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Diógenes Santiago Santos - One of the best experts on this subject based on the ideXlab platform.
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The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis Shikimate dehydrogenase
BMC Research Notes, 2009Co-Authors: Valnes Da Silva Rodrigues, Diógenes Santiago Santos, Ardala Breda, Luiz Augusto BassoAbstract:Background The Shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in Mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. M. tuberculosis aroE-encoded Shikimate dehydrogenase catalyzes the forth reaction in the Shikimate pathway. Structural and functional studies indicate that Lysine69 may be involved in catalysis and/or substrate binding in M. tuberculosis Shikimate dehydrogenase. Investigation of the kinetic properties of mutant enzymes can bring important insights about the role of amino acid residues for M. tuberculosis Shikimate dehydrogenase.
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Shikimate kinase: a potential target for development of novel antitubercular agents.
Current Drug Targets, 2007Co-Authors: Jose Henrique Pereira, Rafael Andrade Caceres, Walter Filgueira De Azevedo, Jaim S. Oliveira, Igor B. Vasconcelos, Luis Augusto Basso, Diógenes Santiago SantosAbstract:Tuberculosis (TB) remains the leading cause of mortality due to a bacterial pathogen, Mycobacterium tuberculosis. However, no new classes of drugs for TB have been developed in the past 30 years. Therefore there is an urgent need to develop faster acting and effective new antitubercular agents, preferably belonging to new structural classes, to better combat TB, including MDR-TB, to shorten the duration of current treatment to improve patient compliance, and to provide effective treatment of latent tuberculosis infection. The enzymes in the Shikimate pathway are potential targets for development of a new generation of antitubercular drugs. The Shikimate pathway has been shown by disruption of aroK gene to be essential for the Mycobacterium tuberculosis. The Shikimate kinase (SK) catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid (Shikimate) using ATP as a co-substrate. SK belongs to family of nucleoside monophosphate (NMP) kinases. The enzyme is an alpha/beta protein consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. The Shikimate kinases are composed of three domains: Core domain, Lid domain and Shikimate-binding domain. The Lid and Shikimate-binding domains are responsible for large conformational changes during catalysis. More recently, the precise interactions between SK and substrate have been elucidated, showing the binding of Shikimate with three charged residues conserved among the SK sequences. The elucidation of interactions between MtSK and their substrates is crucial for the development of a new generation of drugs against tuberculosis through rational drug design.
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Effects of the magnesium and chloride ions and Shikimate on the structure of Shikimate kinase from Mycobacterium tuberculosis.
Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2006Co-Authors: Marcio Vinicius Bertacine Dias, Jaim S. Oliveira, Luiz Augusto Basso, Diógenes Santiago Santos, Lívia Maria Faim, Igor B. Vasconcelos, Walter Filgueira De AzevedoAbstract:Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the Shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts Shikimate to Shikimate-3-phosphate. In this work, the conformational changes that occur on binding of Shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and Shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the Shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.
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Structure of Shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
Acta Crystallographica Section D Biological Crystallography, 2004Co-Authors: Jose Henrique Pereira, Jaim S. Oliveira, Fernanda Canduri, Marcio Vinicius Bertacine Dias, Mario Sergio Palma, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira De AzevedoAbstract:Tuberculosis made a resurgence in the mid-1980s and now kills approximately 3 million people a year. The re-emergence of tuberculosis as a public health threat, the high susceptibility of HIV-infected persons and the proliferation of multi-drug-resistant strains have created a need to develop new drugs. Shikimate kinase and other enzymes in the Shikimate pathway are attractive targets for development of non-toxic antimicrobial agents, herbicides and anti-parasitic drugs, because the pathway is essential in these species whereas it is absent from mammals. The crystal structure of Shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid (Shikimate) has been determined at 2.3 A resolution, clearly revealing the amino-acid residues involved in Shikimate binding. This is the first three-dimensional structure of Shikimate kinase complexed with Shikimate. In MtSK, the Glu61 residue that is strictly conserved in Shikimate kinases forms a hydrogen bond and salt bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for Shikimate binding. The carboxyl group of Shikimate interacts with Arg58, Gly81 and Arg136 and the hydroxyl groups interact with Asp34 and Gly80. The crystal structure of MtSK-MgADP-Shikimate will provide crucial information for the elucidation of the mechanism of the Shikimate kinase-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.
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Interaction of shikimic acid with Shikimate kinase (Retracted Article. See vol 334, pg 967, 2005)
Biochemical and Biophysical Research Communications, 2004Co-Authors: Jadergudson Pereira, Walter Filgueira De Azevedo, Jaim S. Oliveira, Fernanda Canduri, Mario Sergio Palma, Luiz Augusto Basso, Mvb Dias, Diógenes Santiago SantosAbstract:The crystal structure of Shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid (Shikimate) has been determined at 2.3A resolution, clearly revealing the amino acid residues involved in Shikimate binding. In MtSK, the Glu61 strictly conserved in SK forms a hydrogen bond and salt-bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for Shikimate binding. The carboxyl group of Shikimate interacts with Arg58, Gly81, and Arg136, and hydroxyl groups with Asp34 and Gly80. The crystal structure of MtSK-MgADP-Shikimate will provide crucial information for elucidation of the mechanism of SK-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.
Walter Filgueira De Azevedo - One of the best experts on this subject based on the ideXlab platform.
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Molecular modeling and dynamics studies of Shikimate Kinase from Bacillus anthracis
Bioorganic & Medicinal Chemistry, 2008Co-Authors: Ivani Pauli, Rafael Andrade Caceres, Walter Filgueira De AzevedoAbstract:Bacillus anthracis has been used as weapon in bioterrorist activities, with high mortality, despite anti-microbial treatment, which strongly indicates a need of new drugs to treat anthrax. Shikimate Pathway is a seven-step biosynthetic route which generates chorismic acid. The Shikimate pathway is essential for many pathological organisms, whereas it is absent in mammals. Therefore, these enzymes are potential targets for the development of non-toxic anti-microbial agents and herbicides and have been submitted to intensive structural studies. Shikimate Kinase is the fifth enzyme of Shikimate pathway and catalyzes the specific phosphorylation of the 3-hydroxyl group of Shikimate using ATP as a co-substrate, resulting in Shikimate-3-phosphate and ADP. The present work describes for the first time a structural model for the Shikimate Kinase from B. anthracis using molecular modeling approach and molecular dynamics simulations. This study was able to identify the main residues of the ATP-binding and the Shikimate pockets responsible for ligand affinities. Analysis of the molecular dynamics simulations indicates the structural features responsible for the stability of the structure. This study may help in the identification of new inhibitors for this enzyme.
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Shikimate kinase: a potential target for development of novel antitubercular agents.
Current Drug Targets, 2007Co-Authors: Jose Henrique Pereira, Rafael Andrade Caceres, Walter Filgueira De Azevedo, Jaim S. Oliveira, Igor B. Vasconcelos, Luis Augusto Basso, Diógenes Santiago SantosAbstract:Tuberculosis (TB) remains the leading cause of mortality due to a bacterial pathogen, Mycobacterium tuberculosis. However, no new classes of drugs for TB have been developed in the past 30 years. Therefore there is an urgent need to develop faster acting and effective new antitubercular agents, preferably belonging to new structural classes, to better combat TB, including MDR-TB, to shorten the duration of current treatment to improve patient compliance, and to provide effective treatment of latent tuberculosis infection. The enzymes in the Shikimate pathway are potential targets for development of a new generation of antitubercular drugs. The Shikimate pathway has been shown by disruption of aroK gene to be essential for the Mycobacterium tuberculosis. The Shikimate kinase (SK) catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid (Shikimate) using ATP as a co-substrate. SK belongs to family of nucleoside monophosphate (NMP) kinases. The enzyme is an alpha/beta protein consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. The Shikimate kinases are composed of three domains: Core domain, Lid domain and Shikimate-binding domain. The Lid and Shikimate-binding domains are responsible for large conformational changes during catalysis. More recently, the precise interactions between SK and substrate have been elucidated, showing the binding of Shikimate with three charged residues conserved among the SK sequences. The elucidation of interactions between MtSK and their substrates is crucial for the development of a new generation of drugs against tuberculosis through rational drug design.
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Effects of the magnesium and chloride ions and Shikimate on the structure of Shikimate kinase from Mycobacterium tuberculosis.
Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2006Co-Authors: Marcio Vinicius Bertacine Dias, Jaim S. Oliveira, Luiz Augusto Basso, Diógenes Santiago Santos, Lívia Maria Faim, Igor B. Vasconcelos, Walter Filgueira De AzevedoAbstract:Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the Shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts Shikimate to Shikimate-3-phosphate. In this work, the conformational changes that occur on binding of Shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and Shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the Shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.
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Structure of Shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
Acta Crystallographica Section D Biological Crystallography, 2004Co-Authors: Jose Henrique Pereira, Jaim S. Oliveira, Fernanda Canduri, Marcio Vinicius Bertacine Dias, Mario Sergio Palma, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira De AzevedoAbstract:Tuberculosis made a resurgence in the mid-1980s and now kills approximately 3 million people a year. The re-emergence of tuberculosis as a public health threat, the high susceptibility of HIV-infected persons and the proliferation of multi-drug-resistant strains have created a need to develop new drugs. Shikimate kinase and other enzymes in the Shikimate pathway are attractive targets for development of non-toxic antimicrobial agents, herbicides and anti-parasitic drugs, because the pathway is essential in these species whereas it is absent from mammals. The crystal structure of Shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid (Shikimate) has been determined at 2.3 A resolution, clearly revealing the amino-acid residues involved in Shikimate binding. This is the first three-dimensional structure of Shikimate kinase complexed with Shikimate. In MtSK, the Glu61 residue that is strictly conserved in Shikimate kinases forms a hydrogen bond and salt bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for Shikimate binding. The carboxyl group of Shikimate interacts with Arg58, Gly81 and Arg136 and the hydroxyl groups interact with Asp34 and Gly80. The crystal structure of MtSK-MgADP-Shikimate will provide crucial information for the elucidation of the mechanism of the Shikimate kinase-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.
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Interaction of shikimic acid with Shikimate kinase (Retracted Article. See vol 334, pg 967, 2005)
Biochemical and Biophysical Research Communications, 2004Co-Authors: Jadergudson Pereira, Walter Filgueira De Azevedo, Jaim S. Oliveira, Fernanda Canduri, Mario Sergio Palma, Luiz Augusto Basso, Mvb Dias, Diógenes Santiago SantosAbstract:The crystal structure of Shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid (Shikimate) has been determined at 2.3A resolution, clearly revealing the amino acid residues involved in Shikimate binding. In MtSK, the Glu61 strictly conserved in SK forms a hydrogen bond and salt-bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for Shikimate binding. The carboxyl group of Shikimate interacts with Arg58, Gly81, and Arg136, and hydroxyl groups with Asp34 and Gly80. The crystal structure of MtSK-MgADP-Shikimate will provide crucial information for elucidation of the mechanism of SK-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.
Dinesh Christendat - One of the best experts on this subject based on the ideXlab platform.
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Shikimate induced transcriptional activation of protocatechuate biosynthesis genes by quir a lysr type transcriptional regulator in listeria monocytogenes
Journal of Molecular Biology, 2018Co-Authors: Stephanie M Prezioso, Kevin Xue, Nelly Leung, Scott D Grayowen, Dinesh ChristendatAbstract:Abstract Listeria monocytogenes is a common foodborne bacterial pathogen that contaminates plant and animal consumable products. The persistent nature of L. monocytogenes is associated with millions of dollars in food recalls annually. Here, we describe the role of Shikimate in directly modulating the expression of genes encoding enzymes for the conversion of quinate and Shikimate metabolites to protocatechuate. In L. monocytogenes, these genes are found within two operons, named qui1 and qui2. In addition, a gene named quiR, encoding a LysR-Type Transcriptional Regulator (QuiR), is located immediately upstream of the qui1 operon. Transcriptional lacZ-promoter fusion experiments show that QuiR induces gene expression of both qui1 and qui2 operons in the presence of Shikimate. Furthermore, co-crystallization of the QuiR effector binding domain in complex with Shikimate provides insights into the mechanism of activation of this regulator. Together these data show that upon Shikimate accumulation, QuiR activates the transcription of genes encoding enzymes involved in Shikimate and quinate utilization for the production of protocatechuate. Furthermore, the accumulation of protocatechuate leads to the inhibition of Listeria growth. Since protocatechuate is not known to be utilized by Listeria, its role is distinct from those established in other bacteria.
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Structural and Mechanistic Analysis of a Novel Class of Shikimate Dehydrogenases: Evidence for a Conserved Catalytic Mechanism in the Shikimate Dehydrogenase Family
Biochemistry, 2011Co-Authors: James Peek, John G. Lee, Guillermo Senisterra, Dinesh ChristendatAbstract:Shikimate dehydrogenase (SDH) catalyzes the reversible NADPH-dependent reduction of 3-dehydroShikimate to Shikimate. This reaction represents the fourth step of the Shikimate pathway, the essential route for the biosynthesis of the aromatic amino acids in plants, fungi, bacteria, and apicomplexan parasites. The absence of this pathway in animals makes it an attractive target for herbicides and antimicrobials. At least four functionally distinct enzyme classes, AroE, YdiB, SDH-like (SdhL), and AroE-like1 (Ael1), utilize Shikimate as a substrate in vitro and form the SDH family. Crystal structures have been determined for AroE, YdiB, and SdhL. In this study, we have determined the first representative crystal structure of an Ael1 enzyme. We demonstrate that Ael1 shares a similar overall structure with the other members of the SDH family. This high level of structural conservation extends to the active sites of the enzymes. In particular, an ionizable active site lysine and aspartate are present in all SDH h...
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The DHQ-dehydroShikimate-SDH-Shikimate-NADP(H) Complex: Insights into Metabolite Transfer in the Shikimate Pathway†,‡
Crystal Growth & Design, 2007Co-Authors: Sasha A. Singh, Dinesh ChristendatAbstract:Plants encode the bifunctional dehydroquinase-Shikimate dehydrogenase (DHQ-SDH), which catalyzes the third and fourth steps of the Shikimate pathway. We report the Arabidopsis thaliana DHQ-SDH structure in complex with all of its natural substrates. The DHQ-SDH enzyme was first cocrystallized with Shikimate. NADP+ was subsequently added to the crystals yielding the SDH ternary complex. The Pro-R hydrogen of the nicotinamide C4 is 3.35 A from the C3 of Shikimate, the site of hydride transfer. The catalytic Lys 385 and Asp 423 residues are proximal to the C3-hydroxyl of Shikimate, which is deprotonated in the oxidation reaction. The SDH-Shikimate-NADP(H) complex represents the active complex as the oxidation of Shikimate was evidenced by the generation of the product (dehydroShikimate) found in the DHQ site. DHQ-SDH adopts a concave architecture that places the active sites in a face-to-face arrangement. This proximal organization serves to increase the local effective concentration of dehydroShikimate, and...
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Structure of Arabidopsis dehydroquinate dehydratase-Shikimate dehydrogenase and implications for metabolic channeling in the Shikimate pathway.
Biochemistry, 2006Co-Authors: Sasha A. Singh, Dinesh ChristendatAbstract:The bifunctional enzyme dehydroquinate dehydratase-Shikimate dehydrogenase (DHQ-SDH) catalyzes the dehydration of dehydroquinate to dehydroShikimate and the reduction of dehydroShikimate to Shikimate in the Shikimate pathway. We report the first crystal structure of Arabidopsis DHQ-SDH with Shikimate bound at the SDH site and tartrate at the DHQ site. The interactions observed in the DHQ-tartrate complex reveal a conserved mode for substrate binding between the plant and microbial DHQ dehydratase family of enzymes. The SDH-Shikimate complex provides the first direct evidence of the role of active site residues in the catalytic mechanism. Site-directed mutagenesis and mechanistic analysis revealed that Asp 423 and Lys 385 are key catalytic groups and Ser 336 is a key binding group. The arrangement of the two functional domains reveals that the control of metabolic flux through the Shikimate pathway is achieved by increasing the effective concentration of dehydroShikimate through the proximity of the two sites.
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Crystal Structure of a Novel Shikimate Dehydrogenase from Haemophilus influenzae
Journal of Biological Chemistry, 2005Co-Authors: Sasha A. Singh, Sergey Korolev, Olga Koroleva, T. I. Zarembinski, Frank R. Collart, Andrzej Joachimiak, Dinesh ChristendatAbstract:To date two classes of Shikimate dehydrogenases have been identified and characterized, YdiB and AroE. YdiB is a bifunctional enzyme that catalyzes the reversible reductions of dehydroquinate to quinate and dehydroShikimate to Shikimate in the presence of either NADH or NADPH. In contrast, AroE catalyzes the reversible reduction of dehydroShikimate to Shikimate in the presence of NADPH. Here we report the crystal structure and biochemical characterization of HI0607, a novel class of Shikimate dehydrogenase annotated as Shikimate dehydrogenase-like. The kinetic properties of HI0607 are remarkably different from those of AroE and YdiB. In comparison with YdiB, HI0607 catalyzes the oxidation of Shikimate but not quinate. The turnover rate for the oxidation of Shikimate is approximately 1000-fold lower compared with that of AroE. Phylogenetic analysis reveals three independent clusters representing three classes of Shikimate dehydrogenases, namely AroE, YdiB, and this newly characterized Shikimate dehydrogenase-like protein. In addition, mutagenesis studies of two invariant residues, Asp-103 and Lys-67, indicate that they are important catalytic groups that may function as a catalytic pair in the Shikimate dehydrogenase reaction. This is the first study that describes the crystal structure as well as mutagenesis and mechanistic analysis of this new class of Shikimate dehydrogenase.
Luiz Augusto Basso - One of the best experts on this subject based on the ideXlab platform.
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The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis Shikimate dehydrogenase
BMC Research Notes, 2009Co-Authors: Valnes Da Silva Rodrigues, Diógenes Santiago Santos, Ardala Breda, Luiz Augusto BassoAbstract:Background The Shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in Mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. M. tuberculosis aroE-encoded Shikimate dehydrogenase catalyzes the forth reaction in the Shikimate pathway. Structural and functional studies indicate that Lysine69 may be involved in catalysis and/or substrate binding in M. tuberculosis Shikimate dehydrogenase. Investigation of the kinetic properties of mutant enzymes can bring important insights about the role of amino acid residues for M. tuberculosis Shikimate dehydrogenase.
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Effects of the magnesium and chloride ions and Shikimate on the structure of Shikimate kinase from Mycobacterium tuberculosis.
Acta Crystallographica Section F Structural Biology and Crystallization Communications, 2006Co-Authors: Marcio Vinicius Bertacine Dias, Jaim S. Oliveira, Luiz Augusto Basso, Diógenes Santiago Santos, Lívia Maria Faim, Igor B. Vasconcelos, Walter Filgueira De AzevedoAbstract:Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the Shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts Shikimate to Shikimate-3-phosphate. In this work, the conformational changes that occur on binding of Shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and Shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the Shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.
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Structure of Shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
Acta Crystallographica Section D Biological Crystallography, 2004Co-Authors: Jose Henrique Pereira, Jaim S. Oliveira, Fernanda Canduri, Marcio Vinicius Bertacine Dias, Mario Sergio Palma, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira De AzevedoAbstract:Tuberculosis made a resurgence in the mid-1980s and now kills approximately 3 million people a year. The re-emergence of tuberculosis as a public health threat, the high susceptibility of HIV-infected persons and the proliferation of multi-drug-resistant strains have created a need to develop new drugs. Shikimate kinase and other enzymes in the Shikimate pathway are attractive targets for development of non-toxic antimicrobial agents, herbicides and anti-parasitic drugs, because the pathway is essential in these species whereas it is absent from mammals. The crystal structure of Shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid (Shikimate) has been determined at 2.3 A resolution, clearly revealing the amino-acid residues involved in Shikimate binding. This is the first three-dimensional structure of Shikimate kinase complexed with Shikimate. In MtSK, the Glu61 residue that is strictly conserved in Shikimate kinases forms a hydrogen bond and salt bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for Shikimate binding. The carboxyl group of Shikimate interacts with Arg58, Gly81 and Arg136 and the hydroxyl groups interact with Asp34 and Gly80. The crystal structure of MtSK-MgADP-Shikimate will provide crucial information for the elucidation of the mechanism of the Shikimate kinase-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.
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Interaction of shikimic acid with Shikimate kinase (Retracted Article. See vol 334, pg 967, 2005)
Biochemical and Biophysical Research Communications, 2004Co-Authors: Jadergudson Pereira, Walter Filgueira De Azevedo, Jaim S. Oliveira, Fernanda Canduri, Mario Sergio Palma, Luiz Augusto Basso, Mvb Dias, Diógenes Santiago SantosAbstract:The crystal structure of Shikimate kinase from Mycobacterium tuberculosis (MtSK) complexed with MgADP and shikimic acid (Shikimate) has been determined at 2.3A resolution, clearly revealing the amino acid residues involved in Shikimate binding. In MtSK, the Glu61 strictly conserved in SK forms a hydrogen bond and salt-bridge with Arg58 and assists in positioning the guanidinium group of Arg58 for Shikimate binding. The carboxyl group of Shikimate interacts with Arg58, Gly81, and Arg136, and hydroxyl groups with Asp34 and Gly80. The crystal structure of MtSK-MgADP-Shikimate will provide crucial information for elucidation of the mechanism of SK-catalyzed reaction and for the development of a new generation of drugs against tuberculosis.
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Molecular models for Shikimate pathway enzymes of Xylella fastidiosa.
Biochemical and Biophysical Research Communications, 2004Co-Authors: Helen Andrade Arcuri, Jose Henrique Pereira, Jaim S. Oliveira, Fernanda Canduri, Mario Sergio Palma, Luiz Augusto Basso, Diógenes Santiago Santos, Nelson José Freitas Da Silveira, João Carlos Camera, Walter Filgueira De AzevedoAbstract:The Xylella fastidiosa is a bacterium that is the cause of citrus variegated chlorosis (CVC). The Shikimate pathway is of pivotal importance for production of a plethora of aromatic compounds in plants, bacteria, and fungi. Putative structural differences in the enzymes from the Shikimate pathway, between the proteins of bacterial origin and those of plants, could be used for the development of a drug for the control of CVC. However, inhibitors for Shikimate pathway enzymes should have high specificity for X. fastidiosa enzymes, since they are also present in plants. In order to pave the way for structural and functional efforts towards antimicrobial agent development, here we describe the molecular modeling of seven enzymes of the Shikimate pathway of X. fastidiosa. The structural models of Shikimate pathway enzymes, complexed with inhibitors, strongly indicate that the previously identified inhibitors may also inhibit the X. fastidiosa enzymes.
John R. Coggins - One of the best experts on this subject based on the ideXlab platform.
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structures of Shikimate dehydrogenase aroe and its paralog ydib a common structural framework for different activities
Journal of Biological Chemistry, 2003Co-Authors: Gurvan Michel, John R. Coggins, Aleksander W Roszak, Veronique Sauve, John Maclean, Allan Matte, Miroslaw Cygler, Adrian J. LapthornAbstract:Shikimate dehydrogenase catalyzes the fourth step of the Shikimate pathway, the essential route for the biosynthesis of aromatic compounds in plants and microorganisms. Absent in metazoans, this pathway is an attractive target for nontoxic herbicides and drugs. Escherichia coli expresses two Shikimate dehydrogenase paralogs, the NADP-specific AroE and a putative enzyme YdiB. Here we characterize YdiB as a dual specificity quinate/Shikimate dehydrogenase that utilizes either NAD or NADP as a cofactor. Structures of AroE and YdiB with bound cofactors were determined at 1.5 and 2.5 A resolution, respectively. Both enzymes display a similar architecture with two α/β domains separated by a wide cleft. Comparison of their dinucleotide-binding domains reveals the molecular basis for cofactor specificity. Independent molecules display conformational flexibility suggesting that a switch between open and closed conformations occurs upon substrate binding. Sequence analysis and structural comparison led us to propose the catalytic machinery and a model for 3-dehydroShikimate recognition. Furthermore, we discuss the evolutionary and metabolic implications of the presence of two Shikimate dehydrogenases in E. coli and other organisms.
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The Shikimate Pathway and Its Branches in Apicomplexan Parasites
The Journal of Infectious Diseases, 2002Co-Authors: Craig w. Roberts, Fiona Roberts, John R. Coggins, Russell e. Lyons, Michael j. Kirisits, Ernest j Mui, John Finnerty, Jennifer j. Johnson, David j. p. Ferguson, Tino KrellAbstract:The Shikimate pathway is essential for production of a plethora of aromatic compounds in plants, bacteria, and fungi. Seven enzymes of the Shikimate pathway catalyze sequential conversion of erythrose 4-phosphate and phosphoenol pyruvate to chorismate. Chorismate is then used as a substrate for other pathways that culminate in production of folates, ubiquinone, napthoquinones, and the aromatic amino acids tryptophan, phenylalanine, and tyrosine. The Shikimate pathway is absent from animals and present in the apicomplexan parasites Toxoplasma gondii, Plasmodium falciparum, and Cryptosporidium parvum. Inhibition of the pathway by glyphosate is effective in controlling growth of these parasites. These findings emphasize the potential benefits of developing additional effective inhibitors of the Shikimate pathway. Such inhibitors may function as broad-spectrum antimicrobial agents that are effective against bacterial and fungal pathogens and apicomplexan parasites
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Evidence for the Shikimate pathway in apicomplexan parasites
Nature, 1998Co-Authors: Fiona Roberts, Craig W. Roberts, Jennifer J. Johnson, Dennis E. Kyle, Tino Krell, John R. Coggins, Graham H. Coombs, Wilbur K. Milhous, Saul Tzipori, David J. P. FergusonAbstract:Parasites of the phylum Apicomplexa cause substantial morbidity, mortality and economic losses, and new medicines to treat them are needed urgently. The Shikimate pathway is an attractive target for herbicides and antimicrobial agents because it is essential in algae, higher plants, bacteria and fungi, but absent from mammals. Here we present biochemical, genetic and chemotherapeutic evidence for the presence of enzymes of the Shikimate pathway in apicomplexan parasites. In vitro growth of Toxoplasma gondii, Plasmodium falciparum (malaria) and Cryptosporidium parvum was inhibited by the herbicide glyphosate, a well-characterized inhibitor of the Shikimate pathway enzyme 5-enolpyruvyl Shikimate 3-phosphate synthase. This effect on T. gondii and P. falciparum was reversed by treatment with p-aminobenzoate, which suggests that the Shikimate pathway supplies folate precursors for their growth. Glyphosate in combination with pyrimethamine limited T. gondii infection in mice. Four Shikimate pathway enzymes were detected in extracts of T. gondii and glyphosate inhibited 5-enolpyruvyl Shikimate 3-phosphate synthase activity. Genes encoding chorismate synthase, the final Shikimate pathway enzyme, were cloned from T. gondii and P. falciparum. This discovery of a functional Shikimate pathway in apicomplexan parasites provides several targets for the development of new antiparasite agents.
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the three dimensional structure of Shikimate kinase
Journal of Molecular Biology, 1998Co-Authors: Tino Krell, John R. Coggins, Adrian J. LapthornAbstract:The three-dimensional structure of Shikimate kinase from Erwinia chrysanthemi has been determined by multiple isomorphous replacement. Two models are presented: a high resolution 1.9 A model and a 2.6 A model which contains bound Mg-ADP. The enzyme is an alpha/beta protein consisting of a central sheet of five parallel beta-strands flanked by alpha-helices with overall topology similar to adenylate kinase. Evidence is presented that Shikimate kinase undergoes major conformational changes on ligand binding. It resembles adenylate kinase in having a P-loop containing core structure and two flexible domains which undergo induced fit movement on substrate binding. The binding of Mg2+ in the active site of Shikimate kinase involves direct interaction with two protein side-chains which is different from the situation found in adenylate kinase. Shikimate kinase has a readily identifiable Walker A-motif and a recognisable but modified Walker B-motif. Comparison of Shikimate kinase to adenylate kinase has led to the identification of an adenine-binding motif (I/VDAXQ/NXP). Difference Fourier calculations have revealed the Shikimate binding site which corresponds to the location of the AMP-binding site in adenylate kinase. A model for Shikimate-binding is presented.
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the three dimensional structure of Shikimate kinase
Journal of Molecular Biology, 1998Co-Authors: Tino Krell, John R. Coggins, Adrian J. LapthornAbstract:The three-dimensional structure of Shikimate kinase from Erwinia chrysanthemi has been determined by multiple isomorphous replacement. Two models are presented: a high resolution 1.9 A model and a 2.6 A model which contains bound Mg-ADP. The enzyme is an α/β protein consisting of a central sheet of five parallel β-strands flanked by α-helices with overall topology similar to adenylate kinase. Evidence is presented that Shikimate kinase undergoes major conformational changes on ligand binding. It resembles adenylate kinase in having a P-loop containing core structure and two flexible domains which undergo induced fit movement on substrate binding. The binding of Mg2+ in the active site of Shikimate kinase involves direct interaction with two protein side-chains which is different from the situation found in adenylate kinase. Shikimate kinase has a readily identifiable Walker A-motif and a recognisable but modified Walker B-motif. Comparison of Shikimate kinase to adenylate kinase has led to the identification of an adenine-binding motif (I/VDAXQ/NXP). Difference Fourier calculations have revealed the Shikimate binding site which corresponds to the location of the AMP-binding site in adenylate kinase. A model for Shikimate-binding is presented.
