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Wang X, Qiu C, Chen C, Gao C, Wei W, Song W, Wu J, Liu L, Chen X. Metabolic Engineering of Escherichia coli for High-Level Production of l-Phenylalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11029-11040. [PMID: 38699920 DOI: 10.1021/acs.jafc.4c01563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
l-Phenylalanine (l-Phe) is widely used in the food and pharmaceutical industries. However, the biosynthesis of l-Phe using Escherichia coli remains challenging due to its lower tolerance to high concentration of l-Phe. In this study, to efficiently synthesize l-Phe, the l-Phe biosynthetic pathway was reconstructed by expressing the heterologous genes aroK1, aroL1, and pheA1, along with the native genes aroA, aroC, and tyrB in the shikimate-producing strain E. coli SA09, resulting in the engineered strain E. coli PHE03. Subsequently, adaptive evolution was conducted on E. coli PHE03 to enhance its tolerance to high concentrations of l-Phe, resulting in the strain E. coli PHE04, which reduced the cell mortality to 36.2% after 48 h of fermentation. To elucidate the potential mechanisms, transcriptional profiling was conducted, revealing MarA, a DNA-binding transcriptional dual regulator, as playing a crucial role in enhancing cell membrane integrity and fluidity for improving cell tolerance to high concentrations of l-Phe. Finally, the titer, yield, and productivity of l-Phe with E. coli PHE05 overexpressing marA were increased to 80.48 g/L, 0.27 g/g glucose, and 1.68 g/L/h in a 5-L fed-batch fermentation, respectively.
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Affiliation(s)
- Xiaoge Wang
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chong Qiu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Chenghu Chen
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Rios-Soto L, Hernández-Campos A, Tovar-Escobar D, Castillo R, Sierra-Campos E, Valdez-Solana M, Téllez-Valencia A, Avitia-Domínguez C. Inhibition of Shikimate Kinase from Methicillin-Resistant Staphylococcus aureus by Benzimidazole Derivatives. Kinetic, Computational, Toxicological, and Biological Activity Studies. Int J Mol Sci 2024; 25:5077. [PMID: 38791117 PMCID: PMC11121535 DOI: 10.3390/ijms25105077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the biggest threats in modern times. It was estimated that in 2019, 1.27 million deaths occurred around the globe due to AMR. Methicillin-resistant Staphylococcus aureus (MRSA) strains, a pathogen considered of high priority by the World Health Organization, have proven to be resistant to most of the actual antimicrobial treatments. Therefore, new treatments are required to be able to manage this increasing threat. Under this perspective, an important metabolic pathway for MRSA survival, and absent in mammals, is the shikimate pathway, which is involved in the biosynthesis of chorismate, an intermediate for the synthesis of aromatic amino acids, folates, and ubiquinone. Therefore, the enzymes of this route have been considered good targets to design novel antibiotics. The fifth step of the route is performed by shikimate kinase (SK). In this study, an in-house chemical library of 170 benzimidazole derivatives was screened against MRSA shikimate kinase (SaSK). This effort led to the identification of the first SaSK inhibitors, and the two inhibitors with the greatest inhibition activity (C1 and C2) were characterized. Kinetic studies showed that both compounds were competitive inhibitors with respect to ATP and non-competitive for shikimate. Structural analysis through molecular docking and molecular dynamics simulations indicated that both inhibitors interacted with ARG113, an important residue involved in ATP binding, and formed stable complexes during the simulation period. Biological activity evaluation showed that both compounds were able to inhibit the growth of a MRSA strain. Mitochondrial assays showed that both compounds modify the activity of electron transport chain complexes. Finally, ADMETox predictions suggested that, in general, C1 and C2 can be considered as potential drug candidates. Therefore, the benzimidazole derivatives reported here are the first SaSK inhibitors, representing a promising scaffold and a guide to design new drugs against MRSA.
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Affiliation(s)
- Lluvia Rios-Soto
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny, Anitúa S/N, Durango 34000, Mexico;
| | - Alicia Hernández-Campos
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico; (A.H.-C.); (D.T.-E.); (R.C.)
| | - David Tovar-Escobar
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico; (A.H.-C.); (D.T.-E.); (R.C.)
| | - Rafael Castillo
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, México City 04510, Mexico; (A.H.-C.); (D.T.-E.); (R.C.)
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny, Anitúa S/N, Durango 34000, Mexico;
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny, Anitúa S/N, Durango 34000, Mexico;
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3
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Chagaleti BK, Reddy MBR, Saravanan V, B S, D P, Senthil Kumar P, Kathiravan MK. An overview of mechanism and chemical inhibitors of shikimate kinase. J Biomol Struct Dyn 2023; 41:14582-14598. [PMID: 36974959 DOI: 10.1080/07391102.2023.2193985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/04/2023] [Indexed: 03/29/2023]
Abstract
Tuberculosis is a highly infectious disease other than HIV/AIDS and it is one of the top ten causes of death worldwide. Resistance development in the bacteria occurs because of genetic alterations, and the molecular insights suggest that the accumulation of mutation in the individual drug target genes is the primary mechanism of multi-drug resistant tuberculosis. Chorismate is an essential structural fragment for the synthesis of aromatic amino acids and synthesized biochemically by a number of bacteria, including Mycobacterium tuberculosis, utilizing the shikimate pathway. This shikimate kinase is the newer possible target for the generation of novel antitubercular drug because this pathway is expressed only in mycobacterium and not in Mammals. The discovery and development of shikimate kinase inhibitors provide an opportunity for the development of novel selective medications. Multiple shikimate kinase inhibitors have been identified via insilico virtual screening and related protein-ligand interactions along with their in-vitro studies. These inhibitors bind to the active site in a similar fashion to shikimate. In the current review, we present an overview of the biology and chemistry of the shikimate kinase protein and its inhibitors, with special emphasis on the various active scaffold against the enzyme. A variety of chemically diversified synthetic scaffolds including Benzothiazoles, Oxadiazoles, Thiobarbiturates, Naphthoquinones, Thiazoleacetonitriles, Hybridized Pyrazolone derivatives, Orthologous biological macromolecule derivatives, Manzamine Alkaloids derivatives, Dipeptide inhibitor, and Chalcones are discussed in detail. These derivatives bind to the specific target appropriately proving their potential ability through different binding interactions and effectively explored as an effective and selective Sk inhibitor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharath Kumar Chagaleti
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - M B Rahul Reddy
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - Venkatesan Saravanan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - Shanthakumar B
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - Priya D
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
| | - P Senthil Kumar
- Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - M K Kathiravan
- 209, Dr. APJ Abdul Kalam Research Lab, Dept of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu, India
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Russomanno P, Assoni G, Amato J, D'Amore VM, Scaglia R, Brancaccio D, Pedrini M, Polcaro G, La Pietra V, Orlando P, Falzoni M, Cerofolini L, Giuntini S, Fragai M, Pagano B, Donati G, Novellino E, Quintavalle C, Condorelli G, Sabbatino F, Seneci P, Arosio D, Pepe S, Marinelli L. Interfering with the Tumor-Immune Interface: Making Way for Triazine-Based Small Molecules as Novel PD-L1 Inhibitors. J Med Chem 2021; 64:16020-16045. [PMID: 34670084 DOI: 10.1021/acs.jmedchem.1c01409] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The inhibition of the PD-1/PD-L1 axis by monoclonal antibodies has achieved remarkable success in treating a growing number of cancers. However, a novel class of small organic molecules, with BMS-202 (1) as the lead, is emerging as direct PD-L1 inhibitors. Herein, we report a series of 2,4,6-tri- and 2,4-disubstituted 1,3,5-triazines, which were synthesized and assayed for their PD-L1 binding by NMR and homogeneous time-resolved fluorescence. Among them, compound 10 demonstrated to strongly bind with the PD-L1 protein and challenged it in a co-culture of PD-L1 expressing cancer cells (PC9 and HCC827 cells) and peripheral blood mononuclear cells enhanced antitumor immune activity of the latter. Compound 10 significantly increased interferon γ release and apoptotic induction of cancer cells, with low cytotoxicity in healthy cells when compared to 1, thus paving the way for subsequent preclinical optimization and medical applications.
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Affiliation(s)
- Pasquale Russomanno
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
| | - Giulia Assoni
- Department of Cellular, Computational and Integrative Biology, (CIBIO), Università degli Studi di Trento, Via Sommarive 9, Povo I-38123, Trento, Italy.,Chemistry Department, Università degli Studi di Milano, Via C. Golgi 19, Milan 20133, Italy
| | - Jussara Amato
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
| | - Vincenzo Maria D'Amore
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
| | - Riccardo Scaglia
- Chemistry Department, Università degli Studi di Milano, Via C. Golgi 19, Milan 20133, Italy
| | - Diego Brancaccio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
| | - Martina Pedrini
- Chemistry Department, Università degli Studi di Milano, Via C. Golgi 19, Milan 20133, Italy
| | - Giovanna Polcaro
- Dipartimento di Medicina e Chirurgia, Ospedale "San Giovanni di Dio e Ruggi d'Aragona", Università di Salerno, Salerno 84131, Italy
| | - Valeria La Pietra
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
| | - Paolo Orlando
- Chemistry Department, Università degli Studi di Milano, Via C. Golgi 19, Milan 20133, Italy
| | - Marianna Falzoni
- Chemistry Department, Università degli Studi di Milano, Via C. Golgi 19, Milan 20133, Italy
| | - Linda Cerofolini
- Centro di Risonanza Magnetica, CERM, Università di Firenze, Firenze 50019, Italy
| | - Stefano Giuntini
- Centro di Risonanza Magnetica, CERM, Università di Firenze, Firenze 50019, Italy
| | - Marco Fragai
- Centro di Risonanza Magnetica, CERM, Università di Firenze, Firenze 50019, Italy
| | - Bruno Pagano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
| | - Greta Donati
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
| | | | - Cristina Quintavalle
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University, Naples, Italy; Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Naples 80131, Italy
| | - Gerolama Condorelli
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University, Naples, Italy; Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Naples 80131, Italy.,Department of Molecular Medicine and Medical Biotechnology, "Federico II" University, Naples 80131, Italy
| | - Francesco Sabbatino
- Dipartimento di Medicina e Chirurgia, Ospedale "San Giovanni di Dio e Ruggi d'Aragona", Università di Salerno, Salerno 84131, Italy
| | - Pierfausto Seneci
- Chemistry Department, Università degli Studi di Milano, Via C. Golgi 19, Milan 20133, Italy
| | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" (SCITEC), Consiglio Nazionale delle Ricerche (CNR), Via C. Golgi 19, Milan 20133, Italy
| | - Stefano Pepe
- Dipartimento di Medicina e Chirurgia, Ospedale "San Giovanni di Dio e Ruggi d'Aragona", Università di Salerno, Salerno 84131, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, Napoli 80131, Italy
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Hajredini F, Ghose R. An ATPase with a twist: A unique mechanism underlies the activity of the bacterial tyrosine kinase, Wzc. SCIENCE ADVANCES 2021; 7:eabj5836. [PMID: 34550748 PMCID: PMC8457666 DOI: 10.1126/sciadv.abj5836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BY-kinases constitute a protein tyrosine kinase family that encodes unique catalytic domains that deviate from those of eukaryotic kinases resembling P-loop nucleotide triphosphatases (NTPases) instead. We have used computational and supporting biochemical approaches using the catalytic domain of the Escherichia coli BY-kinase, Wzc, to illustrate mechanistic divergences between BY-kinases and NTPases despite their deployment of similar catalytic motifs. In NTPases, the “arginine finger” drives the reactive conformation of ATP while also displacing its solvation shell, thereby making favorable enthalpic and entropic contributions toward βγ-bond cleavage. In BY-kinases, the reactive state of ATP is enabled by ATP·Mg2+-induced global conformational transitions coupled to the conformation of the Walker-A lysine. While the BY-kinase arginine finger does promote the desolvation of ATP, it does so indirectly by generating an ordered active site in combination with other structural elements. Bacteria, using these mechanistic variations, have thus repurposed an ancient fold to phosphorylate on tyrosine.
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Affiliation(s)
- Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA
- Corresponding author.
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Hajredini F, Piserchio A, Ghose R. Long-range dynamic correlations regulate the catalytic activity of the bacterial tyrosine kinase Wzc. SCIENCE ADVANCES 2020; 6:eabd3718. [PMID: 33355134 PMCID: PMC11206214 DOI: 10.1126/sciadv.abd3718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/04/2020] [Indexed: 06/12/2023]
Abstract
BY-kinases represent a highly conserved family of protein tyrosine kinases unique to bacteria without eukaryotic orthologs. BY-kinases are regulated by oligomerization-enabled transphosphorylation on a C-terminal tyrosine cluster through a process with sparse mechanistic detail. Using the catalytic domain (CD) of the archetypal BY-kinase, Escherichia coli Wzc, and enhanced-sampling molecular dynamics simulations, isothermal titration calorimetry and nuclear magnetic resonance measurements, we propose a mechanism for its activation and nucleotide exchange. We find that the monomeric Wzc CD preferentially populates states characterized by distortions at its oligomerization interfaces and by catalytic element conformations that allow high-affinity interactions with ADP but not with ATP·Mg2+ We propose that oligomer formation stabilizes the intermonomer interfaces and results in catalytic element conformations suitable for optimally engaging ATP·Mg2+, facilitating exchange with bound ADP. This sequence of events, oligomerization, i.e., substrate binding, before engaging ATP·Mg2+, facilitates optimal autophosphorylation by preventing a futile cycle of ATP hydrolysis.
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Affiliation(s)
- Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA.
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA
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Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs. Molecules 2020; 25:molecules25061259. [PMID: 32168746 PMCID: PMC7144000 DOI: 10.3390/molecules25061259] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Roughly a third of the world’s population is estimated to have latent Mycobacterium tuberculosis infection, being at risk of developing active tuberculosis (TB) during their lifetime. Given the inefficacy of prophylactic measures and the increase of drug-resistant M. tuberculosis strains, there is a clear and urgent need for the development of new and more efficient chemotherapeutic agents, with selective toxicity, to be implemented on patient treatment. The component enzymes of the shikimate pathway, which is essential in mycobacteria and absent in humans, stand as attractive and potential targets for the development of new drugs to treat TB. This review gives an update on published work on the enzymes of the shikimate pathway and some insight on what can be potentially explored towards selective drug development.
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Sahu PK, Mohapatra PK, Rajani DP, Raval MK. Structure-based Discovery of Narirutin as a Shikimate kinase Inhibitor with Anti-tubercular Potency. Curr Comput Aided Drug Des 2019; 16:523-529. [PMID: 31654517 DOI: 10.2174/1573409915666191025112150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/05/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Shikimate pathway is essential for tubercular bacillus but it is absent in mammals. Therefore, Shikimate kinase and other enzymes in the pathway are potential targets for the development of novel anti-tuberculosis drugs. OBJECTIVE In the present study, Shikimate kinase is selected as the target for in silico screening of phytochemicals with an aim to discover a novel herbal drug against Mycobacterium tuberculosis (Mtb). METHODS A structure-based drug discovery approach is undertaken for the execution of the objective. Virtual screening of phytochemical database NPACT against the target, Shikimate kinase (PDB ID 3BAF), is carried out followed by toxicity and drug-likeness filtration. Finally, a lead, narirutin was selected for in vitro anti-tubercular study. RESULTS Narirutin, present in citrus fruits, emerges as the lead. It is considered to be non-toxic with predicted high LD50 value, 12000 mg/kg body weight. The phytochemical is tested for its antitubercular activity in vitro. It has MIC99 62.5 μg/mL against the MtbH37Rv strain. CONCLUSION This is the first-ever report to show anti-tuberculosis potency of narirutin.
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Affiliation(s)
- Pramod Kumar Sahu
- Department of Chemistry, Gangadhar Meher University, Sambalpur, 768004, Odisha, India
| | - Pranab Kishor Mohapatra
- Department of Chemistry, CV Raman College of Engineering, Bidyanagar, Mahura, Janla, Bhubaneswar 752054, Odisha, India
| | - Dhanji Popatbhai Rajani
- Microcare Laboratory and Tuberculosis Research Center, 105, Manthan Point, Unapani Road, Lal Darwaja, Surat - 395003, Gujarat, India
| | - Mukesh Kumar Raval
- Department of Chemistry, Gangadhar Meher University, Sambalpur, 768004, Odisha, India
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9
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Favela-Candia A, Téllez-Valencia A, Campos-Almazán M, Sierra-Campos E, Valdez-Solana M, Oria-Hernández J, Castillo-Villanueva A, Nájera H, Avitia-Domínguez C. Biochemical, Kinetic, and Computational Structural Characterization of Shikimate Kinase from Methicillin-Resistant Staphylococcus aureus. Mol Biotechnol 2019; 61:274-285. [PMID: 30747382 DOI: 10.1007/s12033-019-00159-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the most widespread pathogens worldwide is methicillin-resistant Staphylococcus aureus, a bacterium that provokes severe life-threatening illnesses both in hospitals and in the community. The principal challenge lies in the resistance of MRSA to current treatments, which encourages the study of different molecular targets that could be used to develop new drugs against this infectious agent. With this goal, a detailed characterization of shikimate kinase from this microorganism (SaSK) is described. The results showed that SaSK has a Km of 0.153 and 224 µM for shikimate and ATP, respectively, and a global reaction rate of 13.4 µmol/min/mg; it is suggested that SaSK utilizes the Bi-Bi Ping Pong reaction mechanism. Furthermore, the physicochemical data indicated that SaSK is an unstable, hydrophilic, and acidic protein. Finally, structural information showed that SaSK presented folding that is typical of its homologous counterparts and contains the typical domains of this family of proteins. Amino acids that have been shown to be important for SaSK protein function are conserved. Therefore, this study provides fundamental information that may aid in the design of inhibitors that could be used to develop new antibacterial agents.
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Affiliation(s)
- Alejandro Favela-Candia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico
| | - Mara Campos-Almazán
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, C.P. 35010, Durango, Mexico
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, C.P. 35010, Durango, Mexico
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica Genética, Secretaría de Salud, Instituto Nacional de Pediatría, C.P. 04534, Ciudad de México, Mexico
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica Genética, Secretaría de Salud, Instituto Nacional de Pediatría, C.P. 04534, Ciudad de México, Mexico
| | - Hugo Nájera
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Delegación Cuajimalpa de Morelos, Av. Vasco de Quiroga 4871, Colonia Santa Fe Cuajimalpa, C.P. 05300, Ciudad de México, Mexico
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico.
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10
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Schoenenberger B, Wszolek A, Meier R, Brundiek H, Obkircher M, Wohlgemuth R. Recombinant AroL-Catalyzed Phosphorylation for the Efficient Synthesis of Shikimic Acid 3-Phosphate. Biotechnol J 2018; 13:e1700529. [PMID: 29697210 DOI: 10.1002/biot.201700529] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 04/03/2018] [Indexed: 01/01/2023]
Abstract
Shikimic acid 3-phosphate, as a central metabolite of the shikimate pathway, is of high interest as enzyme substrate for 5-enolpyruvoyl-shikimate 3-phosphate synthase, a drug target in infectious diseases and a prime enzyme target for the herbicide glyphosate. As the important substrate shikimic acid 3-phosphate is only accessible via a chemical multi-step route, a new straightforward preparative one-step enzymatic phosphorylation of shikimate using a stable recombinant shikimate kinase has been developed for the selective phosphorylation of shikimate in the 3-position. Highly active shikimate kinase is produced by straightforward expression of a synthetic aroL gene in Escherichia coli. The time course of the shikimate kinase-catalyzed phosphorylation is investigated by 1 H- and 31 P-NMR, using the phosphoenolpyruvate/pyruvate kinase system for the regeneration of the ATP cofactor. This enables the development of a quantitative biocatalytic 3-phosphorylation of shikimic acid. After a standard workup procedure, a good yield of shikimic acid 3-phosphate, with high HPLC- and NMR purity, is obtained. This efficient biocatalytic synthesis of shikimic acid 3-phosphate is superior to any other method and has been successfully scaled up to multi-gram scale.
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Affiliation(s)
| | - Agata Wszolek
- Enzymicals, Walther-Rathenau-Strasse 49a, 17489, Greifswald, Germany
| | - Roland Meier
- Sigma-Aldrich, Member of Merck Group, Industriestrasse 25, CH-9470, Buchs, Switzerland
| | - Henrike Brundiek
- Enzymicals, Walther-Rathenau-Strasse 49a, 17489, Greifswald, Germany
| | - Markus Obkircher
- Sigma-Aldrich, Member of Merck Group, Industriestrasse 25, CH-9470, Buchs, Switzerland
| | - Roland Wohlgemuth
- Sigma-Aldrich, Member of Merck Group, Industriestrasse 25, CH-9470, Buchs, Switzerland
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11
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Structure-guided design of Serratia marcescens short-chain dehydrogenase/reductase for stereoselective synthesis of (R)-phenylephrine. Sci Rep 2018; 8:2316. [PMID: 29396495 PMCID: PMC5797133 DOI: 10.1038/s41598-018-19235-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/27/2017] [Indexed: 02/07/2023] Open
Abstract
Bioconversion is useful to produce optically pure enantiomers in the pharmaceutical industry, thereby avoiding problems with side reactions during organic synthesis processes. A short-chain dehydrogenase/reductase from Serratia marcescens BCRC 10948 (SmSDR) can stereoselectively convert 1-(3-hydroxyphenyl)-2-(methylamino) ethanone (HPMAE) into (R)-phenylephrine [(R)-PE], which is marketed medically as a nasal decongestant agent. The whole-cell conversion process for the synthesis of (R)-PE using SmSDR was reported to have an unexpectedly low conversion rate. We reported the crystal structure of the SmSDR and designed profitable variants to improve the enzymatic activity by structure-guided approach. Several important residues in the structure were observed to form hydrophobic clusters that stabilize the mobile loops surrounding the pocket. Of these, Phe98 and Phe202 face toward each other and connect the upper curvature from the two arms (i.e., the α7 helix and loopβ4-α4). The mutant structure of the double substitutions (F98YF202Y) exhibited a hydrogen bond between the curvatures that stabilizes the flexible arms. Site-directed mutagenesis characterization revealed that the mutations (F98Y, F98YF202Y, and F98YF202L) of the flexible loops that stabilize the region exhibited a higher transformation activity toward HPMAE. Together, our results suggest a robust structure-guided approach that can be used to generate a valuable engineered variant for pharmaceutical applications.
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12
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Gudernova I, Balek L, Varecha M, Kucerova JF, Kunova Bosakova M, Fafilek B, Palusova V, Uldrijan S, Trantirek L, Krejci P. Inhibitor repurposing reveals ALK, LTK, FGFR, RET and TRK kinases as the targets of AZD1480. Oncotarget 2017; 8:109319-109331. [PMID: 29312610 PMCID: PMC5752523 DOI: 10.18632/oncotarget.22674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/28/2017] [Indexed: 01/29/2023] Open
Abstract
Many tyrosine kinase inhibitors (TKIs) have failed to reach human use due to insufficient activity in clinical trials. However, the failed TKIs may still benefit patients if their other kinase targets are identified by providing treatment focused on syndromes driven by these kinases. Here, we searched for novel targets of AZD1480, an inhibitor of JAK2 kinase that recently failed phase two cancer clinical trials due to a lack of activity. Twenty seven human receptor tyrosine kinases (RTKs) and 153 of their disease-associated mutants were in-cell profiled for activity in the presence of AZD1480 using a newly developed RTK plasmid library. We demonstrate that AZD1480 inhibits ALK, LTK, FGFR1-3, RET and TRKA-C kinases and uncover a physical basis of this specificity. The RTK activity profiling described here facilitates inhibitor repurposing by enabling rapid and efficient identification of novel TKI targets in cells.
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Affiliation(s)
- Iva Gudernova
- Department of Biology, Faculty of Medicine, 62500 Brno, Czech Republic
| | - Lukas Balek
- Department of Biology, Faculty of Medicine, 62500 Brno, Czech Republic
| | - Miroslav Varecha
- Department of Biology, Faculty of Medicine, 62500 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, 65691 Brno, Czech Republic
| | | | | | - Bohumil Fafilek
- Department of Biology, Faculty of Medicine, 62500 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, 65691 Brno, Czech Republic
| | - Veronika Palusova
- Department of Biology, Faculty of Medicine, 62500 Brno, Czech Republic
| | - Stjepan Uldrijan
- Department of Biology, Faculty of Medicine, 62500 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, 65691 Brno, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, 62500 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, 65691 Brno, Czech Republic
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13
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Verma P, Kar B, Varshney R, Roy P, Sharma AK. Characterization of AICAR transformylase/IMP cyclohydrolase (ATIC) from Staphylococcus lugdunensis. FEBS J 2017; 284:4233-4261. [PMID: 29063699 DOI: 10.1111/febs.14303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/26/2017] [Accepted: 10/19/2017] [Indexed: 01/05/2023]
Abstract
The 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/inosine monophosphate (IMP) cyclohydrolase (ATIC) catalyzes final two steps of purine nucleotide de novo biosynthetic pathway. This study reports the characterization of ATIC from Staphylococcus lugdunensis (SlugATIC). Apart from kinetic analysis and a detailed biophysical characterization of SlugATIC, the role of ATIC in cell proliferation has been demonstrated for the first time. The purified recombinant SlugATIC and its truncated domains exist mainly in dimeric form was revealed in gel-filtration and glutaraldehyde cross-linking studies. The two activities reside on separate domains was demonstrated in kinetic analysis of SlugATIC and reconstituted truncated N-terminal IMP cyclohydrolase (IMPCHase) and C-terminal AICAR transformylase (AICAR TFase) domains. Site-directed mutagenesis showed that Lys255 and His256 are the key catalytic residues, while Asn415 substantially contributes to AICAR TFase activity in SlugATIC. The differential scanning calorimetry (DSC) analysis revealed a molten globule-like structure for independent N-terminal domain as compared with a relatively stable conformational state in full-length SlugATIC signifying the importance of covalently linked domains. Unlike reported crystal structures, the DSC studies revealed significant conformational changes on binding of leading ligand to AICAR TFase domain in SlugATIC. The cell proliferation activity of SlugATIC was observed where it promoted proliferation and viability of NIH 3T3 and RIN-5F cells, exhibited in vitro wound healing in NIH 3T3 fibroblast cells, and rescued RIN-5F cells from the cytotoxic effects of palmitic acid and high glucose. The results suggest that ATIC, an important drug target, can also be exploited for its cell proliferative properties.
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Affiliation(s)
- Preeti Verma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Bibekananda Kar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ritu Varshney
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Partha Roy
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani K Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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14
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Yao J, Wang X, Luo H, Gu P. Understanding the Catalytic Mechanism and the Nature of the Transition State of an Attractive Drug‐Target Enzyme (Shikimate Kinase) by Quantum Mechanical/Molecular Mechanical (QM/MM) Studies. Chemistry 2017; 23:16380-16387. [DOI: 10.1002/chem.201703867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Jianzhuang Yao
- School of Biological Science and Technology University of Jinan Jinan 250022 P.R. China
| | - Xia Wang
- School of Biological Science and Technology University of Jinan Jinan 250022 P.R. China
| | - Haixia Luo
- Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, Life Science School Ningxia University Yinchuan 750021 P.R. China
| | - Pengfei Gu
- School of Biological Science and Technology University of Jinan Jinan 250022 P.R. China
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15
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Vasylenko T, Liou YF, Chiou PC, Chu HW, Lai YS, Chou YL, Huang HL, Ho SY. SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides. BMC Bioinformatics 2016; 17:514. [PMID: 28155663 PMCID: PMC5260027 DOI: 10.1186/s12859-016-1371-4] [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: 01/28/2023] Open
Abstract
Background Bacterial tyrosine-kinases (BY-kinases), which play an important role in numerous cellular processes, are characterized as a separate class of enzymes and share no structural similarity with their eukaryotic counterparts. However, in silico methods for predicting BY-kinases have not been developed yet. Since these enzymes are involved in key regulatory processes, and are promising targets for anti-bacterial drug design, it is desirable to develop a simple and easily interpretable predictor to gain new insights into bacterial tyrosine phosphorylation. This study proposes a novel SCMBYK method for predicting and characterizing BY-kinases. Results A dataset consisting of 797 BY-kinases and 783 non-BY-kinases was established to design the SCMBYK predictor, which achieved training and test accuracies of 97.55 and 96.73%, respectively. Furthermore, the leave-one-phylum-out method was used to predict specific bacterial phyla hosts of target sequences, gaining 97.39% average test accuracy. After analyzing SCMBYK-derived propensity scores, four characteristics of BY-kinases were determined: 1) BY-kinases tend to be composed of α-helices; 2) the amino-acid content of extracellular regions of BY-kinases is expected to be dominated by residues such as Val, Ile, Phe and Tyr; 3) BY-kinases structurally resemble nuclear proteins; 4) different domains play different roles in triggering BY-kinase activity. Conclusions The SCMBYK predictor is an effective method for identification of possible BY-kinases. Furthermore, it can be used as a part of a novel drug repurposing method, which recognizes putative BY-kinases and matches them to approved drugs. Among other results, our analysis revealed that azathioprine could suppress the virulence of M. tuberculosis, and thus be considered as a potential antibiotic for tuberculosis treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1371-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tamara Vasylenko
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yi-Fan Liou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Po-Chin Chiou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsiao-Wei Chu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yung-Sung Lai
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Ling Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hui-Ling Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,College of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, Taiwan.
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,College of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, Taiwan.
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16
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Prado V, Lence E, Thompson P, Hawkins AR, González-Bello C. Freezing the Dynamic Gap for Selectivity: Motion-Based Design of Inhibitors of the Shikimate Kinase Enzyme. Chemistry 2016; 22:17988-18000. [DOI: 10.1002/chem.201602923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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17
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Prado V, Lence E, Maneiro M, Vázquez-Ucha JC, Beceiro A, Thompson P, Hawkins AR, González-Bello C. Targeting the Motion of Shikimate Kinase: Development of Competitive Inhibitors that Stabilize an Inactive Open Conformation of the Enzyme. J Med Chem 2016; 59:5471-87. [DOI: 10.1021/acs.jmedchem.6b00483] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan C. Vázquez-Ucha
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences,
Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences,
Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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18
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Mehra R, Rajput VS, Gupta M, Chib R, Kumar A, Wazir P, Khan IA, Nargotra A. Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition. J Chem Inf Model 2016; 56:930-40. [PMID: 27149193 DOI: 10.1021/acs.jcim.6b00056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis shikimate kinase (Mtb-SK) is a key enzyme involved in the biosynthesis of aromatic amino acids through the shikimate pathway. Since it is proven to be essential for the survival of the microbe and is absent from mammals, it is a promising target for anti-TB drug discovery. In this study, a combined approach of in silico similarity search and pharmacophore building using already reported inhibitors was used to screen a procured library of 20,000 compounds of the commercially available ChemBridge database. From the in silico screening, 15 hits were identified, and these hits were evaluated in vitro for Mtb-SK enzyme inhibition. Two compounds presented significant enzyme inhibition with IC50 values of 10.69 ± 0.9 and 46.22 ± 1.2 μM. The best hit was then evaluated for the in vitro mode of inhibition where it came out to be an uncompetitive and noncompetitive inhibitor with respect to shikimate (SKM) and ATP, respectively, suggesting its binding at an allosteric site. Potential binding sites of Mtb-SK were identified which confirmed the presence of an allosteric binding pocket apart from the ATP and SKM binding sites. The docking simulations were performed at this pocket in order to find the mode of binding of the best hit in the presence of substrates and the products of the enzymatic reaction. Molecular dynamics (MD) simulations elucidated the probability of inhibitor binding at the allosteric site in the presence of ADP and shikimate-3-phosphate (S-3-P), that is, after the formation of products of the reaction. The inhibitor binding may prevent the release of the product from Mtb-SK, thereby inhibiting its activity. The binding stability and the key residue interactions of the inhibitor to this product complex were also revealed by the MD simulations. Residues ARG43, ILE45, and PHE57 were identified as crucial that were involved in interactions with the best hit. This is the first report of an allosteric binding site of Mtb-SK, which could largely address the selectivity issue associated with kinase inhibitors.
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Affiliation(s)
- Rukmankesh Mehra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Vikrant Singh Rajput
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Monika Gupta
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Kumar
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Priya Wazir
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Nargotra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
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19
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Prado V, Lence E, Vallejo JA, Beceiro A, Thompson P, Hawkins AR, González-Bello C. Study of the Phosphoryl-Transfer Mechanism of Shikimate Kinase by NMR Spectroscopy. Chemistry 2016; 22:2758-68. [PMID: 26797764 DOI: 10.1002/chem.201504438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 01/16/2023]
Abstract
The phosphoryl-transfer mechanism of shikimate kinase from Mycobacterium tuberculosis and Helicobacter pylori, which is an attractive target for antibiotic drug discovery, has been studied by 1D (1)H and (31)P NMR spectroscopy. Metaphosphoric acid proved to be a good mimetic of the metaphosphate intermediate and facilitated the ready and rapid evaluation by NMR spectroscopic analysis of a dissociative mechanism. The required closed form of the active site for catalysis was achieved by the use of ADP (product) or two synthetic ADP analogues (AMPNP, AMPCP). Molecular dynamics simulation studies reported here also revealed that the essential arginine (Arg116/Arg117 in H. pylori and M. tuberculosis, respectively), which activates the γ-phosphate group of ATP for catalysis and triggers the release of the product for turnover, would also be involved in the stabilisation of the metaphosphate intermediate during catalysis. We believe that the studies reported here will be helpful for future structure-based design of inhibitors of this attractive target. The approach is also expected be useful for studies on the possible dissociative mechanism of other kinase enzymes.
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Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Juan A Vallejo
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), Hospital Teresa Herrera, As Xubias, 84, 15006 A, Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), Hospital Teresa Herrera, As Xubias, 84, 15006 A, Coruña, Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Alastair R Hawkins
- Institute of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain.
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20
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Sutton KA, Breen J, MacDonald U, Beanan JM, Olson R, Russo TA, Schultz LW, Umland TC. Structure of shikimate kinase, an in vivo essential metabolic enzyme in the nosocomial pathogen Acinetobacter baumannii, in complex with shikimate. ACTA ACUST UNITED AC 2015; 71:1736-44. [PMID: 26249354 DOI: 10.1107/s139900471501189x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/22/2015] [Indexed: 11/10/2022]
Abstract
Acinetobacter baumannii is an opportunistic Gram-negative pathogen that is an important cause of healthcare-associated infections exhibiting high mortality rates. Clinical isolates of multidrug-resistant (MDR) and extremely drug-resistant (XDR) A. baumannii strains are increasingly being observed. Compounding this concern is the dearth of new antibacterial agents in late-stage development that are effective against MDR and XDR A. baumannii. As part of an effort to address these concerns, two genes (aroA and aroC) of the shikimate pathway have previously been determined to be essential for the growth and survival of A. baumannii during host infection (i.e. to be essential in vivo). This study expands upon these results by demonstrating that the A. baumannii aroK gene, encoding shikimate kinase (SK), is also essential in vivo in a rat soft-tissue infection model. The crystal structure of A. baumannii SK in complex with the substrate shikimate and a sulfate ion that mimics the binding interactions expected for the β-phosphate of ATP was then determined to 1.91 Å resolution and the enzyme kinetics were characterized. The flexible shikimate-binding domain and LID region are compared with the analogous regions in other SK crystal structures. The impact of structural differences and sequence divergence between SKs from pathogenic bacteria that may influence antibiotic-development efforts is discussed.
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Affiliation(s)
- Kristin A Sutton
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Jennifer Breen
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Ulrike MacDonald
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Janet M Beanan
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Ruth Olson
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Thomas A Russo
- Department of Medicine and The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - L Wayne Schultz
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | - Timothy C Umland
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
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21
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Gordon S, Simithy J, Goodwin DC, Calderón AI. Selective Mycobacterium tuberculosis Shikimate Kinase Inhibitors as Potential Antibacterials. PERSPECTIVES IN MEDICINAL CHEMISTRY 2015; 7:9-20. [PMID: 25861218 PMCID: PMC4362912 DOI: 10.4137/pmc.s13212] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/19/2015] [Accepted: 01/27/2015] [Indexed: 11/08/2022]
Abstract
Owing to the persistence of tuberculosis (TB) as well as the emergence of multidrug-resistant and extensively drug-resistant (XDR) forms of the disease, the development of new antitubercular drugs is crucial. Developing inhibitors of shikimate kinase (SK) in the shikimate pathway will provide a selective target for antitubercular agents. Many studies have used in silico technology to identify compounds that are anticipated to interact with and inhibit SK. To a much more limited extent, SK inhibition has been evaluated by in vitro methods with purified enzyme. Currently, there are no data on in vivo activity of Mycobacterium tuberculosis shikimate kinase (MtSK) inhibitors available in the literature. In this review, we present a summary of the progress of SK inhibitor discovery and evaluation with particular attention toward development of new antitubercular agents.
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Affiliation(s)
- Sara Gordon
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Johayra Simithy
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Douglas C Goodwin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, USA
| | - Angela I Calderón
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
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Morohoshi T, Tominaga Y, Someya N, Ikeda T. Characterization of a novel thermostable N-acylhomoserine lactonase from the thermophilic bacterium Thermaerobacter marianensis. J Biosci Bioeng 2014; 120:1-5. [PMID: 25529553 DOI: 10.1016/j.jbiosc.2014.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 11/29/2022]
Abstract
Thermaerobacter marianensis is an extremely thermophilic bacterium, which was isolated from the Mariana Trench, with an optimal growth temperature of approximately 75 °C. N-Acylhomoserine lactone (AHL) is a quorum-sensing signal molecule used by many gram-negative bacteria. Here, we report the identification of an AHL-degrading gene homolog (designated aiiT) in the genome of T. marianensis JCM 10246. AiiT has 59.7%, 21.2%, and 11.2% identity to AhlS from Solibacillus silvestris, AiiA from Bacillus cereus, and AidC from Chryseobacterium sp., respectively. Homologs of aiiT were also found in Thermaerobacter nagasakiensis, T. composti, and T. subterraneus. A purified AiiT-maltose binding fusion showed high AHL-degrading activity against N-hexanoyl-L-homoserine lactone, N-octanoyl-L-homoserine lactone, and N-decanoyl-L-homoserine lactone at temperatures ranging from 40 to 80 °C. HPLC analysis revealed that AiiT functions as an AHL-lactonase that catalyzes AHL ring opening by hydrolyzing lactones. AiiT displayed maximal activity at high temperatures (60-80 °C) and showed higher thermostability than other AHL lactonases.
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Affiliation(s)
- Tomohiro Morohoshi
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya 321-8585, Japan.
| | - Yoshiaki Tominaga
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya 321-8585, Japan
| | - Nobutaka Someya
- Hokkaido Agricultural Research Center (HARC), National Agriculture and Food Research Organization (NARO), 9-4 Shinsei-minami, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Tsukasa Ikeda
- Department of Material and Environmental Chemistry, Graduate School of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya 321-8585, Japan
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Simithy J, Reeve N, Hobrath JV, Reynolds RC, Calderón AI. Identification of shikimate kinase inhibitors among anti-Mycobacterium tuberculosis compounds by LC-MS. Tuberculosis (Edinb) 2014; 94:152-8. [DOI: 10.1016/j.tube.2013.12.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 12/14/2013] [Accepted: 12/19/2013] [Indexed: 11/27/2022]
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Mikoulinskaia GV, Taran SA, Skoblov YS, Feofanov SA. The study of the bacteriophage T5 deoxynucleoside monophosphate kinase active site by site-directed mutagenesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013. [DOI: 10.1134/s1068162013060071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Blanco B, Prado V, Lence E, Otero JM, Garcia-Doval C, van Raaij MJ, Llamas-Saiz AL, Lamb H, Hawkins AR, González-Bello C. Mycobacterium tuberculosis shikimate kinase inhibitors: design and simulation studies of the catalytic turnover. J Am Chem Soc 2013; 135:12366-76. [PMID: 23889343 DOI: 10.1021/ja405853p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shikimate kinase (SK) is an essential enzyme in several pathogenic bacteria and does not have any counterpart in human cells, thus making it an attractive target for the development of new antibiotics. The key interactions of the substrate and product binding and the enzyme movements that are essential for catalytic turnover of the Mycobacterium tuberculosis shikimate kinase enzyme (Mt-SK) have been investigated by structural and computational studies. Based on these studies several substrate analogs were designed and assayed. The crystal structure of Mt-SK in complex with ADP and one of the most potent inhibitors has been solved at 2.15 Å. These studies reveal that the fixation of the diaxial conformation of the C4 and C5 hydroxyl groups recognized by the enzyme or the replacement of the C3 hydroxyl group in the natural substrate by an amino group is a promising strategy for inhibition because it causes a dramatic reduction of the flexibility of the LID and shikimic acid binding domains. Molecular dynamics simulation studies showed that the product is expelled from the active site by three arginines (Arg117, Arg136, and Arg58). This finding represents a previously unknown key role of these conserved residues. These studies highlight the key role of the shikimic acid binding domain in the catalysis and provide guidance for future inhibitor designs.
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Affiliation(s)
- Beatriz Blanco
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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26
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Rosado LA, Vasconcelos IB, Palma MS, Frappier V, Najmanovich RJ, Santos DS, Basso LA. The mode of action of recombinant Mycobacterium tuberculosis shikimate kinase: kinetics and thermodynamics analyses. PLoS One 2013; 8:e61918. [PMID: 23671579 PMCID: PMC3646032 DOI: 10.1371/journal.pone.0061918] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 03/14/2013] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis remains as one of the main cause of mortality worldwide due to a single infectious agent, Mycobacterium tuberculosis. The aroK-encoded M. tuberculosis Shikimate Kinase (MtSK), shown to be essential for survival of bacilli, catalyzes the phosphoryl transfer from ATP to the carbon-3 hydroxyl group of shikimate (SKH), yielding shikimate-3-phosphate and ADP. Here we present purification to homogeneity, and oligomeric state determination of recombinant MtSK. Biochemical and biophysical data suggest that the chemical reaction catalyzed by monomeric MtSK follows a rapid-equilibrium random order of substrate binding, and ordered product release. Isothermal titration calorimetry (ITC) for binding of ligands to MtSK provided thermodynamic signatures of non-covalent interactions to each process. A comparison of steady-state kinetics parameters and equilibrium dissociation constant value determined by ITC showed that ATP binding does not increase the affinity of MtSK for SKH. We suggest that MtSK would more appropriately be described as an aroL-encoded type II shikimate kinase. Our manuscript also gives thermodynamic description of SKH binding to MtSK and data for the number of protons exchanged during this bimolecular interaction. The negative value for the change in constant pressure heat capacity (ΔCp) and molecular homology model building suggest a pronounced contribution of desolvation of non-polar groups upon binary complex formation. Thermodynamic parameters were deconvoluted into hydrophobic and vibrational contributions upon MtSK:SKH binary complex formation. Data for the number of protons exchanged during this bimolecular interaction are interpreted in light of a structural model to try to propose the likely amino acid side chains that are the proton donors to bulk solvent following MtSK:SKH complex formation.
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Affiliation(s)
- Leonardo Astolfi Rosado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Igor Bordin Vasconcelos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Mário Sérgio Palma
- Laboratório de Biologia Estrutural e Zooquímica, Centro de Estudos de Insetos Sociais, Departamento de Biologia, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Vincent Frappier
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Rafael Josef Najmanovich
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Diógenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Porto Alegre, RS, Brazil
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Emptage RP, Pemble CW, York JD, Raetz CRH, Zhou P. Mechanistic characterization of the tetraacyldisaccharide-1-phosphate 4'-kinase LpxK involved in lipid A biosynthesis. Biochemistry 2013; 52:2280-90. [PMID: 23464738 DOI: 10.1021/bi400097z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The sixth step in the lipid A biosynthetic pathway involves phosphorylation of the tetraacyldisaccharide-1-phosphate (DSMP) intermediate by the cytosol-facing inner membrane kinase LpxK, a member of the P-loop-containing nucleoside triphosphate (NTP) hydrolase superfamily. We report the kinetic characterization of LpxK from Aquifex aeolicus and the crystal structures of LpxK in complex with ATP in a precatalytic binding state, the ATP analogue AMP-PCP in the closed catalytically competent conformation, and a chloride anion revealing an inhibitory conformation of the nucleotide-binding P-loop. We demonstrate that LpxK activity in vitro requires the presence of a detergent micelle and formation of a ternary LpxK-ATP/Mg(2+)-DSMP complex. Using steady-state kinetics, we have identified crucial active site residues, leading to the proposal that the interaction of D99 with H261 acts to increase the pKa of the imidazole moiety, which in turn serves as the catalytic base to deprotonate the 4'-hydroxyl of the DSMP substrate. The fact that an analogous mechanism has not yet been observed for other P-loop kinases highlights LpxK as a distinct member of the P-loop kinase family, a notion that is also reflected through its localization at the membrane, lipid substrate, and overall structure.
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Affiliation(s)
- Ryan P Emptage
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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28
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Grangeasse C, Nessler S, Mijakovic I. Bacterial tyrosine kinases: evolution, biological function and structural insights. Philos Trans R Soc Lond B Biol Sci 2012; 367:2640-55. [PMID: 22889913 DOI: 10.1098/rstb.2011.0424] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Reversible protein phosphorylation is a major mechanism in the regulation of fundamental signalling events in all living organisms. Bacteria have been shown to possess a versatile repertoire of protein kinases, including histidine and aspartic acid kinases, serine/threonine kinases, and more recently tyrosine and arginine kinases. Tyrosine phosphorylation is today recognized as a key regulatory device of bacterial physiology, linked to exopolysaccharide production, virulence, stress response and DNA metabolism. However, bacteria have evolved tyrosine kinases that share no resemblance with their eukaryotic counterparts and are unique in exploiting the ATP/GTP-binding Walker motif to catalyse autophosphorylation and substrate phosphorylation on tyrosine. These enzymes, named BY-kinases (for Bacterial tYrosine kinases), have been identified in a majority of sequenced bacterial genomes, and to date no orthologues have been found in Eukarya. The aim of this review was to present the most recent knowledge about BY-kinases by focusing primarily on their evolutionary origin, structural and functional aspects, and emerging regulatory potential based on recent bacterial phosphoproteomic studies.
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Affiliation(s)
- Christophe Grangeasse
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, CNRS, Université de Lyon, UMR 5086, 7 passage du Vercors, 69367 Lyon, France.
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29
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Donnini S, De Nisi P, Gabotti D, Tato L, Zocchi G. Adaptive strategies of Parietaria diffusa (M.&K.) to calcareous habitat with limited iron availability. PLANT, CELL & ENVIRONMENT 2012; 35:1171-84. [PMID: 22229865 DOI: 10.1111/j.1365-3040.2012.02481.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The study of native plants growing in hostile environments is useful to understand how these species respond to stress conditions. Parietaria diffusa (M.&K.) is able to survive in highly calcareous soils and extreme environments, such as house walls, without displaying any chlorotic symptoms. Here, we have investigated the existence of Strategy I complementary/alternative mechanism(s) involved in Fe solubilization and uptake and responsible for Parietaria's extraordinary efficiency. After assessing the specific traits involved in a calcicole-behaviour in the field, we have grown plants in conditions of Fe deficiency, either direct (-Fe) or induced by the presence of bicarbonate (+FeBic). Then, the growth performance, physiological and biochemical responses of the plants were investigated. The study shows that in Parietaria+FeBic, the classical responses of Strategy I plants are activated to a lower extent than in -Fe. In addition, there is a greater production of phenolics and organic acids that are both exuded and accumulated in the roots, which in turn show structures similar to 'proteoid-like roots'. We suggest that in the presence of this constraint, Parietaria undergoes some metabolic rearrangements that involve PEP-consuming reactions and an enhancement of the shikimate pathway.
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Affiliation(s)
- Silvia Donnini
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy
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30
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Cheng WC, Chen YF, Wang HJ, Hsu KC, Lin SC, Chen TJ, Yang JM, Wang WC. Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism. PLoS One 2012; 7:e33481. [PMID: 22438938 PMCID: PMC3306394 DOI: 10.1371/journal.pone.0033481] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 02/14/2012] [Indexed: 12/13/2022] Open
Abstract
Shikimate kinase (SK), which catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP, is the enzyme in the fifth step of the shikimate pathway for biosynthesis of aromatic amino acids. This pathway is present in bacteria, fungi, and plants but absent in mammals and therefore represents an attractive target pathway for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here we investigated the detailed structure–activity relationship of SK from Helicobacter pylori (HpSK). Site-directed mutagenesis and isothermal titration calorimetry studies revealed critical conserved residues (D33, F48, R57, R116, and R132) that interact with shikimate and are therefore involved in catalysis. Crystal structures of HpSK·SO4, R57A, and HpSK•shikimate-3-phosphate•ADP show a characteristic three-layer architecture and a conformationally elastic region consisting of F48, R57, R116, and R132, occupied by shikimate. The structure of the inhibitor complex, E114A•162535, was also determined, which revealed a dramatic shift in the elastic LID region and resulted in conformational locking into a distinctive form. These results reveal considerable insight into the active-site chemistry of SKs and a selective inhibitor-induced-fit mechanism.
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Affiliation(s)
- Wen-Chi Cheng
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Yen-Fu Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Hung-Jung Wang
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Kai-Cheng Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shuang-Chih Lin
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Tzu-Jung Chen
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Jinn-Moon Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
- * E-mail: (J-MY); (W-CW)
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
- Biomedical Science and Engineering Center, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (J-MY); (W-CW)
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Surade S, Blundell T. Structural Biology and Drug Discovery of Difficult Targets: The Limits of Ligandability. ACTA ACUST UNITED AC 2012; 19:42-50. [DOI: 10.1016/j.chembiol.2011.12.013] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 11/08/2011] [Accepted: 12/09/2011] [Indexed: 02/05/2023]
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Fucile G, Garcia C, Carlsson J, Sunnerhagen M, Christendat D. Structural and biochemical investigation of two Arabidopsis shikimate kinases: the heat-inducible isoform is thermostable. Protein Sci 2011; 20:1125-36. [PMID: 21520319 PMCID: PMC3149186 DOI: 10.1002/pro.640] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/08/2011] [Accepted: 04/08/2011] [Indexed: 11/12/2022]
Abstract
The expression of plant shikimate kinase (SK; EC 2.7.1.71), an intermediate step in the shikimate pathway to aromatic amino acid biosynthesis, is induced under specific conditions of environmental stress and developmental requirements in an isoform-specific manner. Despite their important physiological role, experimental structures of plant SKs have not been determined and the biochemical nature of plant SK regulation is unknown. The Arabidopsis thaliana genome encodes two SKs, AtSK1 and AtSK2. We demonstrate that AtSK2 is highly unstable and becomes inactivated at 37 °C whereas the heat-induced isoform, AtSK1, is thermostable and fully active under identical conditions at this temperature. We determined the crystal structure of AtSK2, the first SK structure from the plant kingdom, and conducted biophysical characterizations of both AtSK1 and AtSK2 towards understanding this mechanism of thermal regulation. The crystal structure of AtSK2 is generally conserved with bacterial SKs with the addition of a putative regulatory phosphorylation motif forming part of the adenosine triphosphate binding site. The heat-induced isoform, AtSK1, forms a homodimer in solution, the formation of which facilitates its relative thermostability compared to AtSK2. In silico analyses identified AtSK1 site variants that may contribute to AtSK1 stability. Our findings suggest that AtSK1 performs a unique function under heat stress conditions where AtSK2 could become inactivated. We discuss these findings in the context of regulating metabolic flux to competing downstream pathways through SK-mediated control of steady state concentrations of shikimate.
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Affiliation(s)
- Geoffrey Fucile
- Department of Cell and Systems Biology, University of TorontoOntario, Canada
| | - Christel Garcia
- Department of Cell and Systems Biology, University of TorontoOntario, Canada
| | - Jonas Carlsson
- Department of Physics, Chemistry and Biology, Linköping UniversityLinköping, Sweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping UniversityLinköping, Sweden
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of TorontoOntario, Canada
- Center for the Analysis of Genome Evolution and Function, University of TorontoOntario, Canada
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Mulabagal V, Calderón AI. Development of an Ultrafiltration-Liquid Chromatography/Mass Spectrometry (UF-LC/MS) Based Ligand-Binding Assay and an LC/MS Based Functional Assay for Mycobacterium tuberculosis Shikimate Kinase. Anal Chem 2010; 82:3616-21. [DOI: 10.1021/ac902849g] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vanisree Mulabagal
- Department of Pharmacal Sciences, Harrison School of Pharmacy, 4306B Walker Building, Auburn University, Auburn, Alabama 36849
| | - Angela I. Calderón
- Department of Pharmacal Sciences, Harrison School of Pharmacy, 4306B Walker Building, Auburn University, Auburn, Alabama 36849
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Fucile G, Falconer S, Christendat D. Evolutionary diversification of plant shikimate kinase gene duplicates. PLoS Genet 2008; 4:e1000292. [PMID: 19057671 PMCID: PMC2593004 DOI: 10.1371/journal.pgen.1000292] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 11/03/2008] [Indexed: 01/03/2023] Open
Abstract
Shikimate kinase (SK; EC 2.7.1.71) catalyzes the fifth reaction of the shikimate pathway, which directs carbon from the central metabolism pool to a broad range of secondary metabolites involved in plant development, growth, and stress responses. In this study, we demonstrate the role of plant SK gene duplicate evolution in the diversification of metabolic regulation and the acquisition of novel and physiologically essential function. Phylogenetic analysis of plant SK homologs resolves an orthologous cluster of plant SKs and two functionally distinct orthologous clusters. These previously undescribed genes, shikimate kinase-like 1 (SKL1) and -2 (SKL2), do not encode SK activity, are present in all major plant lineages, and apparently evolved under positive selection following SK gene duplication over 400 MYA. This is supported by functional assays using recombinant SK, SKL1, and SKL2 from Arabidopsis thaliana (At) and evolutionary analyses of the diversification of SK-catalytic and -substrate binding sites based on theoretical structure models. AtSKL1 mutants yield albino and novel variegated phenotypes, which indicate SKL1 is required for chloroplast biogenesis. Extant SKL2 sequences show a strong genetic signature of positive selection, which is enriched in a protein–protein interaction module not found in other SK homologs. We also report the first kinetic characterization of plant SKs and show that gene expression diversification among the AtSK inparalogs is correlated with developmental processes and stress responses. This study examines the functional diversification of ancient and recent plant SK gene duplicates and highlights the utility of SKs as scaffolds for functional innovation. Gene duplicates provide an opportunity for functional innovation by buffering their ancestral function. Mutations or genomic rearrangements altering when and where the duplicates are expressed, or the structure/function of the products encoded by the genes, can provide a selective advantage to the organism and are subsequently retained. In this study, we demonstrate that duplicates of genes encoding the metabolic enzyme shikimate kinase (SK) in plants have evolved to acquire novel gene product functions and novel gene expression patterns. We introduce two ancient genes, SKL1 and SKL2, present in all higher plant groups that were previously overlooked due to their overall similarity to the ancestral SKs from which they originated. SKL1 mutants in the model plant Arabidopsis indicate this gene is required for chloroplast biogenesis. We show that SKL2 acquired a protein–protein interaction domain that is evolving under positive selection. We also show that SK duplicates that retained their ancestral enzyme function have acquired new expression patterns correlated with developmental processes and stress responses. These findings demonstrate that plant SK evolution has played an important role in both the acquisition of novel gene function as well as the diversification of metabolic regulation.
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Affiliation(s)
- Geoffrey Fucile
- Department of Cell and Systems Biology, University of Toronto, Canada
| | - Shannon Falconer
- Department of Cell and Systems Biology, University of Toronto, Canada
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, Canada
- * E-mail:
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35
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Olivares-Illana V, Meyer P, Bechet E, Gueguen-Chaignon V, Soulat D, Lazereg-Riquier S, Mijakovic I, Deutscher J, Cozzone AJ, Laprévote O, Morera S, Grangeasse C, Nessler S. Structural basis for the regulation mechanism of the tyrosine kinase CapB from Staphylococcus aureus. PLoS Biol 2008; 6:e143. [PMID: 18547145 PMCID: PMC2422856 DOI: 10.1371/journal.pbio.0060143] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 04/28/2008] [Indexed: 12/19/2022] Open
Abstract
Bacteria were thought to be devoid of tyrosine-phosphorylating enzymes. However, several tyrosine kinases without similarity to their eukaryotic counterparts have recently been identified in bacteria. They are involved in many physiological processes, but their accurate functions remain poorly understood due to slow progress in their structural characterization. They have been best characterized as copolymerases involved in the synthesis and export of extracellular polysaccharides. These compounds play critical roles in the virulence of pathogenic bacteria, and bacterial tyrosine kinases can thus be considered as potential therapeutic targets. Here, we present the crystal structures of the phosphorylated and unphosphorylated states of the tyrosine kinase CapB from the human pathogen Staphylococcus aureus together with the activator domain of its cognate transmembrane modulator CapA. This first high-resolution structure of a bacterial tyrosine kinase reveals a 230-kDa ring-shaped octamer that dissociates upon intermolecular autophosphorylation. These observations provide a molecular basis for the regulation mechanism of the bacterial tyrosine kinases and give insights into their copolymerase function. An idiosyncratic new class of bacterial enzymes, bacterial tyrosine-kinases (BY-kinases), has been characterized. These enzymes, which are involved in an increasing number of physiological processes ranging from stress resistance to pathogenicity, share no sequence similarities with eukaryotic kinases, and their function remains largely unknown. They have nevertheless been described to undergo autophosphorylation on a C-terminal tyrosine cluster and to phosphorylate endogenous protein substrates. We describe here the first crystal structure of a bacterial tyrosine kinase, namely CapB from the pathogen Staphylococcus aureus, in complex with the cytoplasmic domain of the transmembrane stimulatory protein CapA. Our data explain the activation mechanism of CapB by CapA and allow us to propose a regulatory mechanism based on intermolecular autophosphorylation. These results also give new insights onto the phosphorylation of the endogenous substrate CapO, an enzyme involved in the synthesis of polysaccharide precursors. CapA and CapB, among others, are involved as copolymerases in the synthesis of extracellular polysaccharides that are thought to be potent virulence factors. Thus, these structural data provide the basis for designing specific inhibitors for these enzymes, which constitute an original and attractive target for the development of new drugs to treat infectious diseases. Structural analysis of a conserved bacterial tyrosine kinase fromStaphylococcus aureus provides the basis for deciphering its regulatory mechanism, leading to a model for its implication in extracellular polysaccharide synthesis.
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Affiliation(s)
| | - Philippe Meyer
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
| | - Emmanuelle Bechet
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
| | | | - Didier Soulat
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
| | | | - Ivan Mijakovic
- Center for Microbial Biotechnology, BioCentrum, Technical University of Denmark, Lyngby, Denmark
| | - Josef Deutscher
- Laboratory of Microbiology and Molecular Genetics, AgroParisTech, CNRS, INRA, Thiverval-Grignon, France
| | - Alain J Cozzone
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
| | - Olivier Laprévote
- Institut de Chimie des Substances Naturelles, CNRS, Gif sur Yvette, France
| | - Solange Morera
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
| | - Christophe Grangeasse
- Institut de Biologie et Chimie des Protéines, CNRS, Université Lyon 1, Université de Lyon, Lyon, France
- * To whom correspondence should be addressed. E-mail: (CG); (SN)
| | - Sylvie Nessler
- Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
- * To whom correspondence should be addressed. E-mail: (CG); (SN)
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36
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Abstract
This chapter describes in detail the genes and proteins of Escherichia coli involved in the biosynthesis and transport of the three aromatic amino acids tyrosine, phenylalanine, and tryptophan. It provides a historical perspective on the elaboration of the various reactions of the common pathway converting erythrose-4-phosphate and phosphoenolpyruvate to chorismate and those of the three terminal pathways converting chorismate to phenylalanine, tyrosine, and tryptophan. The regulation of key reactions by feedback inhibition, attenuation, repression, and activation are also discussed. Two regulatory proteins, TrpR (108 amino acids) and TyrR (513 amino acids), play a major role in transcriptional regulation. The TrpR protein functions only as a dimer which, in the presence of tryptophan, represses the expression of trp operon plus four other genes (the TrpR regulon). The TyrR protein, which can function both as a dimer and as a hexamer, regulates the expression of nine genes constituting the TyrR regulon. TyrR can bind each of the three aromatic amino acids and ATP and under their influence can act as a repressor or activator of gene expression. The various domains of this protein involved in binding the aromatic amino acids and ATP, recognizing DNA binding sites, interacting with the alpha subunit of RNA polymerase, and changing from a monomer to a dimer or a hexamer are all described. There is also an analysis of the various strategies which allow TyrR in conjunction with particular amino acids to differentially affect the expression of individual genes of the TyrR regulon.
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Structure-based prediction of Mycobacterium tuberculosis shikimate kinase inhibitors by high-throughput virtual screening. Bioorg Med Chem Lett 2008; 18:3152-7. [DOI: 10.1016/j.bmcl.2008.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 04/25/2008] [Accepted: 05/01/2008] [Indexed: 10/22/2022]
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38
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Roy S, Fortin M, Gagnon J, Ghinet MG, Lehoux JG, Dupuis G, Brzezinski R. Quantitative fluorometric analysis of the protective effect of chitosan on thermal unfolding of catalytically active native and genetically-engineered chitosanases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:975-84. [PMID: 17644457 DOI: 10.1016/j.bbapap.2007.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 05/17/2007] [Accepted: 05/29/2007] [Indexed: 10/23/2022]
Abstract
We have taken advantage of the intrinsic fluorescence properties of chitosanases to rapidly and quantitatively evaluate the protective effect of chitosan against thermal denaturation of chitosanases. The studies were done using wild type chitosanases N174 produced by Streptomyces sp. N174 and SCO produced by Streptomyces coelicolor A3(2). In addition, two mutants of N174 genetically engineered by single amino acid substitutions (A104L and K164R) and one "consensus" (N174-CONS) chitosanase designed by multiple amino acid substitutions of N174 were analyzed. Chitosan used had a weight average molecular weight (Mw) of 220 kDa and was 85% deacetylated. Results showed a pH and concentration-dependent protective effect of chitosan in all the cases. However, the extent of thermal protection varied depending on chitosanases, suggesting that key amino acid residues contributed to resistance to heat denaturation. The transition temperatures (T(m)) of N174 were 54 degrees C and 69.5 degrees C in the absence and presence (6 g/l) of chitosan, respectively. T(m) were increased by 11.6 degrees C (N174-CONS), 13.8 degrees C (CSN-A104L), 15.6 degrees C (N174-K164R) and 25.2 degrees C (SCO) in the presence of chitosan (6 g/l). The thermal protective effect was attributed to an enzyme-ligand thermostabilization mechanism since it was not mimicked by the presence of anionic (carboxymethyl cellulose, heparin) or cationic (polyethylene imine) polymers, polyhydroxylated (glycerol, sorbitol) compounds or inorganic salts. Furthermore, the data from fluorometry experiments were in agreement with those obtained by analysis of reaction time-courses performed at 61 degrees C in which case CSN-A104L was rapidly inactivated whereas N174, N174-CONS and N174-K164R remained active over a reaction time of 90 min. This study presents evidence that (1) the fluorometric determination of T(m) in the presence of chitosan is a reliable technique for a rapid assessment of the thermal behavior of chitosanases, (2) it is applicable to structure-function studies of mutant chitosanases and, (3) it can be useful to provide an insight into the mechanism by which mutations can influence chitosanase stability.
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Affiliation(s)
- Sébastien Roy
- Diversified Natural Products Research Laboratory, Institut de Pharmacologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4.
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39
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Han C, Zhang J, Chen L, Chen K, Shen X, Jiang H. Discovery of Helicobacter pylori shikimate kinase inhibitors: Bioassay and molecular modeling. Bioorg Med Chem 2007; 15:656-62. [PMID: 17098431 DOI: 10.1016/j.bmc.2006.10.058] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 10/26/2006] [Accepted: 10/28/2006] [Indexed: 11/29/2022]
Abstract
Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway and catalyzes the phosphate transfer from ATP to shikimate in generating shikimate 3-phosphate and ADP. SK has been developed as a promising target for the discovery of antibacterial agents. In this report, two small molecular inhibitors (compound 1, 3-methoxy-4-{[2-({2-methoxy-4-[(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy}methyl)benzyl]oxy}benzaldehyde; compound 2, 5-bromo-2-(5-{[1-(3,4-dichlorophenyl)-3,5-dioxo-4-pyrazolidinylidene]methyl}-2-furyl)benzoic acid) against Helicobacter pylori SK (HpSK) were successfully identified with IC(50) values of 5.5+/-1.2 and 6.4+/-0.4 microM, respectively. The inhibition kinetics shows that compound 1 is a noncompetitive inhibitor with respect to both shikimate and MgATP, and compound 2 is a competitive inhibitor toward shikimate and noncompetitive inhibitor with respect to MgATP. The surface plasmon resonance (SPR) technology based analysis reveals that the equilibrium dissociation constants (K(D)s) of compounds 1 and 2 with HpSK enzyme are 4.39 and 3.74 microM, respectively. The molecular modeling and docking of two inhibitors with HpSK reveals that the active site of HpSK is rather roomy and deep, forming an L-shape channel on the surface of the protein, and compound 1 prefers the corner area of L-shape channel, while compound 2 binds the short arm of the channel of SK in the binding interactions. It is expected that our current work might supply useful information for the development of novel SK inhibitors.
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Affiliation(s)
- Cong Han
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
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40
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Dias MVB, Faím LM, Vasconcelos IB, de Oliveira JS, Basso LA, Santos DS, de Azevedo WF. Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:1-6. [PMID: 17183161 PMCID: PMC2330112 DOI: 10.1107/s1744309106046823] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Accepted: 11/06/2006] [Indexed: 11/10/2022]
Abstract
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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Affiliation(s)
- Marcio Vinicius Bertacine Dias
- Programa de Pós-Graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000, Brazil
| | - Lívia Maria Faím
- Programa de Pós-Graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000, Brazil
| | - Igor Bordin Vasconcelos
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisa em Biologia Molecular e Funcional, Porto Alegre, RS, Brazil
| | - Jaim Simões de Oliveira
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisa em Biologia Molecular e Funcional, Porto Alegre, RS, Brazil
| | - Luiz Augusto Basso
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisa em Biologia Molecular e Funcional, Porto Alegre, RS, Brazil
| | - Diógenes Santiago Santos
- Pontifícia Universidade Católica do Rio Grande do Sul, Centro de Pesquisa em Biologia Molecular e Funcional, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga, 6681 Porto Alegre-RS, CEP 90619-900, Brazil
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41
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Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD. Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis. J Mol Biol 2006; 364:411-23. [PMID: 17020768 DOI: 10.1016/j.jmb.2006.09.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2006] [Revised: 08/31/2006] [Accepted: 09/01/2006] [Indexed: 10/24/2022]
Abstract
The structural mechanism of the catalytic functioning of shikimate kinase from Mycobacterium tuberculosis was investigated on the basis of a series of high-resolution crystal structures corresponding to individual steps in the enzymatic reaction. The catalytic turnover of shikimate and ATP into the products shikimate-3-phosphate and ADP, followed by release of ADP, was studied in the crystalline environment. Based on a comparison of the structural states before initiation of the reaction and immediately after the catalytic step, we derived a structural model of the transition state that suggests that phosphoryl transfer proceeds with inversion by an in-line associative mechanism. The random sequential binding of shikimate and nucleotides is associated with domain movements. We identified a synergic mechanism by which binding of the first substrate may enhance the affinity for the second substrate.
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Affiliation(s)
- Marcus D Hartmann
- Max Planck Unit for Structural Molecular Biology, MPG-ASMB c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
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42
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Dhaliwal B, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK. Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:710-5. [PMID: 16880539 PMCID: PMC2242935 DOI: 10.1107/s174430910602447x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Accepted: 06/26/2006] [Indexed: 12/02/2022]
Abstract
The crystal structure of Staphylococcus aureus cytidine monophosphate kinase (CMK) in complex with cytidine 5'-monophosphate (CMP) has been determined at 2.3 angstroms resolution. The active site reveals novel features when compared with two orthologues of known structure. Compared with the Streptococcus pneumoniae CMK solution structure of the enzyme alone, S. aureus CMK adopts a more closed conformation, with the NMP-binding domain rotating by approximately 16 degrees towards the central pocket of the molecule, thereby assembling the active site. Comparing Escherichia coli and S. aureus CMK-CMP complex structures reveals differences within the active site, including a previously unreported indirect interaction of CMP with Asp33, the replacement of a serine residue involved in the binding of CDP by Ala12 in S. aureus CMK and an additional sulfate ion in the E. coli CMK active site. The detailed understanding of the stereochemistry of CMP binding to CMK will assist in the design of novel inhibitors of the enzyme. Inhibitors are required to treat the widespread hospital infection methicillin-resistant S. aureus (MRSA), currently a major public health concern.
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Affiliation(s)
- Balvinder Dhaliwal
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Jingshan Ren
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
| | - Michael Lockyer
- Arrow Therapeutics, Britannia House, 7 Trinity Street, London SE1 1DA, England
| | - Ian Charles
- Arrow Therapeutics, Britannia House, 7 Trinity Street, London SE1 1DA, England
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Catherine Cookson Building, Medical School, Framlington Place, University of Newcastle-upon-Tyne, Newcastle-upon-Tyne NE2 4HH, England
| | - David K. Stammers
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, England
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43
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Kotaka M, Dhaliwal B, Ren J, Nichols CE, Angell R, Lockyer M, Hawkins AR, Stammers DK. Structures of S. aureus thymidylate kinase reveal an atypical active site configuration and an intermediate conformational state upon substrate binding. Protein Sci 2006; 15:774-84. [PMID: 16522804 PMCID: PMC2242479 DOI: 10.1110/ps.052002406] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to human health, particularly through hospital acquired infection. The spread of MRSA means that novel targets are required to develop potential inhibitors to combat infections caused by such drug-resistant bacteria. Thymidylate kinase (TMK) is attractive as an antibacterial target as it is essential for providing components for DNA synthesis. Here, we report crystal structures of unliganded and thymidylate-bound forms of S. aureus thymidylate kinase (SaTMK). His-tagged and untagged SaTMK crystallize with differing lattice packing and show variations in conformational states for unliganded and thymidylate (TMP) bound forms. In addition to open and closed forms of SaTMK, an intermediate conformation in TMP binding is observed, in which the site is partially closed. Analysis of these structures indicates a sequence of events upon TMP binding, with helix alpha3 shifting position initially, followed by movement of alpha2 to close the substrate site. In addition, we observe significant conformational differences in the TMP-binding site in SaTMK as compared to available TMK structures from other bacterial species, Escherichia coli and Mycobacterium tuberculosis as well as human TMK. In SaTMK, Arg 48 is situated at the base of the TMP-binding site, close to the thymine ring, whereas a cis-proline occupies the equivalent position in other TMKs. The observed TMK structural differences mean that design of compounds highly specific for the S. aureus enzyme looks possible; such inhibitors could minimize the transfer of drug resistance between different bacterial species.
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Affiliation(s)
- Masayo Kotaka
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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44
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Cheng WC, Chang YN, Wang WC. Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase. J Bacteriol 2005; 187:8156-63. [PMID: 16291688 PMCID: PMC1291267 DOI: 10.1128/jb.187.23.8156-8163.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shikimate kinase (EC 2.7.1.71) catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid in the presence of ATP. As the fifth key step in the shikimate pathway for aromatic amino acid biosynthesis in bacteria, fungi, and plants, but not mammals, shikimate kinase represents an attractive target for the development of new antimicrobial agents, herbicides, and antiparasitic agents. Here, we report the 1.8-Angstroms crystal structure of Helicobacter pylori shikimate kinase (HpSK). The crystal structure shows a three-layer alpha/beta fold consisting of a central sheet of five parallel beta-strands flanked by seven alpha-helices. An HpSK-shikimate-PO(4) complex was also determined and refined to 2.3 Angstroms, revealing induced-fit movement from an open to a closed form on substrate binding. Shikimate is located above a short 3(10) helix formed by a strictly conserved motif (GGGXV) after beta(3). Moreover, several highly conserved charged residues including Asp33 (in a conserved DT/SD motif), Arg57, and Arg132 (interacting with shikimate) are identified, guiding the development of novel inhibitors of shikimate kinase.
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Affiliation(s)
- Wen-Chi Cheng
- Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing Hua University, Hsinchu, Taiwan
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45
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Wu Q, Gee CL, Lin F, Tyndall JD, Martin JL, Grunewald GL, McLeish MJ. Structural, Mutagenic, and Kinetic Analysis of the Binding of Substrates and Inhibitors of Human Phenylethanolamine N-Methyltransferase. J Med Chem 2005; 48:7243-52. [PMID: 16279783 DOI: 10.1021/jm050568o] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The X-ray structure of human phenylethanolamine N-methyltransferase (hPNMT) complexed with its product, S-adenosyl-L-homocysteine (4), and the most potent inhibitor reported to date, SK&F 64139 (7), was used to identify the residues involved in inhibitor binding. Four of these residues, Val53, Lys57, Glu219 and Asp267, were replaced, in turn, with alanine. All variants had increased Km values for phenylethanolamine (10), but only D267A showed a noteworthy (20-fold) decrease in its kcat value. Both WT hPNMT and D267A had similar kcat values for a rigid analogue, anti-9-amino-6-(trifluoromethyl)benzonorbornene (12), suggesting that Asp267 plays an important role in positioning the substrate but does not participate directly in catalysis. The Ki values for the binding of inhibitors such as 7 to the E219A and D267A variants increased by 2-3 orders of magnitude. Further, the inhibitors were shown to bind up to 50-fold more tightly in the presence of S-adenosyl-L-methionine (3), suggesting that the binding of the latter brings about a conformational change in the enzyme.
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Affiliation(s)
- Qian Wu
- Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, USA
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46
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Dhaliwal B, Nichols CE, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK. Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase. FEBS Lett 2004; 574:49-54. [PMID: 15358538 DOI: 10.1016/j.febslet.2004.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2004] [Revised: 07/07/2004] [Accepted: 08/04/2004] [Indexed: 11/19/2022]
Abstract
The X-ray crystal structure of Mycobacterium tuberculosis shikimate kinase (SK) with bound shikimate and adenosine diphosphate (ADP) has been determined to a resolution of 2.15 A. The binding of shikimate in a shikimate kinase crystal structure has not previously been reported. The substrate binds in a pocket lined with hydrophobic residues and interacts with several highly conserved charged residues including Asp34, Arg58, Glu61 and Arg136 which project into the cavity. Comparisons of our ternary SK-ADP-shikimate complex with an earlier binary SK-ADP complex show that conformational changes occur on shikimate binding with the substrate-binding domain rotating by 10 degrees. Detailed knowledge of shikimate binding is an important step in the design of inhibitors of SK, which have potential as novel anti-tuberculosis agents.
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Affiliation(s)
- Balvinder Dhaliwal
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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47
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Cerasoli E, Kelly SM, Coggins JR, Lapthorn AJ, Clarke DT, Price NC. Effects of salts on the function and conformational stability of shikimate kinase. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1648:43-54. [PMID: 12758146 DOI: 10.1016/s1570-9639(03)00110-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The unfolding of shikimate kinase (SK) from Erwinia chrysanthemi by urea and its subsequent refolding on dilution of the denaturing agent has been studied in detail [Eur. J. Biochem. 269 (2002) 2124]. Comparison of the effects of urea on the enzyme with those of guanidinium chloride (GdmCl) and NaCl indicated that chloride ions significantly weakened the binding of shikimate. This finding prompted a more detailed examination of the effects of salts on the structure, function and stability of the enzyme; the effects of NaCl and Na(2)SO(4) were investigated in detail. These salts have very small effects on the secondary structure as judged by far UV CD circular dichroism (CD), although the near UV CD spectra suggest that some limited changes in the environment of aromatic amino acids may occur. Both salts inhibit SK activity and analysis of the kinetic and substrate binding parameters point to a complex mechanism for the inhibition. Inclusion of salts leads to a marked stabilisation against unfolding of the enzyme by urea. When the enzyme is unfolded by incubation in 4 M urea, addition of NaCl or Na(2)SO(4) leads to a relatively slow refolding of the enzyme as judged by the regain of native-like CD and fluorescence. In addition, the refolded enzyme can bind shikimate, though more weakly than the native enzyme. However, the refolded enzyme does not appear to be capable of binding nucleotides, nor does it possess detectable catalytic activity. The refolding process brought about by addition of salt in the presence of 4 M urea is not associated with any change in the fluorescence of the probe 8-anilino-1-naphthalenesulfonic acid (ANS), indicating that an intermediate formed by hydrophobic collapse is unlikely to be significantly populated. The results point to both specific and general effects of salts on SK. These are discussed in the light of the structural information available on the enzyme.
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Affiliation(s)
- Eleonora Cerasoli
- Division of Biochemistry and Molecular Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, Joseph Black Building, Scotland, UK
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48
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Pilloff D, Dabovic K, Romanowski MJ, Bonanno JB, Doherty M, Burley SK, Leyh TS. The kinetic mechanism of phosphomevalonate kinase. J Biol Chem 2003; 278:4510-5. [PMID: 12424232 DOI: 10.1074/jbc.m210551200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphomevalonate kinase catalyzes an essential step in the so-called mevalonate pathway, which appears to be the sole pathway for the biosynthesis of sterols and other isoprenoids in mammals and archea. Despite the well documented importance of this pathway in the cause and prevention of human disease and that it is the biosynthetic root of an enormous diverse class of metabolites, the mechanism of phosphomevalonate kinase from any organism is not yet well characterized. The first structure of a phosphomevalonate kinase from Streptococcus pneumoniae was solved recently. The enzyme exhibits an atypical P-loop that is a conserved defining feature of the GHMP kinase superfamily. In this study, the kinetic mechanism of the S. pneumoniae enzyme is characterized in the forward and reverse directions using a combination of classical initial-rate methods including alternate substrate inhibition using ADPbetaS. The inhibition patterns strongly support that in either direction the substrates bind randomly to the enzyme prior to chemistry, a random sequential bi-bi mechanism. The kinetic constants are as follows: k(cat(forward)) = 3.4 s(-1), K(i(ATP)) = 137 microm, K(m(ATP)) = 74 microm, K(i(pmev)) = 7.7 microm, K(m(pmev)) = 4.2 microm; k(cat(reverse)) = 3.9 s(-1), K(i(ADP)) = 410 microm, K(m(ADP)) = 350 microm, K(i(ppmev)) = 14 microm, K(m(ppmev)) = 12 microm, where pmev and ppmev represent phosphomevalonate and diphosphomevalonate, respectively.
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Affiliation(s)
- Daniel Pilloff
- Department of Biochemistry, The Albert Einstein College of Medicine, Bronx, New York 10461-1926, USA
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Bertoldi M, Gonsalvi M, Contestabile R, Voltattorni CB. Mutation of tyrosine 332 to phenylalanine converts dopa decarboxylase into a decarboxylation-dependent oxidative deaminase. J Biol Chem 2002; 277:36357-62. [PMID: 12118007 DOI: 10.1074/jbc.m204867200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A flexible loop (residues 328-339), presumably covering the active site upon substrate binding, has been revealed in 3,4-dihydroxyphenylalanine decarboxylase by means of kinetic and structural studies. The function of tyrosine 332 has been investigated by substituting it with phenylalanine. Y332F displays coenzyme content and spectroscopic features identical to those of the wild type. Unlike wild type, during reactions with l-aromatic amino acids under both aerobic and anaerobic conditions, Y332F does not catalyze the formation of aromatic amines. However, analysis of the products shows that in aerobiosis, l-aromatic amino acids are converted into the corresponding aromatic aldehydes, ammonia, and CO(2) with concomitant O(2) consumption. Therefore, substitution of Tyr-332 with phenylalanine results in the suppression of the original activity and in the generation of a decarboxylation-dependent oxidative deaminase activity. In anaerobiosis, Y332F catalyzes exclusively a decarboxylation-dependent transamination of l-aromatic amino acids. A role of Tyr-332 in the Calpha protonation step that catalyzes the formation of physiological products has been proposed. Furthermore, Y332F catalyzes oxidative deamination of aromatic amines and half-transamination of d-aromatic amino acids with k(cat) values comparable with those of the wild type. However, for all the mutant-catalyzed reactions, an increase in K(m) values is observed, suggesting that Y --> F replacement also affects substrate binding.
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Affiliation(s)
- Mariarita Bertoldi
- Dipartimento di Scienze Neurologiche e della Visione, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università degli Studi di Verona, Strada Le Grazie, 8, 37134 Verona, Italy
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Runquist JA, Miziorko HM. Anionic substitutes for catalytic aspartic acids in phosphoribulokinase. Arch Biochem Biophys 2002; 405:178-84. [PMID: 12220530 DOI: 10.1016/s0003-9861(02)00367-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mutagenic substitution of the invariant D42 and D169 residues in phosphoribulokinase (PRK) with amino acids that contain neutral side chains (e.g., alanine or asparagine) results in large decreases in catalytic efficiency (10(5)- and 10(4)-fold for replacement of D42 and D169, respectively). To further evaluate the importance of anionic side chains at residues 42 and 169, substitutions of glutamic acid (D42E, D169E) and cysteine (D42C and D169C in an otherwise cysteine-free protein) have been engineered. All purified mutant enzymes bind the fluorescent alternative substrate trinitrophenyl-ATP and the allosteric effector NADH similarly to wild-type PRK. For D42E and D42C, V(max) exhibits substantial decreases of 135- and 220-fold, respectively. Comparable substitutions for D169 result in smaller effects; D169E and D169C exhibit decreases in V(max) of 39- and 26-fold, respectively. Thus, regardless of the type of substitution, changes at D42 more profoundly affect catalytic rate than do comparable changes at D169. Precedent with enzymes in which cysteine replaces an acidic residue suggests that oxidation of the thiolate to a sulfinate can convert low-activity cysteine mutants into enzymes with improved activity. Periodate oxidation of cysteine-free PRK results in a slight decrease in activity. In contrast, comparable treatment of D42C and D169C proteins increases activity by 5- and 7-fold, respectively. Thus, for reasonably efficient catalysis, PRK requires anionic character in the side chains of residues 42 and 169. The enzyme can, however, tolerate substantial structural and chemical variability at these residues.
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Affiliation(s)
- Jennifer A Runquist
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226, USA
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