1
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Jiang X, Shon K, Li X, Cui G, Wu Y, Wei Z, Wang A, Li X, Lu Y. Recent advances in identifying protein targets of bioactive natural products. Heliyon 2024; 10:e33917. [PMID: 39091937 PMCID: PMC11292521 DOI: 10.1016/j.heliyon.2024.e33917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
Background Natural products exhibit structural complexity, diversity, and historical therapeutic significance, boasting attractive functions and biological activities that have significantly influenced drug discovery endeavors. The identification of target proteins of active natural compounds is crucial for advancing novel drug innovation. Currently, methods for identifying targets of natural products can be categorized into labeling and label-free approaches based on whether the natural bioactive constituents are modified into active probes. In addition, there is a new avenue for rapidly exploring the targets of natural products based on their innate functions. Aim This review aimed to summarize recent advancements in both labeling and label-free approaches to the identification of targets for natural products, as well as the novel target identification method based on the natural functions of natural products. Methods We systematically collected relevant articles published in recent years from PubMed, Web of Science, and ScienceDirect, focusing on methods employed for identifying protein targets of bioactive natural products. Furthermore, we systematically summarized the principles, procedures, and successful cases, as well as the advantages and limitations of each method. Results Labeling methods allow for the direct labeling of target proteins and the exclusion of indirectly targeted proteins. However, these methods are not suitable for studying post-modified compounds with abolished activity, chemically challenging synthesis, or trace amounts of natural active compounds. Label-free methods can be employed to identify targets of any natural active compounds, including trace amounts and multicomponent mixtures, but their reliability is not as high as labeling methods. The structural complementarity between natural products and their innate receptors significantly increase the opportunities for finding more promising structural analogues of the natural products, and natural products may interact with several structural analogues of receptors in humans. Conclusion Each approach presents benefits and drawbacks. In practice, a combination of methods is employed to identify targets of natural products. And natural products' innate functions-based approach is a rapid and selective strategy for target identification. This review provides valuable references for future research in this field, offering insights into techniques and methodologies.
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Affiliation(s)
- Xuan Jiang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Kinyu Shon
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaofeng Li
- Department of Biochemistry and Molecular Biology, School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Guoliang Cui
- Department of Gastroenterology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuanyuan Wu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhonghong Wei
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Aiyun Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, 210023, China
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2
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Suresh PS, Kumari S, Sahal D, Sharma U. Innate functions of natural products: A promising path for the identification of novel therapeutics. Eur J Med Chem 2023; 260:115748. [PMID: 37666044 DOI: 10.1016/j.ejmech.2023.115748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
In the course of evolution, living organisms have become well equipped with diverse natural products that serve important functions, including defence from biotic and abiotic stress, growth regulation, reproduction, metabolism, and epigenetic regulation. It seems to be the organism's ecological niche that influences the natural product's structural and functional diversity. Indeed, natural products constitute the nuts and bolts of molecular co-evolution and ecological relationships among different life forms. Since natural products in the form of specialized secondary metabolites exhibit biological functions via interactions with specific target proteins, they can provide a simultaneous glimpse of both new therapeutics and therapeutic targets in humans as well. In this review, we have discussed the innate role of natural products in the ecosystem and how this intrinsic role provides a futuristic opportunity to identify new drugs and therapeutic targets rapidly.
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Affiliation(s)
- Patil Shivprasad Suresh
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Surekha Kumari
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Dinkar Sahal
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Upendra Sharma
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
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3
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Campolo N, Mastrogiovanni M, Mariotti M, Issoglio FM, Estrin D, Hägglund P, Grune T, Davies MJ, Bartesaghi S, Radi R. Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation. J Biol Chem 2023; 299:102941. [PMID: 36702251 PMCID: PMC10011836 DOI: 10.1016/j.jbc.2023.102941] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
Glutamine synthetase (GS), which catalyzes the ATP-dependent synthesis of L-glutamine from L-glutamate and ammonia, is a ubiquitous and conserved enzyme that plays a pivotal role in nitrogen metabolism across all life domains. In vertebrates, GS is highly expressed in astrocytes, where its activity sustains the glutamate-glutamine cycle at glutamatergic synapses and is thus essential for maintaining brain homeostasis. In fact, decreased GS levels or activity have been associated with neurodegenerative diseases, with these alterations attributed to oxidative post-translational modifications of the protein, in particular tyrosine nitration. In this study, we expressed and purified human GS (HsGS) and performed an in-depth analysis of its oxidative inactivation by peroxynitrite (ONOO-) in vitro. We found that ONOO- exposure led to a dose-dependent loss of HsGS activity, the oxidation of cysteine, methionine, and tyrosine residues and also the nitration of tryptophan and tyrosine residues. Peptide mapping by LC-MS/MS through combined H216O/H218O trypsin digestion identified up to 10 tyrosine nitration sites and five types of dityrosine cross-links; these modifications were further scrutinized by structural analysis. Tyrosine residues 171, 185, 269, 283, and 336 were the main nitration targets; however, tyrosine-to-phenylalanine HsGS mutants revealed that their sole nitration was not responsible for enzyme inactivation. In addition, we observed that ONOO- induced HsGS aggregation and activity loss. Thiol oxidation was a key modification to elicit aggregation, as it was also induced by hydrogen peroxide treatment. Taken together, our results indicate that multiple oxidative events at various sites are responsible for the inactivation and aggregation of human GS.
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Affiliation(s)
- Nicolás Campolo
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mauricio Mastrogiovanni
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Michele Mariotti
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Federico M Issoglio
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Buenos Aires, Argentina; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Darío Estrin
- CONICET-Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Buenos Aires, Argentina; Departamento de Química Inorgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Analítica y Química Física, Buenos Aires, Argentina
| | - Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tilman Grune
- Department of Molecular Toxicology, German Institute of Human Nutrition, Potsdam-Rehbrücke, Nuthetal, Germany; German Center for Cardiovascular Research (DZHK), Berlin, Germany; Department of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Silvina Bartesaghi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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4
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Cho SG, Song M, Chuon K, Shim JG, Meas S, Jung KH. Heliorhodopsin binds and regulates glutamine synthetase activity. PLoS Biol 2022; 20:e3001817. [PMID: 36190943 PMCID: PMC9529153 DOI: 10.1371/journal.pbio.3001817] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022] Open
Abstract
Photoreceptors are light-sensitive proteins found in various organisms that respond to light and relay signals into the cells. Heliorhodopsin, a retinal-binding membrane protein, has been recently discovered, however its function remains unknown. Herein, we investigated the relationship between Actinobacteria bacterium IMCC26103 heliorhodopsin (AbHeR) and an adjacent glutamine synthetase (AbGS) in the same operon. We demonstrate that AbHeR binds to AbGS and regulates AbGS activity. More specifically, the dissociation constant (Kd) value of the binding between AbHeR and AbGS is 6.06 μM. Moreover, the absence of positively charged residues within the intracellular loop of AbHeR impacted Kd value as they serve as critical binding sites for AbGS. We also confirm that AbHeR up-regulates the biosynthetic enzyme activity of AbGS both in vitro and in vivo in the presence of light. GS is a key enzyme involved in nitrogen assimilation that catalyzes the conversion of glutamate and ammonia to glutamine. Hence, the interaction between AbHeR and AbGS may be critical for nitrogen assimilation in Actinobacteria bacterium IMCC26103 as it survives in low-nutrient environments. Overall, the findings of our study describe, for the first time, to the best of our knowledge, a novel function of heliorhodopsin as a regulatory rhodopsin with the capacity to bind and regulate enzyme activity required for nitrogen assimilation. A study of heliorhodopsin, an actinobacterial photoreceptor of unknown function, reveals that it interacts with glutamine synthetase, an enzyme involved in nitrogen assimilation, and regulates its activity in the presence of light, highlighting the diverse functions of rhodopsins in different organisms.
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Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - Myungchul Song
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Jin-gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,Department of Biology, Faculty of Science, Royal University of Phnom Penh, Phnom Penh, Cambodia
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, Korea,* E-mail:
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5
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Matsumoto T, Hiramoto S, Niwa T, Machida H, Suto C, Takahashi M. First description of a clinical glutamine-dependent Escherichia coli with a missense mutation in the glnA. J Infect Chemother 2022; 28:1513-1518. [DOI: 10.1016/j.jiac.2022.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/13/2022] [Accepted: 07/28/2022] [Indexed: 10/31/2022]
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6
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Somsri S, Kuwamura N, Kojima T, Yoshinari N, Konno T. Self-assembly of cyclic hexamers of γ-cyclodextrin in a metallosupramolecular framework with d-penicillamine. Chem Sci 2020; 11:9246-9253. [PMID: 34094196 PMCID: PMC8161144 DOI: 10.1039/d0sc03925j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 08/17/2020] [Indexed: 11/21/2022] Open
Abstract
Cyclodextrins are widely used cyclic oligosaccharides of d-glucose whose hydrophilic exterior is covered by hydroxyl groups and whose hydrophobic interior is surrounded by lipophilic moieties. Because of this structural feature, cyclodextrin molecules commonly aggregate into dimensional structures via intermolecular hydrogen bonds, and their aggregation into closed oligomeric architectures has been achieved only via the attachment of functional substituent groups to the cyclodextrin rings. Here, we report the first structurally characterized self-assembly of non-substituted γ-cyclodextrin molecules into cyclic hexamers, which was realized in a chiral coordination framework composed of complex-anions with d-penicillamine rather than l- or dl-penicillamine. The self-assembly is accompanied by the 3D-to-2D structural transformation of porous coordination frameworks to form helical hexagonal cavities that accommodate helical γ-cyclodextrin hexamers. This finding provides new insight into the development of cyclodextrin chemistry and host-guest chemistry based on chiral recognition and crystal engineering processes.
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Affiliation(s)
- Supattra Somsri
- Department of Chemistry, Graduate School of Science, Osaka University Toyonaka Osaka 560-0043 Japan
| | - Naoto Kuwamura
- Department of Chemistry, Graduate School of Science, Osaka University Toyonaka Osaka 560-0043 Japan
| | - Tatsuhiro Kojima
- Department of Chemistry, Graduate School of Science, Osaka University Toyonaka Osaka 560-0043 Japan
| | - Nobuto Yoshinari
- Department of Chemistry, Graduate School of Science, Osaka University Toyonaka Osaka 560-0043 Japan
| | - Takumi Konno
- Department of Chemistry, Graduate School of Science, Osaka University Toyonaka Osaka 560-0043 Japan
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7
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Kumar V, Sushma Sri N, Tripathi N, Sharma VK, Bharatam PV, Garg P, Singh S. Structural exploration of glutamine synthetase from Leishmania donovani: Insights from in silico and in vitro analysis. Int J Biol Macromol 2020; 146:860-874. [DOI: 10.1016/j.ijbiomac.2019.09.209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/26/2019] [Accepted: 09/19/2019] [Indexed: 12/20/2022]
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8
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Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F. De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. Structure 2019; 27:679-691.e14. [PMID: 30744995 DOI: 10.1016/j.str.2019.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022]
Abstract
Electron cryotomography enables 3D visualization of cells in a near-native state at molecular resolution. The produced cellular tomograms contain detailed information about a plethora of macromolecular complexes, their structures, abundances, and specific spatial locations in the cell. However, extracting this information in a systematic way is very challenging, and current methods usually rely on individual templates of known structures. Here, we propose a framework called "Multi-Pattern Pursuit" for de novo discovery of different complexes from highly heterogeneous sets of particles extracted from entire cellular tomograms without using information of known structures. These initially detected structures can then serve as input for more targeted refinement efforts. Our tests on simulated and experimental tomograms show that our automated method is a promising tool for supporting large-scale template-free visual proteomics analysis.
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Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Jitin Singla
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond C Stevens
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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9
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Characterization and improved properties of Glutamine synthetase from Providencia vermicola by site-directed mutagenesis. Sci Rep 2018; 8:15640. [PMID: 30353099 PMCID: PMC6199252 DOI: 10.1038/s41598-018-34022-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/19/2018] [Indexed: 11/08/2022] Open
Abstract
In this study, a novel gene for Glutamine synthetase was cloned and characterized for its activities and stabilities from a marine bacterium Providencia vermicola (PveGS). A mutant S54A was generated by site directed mutagenesis, which showed significant increase in the activity and stabilities at a wide range of temperatures. The Km values of PveGS against hydroxylamine, ADP-Na2 and L-Glutamine were 15.7 ± 1.1, (25.2 ± 1.5) × 10-5 and 32.6 ± 1.7 mM, and the kcat were 17.0 ± 0.6, 9.14 ± 0.12 and 30.5 ± 1.0 s-1 respectively. In-silico-analysis revealed that the replacement of Ser at 54th position with Ala increased the catalytic activity of PveGS. Therefore, catalytic efficiency of mutant S54A had increased by 3.1, 0.89 and 2.9-folds towards hydroxylamine, ADP-Na2 and L-Glutamine respectively as compared to wild type. The structure prediction data indicated that the negatively charged pocket becomes enlarged and hydrogen bonding in Ser54 steadily promotes the product release. Interestingly, the residual activity of S54A mutant was increased by 10.7, 3.8 and 3.8 folds at 0, 10 and 50 °C as compared to WT. Structural analysis showed that S54A located on the loop near to the active site improved its flexibility due to the breaking of hydrogen bonds between product and enzyme. This also facilitated the enzyme to increase its cold adaptability as indicated by higher residual activity shown at 0 °C. Thus, replacement of Ala to Ser54 played a pivotal role to enhance the activities and stabilities at a wide range of temperatures.
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10
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Structural Analysis of Glutamine Synthetase from Helicobacter pylori. Sci Rep 2018; 8:11657. [PMID: 30076387 PMCID: PMC6076278 DOI: 10.1038/s41598-018-30191-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/20/2018] [Indexed: 11/08/2022] Open
Abstract
Glutamine synthetase (GS) is an enzyme that regulates nitrogen metabolism and synthesizes glutamine via glutamate, ATP, and ammonia. GS is a homo-oligomeric protein of eight, ten, or twelve subunits, and each subunit-subunit interface has its own active site. GS can be divided into GS I, GS II, and GS III. GS I and GS III form dodecamer in bacteria and archaea, whereas GS II form decamer in eukaryotes. GS I can be further subdivided into GS I-α and GS I-β according to its sequence and regulatory mechanism. GS is an essential protein for the survival of Helicobacter pylori which its infection could promote gastroduodenal diseases. Here, we determined the crystal structures of the GS from H. pylori (Hpy GS) in its apo- and substrate-bound forms at 2.8 Å and 2.9 Å resolution, respectively. Hpy GS formed a dodecamer composed of two hexameric rings stacked face-to-face. Hpy GS, which belongs to GS I, cannot be clearly classified as either GS I-α or GS I-β based on its sequence and regulatory mechanism. In this study, we propose that Hpy GS could be classified as a new GS-I subfamily and provide structural information on the apo- and substrate-bound forms of the protein.
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11
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Németh E, Nagy Z, Pécsváradi A. Chloroplast Glutamine Synthetase, the Key Regulator of Nitrogen Metabolism in Wheat, Performs Its Role by Fine Regulation of Enzyme Activity via Negative Cooperativity of Its Subunits. FRONTIERS IN PLANT SCIENCE 2018; 9:191. [PMID: 29520285 PMCID: PMC5827528 DOI: 10.3389/fpls.2018.00191] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/01/2018] [Indexed: 05/24/2023]
Abstract
Glutamine synthetase (GS) is of central interest as the main route of ammonia assimilation in plants, and as a connection point between the organic and inorganic worlds. Even though GS activity is critical for producing high yields of crop plants, the autoregulation of substrate consumption of wheat GS remained unknown until now. Here we show kinetic evidence, that the chloroplast localized GS isoform (GS2) of wheat (Triticum aestivum L. cv. Jubilejnaja-50) takes place at the carbon-nitrogen metabolic branch point, where it is a mediator, and its enzymatic activity is regulated in a negatively cooperative allosteric manner. We have discovered that GS2 activity is described by a tetraphasic kinetic curve in response to increasing levels of glutamate supply. We constructed a model that explains the kinetic properties of glutamate consumption and this unique allosteric behavior. We also studied the subunit composition of both wheat leaf GS isoenzymes by a combination of two dimensional gel electrophoresis and protein blotting. Both leaf isozymes have homogeneous subunit composition. Glutamate is both a substrate, and an allosteric regulator of the biosynthetic reaction. We have concluded on the basis of our results and previous reports, that wheat GS2 is probably a homooctamer, and that it processes its substrate in a well-regulated, concentration dependent way, as a result of its negatively cooperative, allosteric activity. Thus, GS2 has a central role as a regulator between the nitrogen and the carbon cycles via maintaining glutamine-glutamate pool in the chloroplast on the level of substrates, in addition to its function in ammonia assimilation.
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Affiliation(s)
- Edit Németh
- Department of Plant Biology, University of Szeged, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- Centre for Agricultural Research, Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Zoltán Nagy
- Cereal Research Non-profit Ltd., Szeged, Hungary
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12
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MacCormack TJ, Rundle AM, Malek M, Raveendran A, Meli MV. Gold nanoparticles partition to and increase the activity of glucose-6-phosphatase in a synthetic phospholipid membrane system. PLoS One 2017; 12:e0183274. [PMID: 28817664 PMCID: PMC5560555 DOI: 10.1371/journal.pone.0183274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/01/2017] [Indexed: 01/27/2023] Open
Abstract
Engineered nanomaterials can alter the structure and/or function of biological membranes and membrane proteins but the underlying mechanisms remain unclear. We addressed this using a Langmuir phospholipid monolayer containing an active transmembrane protein, glucose-6-phosphatase (G6Pase). Gold nanoparticles (nAu) with varying ligand shell composition and hydrophobicity were synthesized, and their partitioning in the membrane and effects on protein activity characterized. nAu incorporation did not alter the macroscopic properties of the membrane. Atomic force microscopy showed that when co-spread with other components prior to membrane compression, nAu preferentially interacted with G6Pase and each other in a functional group-dependent manner. Under these conditions, all nAu formulations reduced G6Pase aggregation in the membrane, enhancing catalytic activity 5-6 fold. When injected into the subphase beneath pre-compressed monolayers, nAu did not affect G6Pase activity over 60 minutes, implying they were unable to interact with the protein under these conditions. A small but significant quenching of tryptophan fluorescence showed that nAu interacted with G6Pase in aqueous suspension. nAu also significantly reduced the hydrodynamic diameter of G6Pase in aqueous suspension and promoted catalytic activity, likely via a similar mechanism to that observed in co-spread monolayers. Overall, our results show that nAu can incorporate into membranes and associate preferentially with membrane proteins under certain conditions and that partitioning is dependent upon ligand shell chemistry and composition. Once incorporated, nAu can alter the distribution of membrane proteins and indirectly affect their function by improving active site accessibility, or potentially by changing their native structure and distribution in the membrane.
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Affiliation(s)
- Tyson J. MacCormack
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada
- * E-mail: (TJM); (MVM)
| | - Amanda M. Rundle
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada
| | - Michael Malek
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada
| | - Abhilash Raveendran
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada
| | - Maria-Victoria Meli
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, NB, Canada
- * E-mail: (TJM); (MVM)
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13
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Issoglio FM, Campolo N, Zeida A, Grune T, Radi R, Estrin DA, Bartesaghi S. Exploring the Catalytic Mechanism of Human Glutamine Synthetase by Computer Simulations. Biochemistry 2016; 55:5907-5916. [DOI: 10.1021/acs.biochem.6b00822] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Federico M. Issoglio
- Departamento
de Química Inorgánica, Analítica y Química-Física
and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Ari Zeida
- Departamento
de Química Inorgánica, Analítica y Química-Física
and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Tilman Grune
- German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, Department of Molecular Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | | | - Dario A. Estrin
- Departamento
de Química Inorgánica, Analítica y Química-Física
and INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvina Bartesaghi
- Departamento
de Educación Médica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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Domínguez-Martín MA, Díez J, García-Fernández JM. Physiological Studies of Glutamine Synthetases I and III from Synechococcus sp. WH7803 Reveal Differential Regulation. Front Microbiol 2016; 7:969. [PMID: 27446010 PMCID: PMC4923085 DOI: 10.3389/fmicb.2016.00969] [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] [Received: 04/06/2016] [Accepted: 06/03/2016] [Indexed: 11/18/2022] Open
Abstract
The marine picocyanobacterium Synechococcus sp. WH7803 possesses two glutamine synthetases (GSs; EC 6.3.1.2), GSI encoded by glnA and GSIII encoded by glnN. This is the first work addressing the physiological regulation of both enzymes in a marine cyanobacterial strain. The increase of GS activity upon nitrogen starvation was similar to that found in other model cyanobacteria. However, an unusual response was found when cells were grown under darkness: the GS activity was unaffected, reflecting adaptation to the environment where they thrive. On the other hand, we found that GSIII did not respond to nitrogen availability, in sharp contrast with the results observed for this enzyme in other cyanobacteria thus far studied. These features suggest that GS activities in Synechococcus sp. WH7803 represent an intermediate step in the evolution of cyanobacteria, in a process of regulatory streamlining where GSI lost the regulation by light, while GSIII lost its responsiveness to nitrogen. This is in good agreement with the phylogeny of Synechococcus sp. WH7803 in the context of the marine cyanobacterial radiation.
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Affiliation(s)
| | | | - José M. García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de CórdobaCórdoba, Spain
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15
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Závodszky P, Hajdú I. Evolution of the concept of conformational dynamics of enzyme functions over half of a century: A personal view. Biopolymers 2016; 99:263-9. [PMID: 23348674 DOI: 10.1002/bip.22159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/07/2012] [Indexed: 01/01/2023]
Abstract
To most physicists, it was always evident that conformational fluctuation is an inherent property of all molecules. Its existence in proteins was mentioned first by Linderström-Lang and Schellman in 1959 based on their hydrogen-deuterium exchange experiments. The "induced fit" mechanism to explain ligand-induced conformational changes was suggested by Koshland in 1958. Straub combined these two concepts in his "fluctuation fit" theory in 1964. The era of protein X-ray crystallography imposed a static view of protein structures. With proteins becoming accessible to NMR analysis, conformational dynamics could be mapped, and a new wave of dynamic interpretation of enzymatic catalysis and molecular recognition appeared. Energy landscapes, energy funnels, conformational selection, conformational distribution shifts are now frequent terms in interpreting biomolecular recognition and enzymatic catalysis. All these interpretations are based on the concept that evolution uses the conformational fluctuations of enzymes to develop efficient and dynamic catalytic machines. In a resurrection of the original "fluctuation fit" concept, it is generally recognized now that spatial and temporal events of catalysis are equally important to describe its mechanism. This special issue, dedicated to the memory of Henryk Eisenberg, prompted us to look back at the last 50 years of development of a concept that-like other important concepts-appeared, evolved and became accepted during the period covered by the scientific lifespan of Henryk.
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Affiliation(s)
- Péter Závodszky
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1113, Budapest, Hungary.
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16
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Zhu C, Zhang G, Shen C, Chen S, Tang Y, Mei B, Song R. Expression of bacterial glutamine synthetase gene in Arabidopsis thaliana increases the plant biomass and level of nitrogen utilization. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Abstract
Detailed studies of the glutamine synthetase (GS) in Escherichia coli and other bacteria have shown that the activity of this enzyme is regulated by at least five different mechanisms: (i) cumulative feedback inhibition by multiple end products of glutamine metabolism, (ii) interconversion between taut and relaxed protein configurations in response to binding and dissociation of divalent cations at one of its two metal binding sites, (iii) dynamic interconversion of the enzyme between covalently modified (adenylylated) and unmodified forms by a novel bicyclic cascade system, (iv) repression and derepression of glutamine synthetase formation by cyclic phosphorylation and dephosphorylation of an RNA factor that governs transcription activities, and (v) regulation of glutamine synthetase turnover by the coupling of site specific metal ion-catalyzed oxidation with proteolytic degradation of the enzyme. Glutamine synthetase activity in E. coli is subject to inhibition by seven different end products of glutamine metabolism, namely, by tryptophan, histidine, carbamyl-phosphate, CTP, AMP, glucose-6-phosphate, and NAD+, and also by serine, alanine, and glycine. The cascade theory predicts that the steady-state level of glutamine synthetase adenylylation and therefore its catalytic activity is determined by the combined effects of all metabolites that affect the kinetic parameters of one or more of the enzymes in the cascade. Furthermore, under conditions where the supplies of ATP and glutamate are not limiting and the production of glutamine exceeds the demand, GS is no longer needed, then it will be converted to the catalytically inactive adenylylated form that is not under protection of ATP and glutamate.
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18
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Kosikowska P, Bochno M, Macegoniuk K, Forlani G, Kafarski P, Berlicki Ł. Bisphosphonic acids as effective inhibitors of Mycobacterium tuberculosis glutamine synthetase. J Enzyme Inhib Med Chem 2015; 31:931-8. [DOI: 10.3109/14756366.2015.1070846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Paulina Kosikowska
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland and
| | - Marta Bochno
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland and
| | - Katarzyna Macegoniuk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland and
| | - Giuseppe Forlani
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland and
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wrocław, Poland and
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19
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Saelices L, Robles-Rengel R, Florencio FJ, Muro-Pastor MI. A core of three amino acids at the carboxyl-terminal region of glutamine synthetase defines its regulation in cyanobacteria. Mol Microbiol 2015; 96:483-96. [PMID: 25626767 DOI: 10.1111/mmi.12950] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2015] [Indexed: 11/28/2022]
Abstract
Glutamine synthetase (GS) type I is a key enzyme in nitrogen metabolism, and its activity is finely controlled by cellular carbon/nitrogen balance. In cyanobacteria, a reversible process that involves protein-protein interaction with two proteins, the inactivating factors IF7 and IF17, regulates GS. Previously, we showed that three arginine residues of IFs are critical for binding and inhibition of GS. In this work, taking advantage of the specificity of GS/IFs interaction in the model cyanobacteria Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, we have constructed a different chimeric GSs from these two cyanobacteria. Analysis of these proteins, together with a site-directed mutagenesis approach, indicates that a core of three residues (E419, N456 and R459) is essential for the inactivation process. The three residues belong to the last 56 amino acids of the C-terminus of Synechocystis GS. A protein-protein docking modeling of Synechocystis GS in complex with IF7 supports the role of the identified core for GS/IF interaction.
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Affiliation(s)
- Lorena Saelices
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Seville, 41092, Spain
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20
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Kim G, Weiss SJ, Levine RL. Methionine oxidation and reduction in proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1840:901-5. [PMID: 23648414 PMCID: PMC3766491 DOI: 10.1016/j.bbagen.2013.04.038] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/24/2013] [Accepted: 04/27/2013] [Indexed: 01/10/2023]
Abstract
BACKGROUND Cysteine and methionine are the two sulfur containing amino acids in proteins. While the roles of protein-bound cysteinyl residues as endogenous antioxidants are well appreciated, those of methionine remain largely unexplored. SCOPE We summarize the key roles of methionine residues in proteins. MAJOR CONCLUSION Recent studies establish that cysteine and methionine have remarkably similar functions. GENERAL SIGNIFICANCE Both cysteine and methionine serve as important cellular antioxidants, stabilize the structure of proteins, and can act as regulatory switches through reversible oxidation and reduction. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.
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Affiliation(s)
- Geumsoo Kim
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, USA
| | - Stephen J. Weiss
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rodney L. Levine
- Laboratory of Biochemistry, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892, USA
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21
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van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 2013; 77:628-95. [PMID: 24296575 PMCID: PMC3973380 DOI: 10.1128/mmbr.00025-13] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
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A sensing role of the glutamine synthetase in the nitrogen regulation network in Fusarium fujikuroi. PLoS One 2013; 8:e80740. [PMID: 24260467 PMCID: PMC3829961 DOI: 10.1371/journal.pone.0080740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/05/2013] [Indexed: 11/29/2022] Open
Abstract
In the plant pathogenic ascomycete Fusarium fujikuroi the synthesis of several economically important secondary metabolites (SM) depends on the nitrogen status of the cells. Of these SMs, gibberellin and bikaverin synthesis is subject to nitrogen catabolite repression (NCR) and is therefore only executed under nitrogen starvation conditions. How the signal of available nitrogen quantity and quality is sensed and transmitted to transcription factors is largely unknown. Earlier work revealed an essential regulatory role of the glutamine synthetase (GS) in the nitrogen regulation network and secondary metabolism as its deletion resulted in total loss of SM gene expression. Here we present extensive gene regulation studies of the wild type, the Δgln1 mutant and complementation strains of the gln1 deletion mutant expressing heterologous GS-encoding genes of prokaryotic and eukaryotic origin or 14 different F. fujikuroi gln1 copies with site-directed mutations. All strains were grown under different nitrogen conditions and characterized regarding growth, expression of NCR-responsive genes and biosynthesis of SM. We provide evidence for distinct roles of the GS in sensing and transducing the signals to NCR-responsive genes. Three site directed mutations partially restored secondary metabolism and GS-dependent gene expression, but not glutamine formation, demonstrating for the first time that the catalytic and regulatory roles of GS can be separated. The distinct mutant phenotypes show that the GS (1) participates in NH4+-sensing and transducing the signal towards NCR-responsive transcription factors and their subsequent target genes; (2) affects carbon catabolism and (3) activates the expression of a distinct set of non-NCR GS-dependent genes. These novel insights into the regulatory role of the GS provide fascinating perspectives for elucidating regulatory roles of GS proteins of different organism in general.
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23
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Esrafili MD, Yourdkhani S. Symmetry-adapted perturbation theory study for some magnesium complexes. CAN J CHEM 2012. [DOI: 10.1139/v2012-062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A systematic theoretical study on Mg–ligand interactions has been carried out employing both ab initio correlated wave function and density functional methods. The interactions of the Mg(CH3N2)2moiety with BF, CO, N2, NH3, and H2O ligands have been investigated by performing calculations at the B3LYP, MP2, MP4, and CCSD(T)/6–311++G(3df,3pd) levels of theory. Results indicate that the interaction energies of the Mg(CH3N2)2–L complexes increase in the order NH3 > H2O > BF > CO > N2. Symmetry-adapted perturbation theory (SAPT) analysis has been carried out to understand the nature of the forces involved in the bonding. The SAPT results indicate that the stabilities of the Mg–L interactions are attributed mainly to electrostatic effects, while induction and dispersion forces also play a significant role. The evaluated SAPT interaction energies for the Mg(CH3N2)2–L complexes are generally in good agreement with those obtained using the supermolecule CCSD(T) methods, suggesting that SAPT is a proper method to study the intermolecular interactions in these complexes. The results also suggest an explanation for the unique role of Mg2+as a carrier of water molecules that mediate enzymatic hydrolysis reactions.
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Affiliation(s)
- Mehdi D. Esrafili
- Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, Maragheh, Iran
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24
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Betti M, García-Calderón M, Pérez-Delgado CM, Credali A, Estivill G, Galván F, Vega JM, Márquez AJ. Glutamine synthetase in legumes: recent advances in enzyme structure and functional genomics. Int J Mol Sci 2012; 13:7994-8024. [PMID: 22942686 PMCID: PMC3430217 DOI: 10.3390/ijms13077994] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 01/12/2023] Open
Abstract
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N(2) fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize here the recent advances carried out concerning the quaternary structure of GS, as well as the functional relationship existing between GS2 and processes such as nodulation, photorespiration and water stress, in this latter case by means of proline production. Functional genomic analysis using GS2-minus mutant reveals the key role of GS2 in the metabolic control of the plants and, more particularly, in carbon metabolism.
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Affiliation(s)
- Marco Betti
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-95-4556917; Fax: +34-95-4626853
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25
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Kim JN, Cann IKO, Mackie RI. Purification, characterization, and expression of multiple glutamine synthetases from Prevotella ruminicola 23. J Bacteriol 2012; 194:176-84. [PMID: 22020637 PMCID: PMC3256599 DOI: 10.1128/jb.05916-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/14/2011] [Indexed: 11/20/2022] Open
Abstract
The Prevotella ruminicola 23 genome encodes three different glutamine synthetase (GS) enzymes: glutamine synthetase I (GSI) (ORF02151), GSIII-1 (ORF01459), and GSIII-2 (ORF02034). GSI, GSIII-1, and GSIII-2 have each been heterologously expressed in and purified from Escherichia coli. The subunit molecular mass of GSI was 56 kDa, while GSIII-1 and GSIII-2 were both 83 kDa. Optimal conditions for γ-glutamyl transferase activity were found to be 35°C at pH 5.6 with 0.25 mM Mn(2+) ions (GSI) or 37°C at pH 6.0 (GSIII-1 and GSIII-2) with 0.50 to 1.00 mM Mn(2+) ions. GSIII biosynthetic activity was found to be optimal at 50 to 60°C and pH 6.8 to 7.0 with 10 mM Mn(2+) ions, while GSI displayed no GS biosynthetic activity. Kinetic analysis revealed K(m) values for glutamate and ammonium as well as for hydrolysis of ATP to be 8.58, 0.48, and 1.91 mM, respectively, for GSIII-1 and 1.72, 0.43, and 2.65 mM, respectively, for GSIII-2. A quantitative reverse transcriptase PCR assay (qRT-PCR) revealed GSIII-2 to be significantly induced by high concentrations of ammonia, and this corresponded with increases in measured GS activity. Collectively, these results show that both GSIII enzymes in P. ruminicola 23 are functional and indicate that GSIII-2, flanked by GOGAT (gltB and gltD genes), plays an important role in the acquisition and metabolism of ammonia, particularly under nonlimiting ammonia growth conditions.
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Affiliation(s)
| | - Isaac K. O. Cann
- Department of Animal Sciences
- Department of Microbiology
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Roderick I. Mackie
- Department of Animal Sciences
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
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26
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Crystal Structure of Type III Glutamine Synthetase: Surprising Reversal of the Inter-Ring Interface. Structure 2011; 19:471-83. [DOI: 10.1016/j.str.2011.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 01/31/2011] [Accepted: 02/07/2011] [Indexed: 11/19/2022]
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27
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Itzen A, Blankenfeldt W, Goody RS. Adenylylation: renaissance of a forgotten post-translational modification. Trends Biochem Sci 2011; 36:221-8. [PMID: 21256032 DOI: 10.1016/j.tibs.2010.12.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/22/2010] [Accepted: 12/22/2010] [Indexed: 01/29/2023]
Abstract
The stable post-translational modification of proteins by adenylylation or uridylylation was discovered more than four decades ago as a mechanism to regulate the activity of enzymes. Although many other processes involving the covalent transfer of an AMP residue to an amino acid side chain have been identified since then, these are transient adenylylation events that essentially use the free energy of ATP hydrolysis to activate specific processes. Recently, new examples of stable adenylylation of small GTPases involved in signal transduction and regulation of cellular events were discovered, which appear to modulate downstream processes such as cytoskeletal rearrangement and vesicular trafficking. We present a survey of the historical and modern phases of research in this area, focusing on the common and differing aspects of protein adenylylation.
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Affiliation(s)
- Aymelt Itzen
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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28
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Stucture of the complex between Mucor pusillus pepsin and the key domain of κ-casein for site-directed mutagenesis: a combined molecular modeling and docking approach. J Mol Model 2010; 17:1661-8. [DOI: 10.1007/s00894-010-0869-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 10/05/2010] [Indexed: 11/25/2022]
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29
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Seabra AR, Carvalho H, Pereira PJB. Crystallization and preliminary crystallographic characterization of glutamine synthetase from Medicago truncatula. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1309-12. [PMID: 20054137 PMCID: PMC2802889 DOI: 10.1107/s1744309109047381] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 11/09/2009] [Indexed: 11/11/2022]
Abstract
The condensation of ammonium and glutamate into glutamine catalyzed by glutamine synthetase (GS) is a fundamental step in nitrogen metabolism in all kingdoms of life. In plants, this is preceded by the reduction of inorganic nitrogen to an ammonium ion and therefore effectively articulates nitrogen fixation and metabolism. Although the three-dimensional structure of the dodecameric bacterial GS was determined quite some time ago, the quaternary architecture of the plant enzyme has long been assumed to be octameric, mostly on the basis of low-resolution electron-microscopy studies. Recently, the crystallographic structure of a monocotyledonous plant GS was reported that revealed a homodecameric organization. In order to unambiguously establish the quaternary architecture of GS from dicotyledonous plants, GS1a from the model legume Medicago truncatula was overexpressed, purified and crystallized. The collection of synchrotron diffraction data to 2.35 A resolution allowed the determination of the three-dimensional structure of this enzyme by molecular replacement.
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Affiliation(s)
- Ana Rita Seabra
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Helena Carvalho
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
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30
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Computational Structural Analysis and Kinetic Studies of a Cytosolic Glutamine Synthetase from Camellia sinensis (L.) O. Kuntze. Protein J 2009; 28:428-34. [DOI: 10.1007/s10930-009-9210-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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He YX, Gui L, Liu YZ, Du Y, Zhou Y, Li P, Zhou CZ. Crystal structure of Saccharomyces cerevisiae glutamine synthetase Gln1 suggests a nanotube-like supramolecular assembly. Proteins 2009; 76:249-54. [PMID: 19322816 DOI: 10.1002/prot.22403] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yong-Xing He
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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32
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Kinoshita S, Isu S, Kaneko G, Yamada H, Hara T, Itoh Y, Watabe S. The occurrence of eukaryotic type III glutamine synthetase in the marine diatom Chaetoceros compressum. Mar Genomics 2009; 2:103-11. [DOI: 10.1016/j.margen.2009.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2009] [Revised: 05/26/2009] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
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33
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Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design. J Mol Biol 2007; 375:217-28. [PMID: 18005987 DOI: 10.1016/j.jmb.2007.10.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Revised: 10/09/2007] [Accepted: 10/11/2007] [Indexed: 11/21/2022]
Abstract
Glutamine synthetase (GS) catalyzes the ligation of glutamate and ammonia to form glutamine, with concomitant hydrolysis of ATP. In mammals, the activity eliminates cytotoxic ammonia, at the same time converting neurotoxic glutamate to harmless glutamine; there are a number of links between changes in GS activity and neurodegenerative disorders, such as Alzheimer's disease. In plants, because of its importance in the assimilation and re-assimilation of ammonia, the enzyme is a target of some herbicides. GS is also a central component of bacterial nitrogen metabolism and a potential drug target. Previous studies had investigated the structures of bacterial and plant GSs. In the present publication, we report the first structures of mammalian GSs. The apo form of the canine enzyme was solved by molecular replacement and refined at a resolution of 3 A. Two structures of human glutamine synthetase represent complexes with: a) phosphate, ADP, and manganese, and b) a phosphorylated form of the inhibitor methionine sulfoximine, ADP and manganese; these structures were refined to resolutions of 2.05 A and 2.6 A, respectively. Loop movements near the active site generate more closed forms of the eukaryotic enzymes when substrates are bound; the largest changes are associated with the binding of the nucleotide. Comparisons with earlier structures provide a basis for the design of drugs that are specifically directed at either human or bacterial enzymes. The site of binding the amino acid substrate is highly conserved in bacterial and eukaryotic GSs, whereas the nucleotide binding site varies to a much larger degree. Thus, the latter site offers the best target for specific drug design. Differences between mammalian and plant enzymes are much more subtle, suggesting that herbicides targeting GS must be designed with caution.
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35
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Antonyuk LP. Glutamine synthetase of the rhizobacterium Azospirillum brasilense: Specific features of catalysis and regulation. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807030039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Ang EL, Obbard JP, Zhao H. Probing the molecular determinants of aniline dioxygenase substrate specificity by saturation mutagenesis. FEBS J 2007; 274:928-39. [PMID: 17269935 DOI: 10.1111/j.1742-4658.2007.05638.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aniline dioxygenase is a multicomponent Rieske nonheme-iron dioxygenase enzyme isolated from Acinetobacter sp. strain YAA. Saturation mutagenesis of the substrate-binding pocket residues, which were identified using a homology model of the alpha subunit of the terminal dioxygenase (AtdA3), was used to probe the molecular determinants of AtdA substrate specificity. The V205A mutation widened the substrate specificity of aniline dioxygenase to include 2-isopropylaniline, for which the wild-type enzyme has no activity. The V205A mutation also made 2-isopropylaniline a better substrate for the enzyme than 2,4-dimethylaniline, a native substrate of the wild-type enzyme. The I248L mutation improved the activity of aniline dioxygenase against aniline and 2,4-dimethylaniline approximately 1.7-fold and 2.1-fold, respectively. Thus, it is shown that the alpha subunit of the terminal dioxygenase indeed plays a part in the substrate specificity as well as the activity of aniline dioxygenase. Interestingly, the equivalent residues of V205 and I248 have not been previously reported to influence the substrate specificity of other Rieske dioxygenases. These results should facilitate future engineering of the enzyme for bioremediation and industrial applications.
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Affiliation(s)
- Ee L Ang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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37
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Wyatt K, White HE, Wang L, Bateman OA, Slingsby C, Orlova EV, Wistow G. Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. Structure 2007; 14:1823-34. [PMID: 17161372 PMCID: PMC1868402 DOI: 10.1016/j.str.2006.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/11/2006] [Accepted: 10/26/2006] [Indexed: 02/01/2023]
Abstract
Lengsin is a major protein of the vertebrate eye lens. It belongs to the hitherto purely prokaryotic GS I branch of the glutamine synthetase (GS) superfamily, but has no enzyme activity. Like the taxon-specific crystallins, Lengsin is the result of the recruitment of an ancient enzyme to a noncatalytic role in the vertebrate lens. Cryo-EM and modeling studies of Lengsin show a dodecamer structure with important similarities and differences with prokaryotic GS I structures. GS homology regions of Lengsin are well conserved, but the N-terminal domain shows evidence of dynamic evolutionary changes. Compared with birds and fish, most mammals have an additional exon corresponding to part of the N-terminal domain; however, in human, this is a nonfunctional pseudoexon. Genes related to Lengsin are also present in the sea urchin, suggesting that this branch of the GS I family, supplanted by GS II enzymes in vertebrates, has an ancient role in metazoans.
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Affiliation(s)
- Keith Wyatt
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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38
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van Rooyen JM, Abratt VR, Sewell BT. Three-dimensional Structure of a Type III Glutamine Synthetase by Single-particle Reconstruction. J Mol Biol 2006; 361:796-810. [PMID: 16879836 DOI: 10.1016/j.jmb.2006.06.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 06/05/2006] [Accepted: 06/12/2006] [Indexed: 10/24/2022]
Abstract
GlnN, the type III glutamine synthetase (GSIII) from the medically important, anaerobic, opportunistic pathogen Bacteroides fragilis, has 82.8 kDa subunits that share only 9% sequence identity with the type I glutamine synthetases (GSI), the only family for which a structure is known. Active GlnN was found predominantly in a single peak that eluted from a calibrated gel-filtration chromatography column at a position equaivalent to 0.86(+/-0.08) MDa. Negative-stain electron microscopy enabled the identification of double-ringed particles and single hexameric rings ("pinwheels") resulting from partial staining. A 2D average of these pinwheels showed marked similarity to the corresponding structures found in preparations of GSI, except that the arms of the subunits were 40% longer. Reconstructions from particles embedded in vitreous ice showed that GlnN has a double-ringed, dodecameric structure with a 6-fold dihedral space group (D6) symmetry and dimensions of 17.0 nm parallel with the 6-fold axis and 18.3 nm parallel with the 2-fold axes. The structures, combined with a sequence alignment based on structural principles, showed how many aspects of the structure of GSI, and most notably the alpha/beta barrel fold active site were preserved. There was evidence for the presence of this structure in the reconstructed volume, thus, identifying the indentations between the pinwheel spokes as putative active sites and suggesting conservation of the overall molecular geometry found in GSI despite their low level of global homology. Furthermore, docking of GSI into the reconstruction left sufficient plausibly located unoccupied density to account for the additional residues in GSIII, thus validating the structure.
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Affiliation(s)
- Jason M van Rooyen
- Electron Microscope Unit, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
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39
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Amaya KR, Kocherginskaya SA, Mackie RI, Cann IKO. Biochemical and mutational analysis of glutamine synthetase type III from the rumen anaerobe Ruminococcus albus 8. J Bacteriol 2005; 187:7481-91. [PMID: 16237031 PMCID: PMC1272975 DOI: 10.1128/jb.187.21.7481-7491.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2005] [Accepted: 08/08/2005] [Indexed: 11/20/2022] Open
Abstract
Two different genes encoding glutamine synthetase type I (GSI) and GSIII were identified in the genome sequence of R. albus 8. The identity of the GSIII protein was confirmed by the presence of its associated conserved motifs. The glnN gene, encoding the GSIII, was cloned and expressed in Escherichia coli BL21 cells. The recombinant protein was purified and subjected to biochemical and physical analyses. Subunit organization suggested a protein present in solution as both monomers and oligomers. Kinetic studies using the forward and the gamma-glutamyl transferase (gamma-GT) assays were carried out. Mutations that changed conserved glutamic acid residues to alanine in the four GSIII motifs resulted in drastic decreases in GS activity using both assays, except for an E380A mutation, which rather resulted in an increase in activity in the forward assay compared to the wild-type protein. Reduced GSIII activity was also exhibited by mutating, individually, two lysines (K308 and K318) located in the putative nucleotide-binding site to alanine. Most importantly, the presence of mRNA transcripts of the glnN gene in R. albus 8 cells grown under ammonia limiting conditions, whereas little or no transcript was detected in cells grown under ammonia sufficient conditions, suggested an important role for the GSIII in the nitrogen metabolism of R. albus 8. Furthermore, the mutational studies on the conserved GSIII motifs demonstrated, for the first time, their importance in the structure and/or function of a GSIII protein.
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Affiliation(s)
- Kensey R. Amaya
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Svetlana A. Kocherginskaya
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Roderick I. Mackie
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Isaac K. O. Cann
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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40
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Hiratake J. Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications. CHEM REC 2005; 5:209-28. [PMID: 16041744 DOI: 10.1002/tcr.20045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Carefully designed molecules that are intimately related to the reaction mechanism of enzymes are often highly selective and potent inhibitors that serve as extremely useful chemical probes for understanding the reaction mechanism and structure of enzymes. This article describes the design, synthesis, and applications of specific inhibitors of two mechanistically distinct groups of enzymes, ATP-dependent amide ligases and Ser- and Thr-hydrolases. Our strategy is based on the premise that stable analogues of the transition state (transition-state analogues) are highly potent inhibitors that serve as good mechanistic probes, and that a key structure of a good inhibitor of one enzyme is also utilized for the inhibitors of other enzymes that share the same chemistry in their catalyzed reactions, irrespective of the degree of structural similarity and evolutionary link between the enzymes. According to these principles, we designed and synthesized a series of phosphinate- and sulfoximine-based transition-state analogue inhibitors of glutathione synthetase, gamma-glutamylcysteine synthetase and asparagine synthetase. For the second group of enzymes, we synthesized a gamma-monofluorophosphono glutamate analogue for mechanism-based affinity labeling of gamma-glutamyltranspeptidase and fluorescent phosphonic acid esters for the active-site titration of lipase. These inhibitors were used successfully as ligands for detailed kinetic analyses, X-ray crystallography, and mass analysis of the enzymes to identify the key amino acid residues responsible for catalysis and substrate recognition in the transition state.
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Affiliation(s)
- Jun Hiratake
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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41
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Dutta S, Berman HM. Large macromolecular complexes in the Protein Data Bank: a status report. Structure 2005; 13:381-8. [PMID: 15766539 DOI: 10.1016/j.str.2005.01.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 01/18/2005] [Accepted: 01/19/2005] [Indexed: 11/24/2022]
Abstract
The growing number of large macromolecular complexes in the Protein Data Bank (PDB) has warranted a closer look at these structures. An overview of the types of molecules that form these large complexes is presented here. Some of the challenges at the PDB in representing, archiving, visualizing, and analyzing these structures are discussed along with possible means to overcome them.
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Affiliation(s)
- Shuchismita Dutta
- The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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42
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Krajewski WW, Jones TA, Mowbray SL. Structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition-state mimic provides functional insights. Proc Natl Acad Sci U S A 2005; 102:10499-504. [PMID: 16027359 PMCID: PMC1180770 DOI: 10.1073/pnas.0502248102] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 06/02/2005] [Indexed: 11/18/2022] Open
Abstract
Glutamine synthetase catalyzes the ligation of glutamate and ammonia to form glutamine, with the resulting hydrolysis of ATP. The enzyme is a central component of bacterial nitrogen metabolism and is a potential drug target. Here, we report a high-yield recombinant expression system for glutamine synthetase of Mycobacterium tuberculosis together with a simple purification. The procedure allowed the structure of a complex with a phosphorylated form of the inhibitor methionine sulfoximine, magnesium, and ADP to be solved by molecular replacement and refined at 2.1-A resolution. To our knowledge, this study provides the first reported structure for a taut form of the M. tuberculosis enzyme, similar to that observed for the Salmonella enzyme earlier. The phospho compound, generated in situ by an active enzyme, mimics the phosphorylated tetrahedral adduct at the transition state. Some differences in ligand interactions of the protein with both phosphorylated compound and nucleotide are observed compared with earlier structures; a third metal ion also is found. The importance of these differences in the catalytic mechanism is discussed; the results will help guide the search for specific inhibitors of potential therapeutic interest.
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Affiliation(s)
- Wojciech W Krajewski
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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43
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Pearson JT, Dabrowski MJ, Kung I, Atkins WM. The central loop of Escherichia coli glutamine synthetase is flexible and functionally passive. Arch Biochem Biophys 2005; 436:397-405. [PMID: 15797252 DOI: 10.1016/j.abb.2005.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 02/02/2005] [Indexed: 10/25/2022]
Abstract
Bacterial glutamine synthetases (GSs) are dodecameric aggregates comprised of two face-to-face hexameric rings, which form a cylindrical aqueous channel. Available crystal structures indicate that each subunit provides a 'central loop' that protrudes into this channel. Residues on either side of this loop contribute directly to substrate or metal ion cofactor binding. Although it has been suggested that this conspicuous structural feature may be functionally important, a systematic structure-function analysis of this loop has not been done. Here, we examine the behavior of a cysteine mutant, E165C, which yields inter-subunit disulfide bonds connecting the central loops. The inter-subunit disulfide bonds are readily detected by electrospray ionization mass spectrometry. Based on molecular models, the disulfide bonds would form only if the engineered cysteines on adjacent subunits moved approximately 5 A. Surprisingly, inter-subunit disulfide bonds between the central loops caused no detectable changes in the KMs for glutamate or ATP, nor the KD for either ATP or the transition state analog (L)-methionine sulfoximine (MSOX). Furthermore, covalent and quantitative adduction of the E165C mutant with iodo-acetamido-pyrene yielded nearly fully active enzyme bearing fluorescent pyrene excimers. The relative contribution of pyrene monomers to excimers in the steady state fluorescence is temperature dependent, suggesting thermal equilibrium between loop conformational states. However, the monomer-excimer ratio is independent of ligands such as MSOX, glutamate, or Mn2+. These results validate the suspected flexibility of the central loop, but raise significant doubt about its direct functional role in GS catalysis via conformational switching, including the proposed regulation of GS via ADP-ribosylation within this loop.
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Affiliation(s)
- Josh T Pearson
- Department of Medicinal Chemistry, University of Washington, Box 357610, Seattle, WA 98195-7610, USA
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44
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Lehmann C, Doseeva V, Pullalarevu S, Krajewski W, Howard A, Herzberg O. YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays. Proteins 2004; 56:376-83. [PMID: 15211520 DOI: 10.1002/prot.20103] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Escherichia coli open reading frame YbdK encodes a member of a large bacterial protein family of unknown biological function. The sequences within this family are remotely related to the sequence of gamma-glutamate-cysteine ligase (gamma-GCS), an enzyme in the glutathione biosynthetic pathway. A gene encoding gamma-GCS in E. coli is already known. The 2.15 A resolution crystal structure of YbdK reveals an overall fold similar to that of glutamine synthetase (GS), a nitrogen metabolism enzyme that ligates glutamate and ammonia to yield glutamine. GS and gamma-GCS perform related chemical reactions and require ATP and Mg2+ for their activity. The Mg2+-dependent binding of ATP to YbdK was confirmed by fluorescence spectroscopy employing 2'(or 3')-O-(trinitrophenyl)adenosine 5'-triphosphate, and yielding a dissociation constant of 3 +/- 0.5 microM. The structure of YbdK contains a crevice that corresponds to the binding sites of ATP, Mg2+ and glutamate in GS. Many of the GS residues that coordinate the metal ions and interact with glutamic acid and the phosphoryl and ribosyl groups of ATP are also present in YbdK. GS amino acids that have been associated with ammonia binding have no obvious counterparts in YbdK, consistent with a substrate specificity that is different from that of GS. Ligase activity between glutamic acid and each of the twenty amino acid residues was tested on high performance liquid chromatography (HPLC) by following the hydrolysis of ATP to ADP. Catalysis was observed only with cysteine. A pyruvate kinase/lactic acid dehydrogenase coupled assay was used to rule out GS activity and to determine that YbdK exhibits gamma-GCS activity. The catalytic rate was found to be approximately 500-fold slower than that reported for authentic gamma-GCS.
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Affiliation(s)
- Christopher Lehmann
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
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45
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Mehta R, Pearson JT, Mahajan S, Nath A, Hickey MJ, Sherman DR, Atkins WM. Adenylylation and catalytic properties of Mycobacterium tuberculosis glutamine synthetase expressed in Escherichia coli versus mycobacteria. J Biol Chem 2004; 279:22477-82. [PMID: 15037612 DOI: 10.1074/jbc.m401652200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial glutamine synthetases (GSs) are complex dodecameric oligomers that play a critical role in nitrogen metabolism, converting ammonia and glutamate to glutamine. Recently published reports suggest that GS from Mycobacterium tuberculosis (MTb) may be a therapeutic target (Harth, G., and Horwitz, M. A. (2003) Infect. Immun. 71, 456-464). In some bacteria, GS is regulated via adenylylation of some or all of the subunits within the aggregate; catalytic activity is inversely proportional to the extent of adenylylation. The adenylylation and deadenylylation of GS are catalyzed by adenylyl transferase (ATase). Here, we demonstrate via electrospray ionization mass spectrometry that GS from pathogenic M. tuberculosis is adenylylated by the Escherichia coli ATase. The adenylyl group can be hydrolyzed by snake venom phosphodiesterase to afford the unmodified enzyme. The site of adenylylation of MTb GS by the E. coli ATase is Tyr-406, as indicated by the lack of adenylylation of the Y406F mutant, and, as expected, is based on amino acid sequence alignments. Using electrospray ionization mass spectroscopy methodology, we found that GS is not adenylylated when obtained directly from MTb cultures that are not supplemented with glutamine. Under these conditions, the highly related but non-pathogenic Mycobacterium bovis BCG yields partially ( approximately 25%) adenylylated enzyme. Upon the addition of glutamine to the cultures, the MTb GS becomes significantly adenylylated ( approximately 30%), whereas the adenylylation of M. bovis BCG GS does not change. Collectively, the results demonstrate that MTb GS is a substrate for E. coli ATase, but only low adenylylation states are accessible. This parallels the low adenylylation states observed for GS from mycobacteria and suggests the intriguing possibility that adenylylation in the pathogenic versus non-pathogenic mycobacteria is differentially regulated.
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Affiliation(s)
- Ranjana Mehta
- Departments of Pathobiology and Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, USA
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46
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Muro-Pastor MI, Barrera FN, Reyes JC, Florencio FJ, Neira JL. The inactivating factor of glutamine synthetase, IF7, is a "natively unfolded" protein. Protein Sci 2003; 12:1443-54. [PMID: 12824490 PMCID: PMC2323932 DOI: 10.1110/ps.0303203] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2003] [Revised: 03/24/2003] [Accepted: 03/28/2003] [Indexed: 10/27/2022]
Abstract
Glutamine synthetase (GS) is the key enzyme responsible for the primary assimilation of ammonium in all living organisms, and it catalyses the synthesis of glutamine from glutamic acid, ATP, and ammonium. One of the recently discovered mechanisms of GS regulation involves protein-protein interactions with a small 65-residue-long protein named IF7. Here, we study the structure and stability of IF7 and its binding properties to GS, by using several biophysical techniques (fluorescence, circular dichroism, Fourier transform infrared and nuclear magnetic resonance spectroscopies, and gel filtration chromatography) which provide complementary structural information. The findings show that IF7 has a small amount of residual secondary structure, but lacks a well defined tertiary structure, and is not compact. Thus, all of the studies indicate that IF7 is a "natively unfolded" protein. The binding of IF7 to GS, its natural binding partner, occurs with an apparent dissociation constant of K(D) = 0.3 +/- 0.1 microM, as measured by fluorescence. We discuss the implications for the GS regulation mechanisms of IF7 being unfolded.
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Affiliation(s)
- M. Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, 41092 Sevilla, Spain
| | - Francisco N. Barrera
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
| | - José C. Reyes
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, 41092 Sevilla, Spain
| | - Francisco J. Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas, 41092 Sevilla, Spain
| | - José L. Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain
- Instituto de Biocomputación y Física de los sistemas complejos, Zaragoza, Spain
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47
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Fisher SH, Brandenburg JL, Wray LV. Mutations in Bacillus subtilis glutamine synthetase that block its interaction with transcription factor TnrA. Mol Microbiol 2002; 45:627-35. [PMID: 12139611 DOI: 10.1046/j.1365-2958.2002.03054.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Bacillus subtilis, the activity of the nitrogen regulatory factor TnrA is regulated through a protein- protein interaction with glutamine synthetase. During growth with excess nitrogen, the feedback-inhibited form of glutamine synthetase binds to TnrA and blocks DNA binding by TnrA. Missense mutations in glutamine synthetase that constitutively express the TnrA-regulated amtB gene were characterized. Four mutant proteins were purified and shown to be defective in their ability to inhibit the in vitro DNA-binding activity of TnrA. Two of the mutant proteins exhibited enzymatic properties similar to those of wild-type glutamine synthetase. A model of B. subtilis glutamine synthetase was derived from a crystal structure of the Salmonella typhimurium enzyme. Using this model, all the mutated amino acid residues were found to be located close to the glutamate entrance of the active site. These results are consistent with the glutamine synthetase protein playing a direct role in regulating TnrA activity.
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Affiliation(s)
- Susan H Fisher
- Department of Microbiology, Boston University School of Medicine, MA 02118, USA.
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48
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Fisher MT. Promotion of the in vitro renaturation of dodecameric glutamine synthetase from Escherichia coli in the presence of GroEL (chaperonin-60) and ATP. Biochemistry 2002; 31:3955-63. [PMID: 1348957 DOI: 10.1021/bi00131a010] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The folding and assembly of dodecameric glutamine synthetase (GS) from Escherichia coli was examined in the absence and presence of the E. coli heat shock protein, GroEL (chaperonin-60). At nonphysiological temperatures (15-20 degrees C), unfolded GS spontaneously renatured to 80-90% of its original activity in the absence of GroEL. At near-physiological temperatures (37 degrees C), only 20-40% of the original activity returns. Under the latter solution conditions, GroEL and ATP enhance the extent of GS renaturation to 70-80% of the original activity at 37 degrees C. In the absence of ATP, GroEL arrests the renaturation of unfolded GS by forming a stable binary complex. The addition of ATP to this complex resulted in the release of GS subunits and formation of active dodecameric GS. The order of addition of ATP or unfolded GS to GroEL results in differences in the t1/2 values where half-maximal GS activity is attained. At a constant GS concentration, the formation of the GroEL.GS complex followed by ATP addition resulted in approximately a 2-fold increase in the observed t1/2 value compared to that observed when GroEL was preincubated with ATP before the GS renaturation reaction was initiated. These differences in renaturation rates may be related to binding affinity differences between the ATP-free and -bound GroEL conformer for unfolded or partially folded protein substrates [Badcoe, I. G., Smith, C. J., Wood, S., Halsall, D. J., Holbrook, J. J., Lund, P., & Clarke, A. R. (1991) Biochemistry 30, 9195-9200].(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M T Fisher
- Laboratory of Biochemistry, National Institutes of Health, National Heart Lung and Blood Institute, Bethesda, Maryland 20892
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49
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Libson AM, Gittis AG, Lattman EE. Crystal Structures of the Binary Ca2+ and pdTp Complexes and the Ternary Complex of the Asp21 .fwdarw. Glu Mutant of Staphylococcal Nuclease. Implications for Catalysis and Ligand Binding. Biochemistry 2002. [DOI: 10.1021/bi00192a004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Zolkiewski M, Ginsburg A. Thermodynamic effects of active-site ligands on the reversible, partial unfolding of dodecameric glutamine synthetase from Escherichia coli: calorimetric studies. Biochemistry 2002; 31:11991-2000. [PMID: 1360813 DOI: 10.1021/bi00163a006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dodecameric glutamine synthetase (GS) from Escherichia coli undergoes reversible, thermally induced partial unfolding without subunit dissociation. A single endotherm for Mn.GS (+/- active-site ligands) in the presence of 1 mM free Mn2+ and 100 mM KCl at pH 7 is observed by differential scanning calorimetry (DSC). Previous deconvolutions of DSC data for Mn.GS showed only two two-state transitions (with similar tm values; 51.6 +/- 2 degrees C), and indicated that cooperative interactions link partial unfolding reactions of all subunits within the Mn.enzyme dodecamer [Ginsburg, A., & Zolkiewski, M. (1991) Biochemistry 30, 9421]. A net uptake of 8.0 equiv of H+ by Mn.GS occurs during partial unfolding, as determined in the present DSC experiments conducted with four buffers having different heats of protonation at 50 degrees C. These data gave a value of 176 +/- 12 kcal (mol of dodecamer)-1 for delta Hcal corrected for buffer protonation. L-Glutamine and L-Met-(SR)-sulfoximine stabilize the Mn.GS dodecamer through the free energies of ligand binding, and these were shown to be partially and totally released, respectively, from the 12 active sites at high temperature. Ligand effects on Tm values from DSC were similar to those from spectral measurements of Trp and Tyr exposures in two subunit domains. Effects of varying [ADP] on DSC profiles of Mn.GS were complex; Tm is increased by low [ADP] and decreased by > 100 microM free ADP. This is due to the exposure of an additional low-affinity ADP binding site per GS subunit at high temperature with log K1' = 4.3 and log K2' = 3.6 at 60 degrees C relative to log K' = 5.5 for ADP binding at 30 degrees C, as determined by isothermal calorimetric and fluorescence titrations. Moreover, delta Hcal at > 27% saturation with ADP (corrected for ADP binding/dissociation) is approximately 80-100 kcal/mol more than in the absence of ligands. Changes in domain interactions could result from ADP bridging subunit contacts in the dodecamer. Each of the active-site ligands investigated here produces different effects on DSC profiles without uncoupling the extremely cooperative, partial unfolding reactions in the Mn.GS dodecamer.
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Affiliation(s)
- M Zolkiewski
- Laboratory of Biochemistry, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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