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Guo N, Luo Q, Zheng Q, Yang S, Zhang S. Current status and progress of research on the ADP-dependent glucokinase gene. Front Oncol 2024; 14:1358904. [PMID: 38590647 PMCID: PMC10999526 DOI: 10.3389/fonc.2024.1358904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 04/10/2024] Open
Abstract
ADP-dependent glucokinase (ADPGK) produces glucose-6-phosphate with adenosine diphosphate (ADP) as the phosphate group donor, in contrast to ATP-dependent hexokinases (HKs). Originally found in archaea, ADPGK is involved in glycolysis. However, its biological function in most eukaryotic organisms is still unclear, and the molecular mechanism of action requires further investigation. This paper provides a concise overview of ADPGK's origin, biological function and clinical application. It aims to furnish scientific information for the diagnosis and treatment of human metabolic diseases, neurological disorders, and malignant tumours, and to suggest new strategies for the development of targeted drugs.
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Affiliation(s)
- Ningjing Guo
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Qiong Luo
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Qixian Zheng
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Sheng Yang
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Suyun Zhang
- Department of Internal Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
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2
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Wilk P, Kuśka K, Wątor E, Małecki PH, Woś K, Tokarz P, Dubin G, Grudnik P. Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2020; 21:E9570. [PMID: 33339113 DOI: 10.3390/ijms21249570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/05/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Glycerol is an organic compound that can be utilized as an alternative source of carbon by various organisms. One of the ways to assimilate glycerol by the cell is the phosphorylative catabolic pathway in which its activation is catalyzed by glycerol kinase (GK) and glycerol-3-phosphate (G3P) is formed. To date, several GK crystal structures from bacteria, archaea, and unicellular eukaryotic parasites have been solved. Herein, we present a series of crystal structures of GK from Chaetomium thermophilum (CtGK) in apo and glycerol-bound forms. In addition, we show the feasibility of an ADP-dependent glucokinase (ADPGK)-coupled enzymatic assay to measure the CtGK activity. New structures described in our work provide structural insights into the GK catalyzed reaction in the filamentous fungus and set the foundation for understanding the glycerol metabolism in eukaryotes.
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Herrera-Morande A, Castro-Fernández V, Merino F, Ramírez-Sarmiento CA, Fernández FJ, Vega MC, Guixé V. Protein topology determines substrate-binding mechanism in homologous enzymes. Biochim Biophys Acta Gen Subj 2018; 1862:2869-2878. [PMID: 30251675 DOI: 10.1016/j.bbagen.2018.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/21/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022]
Abstract
During evolution, some homologs proteins appear with different connectivity between secondary structures (different topology) but conserving the tridimensional arrangement of them (same architecture). These events can produce two types of arrangements; circular permutation or non-cyclic permutations. The first one results in the N and C terminus transferring to a different position on a protein sequence while the second refers to a more complex arrangement of the structural elements. In ribokinase superfamily, two different topologies can be identified, which are related to each other as a non-cyclic permutation occurred during the evolution. Interestingly, this change in topology is correlated with the nucleotide specificity of its members. Thereby, the connectivity of the secondary elements allows us to distinguish an ATP-dependent and an ADP-dependent topology. Here we address the impact of introducing the topology of a homologous ATP-dependent kinase in an ADP-dependent kinase (Thermococcus litoralis glucokinase) in the structure, nucleotide specificity, and substrate binding order of the engineered enzyme. Structural evidence demonstrates that rewiring the topology of TlGK leads to an active and soluble enzyme without modifications on its three-dimensional architecture. The permuted enzyme (PerGK) retains the nucleotide preference of the parent TlGK enzyme but shows a change in the substrate binding order. Our results illustrate how the rearrangement of the protein folding topology during the evolution of the ribokinase superfamily enzymes may have dictated the substrate-binding order in homologous enzymes of this superfamily.
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Affiliation(s)
| | | | - Felipe Merino
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Francisco J Fernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain
| | - M Cristina Vega
- Centro de Investigaciones Biológicas (CIB-CSIC), Structural and Chemical Biology Dep., Madrid, Spain.
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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Grudnik P, Kamiński MM, Rembacz KP, Kuśka K, Madej M, Potempa J, Dawidowski M, Dubin G. Structural basis for ADP-dependent glucokinase inhibition by 8-bromo-substituted adenosine nucleotide. J Biol Chem 2018; 293:11088-11099. [PMID: 29784881 DOI: 10.1074/jbc.ra117.001562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/18/2018] [Indexed: 01/01/2023] Open
Abstract
In higher eukaryotes, several ATP-utilizing enzymes known as hexokinases activate glucose in the glycolysis pathway by phosphorylation to glucose 6-phosphate. In contrast to canonical hexokinases, which use ATP, ADP-dependent glucokinase (ADPGK) catalyzes noncanonical phosphorylation of glucose to glucose 6-phosphate using ADP as a phosphate donor. Initially discovered in Archaea, the human homolog of ADPGK was described only recently. ADPGK's involvement in modified bioenergetics of activated T cells has been postulated, and elevated ADPGK expression has been reported in various cancer tissues. However, the physiological role of ADPGK is still poorly understood, and effective ADPGK inhibitors still await discovery. Here, we show that 8-bromo-substituted adenosine nucleotide inhibits human ADPGK. By solving the crystal structure of archaeal ADPGK in complex with 8-bromoadenosine phosphate (8-Br-AMP) at 1.81 Å resolution, we identified the mechanism of inhibition. We observed that 8-Br-AMP is a competitive inhibitor of ADPGK and that the bromine substitution induces marked structural changes within the protein's active site by engaging crucial catalytic residues. The results obtained using the Jurkat model of activated human T cells suggest its moderate activity in a cellular setting. We propose that our structural insights provide a critical basis for rational development of novel ADPGK inhibitors.
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Affiliation(s)
- Przemysław Grudnik
- From the Faculty of Biochemistry, Biophysics and Biotechnology and .,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
| | - Marcin M Kamiński
- the Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, and
| | | | - Katarzyna Kuśka
- From the Faculty of Biochemistry, Biophysics and Biotechnology and
| | - Mariusz Madej
- From the Faculty of Biochemistry, Biophysics and Biotechnology and.,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
| | - Jan Potempa
- From the Faculty of Biochemistry, Biophysics and Biotechnology and.,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
| | - Maciej Dawidowski
- the Faculty of Pharmacy, Warsaw Medical University, Banacha 1 Street, 02-097 Warsaw, Poland
| | - Grzegorz Dubin
- From the Faculty of Biochemistry, Biophysics and Biotechnology and .,Malopolska Center of Biotechnology Jagiellonian University in Krakow, Gronostajowa 7 Street, 30-387 Krakow, Poland
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5
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Tokarz P, Wiśniewska M, Kamiński MM, Dubin G, Grudnik P. Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii in complex with 5-iodotubercidin reveals phosphoryl transfer mechanism. Protein Sci 2018; 27:790-797. [PMID: 29352744 DOI: 10.1002/pro.3377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 11/11/2022]
Abstract
ADP-dependent glucokinase (ADPGK) is an alternative novel glucose phosphorylating enzyme in a modified glycolysis pathway of hyperthermophilic Archaea. In contrast to classical ATP-dependent hexokinases, ADPGK utilizes ADP as a phosphoryl group donor. Here, we present a crystal structure of archaeal ADPGK from Methanocaldococcus jannaschii in complex with an inhibitor, 5-iodotubercidin, d-glucose, inorganic phosphate, and a magnesium ion. Detailed analysis of the architecture of the active site allowed for confirmation of the previously proposed phosphorylation mechanism and the crucial role of the invariant arginine residue (Arg197). The crystal structure shows how the phosphate ion, while mimicking a β-phosphate group, is positioned in the proximity of the glucose moiety by arginine and the magnesium ion, thus providing novel insights into the mechanism of catalysis. In addition, we demonstrate that 5-iodotubercidin inhibits human ADPGK-dependent T cell activation-induced reactive oxygen species (ROS) release and downstream gene expression, and as such it may serve as a model compound for further screening for hADPGK-specific inhibitors.
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Affiliation(s)
- Piotr Tokarz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7, Krakow, 30-387, Poland.,Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
| | - Magdalena Wiśniewska
- Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
| | - Marcin M Kamiński
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee, 38105
| | - Grzegorz Dubin
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7, Krakow, 30-387, Poland.,Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
| | - Przemysław Grudnik
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7, Krakow, 30-387, Poland.,Malopolska Center of Biotechnology, Jagiellonian University in Krakow, ul. Gronostajowa 7a, Krakow, 30-387, Poland
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Richter JP, Goroncy AK, Ronimus RS, Sutherland-Smith AJ. The Structural and Functional Characterization of Mammalian ADP-dependent Glucokinase. J Biol Chem 2015; 291:3694-704. [PMID: 26555263 DOI: 10.1074/jbc.m115.679902] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Indexed: 12/24/2022] Open
Abstract
The enzyme-catalyzed phosphorylation of glucose to glucose-6-phosphate is a reaction central to the metabolism of all life. ADP-dependent glucokinase (ADPGK) catalyzes glucose-6-phosphate production, utilizing ADP as a phosphoryl donor in contrast to the more well characterized ATP-requiring hexokinases. ADPGK is found in Archaea and metazoa; in Archaea, ADPGK participates in a glycolytic role, but a function in most eukaryotic cell types remains unknown. We have determined structures of the eukaryotic ADPGK revealing a ribokinase-like tertiary fold similar to archaeal orthologues but with significant differences in some secondary structural elements. Both the unliganded and the AMP-bound ADPGK structures are in the "open" conformation. The structures reveal the presence of a disulfide bond between conserved cysteines that is positioned at the nucleotide-binding loop of eukaryotic ADPGK. The AMP-bound ADPGK structure defines the nucleotide-binding site with one of the disulfide bond cysteines coordinating the AMP with its main chain atoms, a nucleotide-binding motif that appears unique to eukaryotic ADPGKs. Key amino acids at the active site are structurally conserved between mammalian and archaeal ADPGK, and site-directed mutagenesis has confirmed residues essential for enzymatic activity. ADPGK is substrate inhibited by high glucose concentration and shows high specificity for glucose, with no activity for other sugars, as determined by NMR spectroscopy, including 2-deoxyglucose, the glucose analogue used for tumor detection by positron emission tomography.
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Affiliation(s)
- Jan P Richter
- From the Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand and
| | - Alexander K Goroncy
- From the Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand and
| | - Ron S Ronimus
- AgResearch Limited, Palmerston North 4442, New Zealand
| | - Andrew J Sutherland-Smith
- From the Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand and
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