1
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Aleshina YA, Aleshin VA. Evolutionary Changes in Primate Glutamate Dehydrogenases 1 and 2 Influence the Protein Regulation by Ligands, Targeting and Posttranslational Modifications. Int J Mol Sci 2024; 25:4341. [PMID: 38673928 PMCID: PMC11050691 DOI: 10.3390/ijms25084341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
There are two paralogs of glutamate dehydrogenase (GDH) in humans encoded by the GLUD1 and GLUD2 genes as a result of a recent retroposition during the evolution of primates. The two human GDHs possess significantly different regulation by allosteric ligands, which is not fully characterized at the structural level. Recent advances in identification of the GDH ligand binding sites provide a deeper perspective on the significance of the accumulated substitutions within the two GDH paralogs. In this review, we describe the evolution of GLUD1 and GLUD2 after the duplication event in primates using the accumulated sequencing and structural data. A new gibbon GLUD2 sequence questions the indispensability of ancestral R496S and G509A mutations for GLUD2 irresponsiveness to GTP, providing an alternative with potentially similar regulatory features. The data of both GLUD1 and GLUD2 evolution not only confirm substitutions enhancing GLUD2 mitochondrial targeting, but also reveal a conserved mutation in ape GLUD1 mitochondrial targeting sequence that likely reduces its transport to mitochondria. Moreover, the information of GDH interactors, posttranslational modification and subcellular localization are provided for better understanding of the GDH mutations. Medically significant point mutations causing deregulation of GDH are considered from the structural and regulatory point of view.
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Affiliation(s)
- Yulia A. Aleshina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vasily A. Aleshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
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2
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Litso I, Plaitakis A, Fadouloglou VE, Providaki M, Kokkinidis M, Zaganas I. Structural Evolution of Primate Glutamate Dehydrogenase 2 as Revealed by In Silico Predictions and Experimentally Determined Structures. Biomolecules 2023; 14:22. [PMID: 38254622 PMCID: PMC10812971 DOI: 10.3390/biom14010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024] Open
Abstract
Glutamate dehydrogenase (GDH) interconverts glutamate to a-ketoglutarate and ammonia, interconnecting amino acid and carbohydrate metabolism. In humans, two functional GDH genes, GLUD1 and GLUD2, encode for hGDH1 and hGDH2, respectively. GLUD2 evolved from retrotransposition of the GLUD1 gene in the common ancestor of modern apes. These two isoenzymes are involved in the pathophysiology of human metabolic, neoplastic, and neurodegenerative disorders. The 3D structures of hGDH1 and hGDH2 have been experimentally determined; however, no information is available about the path of GDH2 structure changes during primate evolution. Here, we compare the structures predicted by the AlphaFold Colab method for the GDH2 enzyme of modern apes and their extinct primate ancestors. Also, we analyze the individual effect of amino acid substitutions emerging during primate evolution. Our most important finding is that the predicted structure of GDH2 in the common ancestor of apes was the steppingstone for the structural evolution of primate GDH2s. Two changes with a strong functional impact occurring at the first evolutionary step, Arg443Ser and Gly456Ala, had a destabilizing and stabilizing effect, respectively, making this step the most important one. Subsequently, GDH2 underwent additional modifications that fine-tuned its enzymatic properties to adapt to the functional needs of modern-day primate tissues.
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Affiliation(s)
- Ionela Litso
- Neurology/Neurogenetics Laboratory, School of Medicine, University of Crete, Voutes, 71003 Heraklion, Greece; (I.L.); (A.P.)
| | - Andreas Plaitakis
- Neurology/Neurogenetics Laboratory, School of Medicine, University of Crete, Voutes, 71003 Heraklion, Greece; (I.L.); (A.P.)
| | - Vasiliki E. Fadouloglou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece;
| | - Mary Providaki
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, 70013 Heraklion, Greece; (M.P.); (M.K.)
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, 70013 Heraklion, Greece; (M.P.); (M.K.)
- Department of Biology, University of Crete, Vasilika Vouton, 71409 Heraklion, Greece
| | - Ioannis Zaganas
- Neurology/Neurogenetics Laboratory, School of Medicine, University of Crete, Voutes, 71003 Heraklion, Greece; (I.L.); (A.P.)
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3
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Vedelek V, Vedelek B, Lőrincz P, Juhász G, Sinka R. A comparative analysis of fruit fly and human glutamate dehydrogenases in Drosophila melanogaster sperm development. Front Cell Dev Biol 2023; 11:1281487. [PMID: 38020911 PMCID: PMC10652781 DOI: 10.3389/fcell.2023.1281487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Glutamate dehydrogenases are enzymes that take part in both amino acid and energy metabolism. Their role is clear in many biological processes, from neuronal function to cancer development. The putative testis-specific Drosophila glutamate dehydrogenase, Bb8, is required for male fertility and the development of mitochondrial derivatives in spermatids. Testis-specific genes are less conserved and could gain new functions, thus raising a question whether Bb8 has retained its original enzymatic activity. We show that while Bb8 displays glutamate dehydrogenase activity, there are significant functional differences between the housekeeping Gdh and the testis-specific Bb8. Both human GLUD1 and GLUD2 can rescue the bb8 ms mutant phenotype, with superior performance by GLUD2. We also tested the role of three conserved amino acids observed in both Bb8 and GLUD2 in Gdh mutants, which showed their importance in the glutamate dehydrogenase function. The findings of our study indicate that Drosophila Bb8 and human GLUD2 could be novel examples of convergent molecular evolution. Furthermore, we investigated the importance of glutamate levels in mitochondrial homeostasis during spermatogenesis by ectopic expression of the mitochondrial glutamate transporter Aralar1, which caused mitochondrial abnormalities in fly spermatids. The data presented in our study offer evidence supporting the significant involvement of glutamate metabolism in sperm development.
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Affiliation(s)
- Viktor Vedelek
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Balázs Vedelek
- Department of Genetics, University of Szeged, Szeged, Hungary
- Hungarian Research Network, Biological Research Centre, Developmental Genetics Unit, Szeged, Hungary
| | - Péter Lőrincz
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
- Hungarian Research Network, Biological Research Centre, Institute of Genetics, Szeged, Hungary
| | - Rita Sinka
- Department of Genetics, University of Szeged, Szeged, Hungary
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4
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Su CC, Lyu M, Zhang Z, Miyagi M, Huang W, Taylor DJ, Yu EW. High-resolution structural-omics of human liver enzymes. Cell Rep 2023; 42:112609. [PMID: 37289586 PMCID: PMC10592444 DOI: 10.1016/j.celrep.2023.112609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/28/2023] [Accepted: 05/20/2023] [Indexed: 06/10/2023] Open
Abstract
We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.
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Affiliation(s)
- Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Meinan Lyu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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5
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Nnatubeugo C, Johnson E, Gisondi S, Roland F, Geldenhuys WJ, Menze MA, Konkle ME. The Mitochondrial Protein MitoNEET as a Probe for the Allostery of Glutamate Dehydrogenase. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238314. [PMID: 36500407 PMCID: PMC9737137 DOI: 10.3390/molecules27238314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022]
Abstract
The proteins glutamate dehydrogenase (GDH) and mitoNEET are both targets of drug development efforts to treat metabolic disorders, cancer, and neurodegenerative diseases. However, these two proteins differ starkly in the current knowledge about ligand binding sites. MitoNEET is a [2Fe-2S]-containing protein with no obvious binding site for small ligands observed in its crystal structures. In contrast, GDH is known to have a variety of ligands at multiple allosteric sites thereby leading to complex regulation in activity. In fact, while GDH can utilize either NAD(H) or NADP(H) for catalysis at the active site, only NAD(H) binds at a regulatory site to inhibit GDH activity. Previously, we found that mitoNEET forms a covalent bond with GDH in vitro and increases the catalytic activity of the enzyme. In this study we evaluated the effects of mitoNEET binding on the allosteric control of GDH conferred by inhibitors. We examined all effectors using NAD or NADP as the coenzyme to determine allosteric linkage by the NAD-binding regulatory site. We found that GDH activity, in the presence of the inhibitory palmitoyl-CoA and EGCG, can be rescued by mitoNEET, regardless of the coenzyme used. This suggests that mitoNEET rescues GDH by stabilizing the open conformation.
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Affiliation(s)
- Chimere Nnatubeugo
- Department of Chemistry, Ball State University, 2000 W. University Avenue, Muncie, IN 47306, USA
| | - Erica Johnson
- Department of Chemistry, Ball State University, 2000 W. University Avenue, Muncie, IN 47306, USA
| | - Sarah Gisondi
- Department of Chemistry, Eastern Illinois University, Charleston, IL 61920, USA
| | - Felicia Roland
- Department of Chemistry, Eastern Illinois University, Charleston, IL 61920, USA
| | - Werner J. Geldenhuys
- Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
- Department of Neuroscience, School of Medicine, West Virginia University, Morgantown, WV 26505, USA
| | - Michael A. Menze
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Mary E. Konkle
- Department of Chemistry, Ball State University, 2000 W. University Avenue, Muncie, IN 47306, USA
- Department of Chemistry, Eastern Illinois University, Charleston, IL 61920, USA
- Correspondence:
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6
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Aleshin VA, Bunik VI, Bruch EM, Bellinzoni M. Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase. Int J Mol Sci 2022; 23:ijms231911306. [PMID: 36232607 PMCID: PMC9570180 DOI: 10.3390/ijms231911306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Glutamate dehydrogenase (GDH) plays a key role in the metabolism of glutamate, an important compound at a cross-road of carbon and nitrogen metabolism and a relevant neurotransmitter. Despite being one of the first discovered allosteric enzymes, GDH still poses challenges for structural characterization of its allosteric sites. Only the structures with ADP, and at low (3.5 Å) resolution, are available for mammalian GDH complexes with allosteric activators. Here, we aim at deciphering a structural basis for the GDH allosteric activation using bovine GDH as a model. For the first time, we report a mammalian GDH structure in a ternary complex with the activators leucine and ADP, co-crystallized with potassium ion, resolved to 2.45 Å. An improved 2.4-angstrom resolution of the GDH complex with ADP is also presented. The ternary complex with leucine and ADP differs from the binary complex with ADP by the conformation of GDH C-terminus, involved in the leucine binding and subunit interactions. The potassium site, identified in this work, may mediate interactions between the leucine and ADP binding sites. Our data provide novel insights into the mechanisms of GDH activation by leucine and ADP, linked to the enzyme regulation by (de)acetylation.
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Affiliation(s)
- Vasily A. Aleshin
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Victoria I. Bunik
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
| | - Eduardo M. Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
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7
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Guan L, Wu F, Ren G, Wang J, Yang X, Huang X, Yu P, Lin Y, Mao L. Role of rare-earth elements in enhancing bioelectrocatalysis for biosensing with NAD +-dependent glutamate dehydrogenase. Chem Sci 2021; 12:13434-13441. [PMID: 34777762 PMCID: PMC8528072 DOI: 10.1039/d1sc00193k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022] Open
Abstract
Dehydrogenases (DHs) are widely explored bioelectrocatalysts in the development of enzymatic bioelectronics like biosensors and biofuel cells. However, the relatively low intrinsic reaction rates of DHs which mostly depend on diffusional coenzymes (e.g., NAD+) have limited their bioelectrocatalytic performance in applications such as biosensors with a high sensitivity. In this study, we find that rare-earth elements (REEs) can enhance the activity of NAD+-dependent glutamate dehydrogenase (GDH) toward highly sensitive electrochemical biosensing of glutamate in vivo. Electrochemical studies show that the sensitivity of the GDH-based glutamate biosensor is remarkably enhanced in the presence of REE cations (i.e., Yb3+, La3+ or Eu3+) in solution, of which Yb3+ yields the highest sensitivity increase (ca. 95%). With the potential effect of REE cations on NAD+ electrochemistry being ruled out, homogeneous kinetic assays by steady-state and stopped-flow spectroscopy reveal a two-fold enhancement in the intrinsic reaction rate of GDH by introducing Yb3+, mainly through accelerating the rate-determining NADH releasing step during the catalytic cycle. In-depth structural investigations using small angle X-ray scattering and infrared spectroscopy indicate that Yb3+ induces the backbone compaction of GDH and subtle β-sheet transitions in the active site, which may reduce the energetic barrier to NADH dissociation from the binding pocket as further suggested by molecular dynamics simulation. This study not only unmasks the mechanism of REE-promoted GDH kinetics but also paves a new way to highly sensitive biosensing of glutamate in vivo.
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Affiliation(s)
- Lihao Guan
- Department of Chemistry, Capital Normal University Beijing 100048 China
| | - Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, University of Chinese Academy of Sciences Beijing 100049 China
| | - Guoyuan Ren
- Department of Chemistry, Capital Normal University Beijing 100048 China
| | - Jialu Wang
- Department of Chemistry, Capital Normal University Beijing 100048 China
| | - Xiaoti Yang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiaohua Huang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University Nanjing 210023 China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, University of Chinese Academy of Sciences Beijing 100049 China
| | - Yuqing Lin
- Department of Chemistry, Capital Normal University Beijing 100048 China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, University of Chinese Academy of Sciences Beijing 100049 China
- College of Chemistry, Beijing Normal University Beijing 100875 China
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8
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Mapping the Intramolecular Communications among Different Glutamate Dehydrogenase States Using Molecular Dynamics. Biomolecules 2021; 11:biom11060798. [PMID: 34072154 PMCID: PMC8228935 DOI: 10.3390/biom11060798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 12/23/2022] Open
Abstract
Glutamate dehydrogenase (GDH) is a ubiquitous enzyme that catalyzes the reversible oxidative deamination of glutamate to α-ketoglutarate. It acts as an important branch-point enzyme between carbon and nitrogen metabolisms. Due to the multifaceted roles of GDH in cancer, hyperinsulinism/hyperammonemia, and central nervous system development and pathologies, tight control of its activity is necessitated. To date, several GDH structures have been solved in its closed form; however, intrinsic structural information in its open and apo forms are still deficient. Moreover, the allosteric communications and conformational changes taking place in the three different GDH states are not well studied. To mitigate these drawbacks, we applied unbiased molecular dynamic simulations (MD) and network analysis to three different GDH states i.e., apo, active, and inactive forms, for investigating their modulatory mechanisms. In this paper, based on MD and network analysis, crucial residues important for signal transduction, conformational changes, and maps of information flow among the different GDH states were elucidated. Moreover, with the recent findings of allosteric modulators, an allosteric wiring illustration of GDH intramolecular signal transductions would be of paramount importance to obtain the process of this enzyme regulation. The structural insights gained from this study will pave way for large-scale screening of GDH regulators and could support researchers in the design and development of new and potent GDH ligands.
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9
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Grzechowiak M, Sliwiak J, Jaskolski M, Ruszkowski M. Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism. FRONTIERS IN PLANT SCIENCE 2020; 11:754. [PMID: 32655590 PMCID: PMC7326016 DOI: 10.3389/fpls.2020.00754] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/12/2020] [Indexed: 05/24/2023]
Abstract
Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)+-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD+-specific, NAD+/NADP+ dual-specific, and NADP+-specific. We determined in this work that the mitochondrial AtGDH1 isozyme from A. thaliana is NAD+-specific. Altogether, A. thaliana expresses three GDH isozymes (AtGDH1-3) targeted to mitochondria, of which AtGDH2 has an extra EF-hand motif and is stimulated by calcium. Our enzymatic assays of AtGDH1 established that its sensitivity to calcium is negligible. In vivo the AtGDH1-3 enzymes form homo- and heterohexamers of varied composition. We solved the crystal structure of recombinant AtGDH1 in the apo-form and in complex with NAD+ at 2.59 and 2.03 Å resolution, respectively. We demonstrate also that both in the apo form and in 1:1 complex with NAD+, it forms D 3-symmetric homohexamers. A subunit of AtGDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme. Most of the subunits in our crystal structures, including those in NAD+ complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD+ hexamer contains a serendipitous 2OG molecule in the active site, causing a dramatic (∼25°) closure of the domains. We provide convincing evidence that the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30). We also identified several MPD [(+/-)-2-methyl-2,4-pentanediol] binding sites with conserved sequence. Although AtGDH1 is insensitive to MPD in our assays, the observation of druggable sites opens a potential for non-competitive herbicide design.
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Affiliation(s)
- Marta Grzechowiak
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Milosz Ruszkowski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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10
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Nassar OM, Wong KY, Lynch GC, Smith TJ, Pettitt BM. Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase. Protein Sci 2019; 28:2080-2088. [PMID: 31610054 DOI: 10.1002/pro.3748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/25/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022]
Abstract
Glutamate dehydrogenase (GDH) is a target for treating insulin-related disorders, such as hyperinsulinism hyperammonemia syndrome. Modeling native ligand binding has shown promise in designing GDH inhibitors and activators. Our computational investigation of the nicotinamide adenine diphosphate hydride (NADH)/adenosine diphosphate (ADP) site presented in this paper provides insight into the opposite allosteric effects induced at a single site of binding inhibitor NADH versus activator ADP to GDH. The computed binding free-energy difference between NADH and ADP using thermodynamic integration is -0.3 kcal/mol, which is within the -0.275 and -1.7 kcal/mol experimental binding free-energy difference range. Our simulations show an interesting model of ADP with dissimilar binding conformations at each NADH/ADP site in the GDH trimer, which explains the poorly understood strong binding but weak activation shown in experimental studies. In contrast, NADH showed similar inhibitory binding conformations at each NADH/ADP site. The structural analysis of the important residues in the NADH/ADP binding site presented in this paper may provide potential targets for mutation studies for allosteric drug design.
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Affiliation(s)
- Omneya M Nassar
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
| | - Ka-Yiu Wong
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Gillian C Lynch
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
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11
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Snyder DT, Panczyk E, Stiving AQ, Gilbert JD, Somogyi A, Kaplan D, Wysocki V. Design and Performance of a Second-Generation Surface-Induced Dissociation Cell for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Native Protein Complexes. Anal Chem 2019; 91:14049-14057. [PMID: 31584811 DOI: 10.1021/acs.analchem.9b03746] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A second-generation ("Gen 2") device capable of surface-induced dissociation (SID) and collision-induced dissociation (CID) for Fourier transform ion cyclotron resonance mass spectrometry of protein complexes has been designed, simulated, fabricated, and experimentally compared to a first-generation device ("Gen 1"). The primary goals of the redesign were to (1) simplify SID by reducing the number of electrodes, (2) increase CID and SID sensitivity by lengthening the collision cell, and (3) increase the mass range of the device for analysis of larger multimeric proteins, all while maintaining the normal instrument configuration and operation. Compared to Gen 1, Gen 2 exhibits an approximately 10× increase in sensitivity in flythrough mode, 7× increase in CID sensitivity for protonated leucine enkephalin (m/z 556), and 14× increase of CID sensitivity of 53 kDa streptavidin tetramer. It also approximately doubles the useful mass range (from m/z 8000 to m/z 15 000) using a rectilinear ion trap with a smaller inscribed radius or triples it (to m/z 22 000) using a hexapole collision cell and yields a 3-10× increase in SID sensitivity. We demonstrate the increased mass range and sensitivity on a variety of model molecules spanning nearly 3 orders of magnitude in absolute mass and present examples where the high resolution of the FT-ICR is advantageous for deconvoluting overlapping SID fragments.
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Affiliation(s)
| | | | | | | | | | - Desmond Kaplan
- KapScience LLC , Tewksbury , Massachusetts 01876 , United States
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12
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Hoffpauir ZA, Sherman E, Smith TJ. Dissecting the Antenna in Human Glutamate Dehydrogenase: Understanding Its Role in Subunit Communication and Allosteric Regulation. Biochemistry 2019; 58:4195-4206. [PMID: 31577135 DOI: 10.1021/acs.biochem.9b00722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate. While GDH is found in all living organisms, only that from animals is highly allosterically regulated by a wide array of metabolites. Because only animal GDH has a 50-residue antenna domain, we hypothesized that it was critical for allostery. To this end, we previously replaced the antenna with the loop found in bacteria, and the resulting chimera was no longer regulated by purine nucleotides. Hence, it seemed logical that the purpose of the antenna is to exert the subunit communication necessary for heterotrophic allosteric regulation. Here, we revisit the antenna deletion studies by retaining 10 more of the human GDH (hGDH) residues without adding the bacterial loop. Unexpectedly, the results were profoundly different than before. The basal activity of the mutant is only ∼13% of that of the wild type but ∼100 times more sensitive to all allosteric activators. In contrast, the mutant is still affected by all of the tested inhibitors to approximately the same degree. The resulting antenna-less mutant retained its negative cooperativity with respect to the coenzyme, again suggesting that intersubunit communication is intact. Finally, the mutant still exhibits substrate inhibition, albeit there are differences in the details. We present a model in which the majority of the antenna is not directly involved in allosteric regulation per se but rather may be responsible for improving enzymatic efficiency by acting as a conduit for substrate binding energy between subunits.
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Affiliation(s)
- Zoe A Hoffpauir
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch at Galveston , 301 University Boulevard, Route 0645 , Galveston , Texas 77555 , United States
| | - Eleena Sherman
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch at Galveston , 301 University Boulevard, Route 0645 , Galveston , Texas 77555 , United States
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology , University of Texas Medical Branch at Galveston , 301 University Boulevard, Route 0645 , Galveston , Texas 77555 , United States
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13
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Glutamate Dehydrogenase from Thermus thermophilus Is Activated by AMP and Leucine as a Complex with Catalytically Inactive Adenine Phosphoribosyltransferase Homolog. J Bacteriol 2019; 201:JB.00710-18. [PMID: 31036724 DOI: 10.1128/jb.00710-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/22/2019] [Indexed: 11/20/2022] Open
Abstract
Glutamate dehydrogenase (GDH) from a thermophilic bacterium, Thermus thermophilus, is composed of two heterologous subunits, GdhA and GdhB. In the heterocomplex, GdhB acts as the catalytic subunit, whereas GdhA lacks enzymatic activity and acts as the regulatory subunit for activation by leucine. In the present study, we performed a pulldown assay using recombinant T. thermophilus, producing GdhA fused with a His tag at the N terminus, and found that TTC1249 (APRTh), which is annotated as adenine phosphoribosyltransferase but lacks the enzymatic activity, was copurified with GdhA. When GdhA, GdhB, and APRTh were coproduced in Escherichia coli cells, they were purified as a ternary complex. The ternary complex exhibited GDH activity that was activated by leucine, as observed for the GdhA-GdhB binary complex. Furthermore, AMP activated GDH activity of the ternary complex, whereas such activation was not observed for the GdhA-GdhB binary complex. This suggests that APRTh mediates the allosteric activation of GDH by AMP. The present study demonstrates the presence of complicated regulatory mechanisms of GDH mediated by multiple compounds to control the carbon-nitrogen balance in bacterial cells.IMPORTANCE GDH, which catalyzes the synthesis and degradation of glutamate using NAD(P)(H), is a widely distributed enzyme among all domains of life. Mammalian GDH is regulated allosterically by multiple metabolites, in which the antenna helix plays a key role to transmit the allosteric signals. In contrast, bacterial GDH was believed not to be regulated allosterically because it lacks the antenna helix. We previously reported that GDH from Thermus thermophilus (TtGDH), which is composed of two heterologous subunits, is activated by leucine. In the present study, we found that AMP activates TtGDH using a catalytically inactive APRTh as the sensory subunit. This suggests that T. thermophilus possesses a complicated regulatory mechanism of GDH to control carbon and nitrogen metabolism.
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14
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VanAernum ZL, Gilbert JD, Belov ME, Makarov AA, Horning SR, Wysocki VH. Surface-Induced Dissociation of Noncovalent Protein Complexes in an Extended Mass Range Orbitrap Mass Spectrometer. Anal Chem 2019; 91:3611-3618. [PMID: 30688442 PMCID: PMC6516482 DOI: 10.1021/acs.analchem.8b05605] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Native mass spectrometry continues to develop as a significant complement to traditional structural biology techniques. Within native mass spectrometry (MS), surface-induced dissociation (SID) has been shown to be a powerful activation method for the study of noncovalent complexes of biological significance. High-resolution mass spectrometers have become increasingly adapted to the analysis of high-mass ions and have demonstrated their importance in understanding how small mass changes can affect the overall structure of large biomolecular complexes. Herein we demonstrate the first adaptation of surface-induced dissociation in a modified high-mass-range, high-resolution Orbitrap mass spectrometer. The SID device was designed to be installed in the Q Exactive series of Orbitrap mass spectrometers with minimal disruption of standard functions. The performance of the SID-Orbitrap instrument has been demonstrated with several protein complex and ligand-bound protein complex systems ranging from 53 to 336 kDa. We also address the effect of ion source temperature on native protein-ligand complex ions as assessed by SID. Results are consistent with previous findings on quadrupole time-of-flight instruments and suggest that SID coupled to high-resolution MS is well-suited to provide information on the interface interactions within protein complexes and ligand-bound protein complexes.
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15
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Hou W, Lu S, Zhao H, Yu Y, Xu H, Yu B, Su L, Lin C, Ruan BH. Propylselen inhibits cancer cell growth by targeting glutamate dehydrogenase at the NADP + binding site. Biochem Biophys Res Commun 2018; 509:262-267. [PMID: 30583861 DOI: 10.1016/j.bbrc.2018.12.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 12/15/2018] [Indexed: 01/18/2023]
Abstract
High levels of glutamate dehydrogenase (GDH) activity are associated with hypoglycemia, cancer, and Parkinson's disease. Propylselen was synthesized to investigate its mechanism of GDH inhibition in comparison with Ebselen and Epigallocatechin gallate (EGCG). Because Ebselen was found to crosslink with the peptide (AA299-341) at the active site of E.coli GDH, the Cys, Pro, and Lys residues of the corresponding peptide were mutagenized to Ala residues. Using enzyme kinetics and biomolecular interaction assays, we found that the conserved GDH P320 residue is important for propylselen binding, C321 for Ebselen binding, and K341 for EGCG binding. In addition, these 3 mutations abolished NADP+ binding to E. coli GDH in the absence of glutamate substrate, but in the presence of glutamate, the catalytic activity of the mutants was reduced only by 2-4 fold, indicating that a substrate-induced fit mechanism exists in E. coli GDH. Furthermore, biochemical analysis showed that NADP+ had high affinity (Kd of 77 nM) for GDH; by targeting the NADP binding site, propylselen effectively inhibited both E. coli and human GDH activity and improved anticancer activity.
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Affiliation(s)
- Wei Hou
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Shiying Lu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Han Zhao
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Yan Yu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Haodong Xu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Biao Yu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Lin Su
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Chenshui Lin
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China
| | - Benfang Helen Ruan
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, Institute of Drug Development & Chemical Biology (IDD & CB), Zhejiang University of Technology, Hangzhou, China.
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16
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Nassar OM, Li C, Stanley CA, Pettitt BM, Smith TJ. Glutamate dehydrogenase: Structure of a hyperinsulinism mutant, corrections to the atomic model, and insights into a regulatory site. Proteins 2018; 87:41-50. [PMID: 30367518 DOI: 10.1002/prot.25620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/10/2018] [Accepted: 10/16/2018] [Indexed: 11/06/2022]
Abstract
Mammalian glutamate dehydrogenase (GDH) has complex allosteric regulation and the loss of GTP inhibition causes the hyperinsulinism/hyperammonemia syndrome (HHS) where insulin is hypersecreted upon consumption of protein. The archetypical HHS lesion is H454Y and lies in the GTP binding pocket. To better understand the mechanism of HHS, we determined the crystal structure of H454Y. When the bovine GDH crystal structures were minimized to prepare for further computational analysis, unusually large deviations were found at the allosteric NADH binding site due to chemical sequence errors. Notably, 387 lies in an allosteric where several activators and inhibitors bind and should be lysine rather than asparagine. All structures were re-refined and the consequence of this sequence error on NADH binding was calculated using free energy perturbation. The binding free energy penalty going from the correct to incorrect sequence found is +5 kcal/mol per site and therefore has a significant impact on drug development. BROADER AUDIENCE ABSTRACT: Glutamate dehydrogenase is a key enzyme involved in amino acid catabolism. As such, it is heavily regulated in animals by a wide array of metabolites. The importance of this regulation is most apparent in a genetic disorder called hyperinsulinism/hyperammonemia (HHS) where patients hypersecrete insulin upon the consumption of protein. We determined the atomic structure of one of these HHS mutants to better understand the disease and also analyzed an allosteric regulatory site.
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Affiliation(s)
- Omneya M Nassar
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
| | - Changhong Li
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Charles A Stanley
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
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17
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Mathioudakis L, Bourbouli M, Daklada E, Kargatzi S, Michaelidou K, Zaganas I. Localization of Human Glutamate Dehydrogenases Provides Insights into Their Metabolic Role and Their Involvement in Disease Processes. Neurochem Res 2018; 44:170-187. [PMID: 29943084 DOI: 10.1007/s11064-018-2575-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/21/2022]
Abstract
Glutamate dehydrogenase (GDH) catalyzes the reversible deamination of L-glutamate to α-ketoglutarate and ammonia. In mammals, GDH contributes to important processes such as amino acid and carbohydrate metabolism, energy production, ammonia management, neurotransmitter recycling and insulin secretion. In humans, two isoforms of GDH are found, namely hGDH1 and hGDH2, with the former being ubiquitously expressed and the latter found mainly in brain, testis and kidney. These two iso-enzymes display highly divergent allosteric properties, especially concerning their basal activity, ADP activation and GTP inhibition. On the other hand, both enzymes are thought to predominantly localize in the mitochondrial matrix, even though alternative localizations have been proposed. To further study the subcellular localization of the two human iso-enzymes, we created HEK293 cell lines stably over-expressing hGDH1 and hGDH2. In these cell lines, immunofluorescence and enzymatic analyses verified the overexpression of both hGDH1 and hGDH2 iso-enzymes, whereas subcellular fractionation followed by immunoblotting showed their predominantly mitochondrial localization. Given that previous studies have only indirectly compared the subcellular localization of the two iso-enzymes, we co-expressed them tagged with different fluorescent dyes (green and red fluorescent protein for hGDH1 and hGDH2, respectively) and found them to co-localize. Despite the wealth of information related to the functional properties of hGDH1 and hGDH2 and the availability of the hGDH1 structure, there is still an ongoing debate concerning their metabolic role and their involvement in disease processes. Data on the localization of hGDHs, as the ones presented here, could contribute to better understanding of the function of these important human enzymes.
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Affiliation(s)
- Lambros Mathioudakis
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Mara Bourbouli
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Elisavet Daklada
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Sofia Kargatzi
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Kleita Michaelidou
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Ioannis Zaganas
- Neurology Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece. .,Department of Neurology, University Hospital of Heraklion, Heraklion, Crete, Greece.
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18
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Jin Y, Li D, Lu S, Zhao H, Chen Z, Hou W, Ruan BH. Ebselen Reversibly Inhibits Human Glutamate Dehydrogenase at the Catalytic Site. Assay Drug Dev Technol 2018; 16:115-122. [PMID: 29470101 DOI: 10.1089/adt.2017.822] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human glutamate dehydrogenase (GDH) plays an important role in neurological diseases, tumor metabolism, and hyperinsulinism-hyperammonemia syndrome (HHS). However, there are very few inhibitors known for human GDH. Recently, Ebselen was reported to crosslink with Escherichia coli GDH at the active site cysteine residue (Cys321), but the sequence alignment showed that the corresponding residue is Ala329 in human GDH. To investigate whether Ebselen could be an inhibitor for human GDH, we cloned and expressed an N-terminal His-tagged human GDH in E. coli. The recombinant human GDH enzyme showed expected properties such as adenosine diphosphate activation and nicotinamide adenine dinucleotide/nicotinamide adenine dinucleotide phosphate dual recognition. Further, we developed a 2-(3-(2-methoxy-4-nitrophenyl)-2-(4-nitrophenyl)-2H-tetrazol-3-ium-5-yl) benzenesulfonate sodium salt (EZMTT)-based assay for human GDH, which was highly sensitive and is suitable for high-throughput screening for potent GDH inhibitors. In addition, ForteBio binding assays demonstrated that Ebselen is a reversible active site inhibitor for human GDH. Since Ebselen is a multifunctional organoselenium compound in Phase III clinical trials for inflammation, an Ebselen-based GDH inhibitor might be valuable for future drug discovery for HHS patients.
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Affiliation(s)
- Yanhong Jin
- College of Pharmaceutical Sciences, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology , Hangzhou, China
| | - Di Li
- College of Pharmaceutical Sciences, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology , Hangzhou, China
| | - Shiying Lu
- College of Pharmaceutical Sciences, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology , Hangzhou, China
| | - Han Zhao
- College of Pharmaceutical Sciences, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology , Hangzhou, China
| | - Zhao Chen
- College of Pharmaceutical Sciences, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology , Hangzhou, China
| | - Wei Hou
- College of Pharmaceutical Sciences, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology , Hangzhou, China
| | - Benfang Helen Ruan
- College of Pharmaceutical Sciences, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology , Hangzhou, China
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19
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Yu Y, Jin Y, Zhou J, Ruan H, Zhao H, Lu S, Zhang Y, Li D, Ji X, Ruan BH. Ebselen: Mechanisms of Glutamate Dehydrogenase and Glutaminase Enzyme Inhibition. ACS Chem Biol 2017; 12:3003-3011. [PMID: 29072450 DOI: 10.1021/acschembio.7b00728] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ebselen modulates target proteins through redox reactions with selenocysteine/cysteine residues, or through binding to the zinc finger domains. However, a recent contradiction in ebselen inhibition of kidney type glutaminase (KGA) stimulated our interest in investigating its inhibition mechanism with glutamate dehydrogenase (GDH), KGA, thioredoxin reductase (TrxR), and glutathione S-transferase. Fluorescein- or biotin-labeled ebselen derivatives were synthesized for mechanistic analyses. Biomolecular interaction analyses showed that only GDH, KGA, and TrxR proteins can bind to the ebselen derivative, and the binding to GDH and KGA could be competed off by glutamine or glutamate. From the gel shift assays, the fluorescein-labeled ebselen derivative could co-migrate with hexameric GDH and monomeric/dimeric TrxR in a dose-dependent manner; it also co-migrated with KGA but disrupted the tetrameric form of the KGA enzyme at a high compound concentration. Further proteomic analysis demonstrated that the ebselen derivative could cross-link with proteins through a specific cysteine at the active site of GDH and TrxR proteins, but for KGA protein, the binding site is at the N-terminal appendix domain outside of the catalytic domain, which might explain why ebselen is not a potent KGA enzyme inhibitor in functional assays. In conclusion, ebselen could inhibit enzyme activity by binding to the catalytic domain or disruption of the protein complex. In addition, ebselen is a relatively potent selective GDH inhibitor that might provide potential therapeutic opportunities for hyperinsulinism-hyperammonemia syndrome patients who have the mutational loss of GTP inhibition.
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Affiliation(s)
- Yan Yu
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Yanhong Jin
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Jie Zhou
- Center
for Medicinal Resources Research, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou, China
| | - Haoqiang Ruan
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Han Zhao
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Shiying Lu
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Yue Zhang
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Di Li
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Xiaoyun Ji
- The
State Key Laboratory of Pharmaceutical Biotechnology, School of Life
Sciences, Nanjing University, Nanjing, China
| | - Benfang Helen Ruan
- College
of Pharmaceutical Science, Collaborative Innovation Center of Yangtza
River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
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20
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Smith HQ, Li C, Stanley CA, Smith TJ. Glutamate Dehydrogenase, a Complex Enzyme at a Crucial Metabolic Branch Point. Neurochem Res 2017; 44:117-132. [PMID: 29079932 DOI: 10.1007/s11064-017-2428-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 12/27/2022]
Abstract
In-vitro, glutamate dehydrogenase (GDH) catalyzes the reversible oxidative deamination of glutamate to α-ketoglutarate (α-KG). GDH is found in all organisms, but in animals is allosterically regulated by a wide array of metabolites. For many years, it was not at all clear why animals required such complex control. Further, in both standard textbooks and some research publications, there has been some controversy as to the directionality of the reaction. Here we review recent work demonstrating that GDH operates mainly in the catabolic direction in-vivo and that the finely tuned network of allosteric regulators allows GDH to meet the varied needs in a wide range of tissues in animals. Finally, we review the progress in using pharmacological agents to activate or inhibit GDH that could impact a wide range of pathologies from insulin disorders to tumor growth.
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Affiliation(s)
- Hong Q Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Changhong Li
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Charles A Stanley
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Thomas James Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA.
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21
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Tomita T, Yin L, Nakamura S, Kosono S, Kuzuyama T, Nishiyama M. Crystal structure of the 2-iminoglutarate-bound complex of glutamate dehydrogenase from Corynebacterium glutamicum. FEBS Lett 2017; 591:1611-1622. [PMID: 28486765 DOI: 10.1002/1873-3468.12667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 11/06/2022]
Abstract
The NADP+ -dependent glutamate dehydrogenase from Corynebacterium glutamicum (CgGDH) is considered to be one of the key enzymes in the industrial fermentation of glutamate due to its high glutamate-producing activity. We determined the crystal structure of CgGDH complexed with NADP+ and 2-iminoglutarate. Among six subunits of hexameric CgGDH-binding NADP+ , only four subunits bind 2-iminoglutarate in a closed form, while the other two are in an open form. In the closed form, 2-iminoglutarate is bound to the substrate-binding site with the 2-imino group stacked by the nicotinamide ring of the coenzyme, suggesting a prehydride transfer state in a hypothesized reaction scheme with the imino intermediate. We also conducted MD simulations and provide insights into the extreme preference for the glutamate-producing reaction of CgGDH. DATABASE The atomic coordinate and structure factors have been deposited in the RCSB PDB database under the accession number 5GUD.
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Affiliation(s)
- Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Lulu Yin
- Biotechnology Research Center, The University of Tokyo, Japan
| | - Shugo Nakamura
- Faculty of Information Networking for Innovation and Design, Toyo University, Tokyo, Japan
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Japan
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22
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Mishra SK, Sankar K, Jernigan RL. Altered dynamics upon oligomerization corresponds to key functional sites. Proteins 2017; 85:1422-1434. [PMID: 28383162 DOI: 10.1002/prot.25302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 12/18/2022]
Abstract
It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse-grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with ¼ of the residues increasing in their mobilities and ¼ having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures. Proteins 2017; 85:1422-1434. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sambit Kumar Mishra
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Kannan Sankar
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, 50011.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, 50011
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23
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The Glutamate Dehydrogenase Pathway and Its Roles in Cell and Tissue Biology in Health and Disease. BIOLOGY 2017; 6:biology6010011. [PMID: 28208702 PMCID: PMC5372004 DOI: 10.3390/biology6010011] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/10/2017] [Accepted: 01/16/2017] [Indexed: 02/07/2023]
Abstract
Glutamate dehydrogenase (GDH) is a hexameric enzyme that catalyzes the reversible conversion of glutamate to α-ketoglutarate and ammonia while reducing NAD(P)⁺ to NAD(P)H. It is found in all living organisms serving both catabolic and anabolic reactions. In mammalian tissues, oxidative deamination of glutamate via GDH generates α-ketoglutarate, which is metabolized by the Krebs cycle, leading to the synthesis of ATP. In addition, the GDH pathway is linked to diverse cellular processes, including ammonia metabolism, acid-base equilibrium, redox homeostasis (via formation of fumarate), lipid biosynthesis (via oxidative generation of citrate), and lactate production. While most mammals possess a single GDH1 protein (hGDH1 in the human) that is highly expressed in the liver, humans and other primates have acquired, via duplication, an hGDH2 isoenzyme with distinct functional properties and tissue expression profile. The novel hGDH2 underwent rapid evolutionary adaptation, acquiring unique properties that enable enhanced enzyme function under conditions inhibitory to its ancestor hGDH1. These are thought to provide a biological advantage to humans with hGDH2 evolution occurring concomitantly with human brain development. hGDH2 is co-expressed with hGDH1 in human brain, kidney, testis and steroidogenic organs, but not in the liver. In human cerebral cortex, hGDH1 and hGDH2 are expressed in astrocytes, the cells responsible for removing and metabolizing transmitter glutamate, and for supplying neurons with glutamine and lactate. In human testis, hGDH2 (but not hGDH1) is densely expressed in the Sertoli cells, known to provide the spermatids with lactate and other nutrients. In steroid producing cells, hGDH1/2 is thought to generate reducing equivalents (NADPH) in the mitochondria for the biosynthesis of steroidal hormones. Lastly, up-regulation of hGDH1/2 expression occurs in cancer, permitting neoplastic cells to utilize glutamine/glutamate for their growth. In addition, deregulation of hGDH1/2 is implicated in the pathogenesis of several human disorders.
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Multiple Forms of Glutamate Dehydrogenase in Animals: Structural Determinants and Physiological Implications. BIOLOGY 2016; 5:biology5040053. [PMID: 27983623 PMCID: PMC5192433 DOI: 10.3390/biology5040053] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/26/2016] [Accepted: 12/07/2016] [Indexed: 11/17/2022]
Abstract
Glutamate dehydrogenase (GDH) of animal cells is usually considered to be a mitochondrial enzyme. However, this enzyme has recently been reported to be also present in nucleus, endoplasmic reticulum and lysosomes. These extramitochondrial localizations are associated with moonlighting functions of GDH, which include acting as a serine protease or an ATP-dependent tubulin-binding protein. Here, we review the published data on kinetics and localization of multiple forms of animal GDH taking into account the splice variants, post-translational modifications and GDH isoenzymes, found in humans and apes. The kinetic properties of human GLUD1 and GLUD2 isoenzymes are shown to be similar to those published for GDH1 and GDH2 from bovine brain. Increased functional diversity and specific regulation of GDH isoforms due to alternative splicing and post-translational modifications are also considered. In particular, these structural differences may affect the well-known regulation of GDH by nucleotides which is related to recent identification of thiamine derivatives as novel GDH modulators. The thiamine-dependent regulation of GDH is in good agreement with the fact that the non-coenzyme forms of thiamine, i.e., thiamine triphosphate and its adenylated form are generated in response to amino acid and carbon starvation.
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Zhang Z, Su B, Wu M, Lin J, Yang L. Strategies for eliminating l-arabinitol in the bioconversion of xylitol. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.08.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Oliveira T, Sharkey MA, Engel PC, Khan AR. Crystal structure of a chimaeric bacterial glutamate dehydrogenase. Acta Crystallogr F Struct Biol Commun 2016; 72:462-6. [PMID: 27303899 PMCID: PMC4909246 DOI: 10.1107/s2053230x16007305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/02/2016] [Indexed: 11/10/2022] Open
Abstract
Glutamate dehydrogenases (EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate using NAD(P)(+) as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD(+) versus NADP(+), but they are not unambiguous predictors of cofactor preference. In the absence of substrate, the two domains move apart as rigid bodies, as shown by the apo structure of glutamate dehydrogenase from Clostridium symbiosum. Here, the crystal structure of a chimaeric clostridial/Escherichia coli enzyme has been determined in the apo state. The enzyme is fully functional and reveals possible determinants of interdomain flexibility at a hinge region following the pivot helix. The enzyme retains the preference for NADP(+) cofactor from the parent E. coli domain II, although there are subtle differences in catalytic activity.
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Affiliation(s)
- Tânia Oliveira
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
| | - Michael A. Sharkey
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul C. Engel
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
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Changes in hydration structure are necessary for collective motions of a multi-domain protein. Sci Rep 2016; 6:26302. [PMID: 27193111 PMCID: PMC4872039 DOI: 10.1038/srep26302] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/25/2016] [Indexed: 01/27/2023] Open
Abstract
Conformational motions of proteins are necessary for their functions. To date, experimental studies measuring conformational fluctuations of a whole protein structure have revealed that water molecules hydrating proteins are necessary to induce protein functional motions. However, the underlying microscopic mechanism behind such regulation remains unsolved. To clarify the mechanism, multi-domain proteins are good targets because it is obvious that water molecules between domains play an important role in domain motions. Here, we show how changes in hydration structure microscopically correlate with large-amplitude motions of a multi-domain protein, through molecular dynamics simulation supported by structural analyses and biochemical experiments. We first identified collective domain motions of the protein, which open/close an active-site cleft between domains. The analyses on changes in hydration structure revealed that changes in local hydration in the depth of the cleft are necessary for the domain motion and vice versa. In particular, ‘wetting’/‘drying’ at a hydrophobic pocket and ‘adsorption’/‘dissociation’ of a few water molecules at a hydrophilic crevice in the cleft were induced by dynamic rearrangements of hydrogen-bond networks, and worked as a switch for the domain motions. Our results microscopically demonstrated the importance of hydrogen-bond networks of water molecules in understanding energy landscapes of protein motions.
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Mechanisms and Dynamics of Protein Acetylation in Mitochondria. Trends Biochem Sci 2016; 41:231-244. [PMID: 26822488 DOI: 10.1016/j.tibs.2015.12.006] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/17/2022]
Abstract
Reversible protein acetylation is a major regulatory mechanism for controlling protein function. Through genetic manipulations, dietary perturbations, and new proteomic technologies, the diverse functions of protein acetylation are coming into focus. Protein acetylation in mitochondria has taken center stage, revealing that 63% of mitochondrially localized proteins contain lysine acetylation sites. We summarize the field and discuss salient topics that cover spurious versus targeted acetylation, the role of SIRT3 deacetylation, nonenzymatic acetylation, and molecular models for regulatory acetylations that display high and low stoichiometry.
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Marques Netto CGC, da Silva DG, Toma SH, Andrade LH, Nakamura M, Araki K, Toma HE. Bovine glutamate dehydrogenase immobilization on magnetic nanoparticles: conformational changes and catalysis. RSC Adv 2016. [DOI: 10.1039/c5ra24637g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Glutamate dehydrogenase (GDH) was immobilized on different supports and systematically investigated in order to provide a better understanding of the immobilization effects on the catalysis of multimeric enzymes.
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Affiliation(s)
| | - Delmárcio G. da Silva
- Supramolecular NanotechLab
- Instituto de Quimica
- Universidade de São Paulo
- São Paulo-SP
- Brazil
| | - Sergio H. Toma
- Supramolecular NanotechLab
- Instituto de Quimica
- Universidade de São Paulo
- São Paulo-SP
- Brazil
| | - Leandro H. Andrade
- Laboratory of Fine Chemistry and Biocatalysis
- Instituto de Química
- Universidade de São Paulo
- São Paulo-SP
- Brazil
| | - Marcelo Nakamura
- Supramolecular NanotechLab
- Instituto de Quimica
- Universidade de São Paulo
- São Paulo-SP
- Brazil
| | - Koiti Araki
- Supramolecular NanotechLab
- Instituto de Quimica
- Universidade de São Paulo
- São Paulo-SP
- Brazil
| | - Henrique E. Toma
- Supramolecular NanotechLab
- Instituto de Quimica
- Universidade de São Paulo
- São Paulo-SP
- Brazil
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30
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Bera S, Lamba S, Rashid M, Sharma AK, Medvinsky AB, Acquisti C, Chakraborty A, Li BL. Robust regulation of hepatic pericentral amination by glutamate dehydrogenase kinetics. Integr Biol (Camb) 2016; 8:1126-1132. [DOI: 10.1039/c6ib00158k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-Ketoglutarate substrate inhibition kinetics of hepatic glutamate dehydrogenase amination activity confers robust control over the ratio between glutamate and ammonium.
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Affiliation(s)
- Soumen Bera
- School of Mathematics
- Statistics and Computational Sciences
- Central University of Rajasthan
- Ajmer
- India
| | - Sanjay Lamba
- School of Mathematics
- Statistics and Computational Sciences
- Central University of Rajasthan
- Ajmer
- India
| | - Mubasher Rashid
- School of Mathematics
- Statistics and Computational Sciences
- Central University of Rajasthan
- Ajmer
- India
| | - Anuj K. Sharma
- School of Chemical Sciences and Pharmacy
- Central University of Rajasthan
- Ajmer
- India
| | | | | | - Amit Chakraborty
- School of Mathematics
- Statistics and Computational Sciences
- Central University of Rajasthan
- Ajmer
- India
| | - Bai-Lian Li
- Ecological Complexity and Modeling Laboratory
- University of California
- Riverside
- USA
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Aluminum and its effect in the equilibrium between folded/unfolded conformation of NADH. J Inorg Biochem 2015; 152:139-46. [PMID: 26346779 DOI: 10.1016/j.jinorgbio.2015.08.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/10/2015] [Accepted: 08/20/2015] [Indexed: 11/22/2022]
Abstract
Nicotinamide adenine dinucleotide (NADH) is one of the most abundant cofactor employed by proteins and enzymes. The molecule is formed by two nucleotides that can lead to two main conformations: folded/closed and unfolded/open. Experimentally, it has been determined that the closed form is about 2 kcal/mol more stable than the open formed. Computationally, a correct description of the NADH unfolding process is challenging due to different reasons: 1) The unfolding process shows a very low energy difference between the two conformations 2) The molecule can form a high number of internal hydrogen bond interactions 3) Subtle effects such as dispersion may be important. In order to tackle all these effects, we have employed a number of different state of the art computational techniques, including: a) well-tempered metadynamics, b) geometry optimizations, and c) Quantum Theory of Atoms in Molecules (QTAIM) calculations, to investigate the conformational change of NADH in solution and interacting with aluminum. All the results indicate that aluminum indeed favors the closed conformation of NADH, due mainly to the formation of a more rigid structure through key hydrogen bond interactions.
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Masuda S, Tomohiro T, Yamaguchi S, Morimoto S, Hatanaka Y. Structure-assisted ligand-binding analysis using fluorogenic photoaffinity labeling. Bioorg Med Chem Lett 2015; 25:1675-1678. [DOI: 10.1016/j.bmcl.2015.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 11/29/2022]
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Son HF, Kim IK, Kim KJ. Structural insights into domain movement and cofactor specificity of glutamate dehydrogenase from Corynebacterium glutamicum. Biochem Biophys Res Commun 2015; 459:387-92. [PMID: 25727019 DOI: 10.1016/j.bbrc.2015.02.109] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 10/23/2022]
Abstract
Glutamate dehydrogenase (GDH) is an enzyme involved in the synthesis of amino acids by converting glutamate to α-ketoglutarate, and vice versa. To investigate the molecular mechanism of GDH, we determined a crystal structure of the Corynebacterium glutamicum-derived GDH (CgGDH) in complex with its NADP cofactor and α-ketoglutarate substrate. CgGDH functions as a hexamer, and each CgGDH monomer comprises 2 separate domains; a Rossmann fold cofactor-binding domain and a substrate-binding domain. The structural comparison between the apo- and cofactor/substrate-binding forms revealed that the CgGDH enzyme undergoes a domain movement during catalysis. In the apo-form, CgGDH exists as an open state, and upon binding of the substrate and cofactor the protein undergoes a conformation change to a closed state. Our structural study also revealed that CgGDH has cofactor specificity for NADP, but not NAD, and this was confirmed by GDH activity measurements. Residues involved in the stabilization of the NADP cofactor and the α-ketoglutarate substrate were identified, and their roles in substrate/cofactor binding were confirmed by site-directed mutagenesis experiments.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Il-Kwon Kim
- Paik Kwang Industrial Company Ltd., 57 Oehang-4 Gil, Gunsan, Jellabuk-do 573-879, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
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Polónia ARM, Cleary DFR, Freitas R, de Voogd NJ, Gomes NCM. The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment. Mol Ecol 2015; 24:409-23. [DOI: 10.1111/mec.13024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 11/23/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Ana R. M. Polónia
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Daniel F. R. Cleary
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Rossana Freitas
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Nicole J. de Voogd
- Naturalis Biodiversity Center; PO Box 9517 2300 RA Leiden The Netherlands
| | - Newton C. M. Gomes
- Department of Biology; CESAM; Universidade de Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
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35
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Quantitative determination of glycine in aqueous solution using glutamate dehydrogenase-immobilized glyoxal agarose beads. Appl Biochem Biotechnol 2014; 172:289-97. [PMID: 24078189 DOI: 10.1007/s12010-013-0543-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
Abstract
In this study, an enzymatic procedure for the determination of glycine (Gly) was developed by using a column containing immobilized glutamate dehydrogenase (GDH) on glyoxal agarose beads. Ammonia is produced from the enzymatic reactions between Gly and GDH with NAD(+) in phosphate buffer medium. The indophenol blue method was used for ammonia detection based on the spectrophotometric measurements of blue-colored product absorbing at 640 nm. The calibration graph is linear in the range of 0.1-10 mM of Gly concentrations. The effect of pH, temperature, and time interval was studied to find column stability, and also the interference effects of other amino acids was investigated. The interaction between GDH and glyoxal agarose beads was analyzed by Fourier transform infrared (FTIR) spectroscopy. The morphology of the immobilized and non-immobilized agarose beads were characterized by atomic force microscopy (AFM).
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Ma X, Zhou M, Wysocki VH. Surface induced dissociation yields quaternary substructure of refractory noncovalent phosphorylase B and glutamate dehydrogenase complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:368-379. [PMID: 24452296 DOI: 10.1007/s13361-013-0790-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/11/2013] [Accepted: 11/19/2013] [Indexed: 06/03/2023]
Abstract
Ion mobility (IM) and tandem mass spectrometry (MS/MS) coupled with native MS are useful for studying noncovalent protein complexes. Collision induced dissociation (CID) is the most common MS/MS dissociation method. However, some protein complexes, including glycogen phosphorylase B kinase (PHB) and L-glutamate dehydrogenase (GDH) examined in this study, are resistant to dissociation by CID at the maximum collision energy available in the instrument. Surface induced dissociation (SID) was applied to dissociate the two refractory protein complexes. Different charge state precursor ions of the two complexes were examined by CID and SID. The PHB dimer was successfully dissociated to monomers and the GDH hexamer formed trimeric subcomplexes that are informative of its quaternary structure. The unfolding of the precursor and the percentages of the distinct products suggest that the dissociation pathways vary for different charge states. The precursors at lower charge states (+21 for PHB dimer and +27 for GDH hexamer) produce a higher percentage of folded fragments and dissociate more symmetrically than the precusors at higher charge states (+29 for PHB dimer and +39 for GDH hexamer). The precursors at lower charge state may be more native-like than the higher charge state because a higher percentage of folded fragments and a lower percentage of highly charged unfolded fragments are detected. The combination of SID and charge reduction is shown to be a powerful tool for quaternary structure analysis of refractory noncovalent protein complexes, as illustrated by the data for PHB dimer and GDH hexamer.
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Affiliation(s)
- Xin Ma
- Department of Chemistry and Biochemistry, The Ohio State University, 876 Biological Sciences Building, 484 W 12th Ave, Columbus, OH, 43210, USA
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Evaluation of sub-cellular distribution of glutamate dehydrogenase (GDH) in Drosophila melanogaster larvae. Acta Histochem 2014; 116:297-303. [PMID: 24139688 DOI: 10.1016/j.acthis.2013.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 08/06/2013] [Accepted: 08/07/2013] [Indexed: 11/20/2022]
Abstract
Glutamate dehydrogenase (GDH) enzyme was conventionally known as a mitochondrial marker. However, subsequently it was reported to be present in the nuclei as well. So far, the nuclear distribution of GDH has been reported in a number of organisms including yeast, rat, cow, chicken. However, the sub-cellular distribution of GDH, illustrated by in situ methods still remains elusive. Here, by assaying the GDH activity and by immuno-blotting using anti-GDH antibody in the fractionated nuclear and cytoplasmic fractions of Drosophila larvae, we demonstrate the cytoplasmic distribution of GDH. This observation was further supported by in situ immunostaining of salivary gland, Malpighian tubules and eye imaginal discs of Drosophila larvae. Collectively, our results demonstrate that in Drosophila larvae, GDH is not found in the nucleus, but is localized exclusively in the cytoplasm.
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The Odyssey of a Young Gene: Structure–Function Studies in Human Glutamate Dehydrogenases Reveal Evolutionary-Acquired Complex Allosteric Regulation Mechanisms. Neurochem Res 2014; 39:471-86. [DOI: 10.1007/s11064-014-1251-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/24/2014] [Accepted: 01/29/2014] [Indexed: 01/13/2023]
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39
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El-Sayed ASA, Ibrahim H, Sitohy MZ. Co-immobilization of PEGylated Aspergillus flavipes L-methioninase with glutamate dehydrogenase: a novel catalytically stable anticancer consortium. Enzyme Microb Technol 2013; 54:59-69. [PMID: 24267569 DOI: 10.1016/j.enzmictec.2013.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/15/2013] [Accepted: 10/10/2013] [Indexed: 11/19/2022]
Abstract
Aspergillus flavipes L-methioninase (AfMETase) exhibits reliable pharmacokinetic properties and anticancer potency in vitro[10]. To maximize its therapeutic efficiency as protection against in vivo proteolysis, reduction of antigenicity and hyperammoniemia, the enzyme was PEGylated and coupled with glutamate dehydrogenase (GDH). The highest degree of PEGylation was measured at 40-50/1 molar ratio of PEG to AfMETase, with a lower mobility on SDS-PGE, compared to the native AfMETase. The activity of free AfMETase was reduced to 66.2% and further to 50% upon PEGylation and GDH conjugation, respectively. The highest degree of surface NH2 modification of AfMETase-GDH co-immobilizates (65%), was reported using 300 mM glutaraldehyde, with 31% methionine conversion. Using L-cysteine and L-methionine as active site protectors, the activity of PEG-AfMETase and PEG-AfMETase-GDH was increased by 14.4 and 32.9-fold, respectively. At 45°C, PEG-AfMETase, PEG-AfMETase-GDH and AfMETase-GDH conjugate have a T1/2 10.3, 8.5 and 7.6 h, inactivation rate (Kr) 0.021, 0.03 and 0.016 min, with 2.0, 1.65 and 1.47-fold stabilization, respectively. Kinetically, the three immobilizates have a relatively similar Km values for L-methionine (7.4-7.9 mM), with lower affinity to homocysteine and cysteine, with stability to PLP-enzyme inhibitors (propargylglycine and hydroxylamine), indicating the protective effect by PEG moieties on the enzyme structure. Also, the three immobilizates exhibited improved stability against proteolysis in vitro, comparing to free AfMETase.
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40
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Li M, Li C, Allen A, Stanley CA, Smith TJ. Glutamate dehydrogenase: structure, allosteric regulation, and role in insulin homeostasis. Neurochem Res 2013; 39:433-45. [PMID: 24122080 DOI: 10.1007/s11064-013-1173-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/26/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023]
Abstract
Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine and inhibitors include GTP, palmitoyl CoA, and ATP. Spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed light as to why mammalian GDH is so tightly regulated. Patients with HHS exhibit hypersecretion of insulin upon consumption of protein and concomitantly extremely high levels of ammonium in the serum. The atomic structures of four new inhibitors complexed with GDH complexes have identified three different allosteric binding sites. Using a transgenic mouse model expressing the human HHS form of GDH, at least three of these compounds blocked the dysregulated form of GDH in pancreatic tissue. EGCG from green tea prevented the hyper-response to amino acids in whole animals and improved basal serum glucose levels. The atomic structure of the ECG-GDH complex and mutagenesis studies is directing structure-based drug design using these polyphenols as a base scaffold. In addition, all of these allosteric inhibitors are elucidating the atomic mechanisms of allostery in this complex enzyme.
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Affiliation(s)
- Ming Li
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO, 63132, USA
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41
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Sharkey MA, Oliveira TF, Engel PC, Khan AR. Structure of NADP(+)-dependent glutamate dehydrogenase from Escherichia coli--reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases. FEBS J 2013; 280:4681-92. [PMID: 23879525 DOI: 10.1111/febs.12439] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/10/2013] [Accepted: 07/16/2013] [Indexed: 11/26/2022]
Abstract
Glutamate dehydrogenases (GDHs; EC 1.4.1.2-4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate, using NAD(+) and/or NADP(+) as a cofactor. Subunits of homo-hexameric bacterial enzymes comprise a substrate-binding domain I followed by a nucleotide-binding domain II. The reaction occurs in a catalytic cleft between the two domains. Although conserved residues in the nucleotide-binding domains of various dehydrogenases have been linked to cofactor preferences, the structural basis for specificity in the GDH family remains poorly understood. Here, the refined crystal structure of Escherichia coli GDH in the absence of reactants is described at 2.5-Å resolution. Modelling of NADP(+) in domain II reveals the potential contribution of positively charged residues from a neighbouring α-helical hairpin to phosphate recognition. In addition, a serine that follows the P7 aspartate is presumed to form a hydrogen bond with the 2'-phosphate. Mutagenesis and kinetic analysis confirms the importance of these residues in NADP(+) recognition. Surprisingly, one of the positively charged residues is conserved in all sequences of NAD(+)-dependent enzymes, but the conformations adopted by the corresponding regions in proteins whose structure has been solved preclude their contribution to the coordination of the 2'-ribose phosphate of NADP(+). These studies clarify the sequence-structure relationships in bacterial GDHs, revealing that identical residues may specify different coenzyme preferences, depending on the structural context. Primary sequence alone is therefore not a reliable guide for predicting coenzyme specificity. We also consider how it is possible for a single sequence to accommodate both coenzymes in the dual-specificity GDHs of animals.
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Affiliation(s)
- Michael A Sharkey
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Ireland
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Engel PC. Glutamate dehydrogenases: the why and how of coenzyme specificity. Neurochem Res 2013; 39:426-32. [PMID: 23761034 DOI: 10.1007/s11064-013-1089-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 05/23/2013] [Accepted: 05/25/2013] [Indexed: 11/28/2022]
Abstract
NAD(+) and NADP(+), chemically similar and with almost identical standard oxidation-reduction potentials, nevertheless have distinct roles, NAD(+) serving catabolism and ATP generation whereas NADPH is the biosynthetic reductant. Separating these roles requires strict specificity for one or the other coenzyme for most dehydrogenases. In many organisms this holds also for glutamate dehydrogenases (GDH), NAD(+)-dependent for glutamate oxidation, NADP(+)-dependent for fixing ammonia. In higher animals, however, GDH has dual specificity. It has been suggested that GDH in mitochondria reacts only with NADP(H), the NAD(+) reaction being an in vitro artefact. However, contrary evidence suggests mitochondrial GDH not only reacts with NAD(+) but maintains equilibrium using the same pool as accessed by β-hydroxybutyrate dehydrogenase. Another complication is the presence of an energy-linked dehydrogenase driving NADP(+) reduction by NADH, maintaining the coenzyme pools at different oxidation-reduction potentials. Its coexistence with GDH makes possible a futile cycle, control of which is not yet properly explained. Structural studies show NAD(+)-dependent, NADP(+)-dependent and dual-specificity GDHs are closely related and a few site-directed mutations can reverse specificity. Specificity for NAD(+) or for NADP(+) has probably emerged repeatedly during evolution, using different structural solutions on different occasions. In various GDHs the P7 position in the coenzyme-binding domain plays a key role. However, whereas in other dehydrogenases an acidic P7 residue usually hydrogen bonds to the 2'- and 3'-hydroxyls, dictating NAD(+) specificity, among GDHs, depending on detailed conformation of surrounding residues, an acidic P7 may permit binding of NAD(+) only, NADP(+) only, or in higher animals both.
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Affiliation(s)
- Paul C Engel
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland,
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Pajęcka K, Nielsen CW, Hauge A, Zaganas I, Bak LK, Schousboe A, Plaitakis A, Waagepetersen HS. Glutamate dehydrogenase isoforms with N-terminal (His)6- or FLAG-tag retain their kinetic properties and cellular localization. Neurochem Res 2013; 39:487-99. [PMID: 23619558 DOI: 10.1007/s11064-013-1042-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
Abstract
Glutamate dehydrogenase (GDH) is a crucial enzyme on the crossroads of amino acid and energy metabolism and it is operating in all domains of life. According to current knowledge GDH is present only in one functional isoform in most animals, including mice. In addition to this housekeeping enzyme (hGDH1 in humans), humans and apes have acquired a second isoform (hGDH2) with a distinct tissue expression profile. In the current study we have cloned both mouse and human GDH constructs containing FLAG and (His)6 small genetically-encoded tags, respectively. The hGDH1 and hGDH2 constructs containing N-terminal (His)6 tags were successfully expressed in Sf9 cells and the recombinant proteins were isolated to ≥95 % purity in a two-step procedure involving ammonium sulfate precipitation and Ni(2+)-based immobilized metal ion affinity chromatography. To explore whether the presence of the FLAG and (His)6 tags affects the cellular localization and functionality of the GDH isoforms, we studied the subcellular distribution of the expressed enzymes as well as their regulation by adenosine diphosphate monopotassium salt (ADP) and guanosine-5'-triphosphate sodium salt (GTP). Through immunoblot analysis of the mitochondrial and cytosolic fraction of the HEK cells expressing the recombinant proteins we found that neither FLAG nor (His)6 tag disturbs the mitochondrial localization of GDH. The addition of the small tags to the N-terminus of the mature mitochondrial mouse GDH1 or human hGDH1 and hGDH2 did not change the ADP activation or GTP inhibition pattern of the proteins as compared to their untagged counterparts. However, the addition of FLAG tag to the C-terminus of the mouse GDH left the recombinant protein fivefold less sensitive to ADP activation. This finding highlights the necessity of the functional characterization of recombinant proteins containing even the smallest available tags.
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Affiliation(s)
- Kamilla Pajęcka
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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Plaitakis A, Zaganas I, Spanaki C. Deregulation of glutamate dehydrogenase in human neurologic disorders. J Neurosci Res 2013; 91:1007-17. [PMID: 23463419 DOI: 10.1002/jnr.23176] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/15/2012] [Accepted: 10/19/2012] [Indexed: 11/09/2022]
Abstract
Mammalian glutamate dehydrogenase is an allosterically regulated enzyme that is central to glutamate metabolism. It contributes to important cellular processes, including Krebs cycle anaplerotic mechanisms, energy production, and ammonia homeostasis. In addition to this housekeeping hGDH1, humans have acquired through duplication an hGDH2 isoenzyme expressed in neural tissues with distinct regulatory properties. There is increasing evidence that deregulation of human GDHs leads to human disorders. Thus, in hGDH1, regulatory mutations that attenuate GTP inhibition can result in the hyperinsulinism/hyperammonemia syndrome, which is often associated with epileptic seizures, mental retardation, and generalized dystonia. Also, transgenic overexpression of GLUD1 in neurons has resulted in age-dependent degeneration of the CA1 behippocampal region, associated with upregulation of α-synuclein and other proteins linked to major human movement disorders. With regard to hGDH2, a rare T1492G variation in the GLUD2 gene, resulting in substitution of Ala for Ser445 in the regulatory domain of hGDH2, interacts significantly with Parkinson's disease (PD) onset. In two independent Greek and one North American PD cohorts, Ser445Ala hemizygous males, but not heterozygous females, developed PD 6-13 years earlier than subjects with other genotypes. The Ala445-hGDH2 variant displays increased catalytic activity that is amenable to inhibition by estrogens. Enhanced glutamate oxidation by Ala445-hGDH2 is thought to accelerate nigral cell degeneration in hemizygous males, and inhibition of the overactive variant by estrogens may protect heterozygous females. Hence, deregulation of hGDH1 and hGDH2 may play a role in degenerative processes, so these observations identify novel targets for therapeutic intervention in human disorders.
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Affiliation(s)
- Andreas Plaitakis
- Department of Neurology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece.
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Intertissue Differences for the Role of Glutamate Dehydrogenase in Metabolism. Neurochem Res 2013; 39:516-26. [DOI: 10.1007/s11064-013-0998-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/24/2013] [Accepted: 02/01/2013] [Indexed: 11/26/2022]
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Computational design of glutamate dehydrogenase in Bacillus subtilis natto. J Mol Model 2013; 19:1919-27. [PMID: 23338837 DOI: 10.1007/s00894-013-1755-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
Abstract
Bacillus subtilis natto is widely used in industry to produce natto, a traditional and popular Japanese soybean food. However, during its secondary fermentation, high amounts of ammonia are released to give a negative influence on the flavor of natto. Glutamate dehydrogenase (GDH) is a key enzyme for the ammonia produced and released, because it catalyzes the oxidative deamination of glutamate to alpha-ketoglutarate using NAD(+) or NADP(+) as co-factor during carbon and nitrogen metabolism processes. To solve this problem, we employed multiple computational methods model and re-design GDH from Bacillus subtilis natto. Firstly, a structure model of GDH with cofactor NADP(+) was constructed by threading and ab initio modeling. Then the substrate glutamate were flexibly docked into the structure model to form the substrate-binding mode. According to the structural analysis of the substrate-binding mode, Lys80, Lys116, Arg196, Thr200, and Ser351 in the active site were found could form a significant hydrogen bonding network with the substrate, which was thought to play a crucial role in the substrate recognition and position. Thus, these residues were then mutated into other amino acids, and the substrate binding affinities for each mutant were calculated. Finally, three single mutants (K80A, K116Q, and S351A) were found to have significant decrease in the substrate binding affinities, which was further supported by our biochemical experiments.
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Biswas D, Pandya V, Singh AK, Mondal AK, Kumaran S. Co-factor binding confers substrate specificity to xylose reductase from Debaryomyces hansenii. PLoS One 2012; 7:e45525. [PMID: 23049810 PMCID: PMC3458928 DOI: 10.1371/journal.pone.0045525] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/21/2012] [Indexed: 01/07/2023] Open
Abstract
Binding of substrates into the active site, often through complementarity of shapes and charges, is central to the specificity of an enzyme. In many cases, substrate binding induces conformational changes in the active site, promoting specific interactions between them. In contrast, non-substrates either fail to bind or do not induce the requisite conformational changes upon binding and thus no catalysis occurs. In principle, both lock and key and induced-fit binding can provide specific interactions between the substrate and the enzyme. In this study, we present an interesting case where cofactor binding pre-tunes the active site geometry to recognize only the cognate substrates. We illustrate this principle by studying the substrate binding and kinetic properties of Xylose Reductase from Debaryomyces hansenii (DhXR), an AKR family enzyme which catalyzes the reduction of carbonyl substrates using NADPH as co-factor. DhXR reduces D-xylose with increased specificity and shows no activity towards "non-substrate" sugars like L-rhamnose. Interestingly, apo-DhXR binds to D-xylose and L-rhamnose with similar affinity (K(d)∼5.0-10.0 mM). Crystal structure of apo-DhXR-rhamnose complex shows that L-rhamnose is bound to the active site cavity. L-rhamnose does not bind to holo-DhXR complex and thus, it cannot competitively inhibit D-xylose binding and catalysis even at 4-5 fold molar excess. Comparison of K(d) values with K(m) values reveals that increased specificity for D-xylose is achieved at the cost of moderately reduced affinity. The present work reveals a latent regulatory role for cofactor binding which was previously unknown and suggests that cofactor induced conformational changes may increase the complimentarity between D-xylose and active site similar to specificity achieved through induced-fit mechanism.
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Affiliation(s)
- Dipanwita Biswas
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| | - Vaibhav Pandya
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| | - Appu Kumar Singh
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| | - Alok K. Mondal
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| | - S. Kumaran
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
- * E-mail:
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Spanaki C, Zaganas I, Kounoupa Z, Plaitakis A. The complex regulation of human glud1 and glud2 glutamate dehydrogenases and its implications in nerve tissue biology. Neurochem Int 2012; 61:470-81. [PMID: 22658952 DOI: 10.1016/j.neuint.2012.05.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 05/20/2012] [Accepted: 05/21/2012] [Indexed: 12/01/2022]
Abstract
Mammalian glutamate dehydrogenase (GDH) is a housekeeping mitochondrial enzyme (hGDH1 in the human) that catalyses the reversible inter-conversion of glutamate to α-ketoglutarate and ammonia, thus interconnecting amino acid and carbohydrate metabolism. It displays an energy sensing mechanism, which permits enzyme activation under low cellular energy states. As GDH is at the crossroads of important metabolic pathways, a tight control of its activity is essential. Indeed, to fulfill its role in metabolism and cellular energetics, mammalian GDH has evolved into a highly regulated enzyme subject to allosteric modulation by diverse compounds. The recent emergence (<23 million years ago) in apes and humans of a hGDH2 isoenzyme with distinct regulatory properties, as well as, the detection of gain-of-function variants in hGDH1 and hGDH2 that affect the nervous system, have introduced additional complexities. The properties of the two highly homologous human GDHs were studied using purified recombinant hGDH1 and hGDH2 obtained by expression of the corresponding cDNAs in Sf21 cells. Results showed that, in contrast to hGDH1 that maintains substantial basal activity (35-40% of its maximal capacity), hGDH2 displays low basal activity (3-8% of maximal) that is remarkably responsive to activation by rising levels of ADP and/or l-leucine. This is primarily due to the Arg443Ser evolutionary change, which also made hGDH2 markedly sensitive to estrogens and neuroleptic drugs. In contrast to hGDH1, which is subject to potent GTP inhibition, hGDH2 has dissociated its function from this energy switch, being able to metabolize glutamate even when the Krebs cycle generates GTP levels sufficient to inactivate the housekeeping hGDH1. Our data also show that spermidine, a polyamine thought to reduce oxidative stress and to prolong survival, and EGCG, a green tea polyphenol, inhibit hGDH2 at lower concentrations than hGDH1. The implications of these findings in nerve tissue biology are discussed.
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Affiliation(s)
- Cleanthe Spanaki
- Department of Neurology, Medical School, University of Crete, Heraklion, Crete, Greece
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Zocher K, Fritz-Wolf K, Kehr S, Fischer M, Rahlfs S, Becker K. Biochemical and structural characterization of Plasmodium falciparum glutamate dehydrogenase 2. Mol Biochem Parasitol 2012; 183:52-62. [DOI: 10.1016/j.molbiopara.2012.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 01/23/2012] [Accepted: 01/31/2012] [Indexed: 02/01/2023]
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L-aspartate dehydrogenase: features and applications. Appl Microbiol Biotechnol 2011; 93:503-16. [PMID: 22120624 DOI: 10.1007/s00253-011-3730-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/30/2011] [Accepted: 11/14/2011] [Indexed: 10/15/2022]
Abstract
L-amino acid dehydrogenases are a group of enzymes that catalyze the reversible oxidative deamination of L-amino acids to their corresponding 2-oxoacids, using either nicotinamide adenine dinucleotide (NAD(+)) or nicotinamide adenine dinucleotide phosphate (NADP(+)) as cofactors. These enzymes have been studied widely because of their potential applications in the synthesis of amino acids for use in production of pharmaceutical peptides, herbicides and insecticides, in biosensors or diagnostic kits, and development of coenzyme regeneration systems for industrial processes. This article presents a review of the currently available data about the recently discovered amino acid dehydrogenase superfamily member L-aspartate dehydrogenase (L-AspDH), their relevant catalytic properties and speculated physiological roles, and potential for biotechnological applications. The proposed classification of L-AspDH on the basis of bioinformatic information and potential role in vivo into NadB (NAD biosynthesis-related) and non-NadB type is unique. In particular, the mesophilic non-NadB type L-AspDH is a novel group of amino acid dehydrogenases with great promise as potential industrial biocatalysts owing to their relatively high catalytic properties at room temperature. Considering that only a few L-AspDH homologs have been characterized so far, identification and prodigious enzymological research of the new members will be necessary to shed light on the gray areas pertaining to these enzymes.
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