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Light SH, Krishna SN, Minasov G, Anderson WF. An Unusual Cation-Binding Site and Distinct Domain-Domain Interactions Distinguish Class II Enolpyruvylshikimate-3-phosphate Synthases. Biochemistry 2016; 55:1239-45. [PMID: 26813771 DOI: 10.1021/acs.biochem.5b00553] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a critical step in the biosynthesis of a number of aromatic metabolites. An essential prokaryotic enzyme and the molecular target of the herbicide glyphosate, EPSPSs are the subject of both pharmaceutical and commercial interest. Two EPSPS classes that exhibit low sequence homology, differing substrate/glyphosate affinities, and distinct cation activation properties have previously been described. Here, we report structural studies of the monovalent cation-binding class II Coxiella burnetii EPSPS (cbEPSPS). Three cbEPSPS crystal structures reveal that the enzyme undergoes substantial conformational changes that alter the electrostatic potential of the active site. A complex with shikimate-3-phosphate, inorganic phosphate (Pi), and K(+) reveals that ligand induced domain closure produces an unusual cation-binding site bordered on three sides by the N-terminal domain, C-terminal domain, and the product Pi. A crystal structure of the class I Vibrio cholerae EPSPS (vcEPSPS) clarifies the basis of differential class I and class II cation responsiveness, showing that in class I EPSPSs a lysine side chain occupies the would-be cation-binding site. Finally, we identify distinct patterns of sequence conservation at the domain-domain interface and propose that the two EPSPS classes have evolved to differently optimize domain opening-closing dynamics.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Sankar N Krishna
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University , 303 East Chicago Avenue, Chicago, Illinois 60611, United States
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Vega S, Abian O, Velazquez-Campoy A. A unified framework based on the binding polynomial for characterizing biological systems by isothermal titration calorimetry. Methods 2014; 76:99-115. [PMID: 25305413 DOI: 10.1016/j.ymeth.2014.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 01/10/2023] Open
Abstract
Isothermal titration calorimetry (ITC) has become the gold-standard technique for studying binding processes due to its high precision and sensitivity, as well as its capability for the simultaneous determination of the association equilibrium constant, the binding enthalpy and the binding stoichiometry. The current widespread use of ITC for biological systems has been facilitated by technical advances and the availability of commercial calorimeters. However, the complexity of data analysis for non-standard models is one of the most significant drawbacks in ITC. Many models for studying macromolecular interactions can be found in the literature, but it looks like each biological system requires specific modeling and data analysis approaches. The aim of this article is to solve this lack of unity and provide a unified methodological framework for studying binding interactions by ITC that can be applied to any experimental system. The apparent complexity of this methodology, based on the binding polynomial, is overcome by its easy generalization to complex systems.
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Affiliation(s)
- Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; IIS Aragón, Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain.
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain; Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain; Fundacion ARAID, Government of Aragon, Spain.
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Martinez-Julvez M, Abian O, Vega S, Medina M, Velazquez-Campoy A. Studying the allosteric energy cycle by isothermal titration calorimetry. Methods Mol Biol 2012; 796:53-70. [PMID: 22052485 DOI: 10.1007/978-1-61779-334-9_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Isothermal titration calorimetry (ITC) is a powerful biophysical technique which allows a complete thermodynamic characterization of protein interactions with other molecules. The possibility of dissecting the Gibbs energy of interaction into its enthalpic and entropic contributions, as well as the detailed additional information experimentally accessible on the intermolecular interactions (stoichiometry, cooperativity, heat capacity changes, and coupled equilibria), make ITC a suitable technique for studying allosteric interactions in proteins. Two experimental methodologies for the characterization of allosteric heterotropic ligand interactions by ITC are described in this chapter, illustrated with two proteins with markedly different structural and functional features: a photosynthetic electron transfer protein and a drug target viral protease.
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Affiliation(s)
- Marta Martinez-Julvez
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain.
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Funke T, Yang Y, Han H, Healy-Fried M, Olesen S, Becker A, Schönbrunn E. Structural basis of glyphosate resistance resulting from the double mutation Thr97 -> Ile and Pro101 -> Ser in 5-enolpyruvylshikimate-3-phosphate synthase from Escherichia coli. J Biol Chem 2009; 284:9854-60. [PMID: 19211556 PMCID: PMC2665107 DOI: 10.1074/jbc.m809771200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 02/11/2009] [Indexed: 11/06/2022] Open
Abstract
The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the target of the broad spectrum herbicide glyphosate. The genetic engineering of EPSPS led to the introduction of glyphosate-resistant crops worldwide. The genetically engineered corn lines NK603 and GA21 carry distinct EPSPS enzymes. CP4 EPSPS, expressed in NK603 corn and transgenic soybean, cotton, and canola, belongs to class II EPSPS, glyphosate-insensitive variants of this enzyme isolated from certain Gram-positive bacteria. GA21 corn, on the other hand, was created by point mutations of class I EPSPS, such as the enzymes from Zea mays or Escherichia coli, which are sensitive to low glyphosate concentrations. The structural basis of the glyphosate resistance resulting from these point mutations has remained obscure. We studied the kinetic and structural effects of the T97I/P101S double mutation, the molecular basis for GA21 corn, using EPSPS from E. coli. The T97I/P101S enzyme is essentially insensitive to glyphosate (K(i) = 2.4 mm) but maintains high affinity for the substrate phosphoenolpyruvate (PEP) (K(m) = 0.1 mm). The crystal structure at 1.7-A resolution revealed that the dual mutation causes a shift of residue Gly(96) toward the glyphosate binding site, impairing efficient binding of glyphosate, while the side chain of Ile(97) points away from the substrate binding site, facilitating PEP utilization. The single site T97I mutation renders the enzyme sensitive to glyphosate and causes a substantial decrease in the affinity for PEP. Thus, only the concomitant mutations of Thr(97) and Pro(101) induce the conformational changes necessary to produce catalytically efficient, glyphosate-resistant class I EPSPS.
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Affiliation(s)
- Todd Funke
- Drug Discovery Department, Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, USA
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Funke T, Han H, Healy-Fried ML, Fischer M, Schönbrunn E. Molecular basis for the herbicide resistance of Roundup Ready crops. Proc Natl Acad Sci U S A 2006; 103:13010-5. [PMID: 16916934 PMCID: PMC1559744 DOI: 10.1073/pnas.0603638103] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Indexed: 11/18/2022] Open
Abstract
The engineering of transgenic crops resistant to the broad-spectrum herbicide glyphosate has greatly improved agricultural efficiency worldwide. Glyphosate-based herbicides, such as Roundup, target the shikimate pathway enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the functionality of which is absolutely required for the survival of plants. Roundup Ready plants carry the gene coding for a glyphosate-insensitive form of this enzyme, obtained from Agrobacterium sp. strain CP4. Once incorporated into the plant genome, the gene product, CP4 EPSP synthase, confers crop resistance to glyphosate. Although widely used, the molecular basis for this glyphosate-resistance has remained obscure. We generated a synthetic gene coding for CP4 EPSP synthase and characterized the enzyme using kinetics and crystallography. The CP4 enzyme has unexpected kinetic and structural properties that render it unique among the known EPSP synthases. Glyphosate binds to the CP4 EPSP synthase in a condensed, noninhibitory conformation. Glyphosate sensitivity can be restored through a single-site mutation in the active site (Ala-100-Gly), allowing glyphosate to bind in its extended, inhibitory conformation.
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Affiliation(s)
- Todd Funke
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045; and
| | - Huijong Han
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045; and
| | | | - Markus Fischer
- Department of Organic Chemistry and Biochemistry, Technical University Munich, D-85747 Garching, Germany
| | - Ernst Schönbrunn
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045; and
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Borges JC, Pereira JH, Vasconcelos IB, dos Santos GC, Olivieri JR, Ramos CHI, Palma MS, Basso LA, Santos DS, de Azevedo WF. Phosphate closes the solution structure of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Mycobacterium tuberculosis. Arch Biochem Biophys 2006; 452:156-64. [PMID: 16876105 DOI: 10.1016/j.abb.2006.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 04/24/2006] [Accepted: 05/12/2006] [Indexed: 11/30/2022]
Abstract
The 5-enolpyruvylshikimate-3-phosphate synthase catalyses the sixth step of the shikimate pathway that is responsible for synthesizing aromatic compounds and is absent in mammals, which makes it a potential target for drugs development against microbial diseases. Here, we report the phosphate binding effects at the structure of the 5-enolpyruvylshikimate-3-phosphate synthase from Mycobacterium tuberculosis. This enzyme is formed by two similar domains that close on each other induced by ligand binding, showing the occurrence of a large conformation change. We have monitored the phosphate binding effects using analytical ultracentrifugation, small angle X-ray scattering and, circular dichroism techniques. The low resolution results showed that the enzyme in the presence of phosphate clearly presented a more compact structure. Thermal-induced unfolding experiments followed by circular dichroism suggested that phosphate rigidified the enzyme. Summarizing, these data suggested that the phosphate itself is able to induce conformational change resulting in the closure movement in the M. tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase.
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Affiliation(s)
- Júlio C Borges
- Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000, Brazil
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Velazquez-Campoy A, Goñi G, Peregrina JR, Medina M. Exact analysis of heterotropic interactions in proteins: Characterization of cooperative ligand binding by isothermal titration calorimetry. Biophys J 2006; 91:1887-904. [PMID: 16766617 PMCID: PMC1544317 DOI: 10.1529/biophysj.106.086561] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intramolecular interaction networks in proteins are responsible for heterotropic ligand binding cooperativity, a biologically important, widespread phenomenon in nature (e.g., signaling transduction cascades, enzymatic cofactors, enzymatic allosteric activators or inhibitors, gene transcription, or repression). The cooperative binding of two (or more) different ligands to a macromolecule is the underlying principle. To date, heterotropic effects have been studied mainly kinetically in enzymatic systems. Until now, approximate approaches have been employed for studying equilibrium heterotropic ligand binding effects, except in two special cases in which an exact analysis was developed: independent binding (no cooperativity) and competitive binding (maximal negative cooperativity). The exact analysis and methodology for characterizing ligand binding cooperativity interactions in the general case (any degree of cooperativity) using isothermal titration calorimetry are presented in this work. Intramolecular interaction pathways within the allosteric macromolecule can be identified and characterized using this methodology. As an example, the thermodynamic characterization of the binding interaction between ferredoxin-NADP+ reductase and its three substrates, NADP+, ferredoxin, and flavodoxin, as well as the characterization of their binding cooperativity interaction, is presented.
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Affiliation(s)
- Adrian Velazquez-Campoy
- Institute of Biocomputation and Complex Systems Physics (BIFI), Universidad de Zaragoza, Zaragoza, Spain.
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Priestman MA, Funke T, Singh IM, Crupper SS, Schönbrunn E. 5-Enolpyruvylshikimate-3-phosphate synthase from Staphylococcus aureus is insensitive to glyphosate. FEBS Lett 2005; 579:728-32. [PMID: 15670836 DOI: 10.1016/j.febslet.2004.12.057] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Revised: 12/17/2004] [Accepted: 12/17/2004] [Indexed: 11/18/2022]
Abstract
The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the penultimate step of the shikimate pathway, and is the target of the broad-spectrum herbicide glyphosate. Kinetic analysis of the cloned EPSPS from Staphylococcus aureus revealed that this enzyme exerts a high tolerance to glyphosate, while maintaining a high affinity for its substrate phosphoenolpyruvate. Enzymatic activity is markedly influenced by monovalent cations such as potassium or ammonium, which is due to an increase in catalytic turnover. However, insensitivity to glyphosate appears to be independent from the presence of cations. Therefore, we propose that the Staphylococcus aureus EPSPS should be classified as a class II EPSPS. This research illustrates a critical mechanism of glyphosate resistance naturally occurring in certain pathogenic bacteria.
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Affiliation(s)
- Melanie A Priestman
- Department of Medicinal Chemistry, University of Kansas, 4040a Malott Hall, Lawrence, KS 66049, USA
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Abstract
Because shikimic acid is the key intermediate in the shikimate pathway in plants and microorganisms, shikimic acid and its derivatives have been described as herbicides and anti-microbial agents. Triacetylshikimic acid (TSA) is an acetylate derivative of shikimic acid. The possible anti-platelet activity and anti-thrombotic efficacy of TSA were evaluated and its effect on arachidonic acid (AA) metabolism and second messengers including cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) was evaluated. After oral pretreatment with TSA, adenosine diphosphate (ADP)-, collagen-, and AA-induced rat platelet aggregation was inhibited ex vivo in a dose-dependent manner. In an arteriovenous-shunt thrombosis model, oral administration of TSA resulted in a dose-dependent inhibition of thrombus growth. TSA markedly increased the cAMP level and showed no effect on the cGMP level in rat platelets. Also, no significant changes in ADP-induced thromboxane B2 formation in rat platelets or 6-keto-prostaglandin F 1alpha production from the abdominal aorta were observed after oral administration of low and medium doses of TSA (12.5 and 50 mg/kg). Additionally, prothrombin time, activated partial thromboplastin time, and thrombin time were unchanged at effective anti-platelet doses of TSA. These results demonstrate that TSA exerts oral anti-platelet and anti-thrombotic efficacy without perturbation of systemic hemostasis in rats, which was partially concerned with the elevation of cAMP in platelets.
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Affiliation(s)
- Fengyang Huang
- Pharmacobiology Department, CINVESTAV-I.P.N., Mexico City, Mexico.
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