct strains, which are responsible for the blinding eye disease known as trachoma, abrogate tryptophan synthesis from indole. We examined serial urogenital samples from a woman who had recurrent Ct infections over 4 years despite antibiotic treatment. The Ct isolates from each infection episode were genome sequenced and analyzed for phenotypic, structural, and functional characteristics. All isolates contained identical mutations in trpA and developed aberrant bodies within intracellular inclusions, visualized by transmission electron microscopy, even when supplemented with indole following IFN-γ treatment. Each isolate displayed an altered αββα structure, could not synthesize tryptophan from indole, and had significantly lower trpBA expression but higher intracellular tryptophan levels compared with those of reference Ct strain F/IC-Cal3. Our data indicate that emergent mutations in the tryptophan operon, which were previously thought to be restricted only to ocular Ct strains, likely resulted in in vivo persistence in the described patient and represents a novel host-pathogen adaptive strategy for survival.IMPORTANCEChlamydia trachomatis (Ct) is the most common sexually transmitted bacterium with more than 131 million cases occurring annually worldwide. Ct infections are often asymptomatic, persisting for many years despite treatment. In vitro recovery from persistence occurs when indole is utilized by the organism's tryptophan synthase to synthesize tryptophan, an essential amino acid for replication. Ocular but not urogenital Ct strains contain mutations in the synthase that abrogate tryptophan synthesis. Here, we discovered that the genomes of serial isolates from a woman with recurrent, treated Ct STIs over many years were identical with a novel synthase mutation. This likely allowed long-term in vivo persistence where active infection resumed only when tryptophan became available. Our findings indicate an emerging adaptive host-pathogen evolutionary strategy for survival in the urogenital tract that will prompt the field to further explore chlamydial persistence, evaluate the genetics of mutant Ct strains and fitness within the host, and their implications for disease pathogenesis.
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Affiliation(s)
- Naraporn Somboonna
- Center for Immunobiology and Vaccine Development, University of California San Francisco Benioff Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Noa Ziklo
- Center for Immunobiology and Vaccine Development, University of California San Francisco Benioff Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
| | - Jung Hyuk Suh
- Center for Immunobiology and Vaccine Development, University of California San Francisco Benioff Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, University of California San Francisco Benioff Children's Hospital Oakland Research Institute, Oakland, California, USA
- Department of Bioengineering, University of California Berkeley and University of California San Francisco Joint Graduate Group, Berkeley and San Francisco, California, USA
- Department of Medicine and Pediatrics, University of California, San Francisco, California, USA
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22
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Michalska K, Gale J, Joachimiak G, Chang C, Hatzos-Skintges C, Nocek B, Johnston SE, Bigelow L, Bajrami B, Jedrzejczak RP, Wellington S, Hung DT, Nag PP, Fisher SL, Endres M, Joachimiak A. Conservation of the structure and function of bacterial tryptophan synthases. IUCRJ 2019; 6:649-664. [PMID: 31316809 PMCID: PMC6608616 DOI: 10.1107/s2052252519005955] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/29/2019] [Indexed: 06/10/2023]
Abstract
Tryptophan biosynthesis is one of the most characterized processes in bacteria, in which the enzymes from Salmonella typhimurium and Escherichia coli serve as model systems. Tryptophan synthase (TrpAB) catalyzes the final two steps of tryptophan biosynthesis in plants, fungi and bacteria. This pyridoxal 5'-phosphate (PLP)-dependent enzyme consists of two protein chains, α (TrpA) and β (TrpB), functioning as a linear αββα heterotetrameric complex containing two TrpAB units. The reaction has a complicated, multistep mechanism resulting in the β-replacement of the hydroxyl group of l-serine with an indole moiety. Recent studies have shown that functional TrpAB is required for the survival of pathogenic bacteria in macrophages and for evading host defense. Therefore, TrpAB is a promising target for drug discovery, as its orthologs include enzymes from the important human pathogens Streptococcus pneumoniae, Legionella pneumophila and Francisella tularensis, the causative agents of pneumonia, legionnaires' disease and tularemia, respectively. However, specific biochemical and structural properties of the TrpABs from these organisms have not been investigated. To fill the important phylogenetic gaps in the understanding of TrpABs and to uncover unique features of TrpAB orthologs to spearhead future drug-discovery efforts, the TrpABs from L. pneumophila, F. tularensis and S. pneumoniae have been characterized. In addition to kinetic properties and inhibitor-sensitivity data, structural information gathered using X-ray crystallo-graphy is presented. The enzymes show remarkable structural conservation, but at the same time display local differences in both their catalytic and allosteric sites that may be responsible for the observed differences in catalysis and inhibitor binding. This functional dissimilarity may be exploited in the design of species-specific enzyme inhibitors.
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Affiliation(s)
- Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Jennifer Gale
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Grazyna Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Changsoo Chang
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Catherine Hatzos-Skintges
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60367, USA
| | - Boguslaw Nocek
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | | | - Lance Bigelow
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Besnik Bajrami
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Robert P. Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | | | - Deborah T. Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Partha P. Nag
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Michael Endres
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
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23
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O'Rourke KF, Axe JM, D'Amico RN, Sahu D, Boehr DD. Millisecond Timescale Motions Connect Amino Acid Interaction Networks in Alpha Tryptophan Synthase. Front Mol Biosci 2018; 5:92. [PMID: 30467546 PMCID: PMC6236060 DOI: 10.3389/fmolb.2018.00092] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/18/2018] [Indexed: 11/13/2022] Open
Abstract
Tryptophan synthase is a model system for understanding allosteric regulation within enzyme complexes. Amino acid interaction networks were previously delineated in the isolated alpha subunit (αTS) in the absence of the beta subunit (βTS). The amino acid interaction networks were different between the ligand-free enzyme and the enzyme actively catalyzing turnover. Previous X-ray crystallography studies indicated only minor localized changes when ligands bind αTS, and so, structural changes alone could not explain the changes to the amino acid interaction networks. We hypothesized that the network changes could instead be related to changes in conformational dynamics. As such, we conducted nuclear magnetic resonance relaxation studies on different substrate- and products-bound complexes of αTS. Specifically, we collected 15N R2 relaxation dispersion data that reports on microsecond-to-millisecond timescale motion of backbone amide groups. These experiments indicated that there are conformational exchange events throughout αTS. Substrate and product binding change specific motional pathways throughout the enzyme, and these pathways connect the previously identified network residues. These pathways reach the αTS/βTS binding interface, suggesting that the identified dynamic networks may also be important for communication with the βTS subunit.
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Affiliation(s)
- Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Jennifer M Axe
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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Buller AR, van Roye P, Cahn JK, Scheele RA, Herger M, Arnold FH. Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble. J Am Chem Soc 2018; 140:7256-7266. [PMID: 29712420 PMCID: PMC5999571 DOI: 10.1021/jacs.8b03490] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric enzymes contain a wealth of catalytic diversity that remains distinctly underutilized for biocatalysis. Tryptophan synthase is a model allosteric system and a valuable enzyme for the synthesis of noncanonical amino acids (ncAA). Previously, we evolved the β-subunit from Pyrococcus furiosus, PfTrpB, for ncAA synthase activity in the absence of its native partner protein PfTrpA. However, the precise mechanism by which mutation activated TrpB to afford a stand-alone catalyst remained enigmatic. Here, we show that directed evolution caused a gradual change in the rate-limiting step of the catalytic cycle. Concomitantly, the steady-state distribution of the intermediates shifts to favor covalently bound Trp adducts, which have increased thermodynamic stability. The biochemical properties of these evolved, stand-alone TrpBs converge on those induced in the native system by allosteric activation. High-resolution crystal structures of the wild-type enzyme, an intermediate in the lineage, and the final variant, encompassing five distinct chemical states, show that activating mutations have only minor structural effects on their immediate environment. Instead, mutation stabilizes the large-scale motion of a subdomain to favor an otherwise transiently populated closed conformational state. This increase in stability enabled the first structural description of Trp covalently bound in a catalytically active TrpB, confirming key features of catalysis. These data combine to show that sophisticated models of allostery are not a prerequisite to recapitulating its complex effects via directed evolution, opening the way to engineering stand-alone versions of diverse allosteric enzymes.
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Affiliation(s)
- Andrew R. Buller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, Wisconsin 53706, United States
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Paul van Roye
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Jackson K.B. Cahn
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, Zurich 8093, Switzerland
| | - Remkes A. Scheele
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Michael Herger
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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25
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Loutchko D, Eisbach M, Mikhailov AS. Stochastic thermodynamics of a chemical nanomachine: The channeling enzyme tryptophan synthase. J Chem Phys 2017; 146:025101. [DOI: 10.1063/1.4973544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Buller AR, van Roye P, Murciano-Calles J, Arnold FH. Tryptophan Synthase Uses an Atypical Mechanism To Achieve Substrate Specificity. Biochemistry 2016; 55:7043-7046. [PMID: 27935677 PMCID: PMC5207025 DOI: 10.1021/acs.biochem.6b01127] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tryptophan synthase (TrpS) catalyzes the final steps in the biosynthesis of l-tryptophan from l-serine (Ser) and indole-3-glycerol phosphate (IGP). We report that native TrpS can also catalyze a productive reaction with l-threonine (Thr), leading to (2S,3S)-β-methyltryptophan. Surprisingly, β-substitution occurs in vitro with a 3.4-fold higher catalytic efficiency for Ser over Thr using saturating indole, despite a >82000-fold preference for Ser in direct competition using IGP. Structural data identify a novel product binding site, and kinetic experiments clarify the atypical mechanism of specificity: Thr binds efficiently but decreases the affinity for indole and disrupts the allosteric signaling that regulates the catalytic cycle.
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Affiliation(s)
- Andrew R. Buller
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Paul van Roye
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Javier Murciano-Calles
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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27
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Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools. Catalysts 2016; 6. [PMID: 27885336 PMCID: PMC5119520 DOI: 10.3390/catal6060082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations.
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Hilario E, Caulkins BG, Huang YMM, You W, Chang CEA, Mueller LJ, Dunn MF, Fan L. Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1864:268-279. [PMID: 26708480 PMCID: PMC4732270 DOI: 10.1016/j.bbapap.2015.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/20/2015] [Accepted: 12/01/2015] [Indexed: 02/02/2023]
Abstract
Four new X-ray structures of tryptophan synthase (TS) crystallized with varying numbers of the amphipathic N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) molecule are presented. These structures show one of the F6 ligands threaded into the tunnel from the β-site and reveal a distinct hydrophobic region. Over this expanse, the interactions between F6 and the tunnel are primarily nonpolar, while the F6 phosphoryl group fits into a polar pocket of the β-subunit active site. Further examination of TS structures reveals that one portion of the tunnel (T1) binds clusters of water molecules, whereas waters are not observed in the nonpolar F6 binding region of the tunnel (T2). MD simulation of another TS structure with an unobstructed tunnel also indicates the T2 region of the tunnel excludes water, consistent with a dewetted state that presents a significant barrier to the transfer of water into the closed β-site. We conclude that hydrophobic molecules can freely diffuse between the α- and β-sites via the tunnel, while water does not. We propose that exclusion of water serves to inhibit reaction of water with the α-aminoacrylate intermediate to form ammonium ion and pyruvate, a deleterious side reaction in the αβ-catalytic cycle. Finally, while most TS structures show βPhe280 partially blocking the tunnel between the α- and β-sites, new structures show an open tunnel, suggesting the flexibility of the βPhe280 side chain. Flexible docking studies and MD simulations confirm that the dynamic behavior of βPhe280 allows unhindered transfer of indole through the tunnel, therefore excluding a gating role for this residue.
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Affiliation(s)
- Eduardo Hilario
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Bethany G Caulkins
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Yu-Ming M Huang
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Wanli You
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Leonard J Mueller
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Michael F Dunn
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA
| | - Li Fan
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA
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29
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Loutchko D, Gonze D, Mikhailov AS. Single-Molecule Stochastic Analysis of Channeling Enzyme Tryptophan Synthase. J Phys Chem B 2016; 120:2179-86. [PMID: 26863529 DOI: 10.1021/acs.jpcb.5b12229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine. It possesses two active centers and, as a single molecule, catalyzes 13 different reaction steps with a complex pattern of allosteric regulation and with an intermediate product channeled from one active center to another. Here, the first single-molecule stochastic model of the enzyme is proposed and analyzed. All its transition rate constants were deduced from the experimental data available, and no fitting parameters were thus employed. Numerical simulations reveal strong correlations in the states of the active centers and the emergent synchronization of intramolecular processes in tryptophan synthase.
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Affiliation(s)
- Dimitri Loutchko
- Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society , 14195 Berlin, Germany
| | - Didier Gonze
- Unité de Chronobiologie théorique, Faculté des Sciences, Université Libre de Bruxelles , 1050 Brussels, Belgium
| | - Alexander S Mikhailov
- Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society , 14195 Berlin, Germany.,Department of Mathematical and Life Sciences, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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30
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Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation. Proc Natl Acad Sci U S A 2015; 112:14599-604. [PMID: 26553994 DOI: 10.1073/pnas.1516401112] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes in heteromeric, allosterically regulated complexes catalyze a rich array of chemical reactions. Separating the subunits of such complexes, however, often severely attenuates their catalytic activities, because they can no longer be activated by their protein partners. We used directed evolution to explore allosteric regulation as a source of latent catalytic potential using the β-subunit of tryptophan synthase from Pyrococcus furiosus (PfTrpB). As part of its native αββα complex, TrpB efficiently produces tryptophan and tryptophan analogs; activity drops considerably when it is used as a stand-alone catalyst without the α-subunit. Kinetic, spectroscopic, and X-ray crystallographic data show that this lost activity can be recovered by mutations that reproduce the effects of complexation with the α-subunit. The engineered PfTrpB is a powerful platform for production of Trp analogs and for further directed evolution to expand substrate and reaction scope.
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31
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Huang YMM, You W, Caulkins BG, Dunn MF, Mueller LJ, Chang CEA. Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase. Protein Sci 2015; 25:166-83. [PMID: 26013176 DOI: 10.1002/pro.2709] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022]
Abstract
The importance of protonation states and proton transfer in pyridoxal 5'-phosphate (PLP)-chemistry can hardly be overstated. Although experimental approaches to investigate pKa values can provide general guidance for assigning proton locations, only static pictures of the chemical species are available. To obtain the overall protein dynamics for the interpretation of detailed enzyme catalysis in this study, guided by information from solid-state NMR, we performed molecular dynamics (MD) simulations for the PLP-dependent enzyme tryptophan synthase (TRPS), whose catalytic mechanism features multiple quasi-stable intermediates. The primary objective of this work is to elucidate how the position of a single proton on the reacting substrate affects local and global protein dynamics during the catalytic cycle. In general, proteins create a chemical environment and an ensemble of conformational motions to recognize different substrates with different protonations. The study of these interactions in TRPS shows that functional groups on the reacting substrate, such as the phosphoryl group, pyridine nitrogen, phenolic oxygen and carboxyl group, of each PLP-bound intermediate play a crucial role in constructing an appropriate molecular interface with TRPS. In particular, the protonation states of the ionizable groups on the PLP cofactor may enhance or weaken the attractions between the enzyme and substrate. In addition, remodulation of the charge distribution for the intermediates may help generate a suitable environment for chemical reactions. The results of our study enhance knowledge of protonation states for several PLP intermediates and help to elucidate their effects on protein dynamics in the function of TRPS and other PLP-dependent enzymes.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Wanli You
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Bethany G Caulkins
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, California, 92521
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, California, 92521
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, California, 92521
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32
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Huang YMM, Kang M, Chang CEA. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. J Mol Recognit 2015; 27:537-48. [PMID: 25042708 DOI: 10.1002/jmr.2377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 11/05/2022]
Abstract
Revealing the processes of ligand-protein associations deepens our understanding of molecular recognition and binding kinetics. Hydrogen bonds (H-bonds) play a crucial role in optimizing ligand-protein interactions and ligand specificity. In addition to the formation of stable H-bonds in the final bound state, the formation of transient H-bonds during binding processes contributes binding kinetics that define a ligand as a fast or slow binder, which also affects drug action. However, the effect of forming the transient H-bonds on the kinetic properties is little understood. Guided by results from coarse-grained Brownian dynamics simulations, we used classical molecular dynamics simulations in an implicit solvent model and accelerated molecular dynamics simulations in explicit waters to show that the position and distribution of the H-bond donor or acceptor of a drug result in switching intermolecular and intramolecular H-bond pairs during ligand recognition processes. We studied two major types of HIV-1 protease ligands: a fast binder, xk263, and a slow binder, ritonavir. The slow association rate in ritonavir can be attributed to increased flexibility of ritonavir, which yields multistep transitions and stepwise entering patterns and the formation and breaking of complex H-bond pairs during the binding process. This model suggests the importance of conversions of spatiotemporal H-bonds during the association of ligands and proteins, which helps in designing inhibitors with preferred binding kinetics.
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Affiliation(s)
- Yu-ming M Huang
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
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Catalytic roles of βLys87 in tryptophan synthase: (15)N solid state NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1194-9. [PMID: 25688830 DOI: 10.1016/j.bbapap.2015.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
Abstract
The proposed mechanism for tryptophan synthase shows βLys87 playing multiple catalytic roles: it bonds to the PLP cofactor, activates C4' for nucleophilic attack via a protonated Schiff base nitrogen, and abstracts and returns protons to PLP-bound substrates (i.e. acid-base catalysis). ε-¹⁵N-lysine TS was prepared to access the protonation state of βLys87 using ¹⁵N solid-state nuclear magnetic resonance (SSNMR) spectroscopy for three quasi-stable intermediates along the reaction pathway. These experiments establish that the protonation state of the ε-amino group switches between protonated and neutral states as the β-site undergoes conversion from one intermediate to the next during catalysis, corresponding to mechanistic steps where this lysine residue has been anticipated to play alternating acid and base catalytic roles that help steer reaction specificity in tryptophan synthase catalysis. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. Guest Editors: Andrea Mozzarelli and Loredano Pollegioni.
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Hiyama T, Sato T, Imanaka T, Atomi H. The tryptophan synthase β-subunit paralogs TrpB1 and TrpB2 in Thermococcus kodakarensis are both involved in tryptophan biosynthesis and indole salvage. FEBS J 2014; 281:3113-25. [PMID: 24835339 DOI: 10.1111/febs.12845] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/01/2014] [Accepted: 05/13/2014] [Indexed: 11/26/2022]
Abstract
The last two steps of l-tryptophan (Trp) biosynthesis are catalyzed by Trp synthase, a heterotetramer composed of TrpA and TrpB. TrpB catalyzes the condensation of indole, synthesized by TrpA, and serine to Trp. In the hyperthermophilic archaeon Thermococcus kodakarensis, trpA and trpB (trpB1) are located adjacently in the trpCDEGFB1A operon. Interestingly, several organisms possess a second trpB gene (trpB2) encoding TrpB2, located outside of the trp operon in T. kodakarensis. Until now, the physiological function of trpB2 has not been examined genetically. In the present study, we report the biochemical and physiological analyses of TrpB2 from T. kodakarensis. Kinetic analysis indicated that TrpB2 catalyzed the TrpB reaction but did not interact with TrpA as in the case of TrpB1. When growth phenotypes were examined for gene disruption strains, the double-deletion mutant (ΔtrpB1ΔtrpB2) displayed Trp auxotrophy, whereas individual single mutants (ΔtrpB1 and ΔtrpB2 strains) did not. It has been proposed previously that, in Thermotoga maritima, TrpB2 provides an alternate route to generate Trp from serine and free indole (indole salvage). To accurately examine the capacity of TrpB1 and TrpB2 in Trp synthesis via indole salvage, we constructed ΔtrpEB1 and ΔtrpEB2 strains using strain KUW1 (ΔpyrFΔtrpE) as a host, eliminating the route for endogenous indole synthesis. Indole complemented the Trp auxotrophies of ΔtrpEB1 (ΔpyrFΔtrpEΔtrpB1) and ΔtrpEB2 (ΔpyrFΔtrpEΔtrpB2) to similar levels. The results indicate that TrpB1 and TrpB2 both contribute to Trp biosynthesis in T. kodakarensis and can utilize free indole, and that indole salvage does not necessarily rely on TrpB2 to a greater extent.
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Affiliation(s)
- Takayoshi Hiyama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Japan
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35
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Mueller LJ, Dunn MF. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase. Acc Chem Res 2013; 46:2008-17. [PMID: 23537227 DOI: 10.1021/ar3003333] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of NMR crystallography applied to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation.
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Affiliation(s)
- Leonard J. Mueller
- Department of Chemistry and ‡Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Michael F. Dunn
- Department of Chemistry and ‡Department of Biochemistry, University of California, Riverside, California 92521, United States
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Niks D, Hilario E, Dierkers A, Ngo H, Borchardt D, Neubauer TJ, Fan L, Mueller LJ, Dunn MF. Allostery and substrate channeling in the tryptophan synthase bienzyme complex: evidence for two subunit conformations and four quaternary states. Biochemistry 2013; 52:6396-411. [PMID: 23952479 DOI: 10.1021/bi400795e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The allosteric regulation of substrate channeling in tryptophan synthase involves ligand-mediated allosteric signaling that switches the α- and β-subunits between open (low activity) and closed (high activity) conformations. This switching prevents the escape of the common intermediate, indole, and synchronizes the α- and β-catalytic cycles. (19)F NMR studies of bound α-site substrate analogues, N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) and N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), were found to be sensitive NMR probes of β-subunit conformation. Both the internal and external aldimine F6 complexes gave a single bound peak at the same chemical shift, while α-aminoacrylate and quinonoid F6 complexes all gave a different bound peak shifted by +1.07 ppm. The F9 complexes exhibited similar behavior, but with a corresponding shift of -0.12 ppm. X-ray crystal structures show the F6 and F9 CF3 groups located at the α-β subunit interface and report changes in both the ligand conformation and the surrounding protein microenvironment. Ab initio computational modeling suggests that the change in (19)F chemical shift results primarily from changes in the α-site ligand conformation. Structures of α-aminoacrylate F6 and F9 complexes and quinonoid F6 and F9 complexes show the α- and β-subunits have closed conformations wherein access of ligands into the α- and β-sites from solution is blocked. Internal and external aldimine structures show the α- and β-subunits with closed and open global conformations, respectively. These results establish that β-subunits exist in two global conformational states, designated open, where the β-sites are freely accessible to substrates, and closed, where the β-site portal into solution is blocked. Switching between these conformations is critically important for the αβ-catalytic cycle.
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Affiliation(s)
- Dimitri Niks
- Department of Biochemistry, University of California at Riverside , Riverside, California 92521, United States
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37
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Ligand binding and unfolding of tryptophan synthase revealed by ion mobility-tandem mass spectrometry employing collision and surface induced dissociation. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0126-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Axe JM, Boehr DD. Long-range interactions in the α subunit of tryptophan synthase help to coordinate ligand binding, catalysis, and substrate channeling. J Mol Biol 2013; 425:1527-45. [PMID: 23376097 DOI: 10.1016/j.jmb.2013.01.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/23/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
Abstract
The α-subunit of tryptophan synthase (αTS) catalyzes the conversion of indole-3-glycerol phosphate to d-glyceraldehyde-3-phosphate and indole. We propose that allosteric networks intrinsic to αTS are modulated by the binding of the β-subunit to regulate αTS function. Understanding these long-range amino acid networks in αTS thus gives insight into the coordination of the two active sites within TS. In this study, we have used Ala residues as probes for structural and dynamic changes of αTS throughout its catalytic cycle, in the absence of the β-subunit. Projection analysis of the chemical shift changes by site-specific amino acid substitutions and ligand titrations indicates that αTS has three important conformational states: ligand-free, glyceraldehyde-3-phosphate-bound(like), and the active states. The amino acid networks within these conformations are different, as suggested by chemical shift correlation analysis. In particular, there are long-range connections, only in the active state, between Ala47, which reports on structural and dynamic changes associated with the general acid/base Glu49, and residues within the β2α2 loop, which contains the catalytically important Asp60 residue. These long-range interactions are likely important for coordinating chemical catalysis. In the free state, but not in the active state, there are connections between the β2α2 and β6α6 loops that likely help to coordinate substrate binding. Changes in the allosteric networks are also accompanied by protein dynamic changes. During catalytic turnover, the protein becomes more rigid on the millisecond timescale and the active-site dynamics are driven to a faster nanosecond timescale.
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Affiliation(s)
- Jennifer M Axe
- Department of Chemistry, Pennsylvania State University, 240 Chemistry Building, University Park, PA 16802, USA
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39
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Phillips RS, Wang AK, Marchal S, Lange R. Effects of Pressure and Osmolytes on the Allosteric Equilibria of Salmonella typhimurium Tryptophan Synthase. Biochemistry 2012; 51:9354-63. [DOI: 10.1021/bi301002q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert S. Phillips
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United
States
| | - Alexandre Kim Wang
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Stephane Marchal
- Inserm U710, Montpellier, F-34095 France, Université de Montpellier 2, Montpellier, F-34095 France, and EPHE, Paris, F-75007 France
| | - Reinhard Lange
- Inserm U710, Montpellier, F-34095 France, Université de Montpellier 2, Montpellier, F-34095 France, and EPHE, Paris, F-75007 France
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40
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Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MRN. Crystal structure of Escherichia coli diaminopropionate ammonia-lyase reveals mechanism of enzyme activation and catalysis. J Biol Chem 2012; 287:20369-81. [PMID: 22505717 PMCID: PMC3370218 DOI: 10.1074/jbc.m112.351809] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/12/2012] [Indexed: 11/06/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize the unique chemistry of a pyridine ring to carry out diverse reactions involving amino acids. Diaminopropionate (DAP) ammonia-lyase (DAPAL) is a prokaryotic PLP-dependent enzyme that catalyzes the degradation of d- and l-forms of DAP to pyruvate and ammonia. Here, we report the first crystal structure of DAPAL from Escherichia coli (EcDAPAL) in tetragonal and monoclinic forms at 2.0 and 2.2 Å resolutions, respectively. Structures of EcDAPAL soaked with substrates were also determined. EcDAPAL has a typical fold type II PLP-dependent enzyme topology consisting of a large and a small domain with the active site at the interface of the two domains. The enzyme is a homodimer with a unique biological interface not observed earlier. Structure of the enzyme in the tetragonal form had PLP bound at the active site, whereas the monoclinic structure was in the apo-form. Analysis of the apo and holo structures revealed that the region around the active site undergoes transition from a disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. EcDAPAL soaked with dl-DAP revealed density at the active site appropriate for the reaction intermediate aminoacrylate, which is consistent with the observation that EcDAPAL has low activity under crystallization conditions. Based on the analysis of the structure and results of site-directed mutagenesis, a two-base mechanism of catalysis involving Asp(120) and Lys(77) is suggested.
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Affiliation(s)
| | | | | | | | - Farida Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Appaji N. Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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41
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Allosteric regulation of substrate channeling and catalysis in the tryptophan synthase bienzyme complex. Arch Biochem Biophys 2012; 519:154-66. [PMID: 22310642 DOI: 10.1016/j.abb.2012.01.016] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/23/2012] [Accepted: 01/25/2012] [Indexed: 11/24/2022]
Abstract
The tryptophan synthase α2β2 bi-enzyme complex catalyzes the last two steps in the synthesis of l-tryptophan (l-Trp). The α-subunit catalyzes cleavage of 3-indole-d-glycerol 3'-phosphate (IGP) to give indole and d-glyceraldehyde 3'-phosphate (G3P). Indole is then transferred (channeled) via an interconnecting 25Å-long tunnel, from the α-subunit to the β-subunit where it reacts with l-Ser in a pyridoxal 5'-phosphate-dependent reaction to give l-Trp and a water molecule. The efficient utilization of IGP and l-Ser by tryptophan synthase to synthesize l-Trp utilizes a system of allosteric interactions that (1) function to switch the α-site on and off at different stages of the β-subunit catalytic cycle, and (2) prevent the escape of the channeled intermediate, indole, from the confines of the α- and β-catalytic sites and the interconnecting tunnel. This review discusses in detail the chemical origins of the allosteric interactions responsible both for switching the α-site on and off, and for triggering the conformational changes between open and closed states which prevent the escape of indole from the bienzyme complex.
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42
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Lai J, Niks D, Wang Y, Domratcheva T, Barends TRM, Schwarz F, Olsen RA, Elliott DW, Fatmi MQ, Chang CEA, Schlichting I, Dunn MF, Mueller LJ. X-ray and NMR Crystallography in an Enzyme Active Site: The Indoline Quinonoid Intermediate in Tryptophan Synthase. J Am Chem Soc 2010; 133:4-7. [DOI: 10.1021/ja106555c] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinfeng Lai
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Dimitri Niks
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Yachong Wang
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Tatiana Domratcheva
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas R. M. Barends
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Friedrich Schwarz
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Ryan A. Olsen
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Douglas W. Elliott
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - M. Qaiser Fatmi
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Chia-en A. Chang
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Michael F. Dunn
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Leonard J. Mueller
- Departments of Chemistry and Biochemistry, University of California, Riverside, California 92521, United States, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
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43
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Ehrmann A, Richter K, Busch F, Reimann J, Albers SV, Sterner R. Ligand-induced formation of a transient tryptophan synthase complex with αββ subunit stoichiometry. Biochemistry 2010; 49:10842-53. [PMID: 21090805 DOI: 10.1021/bi1016815] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prototypical tryptophan synthases form a stable heterotetrameric αββα complex in which the constituting TrpA and TrpB1 subunits activate each other in a bidirectional manner. The hyperthermophilic archaeon Sulfolobus solfataricus does not contain a TrpB1 protein but instead two members of the phylogenetically distinct family of TrpB2 proteins, which are encoded within (sTrpB2i) and outside (sTrpB2a) the tryptophan operon. It has previously been shown that sTrpB2a does not functionally or structurally interact with sTrpA, whereas sTrpB2i substantially activates sTrpA in a unidirectional manner. However, in the absence of catalysis, no physical complex between sTrpB2i and sTrpA could be detected. In order to elucidate the structural requirements for complex formation, we have analyzed the interaction between sTrpA (α-monomer) and sTrpB2i (ββ-dimer) by means of spectroscopy, analytical gel filtration, and analytical ultracentrifugation, as well as isothermal titration calorimetry. In the presence of the TrpA ligand glycerol 3-phosphate (GP) and the TrpB substrate l-serine, sTrpA and sTrpB2i formed a physical complex with a thermodynamic dissociation constant of about 1 μM, indicating that the affinity between the α- and ββ-subunits is weaker by at least 1 order of magnitude than the affinity between the corresponding subunits of prototypical tryptophan synthases. The observed stoichiometry of the complex was 1 subunit of sTrpA per 2 subunits of sTrpB2i, which corresponds to a αββ quaternary structure and testifies to a strong negative cooperativity for the binding of the α-monomers to the ββ-dimer. The analysis of the interaction between sTrpB2i and sTrpA in the presence of several substrate, transition state, and product analogues suggests that the αββ complex remains stable during the whole catalytic cycle and disintegrates into α- and ββ-subunits upon the release of the reaction product tryptophan. The formation of a transient tryptophan synthase complex, together with the observed low affinity of sTrpB2i for l-serine, couples the rate of tryptophan biosynthesis in S. solfataricus to the cytosolic availability of l-serine.
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Affiliation(s)
- Alexander Ehrmann
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Ai R, Qaiser Fatmi M, Chang CEA. T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles. J Comput Aided Mol Des 2010; 24:819-27. [PMID: 20689979 PMCID: PMC2940022 DOI: 10.1007/s10822-010-9376-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 07/26/2010] [Indexed: 11/08/2022]
Abstract
T-Analyst is a user-friendly computer program for analyzing trajectories from molecular modeling. Instead of using Cartesian coordinates for protein conformational analysis, T-Analyst is based on internal bond-angle-torsion coordinates in which internal torsion angle movements, such as side-chain rotations, can be easily detected. The program computes entropy and automatically detects and corrects angle periodicity to produce accurate rotameric states of dihedrals. It also clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. Correlated motions between selected dihedrals can also be observed from the correlation map. T-Analyst focuses on showing changes in protein flexibility between different states and selecting representative protein conformations for molecular docking studies. The program is provided with instructions and full source code in Perl.
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Affiliation(s)
- Rizi Ai
- Department of Chemistry, University of California Riverside, Riverside, CA 92521 USA
| | - M. Qaiser Fatmi
- Department of Chemistry, University of California Riverside, Riverside, CA 92521 USA
| | - Chia-en A. Chang
- Department of Chemistry, University of California Riverside, Riverside, CA 92521 USA
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45
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de la Fuente IM. Quantitative analysis of cellular metabolic dissipative, self-organized structures. Int J Mol Sci 2010; 11:3540-99. [PMID: 20957111 PMCID: PMC2956111 DOI: 10.3390/ijms11093540] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 09/11/2010] [Accepted: 09/12/2010] [Indexed: 11/16/2022] Open
Abstract
One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life.
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Affiliation(s)
- Ildefonso Martínez de la Fuente
- Institute of Parasitology and Biomedicine "López-Neyra" (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento s/n, 18100 Armilla (Granada), Spain; E-Mail: ; Tel.: +34-958-18-16-21
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46
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Wang W, Baker P, Seah SYK. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 2010; 49:3774-82. [PMID: 20364820 DOI: 10.1021/bi100251u] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HpaI and BphI are two pyruvate class II aldolases found in aromatic meta-cleavage degradation pathways that catalyze similar reactions but are not related in sequence. Steady-state kinetic analysis of the aldol addition reactions and product inhibition assays showed that HpaI exhibits a rapid equilibrium random order mechanism while BphI exhibits a compulsory order mechanism, with pyruvate binding first. Both aldolases are able to utilize aldehyde acceptors two to five carbons in length; however, HpaI showed broader specificity and had a preference for aldehydes containing longer linear alkyl chains or C2-OH substitutions. Both enzymes were able to bind 2-keto acids larger than pyruvate, but only HpaI was able to utilize both pyruvate and 2-ketobutanoate as carbonyl donors in the aldol addition reaction. HpaI lacks stereospecific control producing racemic mixtures of 4-hydroxy-2-oxopentanoate (HOPA) from pyruvate and acetaldehyde while BphI synthesizes only (4S)-HOPA. BphI is also able to utilize acetaldehyde produced by the reduction of acetyl-CoA catalyzed by the associated aldehyde dehydrogenase, BphJ. This aldehyde was directly channeled from the dehydrogenase to the aldolase active sites, with an efficiency of 84%. Furthermore, the BphJ reductive deacylation reaction increased 4-fold when BphI was catalyzing the aldol addition reaction. Therefore, the BphI-BphJ enzyme complex exhibits unique bidirectionality in substrate channeling and allosteric activation.
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Affiliation(s)
- Weijun Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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47
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Phillips RS, Miles EW, McPhie P, Marchal S, Lange R, Holtermann G, Goody RS. Effects of hydrostatic pressure on the conformational equilibrium of tryptophan synthase from Salmonella typhimurium. Ann N Y Acad Sci 2010; 1189:95-103. [PMID: 20233374 DOI: 10.1111/j.1749-6632.2009.05201.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A wide range of parameters influence allosteric communications between the alpha- and beta-subunits of the Trp synthase alpha(2)beta(2) multienzyme complex with L-Ser, including monovalent cations, pH, temperature, ligands, organic solvents, and hydrostatic pressure. The conformational change from closed to open can be monitored either by absorbance at 423 nm or fluorescence at 495 nm from the pyridoxal-5'-phosphate-L-Ser complex. Pressure perturbation was used to quantify the effects of monovalent cations, ligands, and mutations on the conformational equilibrium of Trp synthase. P-jump kinetics in the presence of Na(+), NH(4) (+), and Na(+) together with benzimidazole were also examined. The plots of lnk versus P are nonlinear and require a compressibility (beta(double dagger) (o)) term to obtain a good fit. beta(double dagger) (o) is positive for the Na(+) enzyme but negative for NH(4) (+) and Na(+) with benzimidazole. These results suggest that there is a large contribution of solvation to the kinetics of the conformational change of Trp synthase. The relaxation kinetics are also different if the P-jumps are made by increasing or decreasing pressure, suggesting that the enzyme conformations are ensembles of microstates.
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48
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Nishio K, Ogasahara K, Morimoto Y, Tsukihara T, Lee SJ, Yutani K. Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding. FEBS J 2010; 277:2157-70. [PMID: 20370823 DOI: 10.1111/j.1742-4658.2010.07631.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To understand the basis for the lower activity of the tryptophan synthase beta(2) subunit in comparison to the alpha(2)beta(2) complex, we determined the crystal structures of apo-beta(2) and holo-beta(2) from Escherichia coli at 3.0 and 2.9 A resolutions, respectively. To our knowledge, this is the first report of both beta(2) subunit structures with and without pyridoxal-5'-phosphate. The apo-type molecule retained a dimeric form in solution, as in the case of the holo-beta(2) subunit. The subunit structures of both the apo-beta(2) and the holo-beta(2) forms consisted of two domains, namely the N domain and the C domain. Although there were significant structural differences between the apo- and holo-structures, they could be easily superimposed with a 22 degrees rigid body rotation of the C domain. The pyridoxal-5'-phosphate-bound holo-form had multiple interactions between the two domains and a long loop (residues 260-310), which were missing in the apo-form. Comparison of the structures of holo-Ecbeta(2) and Stbeta(2) in the alpha(2)beta(2) complex from Salmonella typhimurium (Stalpha(2)beta(2)) identified the cause of the lower enzymatic activity of holo-Ecbeta(2) in comparison with Stalpha(2)beta(2). The substrate (indole) gate residues, Tyr279 and Phe280, block entry of the substrate into the beta(2) subunit, although the indole can directly access the active site as a result of a wider cleft between the N and C domains in the holo-Ecbeta(2) subunit. In addition, the structure around betaAsp305 of the holo-Ecbeta(2) subunit was similar to the open state of Stalpha(2)beta(2) with low activity, resulting in lower activity of holo-Ecbeta(2).
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Affiliation(s)
- Kazuya Nishio
- Institute for Protein Research, Osaka University, Japan
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49
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Dierkers AT, Niks D, Schlichting I, Dunn MF. Tryptophan synthase: structure and function of the monovalent cation site. Biochemistry 2009; 48:10997-1010. [PMID: 19848417 DOI: 10.1021/bi9008374] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The monovalent cation (MVC) site of the tryptophan synthase from Salmonella typhimurium plays essential roles in catalysis and in the regulation of substrate channeling. In vitro, MVCs affect the equilibrium distribution of intermediates formed in the reaction of l-Ser with the alpha(2)beta(2) complex; the MVC-free, Cs(+)-bound, and NH(4)(+)-bound enzymes stabilize the alpha-aminoacrylate species, E(A-A), while Na(+) binding stabilizes the l-Ser external aldimine species, E(Aex(1)). Two probes of beta-site reactivity and conformation were used herein, the reactive indole analogue, indoline, and the l-Trp analogue, l-His. MVC-bound E(A-A) reacts rapidly with indoline to give the indoline quinonoid species, E(Q)(indoline), which slowly converts to dihydroiso-l-tryptophan. MVC-free E(A-A) gives very little E(Q)(indoline), and turnover is strongly impaired; the fraction of E(Q)(indoline) formed is <3.5% of that given by the Na(+)-bound form. The reaction of l-Ser with the MVC-free internal aldimine species, E(Ain), initially gives small amounts of an active E(A-A) which converts to an inactive species on a slower, conformational, time scale. This inactivation is abolished by the binding of MVCs. The inactive E(A-A) appears to have a closed beta-subunit conformation with an altered substrate binding site that is different from the known conformations of tryptophan synthase. Reaction of l-His with E(Ain) gives an equilibrating mixture of external aldimine and quinonoid species, E(Aex)(his) and E(Q)(his). The MVC-free and Na(+) forms of the enzyme gave trace amounts of E(Q)(his) ( approximately 1% of the beta-sites). The Cs(+) and NH(4)(+) forms gave approximately 17 and approximately 14%, respectively. The reactivity of MVC-free E(Ain) was restored by the binding of an alpha-site ligand. These studies show MVCs and alpha-site ligands act synergistically to modulate the switching of the beta-subunit from the open to the closed conformation, and this switching is crucial to the regulation of beta-site catalytic activity. Comparison of the structures of Na(+) and Cs(+) forms of the enzyme shows Cs(+) favors complexes with open indole binding sites poised for the conformational transition to the closed state, whereas the Na(+) form does not. The beta-subunits of Cs(+) complexes exhibit preformed indole subsites; the indole subsites of the open Na(+) complexes are collapsed, distorted, and too small to accommodate indole.
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Affiliation(s)
- Adam T Dierkers
- Department of Biochemistry, University of California, Riverside, California 92521, USA
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50
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Raboni S, Bettati S, Mozzarelli A. Tryptophan synthase: a mine for enzymologists. Cell Mol Life Sci 2009; 66:2391-403. [PMID: 19387555 PMCID: PMC11115766 DOI: 10.1007/s00018-009-0028-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/30/2009] [Accepted: 03/31/2009] [Indexed: 01/12/2023]
Abstract
Tryptophan synthase is a pyridoxal 5'-phosphate-dependent alpha(2)beta(2) complex catalyzing the last two steps of tryptophan biosynthesis in bacteria, plants and fungi. Structural, dynamic and functional studies, carried out over more than 40 years, have unveiled that: (1) alpha- and beta-active sites are separated by about 20 A and communicate via the selective stabilization of distinct conformational states, triggered by the chemical nature of individual catalytic intermediates and by allosteric ligands; (2) indole, formed at alpha-active site, is intramolecularly channeled to the beta-active site; and (3) naturally occurring as well as genetically generated mutants have allowed to pinpoint functional and regulatory roles for several individual amino acids. These key features have made tryptophan synthase a text-book case for the understanding of the interplay between chemistry and conformational energy landscapes.
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Affiliation(s)
- Samanta Raboni
- Department of Biochemistry and Molecular Biology, University of Parma, Viale GP Usberti 23/A, 43100 Parma, Italy
- Present Address: CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | - Stefano Bettati
- Department of Biochemistry and Molecular Biology, University of Parma, Viale GP Usberti 23/A, 43100 Parma, Italy
- Italian National Institute of Biostructures and Biosystems, Parma, Italy
| | - Andrea Mozzarelli
- Department of Biochemistry and Molecular Biology, University of Parma, Viale GP Usberti 23/A, 43100 Parma, Italy
- Italian National Institute of Biostructures and Biosystems, Parma, Italy
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