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Gasper WC, Gardner S, Ross A, Oppelt SA, Allen KN, Tolan DR. Michaelis-like complex of mouse ketohexokinase isoform C. Acta Crystallogr D Struct Biol 2024; 80:377-385. [PMID: 38805243 DOI: 10.1107/s2059798324003723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Over the past forty years there has been a drastic increase in fructose-related diseases, including obesity, heart disease and diabetes. Ketohexokinase (KHK), the first enzyme in the liver fructolysis pathway, catalyzes the ATP-dependent phosphorylation of fructose to fructose 1-phosphate. Understanding the role of KHK in disease-related processes is crucial for the management and prevention of this growing epidemic. Molecular insight into the structure-function relationship in ligand binding and catalysis by KHK is needed for the design of therapeutic inhibitory ligands. Ketohexokinase has two isoforms: ketohexokinase A (KHK-A) is produced ubiquitously at low levels, whereas ketohexokinase C (KHK-C) is found at much higher levels, specifically in the liver, kidneys and intestines. Structures of the unliganded and liganded human isoforms KHK-A and KHK-C are known, as well as structures of unliganded and inhibitor-bound mouse KHK-C (mKHK-C), which shares 90% sequence identity with human KHK-C. Here, a high-resolution X-ray crystal structure of mKHK-C refined to 1.79 Å resolution is presented. The structure was determined in a complex with both the substrate fructose and the product of catalysis, ADP, providing a view of the Michaelis-like complex of the mouse ortholog. Comparison to unliganded structures suggests that KHK undergoes a conformational change upon binding of substrates that places the enzyme in a catalytically competent form in which the β-sheet domain from one subunit rotates by 16.2°, acting as a lid for the opposing active site. Similar kinetic parameters were calculated for the mouse and human enzymes and indicate that mice may be a suitable animal model for the study of fructose-related diseases. Knowledge of the similarity between the mouse and human enzymes is important for understanding preclinical efforts towards targeting this enzyme, and this ground-state, Michaelis-like complex suggests that a conformational change plays a role in the catalytic function of KHK-C.
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Affiliation(s)
- William C Gasper
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Sarah Gardner
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Adam Ross
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Sarah A Oppelt
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Karen N Allen
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
| | - Dean R Tolan
- Program in Biochemistry and Molecular Biology, Boston University, Boston, MA 02215, USA
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De Vitto H, Belfon KKJ, Sharma N, Toay S, Abendroth J, Dranow DM, Lukacs CM, Choi R, Udell HS, Willis S, Barrera G, Beyer O, Li TD, Hicks KA, Torelli AT, French JB. Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate. Biochemistry 2024. [PMID: 38306231 DOI: 10.1021/acs.biochem.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Thiamin and its phosphate derivatives are ubiquitous molecules involved as essential cofactors in many cellular processes. The de novo biosynthesis of thiamin employs the parallel synthesis of 4-methyl-5-(2-hydroxyethyl)thiazole (THZ-P) and 4-amino-2-methyl-5(diphosphooxymethyl) pyrimidine (HMP) pyrophosphate (HMP-PP), which are coupled to generate thiamin phosphate. Most organisms that can biosynthesize thiamin employ a kinase (HMPK or ThiD) to generate HMP-PP. In nearly all cases, this enzyme is bifunctional and can also salvage free HMP, producing HMP-P, the monophosphate precursor of HMP-PP. Here we present high-resolution crystal structures of an HMPK from Acinetobacter baumannii (AbHMPK), both unliganded and with pyridoxal 5-phosphate (PLP) noncovalently bound. Despite the similarity between HMPK and pyridoxal kinase enzymes, our kinetics analysis indicates that AbHMPK accepts HMP exclusively as a substrate and cannot turn over pyridoxal, pyridoxamine, or pyridoxine nor does it display phosphatase activity. PLP does, however, act as a weak inhibitor of AbHMPK with an IC50 of 768 μM. Surprisingly, unlike other HMPKs, AbHMPK catalyzes only the phosphorylation of HMP and does not generate the diphosphate HMP-PP. This suggests that an additional kinase is present in A. baumannii, or an alternative mechanism is in operation to complete the biosynthesis of thiamin.
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Affiliation(s)
- Humberto De Vitto
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kafi K J Belfon
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Nandini Sharma
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Sarah Toay
- Department of Biological Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - David M Dranow
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Christine M Lukacs
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Hannah S Udell
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Sydney Willis
- Department of Chemistry, Rollins College, Winter Park, Florida 32789, United States
| | - George Barrera
- Department of Chemistry and Biochemistry, Weber State University, Ogden, Utah 84408, United States
| | - Olive Beyer
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Teng Da Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Katherine A Hicks
- Chemistry Department, State University of New York at Cortland, Cortland, New York 13045, United States
| | - Andrew T Torelli
- Department of Chemistry, Ithaca College, Ithaca, New York 14850, United States
| | - Jarrod B French
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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3
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Banerjee P, Chandra A, Mohammad T, Singh N, Hassan MI, Qamar I. Identification of high-affinity pyridoxal kinase inhibitors targeting cancer therapy: an integrated docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2023:1-18. [PMID: 37578056 DOI: 10.1080/07391102.2023.2246580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/05/2023] [Indexed: 08/15/2023]
Abstract
Pyridoxal kinase (PDXK) is a vitamin B6-dependent transferase enzyme encoded by the PDXK gene, crucial for leukemic cell proliferation. Disruption of its activity causes altered metabolism and reduced levels of nucleotides and polyamines. PDXK and pyridoxal 5'-phosphate (PLP) are overexpressed in various carcinomas, making them promising targets for drug design against cancer. Targeting PDXK may hold promise as a therapeutic approach for cancer treatment. This study focused on discovering potential inhibitors that could selectively interrupt the binding of pyridoxal phosphate (PLP) to pyridoxal kinase (PDXK). A commercially available library of 7,28,747 natural and druglike compounds was virtually screened using a molecular docking approach to target the substrate binding pocket of PDXK. Six promising inhibitors were identified, and all-atom molecular dynamics simulations were conducted on the PDXK-ligand complexes for 100 ns to assess their binding conformational stability. The simulation results indicated that the binding of ZINC095099376, ZINC01612996, ZINC049841390, ZINC095098959, ZINC01482077, and ZINC03830976 induced a slight structural change and stabilized the PDXK structure. This analysis provided valuable information about the critical residues involved in the PDXK-PLP complex formation and can be utilized in designing specific and effective PDXK inhibitors. According to this study, these compounds could be developed as anticancer agents targeting PDXK as a potential candidate for further study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pallabi Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Anshuman Chandra
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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Liang L, Yang LL, Wang W, Ji C, Zhang L, Jia Y, Chen Y, Wang X, Tan J, Sun ZJ, Yuan Q, Tan W. Calcium Phosphate-Reinforced Metal-Organic Frameworks Regulate Adenosine-Mediated Immunosuppression. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102271. [PMID: 34554618 DOI: 10.1002/adma.202102271] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Indexed: 05/26/2023]
Abstract
Long-term accumulation of adenosine (Ado) in tumor tissues helps to establish the immunosuppressive tumor microenvironment and to promote tumor development. Regulation of Ado metabolism is particularly pivotal for blocking Ado-mediated immunosuppression. The activity of adenosine kinase (ADK) for catalyzing the phosphorylation of Ado plays an essential role in regulating Ado metabolism. Specifically, accumulated Ado in the tumor microenvironment occupies the active site of ADK, inhibiting the phosphorylation of Ado. Phosphate can protect ADK from inactivation and restore the activity of ADK. Herein, calcium phosphate-reinforced iron-based metal-organic frameworks (CaP@Fe-MOFs) are designed to reduce Ado accumulation and to inhibit Ado-mediated immunosuppressive response in the tumor microenvironment. CaP@Fe-MOFs are found to regulate the Ado metabolism by promoting ADK-mediated phosphorylation and relieving the hypoxic tumor microenvironment. Moreover, CaP@Fe-MOFs can enhance the antitumor immune response via Ado regulation, including the increase of T lymphocytes and dendritic cells and the decrease of regulatory T lymphocytes. Finally, CaP@Fe-MOFs are used for cancer treatment in mice, alleviating the Ado-mediated immunosuppressive response and achieving tumor suppression. This study may offer a general strategy for blocking the Ado-mediated immunosuppression in the tumor microenvironment and further for enhancing the immunotherapy efficacy in vivo.
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Affiliation(s)
- Ling Liang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Lei-Lei Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenjie Wang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Cailing Ji
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Lei Zhang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yiyi Jia
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yuxia Chen
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Xueqiang Wang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jie Tan
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Zhi-Jun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Quan Yuan
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Weihong Tan
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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Timofeev VI, Abramchik YA, Muravyova TI, Zhukhlistova NE, Esipov RS, Kuranova IP. Three-Dimensional Structure of Recombinant Thermophilic Ribokinase from Thermus speсies 2.9 in Complex with Adenosine Diphosphate. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Implications of Oxidative Stress in Glioblastoma Multiforme Following Treatment with Purine Derivatives. Antioxidants (Basel) 2021; 10:antiox10060950. [PMID: 34204594 PMCID: PMC8231124 DOI: 10.3390/antiox10060950] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
Recently, small compound-based therapies have provided new insights into the treatment of glioblastoma multiforme (GBM) by inducing oxidative impairment. Kinetin riboside (KR) and newly designed derivatives (8-azaKR, 7-deazaKR) selectively affect the molecular pathways crucial for cell growth by interfering with the redox status of cancer cells. Thus, these compounds might serve as potential alternatives in the oxidative therapy of GBM. The increased basal levels of reactive oxygen species (ROS) in GBM support the survival of cancer cells and cause drug resistance. The simplest approach to induce cell death is to achieve the redox threshold and circumvent the antioxidant defense mechanisms. Consequently, cells become more sensitive to oxidative stress (OS) caused by exogenous agents. Here, we investigated the effect of KR and its derivatives on the redox status of T98G cells in 2D and 3D cell culture. The use of spheroids of T98G cells enabled the selection of one derivative-7-deazaKR-with comparable antitumor activity to KR. Both compounds induced ROS generation and genotoxic OS, resulting in lipid peroxidation and leading to apoptosis. Taken together, these results demonstrated that KR and 7-deazaKR modulate the cellular redox environment of T98G cells, and vulnerability of these cells is dependent on their antioxidant capacity.
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Paramashivam S, Balasubramaniam S, Dhiraviam KN. Computational exploration of vicine - an alkaloid glycoside mediated pathological hallmark of adenosine kinase to promote neurological disorder. Metab Brain Dis 2021; 36:653-667. [PMID: 33496919 DOI: 10.1007/s11011-021-00674-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/14/2021] [Indexed: 10/22/2022]
Abstract
Epilepsy disease is characterized by the neuronal dysfunction or abnormal neuronal activity of the brain which is regulated by astrocytes. These are glial cells and found to be the major regulators of the brain which are guided by the occurrence of adenosine kinase (ADK) enzyme in the central nervous system (CNS). During the normal physiological environment, ADK maintains the level of adenosine in the CNS. Dysfunction of ADK levels results in accumulation of adenosine levels in the CNS that leads to the pathophysiology of the brain such as astrogliosis which is a pathological hallmark of epileptic seizures. Vicine, an alkaloid glycoside in bitter gourd juice (Momordica charantia) is found to be toxic to the human system if the bitter gourd juice is consumed more. This compound inhibits ADK enzyme activity to lead epilepsy and seizure. Here, the toxic effect of vicine targeting ADK using computational predictions was investigated. The 3-dimensional structure of ADK has been constructed using I-Tasser, which has been refined by ModRefiner, GalaxyRefine, and 3D refine and it was endorsed using PROCHECK, ERRAT, and VADAR. 3D structure of the ligand molecule has been obtained from PubChem. Molecular docking has been achieved using AutoDock 4.2 software, from which the outcome showed the effective interaction between vicine and ADK, which attains binding free energy (∆G) of - 4.13 kcal/mol. Vicine molecule interacts with the active region ARG 149 of ADK and inhibits the functions of ADK that may cause imbalance in energy homeostasis. Also, pre-ADMET results robustly propose in which vicine possesses toxicity, and meanwhile, from the Ames test, it was shown as mutagenic. Hence, the results from our study suggest that vicine was shown to be toxic that suppresses the ADK activity to undergo pathological conditions in the neuronal junctions to lead epilepsy.
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Affiliation(s)
- SathishKumar Paramashivam
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamilnadu, 625021, India
| | | | - Kannan Narayanan Dhiraviam
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamilnadu, 625021, India.
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An Evolutionary Marker of the Ribokinase Superfamily Is Responsible for Zinc-Mediated Regulation of Human Pyridoxal Kinase. Catalysts 2020. [DOI: 10.3390/catal10050555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The ribokinase superfamily catalyzes the phosphorylation of a vast diversity of substrates, and its members are characterized by the conservation of a common structural fold along with highly conserved sequence motifs responsible for phosphoryl transfer (GXGD) and stabilization of the metal-nucleotide complex (NXXE). Recently, a third motif (HXE) exclusive from ADP-dependent enzymes was identified, with its glutamic acid participating in water-mediated interactions with the metal-nucleotide complex and in stabilization of the ternary complex during catalysis. In this work, we bioinformatically determine that the aspartic acid of another motif (DPV), exclusively found in hydroxyethyl thiazole (THZK), hydroxymethyl pyrimidine (HMPK) and pyridoxal kinases (PLK), is structurally equivalent to the acidic residue in the HXE motif. Moreover, this residue is highly conserved among all ribokinase superfamily members. To determine whether the functional role of the DPV motif is similar to the HXE motif, we employed molecular dynamics simulations using crystal structures of phosphoryl donor substrate-complexed THZK and PLK, showing that its aspartic acid participated in water-mediated or direct interactions with the divalent metal of the metal-nucleotide complex. Lastly, enzyme kinetic assays on human PLK, an enzyme that utilizes zinc, showed that site-directed mutagenesis of the aspartic acid from the DPV motif abolishes the inhibition of this enzyme by increasing free zinc concentrations. Altogether, our results highlight that the DPV and HXE motifs are evolutionary markers of the functional and structural divergence of the ribokinase superfamily and evidence the role of the DPV motif in the interaction with both free and nucleotide-complexed divalent metals in the binding site of these enzymes.
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Cheng X, Cheng G, Xing X, Yin C, Cheng Y, Zhou X, Jiang S, Tao F, Deng H, Li Z. Controlled release of adenosine from core-shell nanofibers to promote bone regeneration through STAT3 signaling pathway. J Control Release 2020; 319:234-245. [DOI: 10.1016/j.jconrel.2019.12.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/16/2019] [Accepted: 12/28/2019] [Indexed: 12/13/2022]
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Are S, Gatreddi S, Jakkula P, Qureshi IA. Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani. Int J Biol Macromol 2020; 152:812-827. [PMID: 32105687 DOI: 10.1016/j.ijbiomac.2020.02.257] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/22/2020] [Accepted: 02/23/2020] [Indexed: 11/26/2022]
Abstract
The enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal-5'-phosphate (PLP) using ATP as the co-factor. The product pyridoxal-5'-phosphate plays a key role in several biological processes such as transamination, decarboxylation and deamination. In the present study, full-length ORF of PdxK from Leishmania donovani (LdPdxK) was cloned and then purified using affinity chromatography. LdPdxK exists as a homo-dimer in solution and shows more activity at near to physiological pH. Biochemical analysis of LdPdxK with pyridoxal, pyridoxamine, pyridoxine and ginkgotoxin revealed its affinity preference towards different substrates. The secondary structure analysis using circular dichroism spectroscopy showed LdPdxK to be predominantly α-helical in organization which tends to decline at lower and higher pH. Simultaneously, LdPdxK was crystallized and its three-dimensional structure in complex with ADP and different substrates were determined. Crystal structure of LdPdxK delineated that it has a central core of β-sheets surrounded by α-helices with a conserved GTGD ribokinase motif. The structures of LdPdxK disclosed no major structural changes between ADP and ADP- substrate bound structures. In addition, comparative structural analysis highlighted the key differences between the active site pockets of leishmanial and human PdxK, rendering LdPdxK an attractive candidate for the designing of novel and specific inhibitors.
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Affiliation(s)
- Sayanna Are
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Santhosh Gatreddi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Pranay Jakkula
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India.
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Kubota M, Nainar S, Parker SM, England W, Furche F, Spitale RC. Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry. ACS Chem Biol 2019; 14:1698-1707. [PMID: 31310712 PMCID: PMC8061575 DOI: 10.1021/acschembio.9b00079] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Optimized and stringent chemical methods to profile nascent RNA expression are still in demand. Herein, we expand the toolkit for metabolic labeling of RNA through application of inverse electron demand Diels-Alder (IEDDA) chemistry. Structural examination of metabolic enzymes guided the design and synthesis of vinyl-modified nucleosides, which we systematically tested for their ability to be installed through cellular machinery. Further, we tested these nucleosides against a panel of tetrazines to identify those which are able to react with a terminal alkene, but are stable enough for selective conjugation. The selected pairings then facilitated RNA functionalization with biotin and fluorophores. We found that this chemistry not only is amenable to preserving RNA integrity but also endows the ability to both tag and image RNA in cells. These key findings represent a significant advancement in methods to profile the nascent transcriptome using chemical approaches.
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12
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Jarvis MF. Therapeutic potential of adenosine kinase inhibition-Revisited. Pharmacol Res Perspect 2019; 7:e00506. [PMID: 31367385 PMCID: PMC6646803 DOI: 10.1002/prp2.506] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
Adenosine (ADO) is an endogenous protective regulator that restores cellular energy balance in response to tissue trauma. Extracellular ADO has a half-life of the order of seconds thus restricting its actions to tissues and cellular sites where it is released. Adenosine kinase (AK, ATP:adenosine 5'-phosphotransferase, EC 2.7.1.20) is a cytosolic enzyme that is the rate-limiting enzyme controlling extracellular ADO concentrations. Inhibition of AK can effectively increase ADO extracellular concentrations at tissue sites where pathophysiological changes occur. Highly potent and selective nucleoside and non-nucleoside AK inhibitors were discovered in the late 1990s that showed in vivo effects consistent with the augmentation of the actions of endogenous ADO in experimental models of pain, inflammation, and seizure activity. These data supported clinical development of several AK inhibitors for the management of epilepsy and chronic pain. However, early toxicological data demonstrated that nucleoside and non-nucleoside chemotypes produced hemorrhagic microfoci in brain in an apparent ADO receptor-dependent fashion. An initial oral report of these important toxicological findings was presented at an international conference but a detailed description of these data has not appeared in the peer-reviewed literature. In the two decades following the demise of these early AK-based clinical candidates, interest in AK inhibition has renewed based on preclinical data in the areas of renal protection, diabetic retinopathy, cardioprotection, and neurology. This review provides a summary of the pharmacology and toxicology data for several AK inhibitor chemotypes and the resulting translational issues associated with the development of AK inhibitors as viable therapeutic interventions.
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Song K, Li Y, He H, Liu L, Zhao P, Xia Q, Wang Y. A Novel Adenosine Kinase from Bombyx mori: Enzymatic Activity, Structure, and Biological Function. Int J Mol Sci 2019; 20:ijms20153732. [PMID: 31370143 PMCID: PMC6695918 DOI: 10.3390/ijms20153732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 02/04/2023] Open
Abstract
Adenosine kinase (ADK) is the first enzyme in the adenosine remediation pathway that catalyzes adenosine phosphorylation into adenosine monophosphate, thus regulating adenosine homeostasis in cells. To obtain new insights into ADK from Bombyx mori (BmADK), we obtained recombinant BmADK, and analyzed its activity, structure, and function. Gel-filtration showed BmADK was a monomer with molecular weight of approximately 38 kDa. Circular dichroism spectra indicated BmADK had 36.8% α-helix and 29.9% β-strand structures, respectively. The structure of BmADK was stable in pH 5.0–11.0, and not affected under 30 °C. The melting temperature and the enthalpy and entropy changes in the thermal transition of BmADK were 46.51 ± 0.50 °C, 253.43 ± 0.20 KJ/mol, and 0.79 ± 0.01 KJ/(mol·K), respectively. Site-directed mutagenesis demonstrated G68, S201, E229, and D303 were key amino acids for BmADK structure and activity. In particular, S201A mutation significantly increased the α-helix content of BmADK and its activity. BmADK was located in the cytoplasm and highly expressed in the silk gland during the pre-pupal stage. RNA interference revealed the downregulation of BmADK decreased ATG-8, Caspase-9, Ec-R, E74A, and Br-C expression, indicating it was likely involved in 20E signaling, apoptosis, and autophagy to regulate silk gland degeneration and silkworm metamorphosis. Our study greatly expanded the knowledge on the activity, structure, and role of ADK.
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Affiliation(s)
- Kai Song
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
| | - Yu Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
| | - Huawei He
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
- College of Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing 400715, China.
| | - Lina Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing 400715, China
| | - Yejing Wang
- College of Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
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14
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Crespo R, Dang Q, Zhou NE, Guthrie LM, Snavely TC, Dong W, Loesch KA, Suzuki T, You L, Wang W, O’Malley T, Parish T, Olsen DB, Sacchettini JC. Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase. J Med Chem 2019; 62:4483-4499. [PMID: 31002508 PMCID: PMC6511943 DOI: 10.1021/acs.jmedchem.9b00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis adenosine kinase (MtbAdoK) is an essential enzyme of Mtb and forms part of the purine salvage pathway within mycobacteria. Evidence suggests that the purine salvage pathway might play a crucial role in Mtb survival and persistence during its latent phase of infection. In these studies, we adopted a structural approach to the discovery, structure-guided design, and synthesis of a series of adenosine analogues that displayed inhibition constants ranging from 5 to 120 nM against the enzyme. Two of these compounds exhibited low micromolar activity against Mtb with half maximal effective inhibitory concentrations of 1.7 and 4.0 μM. Our selectivity and preliminary pharmacokinetic studies showed that the compounds possess a higher degree of specificity against MtbAdoK when compared with the human counterpart and are well tolerated in rodents, respectively. Finally, crystallographic studies showed the molecular basis of inhibition, potency, and selectivity and revealed the presence of a potentially therapeutically relevant cavity unique to the MtbAdoK homodimer.
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Affiliation(s)
- Roberto
A. Crespo
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Qun Dang
- Merck
Sharp Dohme Corporation, West Point Pennsylvania 19486, United States
| | - Nian E. Zhou
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Liam M. Guthrie
- College
of Medicine, Texas A&M University Health
Science Center, Bryan, Texas 77807, United
States
| | - Thomas C. Snavely
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Wen Dong
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kimberly A. Loesch
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Takao Suzuki
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Lanying You
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Wei Wang
- WuXi
AppTec, 288 Fute Zhong Road, Shanghai 200131, China
| | - Theresa O’Malley
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue E, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue E, Seattle, Washington 98102, United States
| | - David B. Olsen
- Merck
Sharp Dohme Corporation, West Point Pennsylvania 19486, United States,E-mail: . Phone: 215-652-5250 (D.B.O.)
| | - James C. Sacchettini
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States,E-mail: . Phone: (979) 845-8548 (J.C.S.)
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15
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Abstract
Carbohydrate kinases activate a wide variety of monosaccharides by adding a phosphate group, usually from ATP. This modification is fundamental to saccharide utilization, and it is likely a very ancient reaction. Modern organisms contain carbohydrate kinases from at least five main protein families. These range from the highly specialized inositol kinases, to the ribokinases and galactokinases, which belong to families that phosphorylate a wide range of substrates. The carbohydrate kinases utilize a common strategy to drive the reaction between the sugar hydroxyl and the donor phosphate. Each sugar is held in position by a network of hydrogen bonds to the non-reactive hydroxyls (and other functional groups). The reactive hydroxyl is deprotonated, usually by an aspartic acid side chain acting as a catalytic base. The deprotonated hydroxyl then attacks the donor phosphate. The resulting pentacoordinate transition state is stabilized by an adjacent divalent cation, and sometimes by a positively charged protein side chain or the presence of an anion hole. Many carbohydrate kinases are allosterically regulated using a wide variety of strategies, due to their roles at critical control points in carbohydrate metabolism. The evolution of a similar mechanism in several folds highlights the elegance and simplicity of the catalytic scheme.
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16
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Large-scale conformational changes and redistribution of surface negative charge upon sugar binding dictate the fidelity of phosphorylation in Vibrio cholerae fructokinase. Sci Rep 2018; 8:16925. [PMID: 30446722 PMCID: PMC6240065 DOI: 10.1038/s41598-018-35236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/25/2018] [Indexed: 11/24/2022] Open
Abstract
Fructokinase (FRK) catalyzes the first step of fructose metabolism i.e., D-fructose to D-fructose-6-phosphate (F6P), however, the mechanistic insights of this reaction are elusive yet. Here we demonstrate that the putative Vibrio cholerae fructokinase (VcFRK) exhibit strong fructose-6-kinase activity allosterically modulated by K+/Cs+. We have determined the crystal structures of apo-VcFRK and its complex with fructose, fructose-ADP-Ca2+, fructose-ADP-Ca2+-BeF3−. Collectively, we propose the catalytic mechanism and allosteric activation of VcFRK in atomistic details explaining why K+/Cs+ are better activator than Na+. Structural results suggest that apo VcFRK allows entry of fructose in the active site, sequester it through several conserved H-bonds and attains a closed form through large scale conformational changes. A double mutant (H108C/T261C-VcFRK), that arrests the closed form but unable to reopen for F6P release, is catalytically impotent highlighting the essentiality of this conformational change. Negative charge accumulation around ATP upon fructose binding, is presumed to redirect the γ-phosphate towards fructose for efficient phosphotransfer. Reduced phosphotransfer rate of the mutants E205Q and E110Q supports this view. Atomic resolution structure of VcFRK-fructose-ADP-Ca2+-BeF3−, reported first time for any sugar kinase, suggests that BeF3− moiety alongwith R176, Ca2+ and ‘anion hole’ limit the conformational space for γ-phosphate favoring in-line phospho-transfer.
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17
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Kumar V, Sharma M, Rakesh BR, Malik CK, Neelagiri S, Neerupudi KB, Garg P, Singh S. Pyridoxal kinase: A vitamin B6 salvage pathway enzyme from Leishmania donovani. Int J Biol Macromol 2018; 119:320-334. [DOI: 10.1016/j.ijbiomac.2018.07.095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/21/2022]
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18
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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] [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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19
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Adenosine Kinase couples sensing of cellular potassium depletion to purine metabolism. Sci Rep 2018; 8:11988. [PMID: 30097648 PMCID: PMC6086891 DOI: 10.1038/s41598-018-30418-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/30/2018] [Indexed: 01/07/2023] Open
Abstract
Adenosine Kinase (ADK) regulates the cellular levels of adenosine (ADO) by fine-tuning its metabolic clearance. The transfer of γ-phosphate from ATP to ADO by ADK involves regulation by the substrates and products, as well as by Mg2+ and inorganic phosphate. Here we present new crystal structures of mouse ADK (mADK) binary (mADK:ADO; 1.2 Å) and ternary (mADK:ADO:ADP; 1.8 Å) complexes. In accordance with the structural demonstration of ADO occupancy of the ATP binding site, kinetic studies confirmed a competitive model of auto-inhibition of ADK by ADO. In the ternary complex, a K+ ion is hexacoordinated between loops adjacent to the ATP binding site, where Asp310 connects the K+ coordination sphere to the ATP binding site through an anion hole structure. Nuclear Magnetic Resonance 2D 15N-1H HSQC experiments revealed that the binding of K+ perturbs Asp310 and residues of adjacent helices 14 and 15, engaging a transition to a catalytically productive structure. Consistent with the structural data, the mutants D310A and D310P are catalytically deficient and loose responsiveness to K+. Saturation Transfer Difference spectra of ATPγS provided evidence for an unfavorable interaction of the mADK D310P mutant for ATP. Reductions in K+ concentration diminish, whereas increases enhance the in vitro activity of mADK (maximum of 2.5-fold; apparent Kd = 10.4 mM). Mechanistically, K+ increases the catalytic turnover (Kcat) but does not affect the affinity of mADK for ADO or ATP. Depletion of intracellular K+ inhibited, while its restoration was accompanied by a full recovery of cellular ADK activity. Together, this novel dataset reveals the molecular basis of the allosteric activation of ADK by K+ and highlights the role of ADK in connecting depletion of intracellular K+ to the regulation of purine metabolism.
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20
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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] [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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21
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Zamora RA, Gonzalez-Órdenes F, Castro-Fernández V, Guixé V. ADP-dependent phosphofructokinases from the archaeal order Methanosarcinales display redundant glucokinase activity. Arch Biochem Biophys 2017; 633:85-92. [PMID: 28919057 DOI: 10.1016/j.abb.2017.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/01/2017] [Accepted: 09/11/2017] [Indexed: 11/26/2022]
Abstract
The genome of Methanosarcinales organisms presents both ADP-dependent glucokinase and phosphofructokinase genes. However, Methanococcoides burtonii has a truncate glucokinase gene with a large deletion at the C-terminal, where the catalytic GXGD motif is located. Characterization of its phosphofructokinase annotated protein shows that is a bifunctional enzyme able to supply the absence of the glucokinase activity. Moreover, kinetic analyses of the phosphofructokinase annotated enzyme from, Methanohalobium evestigatum demonstrated that this enzyme is also bifunctional. The high conservation of the active site residues of all the enzymes from the order Methanosarcinales suggest that they should be bifunctional, as was previously reported for the ADP-dependent kinases from Methanococcales, highlighting the redundancy of the glucokinase activity in this archaeal group. The presence of active glycolytic enzymes would be important when glycogen storage of these organisms needs to be degraded to be used as energy source. Kinetic and structural information allows us to establish a substrate specificity signature that identifies specific GK or PFK, and bifunctional enzymes in this family.
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Affiliation(s)
- Ricardo A Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Felipe Gonzalez-Órdenes
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Victor Castro-Fernández
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile.
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile.
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22
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9-(2'-Deoxy-2'-Fluoro-β-d-Arabinofuranosyl) Adenine Is a Potent Antitrypanosomal Adenosine Analogue That Circumvents Transport-Related Drug Resistance. Antimicrob Agents Chemother 2017; 61:AAC.02719-16. [PMID: 28373184 PMCID: PMC5444181 DOI: 10.1128/aac.02719-16] [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: 12/23/2016] [Accepted: 03/27/2017] [Indexed: 01/25/2023] Open
Abstract
Current chemotherapy against African sleeping sickness, a disease caused by the protozoan parasite Trypanosoma brucei, is limited by toxicity, inefficacy, and drug resistance. Nucleoside analogues have been successfully used to cure T. brucei-infected mice, but they have the limitation of mainly being taken up by the P2 nucleoside transporter, which, when mutated, is a common cause of multidrug resistance in T. brucei We report here that adenine arabinoside (Ara-A) and the newly tested drug 9-(2'-deoxy-2'-fluoro-β-d-arabinofuranosyl) adenine (FANA-A) are instead taken up by the P1 nucleoside transporter, which is not associated with drug resistance. Like Ara-A, FANA-A was found to be resistant to cleavage by methylthioadenosine phosphorylase, an enzyme that protects T. brucei against the antitrypanosomal effects of deoxyadenosine. Another important factor behind the selectivity of nucleoside analogues is how well they are phosphorylated within the cell. We found that the T. brucei adenosine kinase had a higher catalytic efficiency with FANA-A than the mammalian enzyme, and T. brucei cells treated with FANA-A accumulated high levels of FANA-A triphosphate, which even surpassed the level of ATP and led to cell cycle arrest, inhibition of DNA synthesis, and the accumulation of DNA breaks. FANA-A inhibited nucleic acid biosynthesis and parasite proliferation with 50% effective concentrations (EC50s) in the low nanomolar range, whereas mammalian cell proliferation was inhibited in the micromolar range. Both Ara-A and FANA-A, in combination with deoxycoformycin, cured T. brucei-infected mice, but FANA-A did so at a dose 100 times lower than that of Ara-A.
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23
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Sarkar B, Kulharia M, Mantha AK. Understanding human thiol dioxygenase enzymes: structure to function, and biology to pathology. Int J Exp Pathol 2017; 98:52-66. [PMID: 28439920 DOI: 10.1111/iep.12222] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/18/2017] [Indexed: 12/15/2022] Open
Abstract
Amino acid metabolism is a significant metabolic activity in humans, especially of sulphur-containing amino acids, methionine and cysteine (Cys). Cys is cytotoxic and neurotoxic in nature; hence, mammalian cells maintain a constant intracellular level of Cys. Metabolism of Cys is mainly regulated by two thiol dioxygenases: cysteine dioxygenase (CDO) and 2-aminoethanethiol dioxygenase (ADO). CDO and ADO are the only human thiol dioxygenases reported with a role in Cys metabolism and localized to mitochondria. This metabolic pathway is important in various human disorders, as it is responsible for the synthesis of antioxidant glutathione and is also for the synthesis of hypotaurine and taurine. CDO is the most extensively studied protein, whose high-resolution crystallographic structures have been solved. As compared to CDO, ADO is less studied, even though it has a key role in cysteamine metabolism. To further understand ADO's structure and function, the three-dimensional structures have been predicted from I-TASSER and SWISS-MODEL servers and validated with PROCHECK software. Structural superimposition approach using iPBA web server further confirmed near-identical structures (including active sites) for the predicted protein models of ADO as compared to CDO. In addition, protein-protein interaction and their association in patho-physiology are crucial in understanding protein functions. Both ADO and CDO interacting partner profiles have been presented using STRING database. In this study, we have predicted a 3D model structure for ADO and summarized the biological roles and the pathological consequences which are associated with the altered expression and functioning of ADO and CDO in case of cancer, neurodegenerative disorders and other human diseases.
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Affiliation(s)
- Bibekananda Sarkar
- Center for Animal Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Mahesh Kulharia
- Center for Computational Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Anil K Mantha
- Center for Animal Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab, India
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24
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Abramchik YA, Timofeev VI, Muravieva TI, Esipov RS, Kuranova IP. Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s106377451606002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Raschka S, Bemister-Buffington J, Kuhn LA. Detecting the native ligand orientation by interfacial rigidity: SiteInterlock. Proteins 2016; 84:1888-1901. [DOI: 10.1002/prot.25172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/19/2016] [Accepted: 09/27/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Sebastian Raschka
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing Michigan 48824 USA
| | - Joseph Bemister-Buffington
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing Michigan 48824 USA
| | - Leslie A. Kuhn
- Department of Biochemistry and Molecular Biology; Michigan State University; East Lansing Michigan 48824 USA
- Department of Computer Science and Engineering; Michigan State University; East Lansing Michigan 48824 USA
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26
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An Adenosine-Mediated Glial-Neuronal Circuit for Homeostatic Sleep. J Neurosci 2016; 36:3709-21. [PMID: 27030757 DOI: 10.1523/jneurosci.3906-15.2016] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/15/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Sleep homeostasis reflects a centrally mediated drive for sleep, which increases during waking and resolves during subsequent sleep. Here we demonstrate that mice deficient for glial adenosine kinase (AdK), the primary metabolizing enzyme for adenosine (Ado), exhibit enhanced expression of this homeostatic drive by three independent measures: (1) increased rebound of slow-wave activity; (2) increased consolidation of slow-wave sleep; and (3) increased time constant of slow-wave activity decay during an average slow-wave sleep episode, proposed and validated here as a new index for homeostatic sleep drive. Conversely, mice deficient for the neuronal adenosine A1 receptor exhibit significantly decreased sleep drive as judged by these same indices. Neuronal knock-out of AdK did not influence homeostatic sleep need. Together, these findings implicate a glial-neuronal circuit mediated by intercellular Ado, controlling expression of homeostatic sleep drive. Because AdK is tightly regulated by glial metabolic state, our findings suggest a functional link between cellular metabolism and sleep homeostasis. SIGNIFICANCE STATEMENT The work presented here provides evidence for an adenosine-mediated regulation of sleep in response to waking (i.e., homeostatic sleep need), requiring activation of neuronal adenosine A1 receptors and controlled by glial adenosine kinase. Adenosine kinase acts as a highly sensitive and important metabolic sensor of the glial ATP/ADP and AMP ratio directly controlling intracellular adenosine concentration. Glial equilibrative adenosine transporters reflect the intracellular concentration to the extracellular milieu to activate neuronal adenosine receptors. Thus, adenosine mediates a glial-neuronal circuit linking glial metabolic state to neural-expressed sleep homeostasis. This indicates a metabolically related function(s) for this glial-neuronal circuit in the buildup and resolution of our need to sleep and suggests potential therapeutic targets more directly related to sleep function.
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27
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Toti KS, Osborne D, Ciancetta A, Boison D, Jacobson KA. South (S)- and North (N)-Methanocarba-7-Deazaadenosine Analogues as Inhibitors of Human Adenosine Kinase. J Med Chem 2016; 59:6860-77. [PMID: 27410258 PMCID: PMC5032833 DOI: 10.1021/acs.jmedchem.6b00689] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Adenosine kinase (AdK) inhibitors raise endogenous adenosine levels, particularly in disease states, and have potential for treatment of seizures, neurodegeneration, and inflammation. On the basis of the South (S) ribose conformation and molecular dynamics (MD) analysis of nucleoside inhibitors bound in AdK X-ray crystallographic structures, (S)- and North (N)-methanocarba (bicyclo[3.1.0]hexane) derivatives of known inhibitors were prepared and compared as human (h) AdK inhibitors. 5'-Hydroxy (34, MRS4202 (S); 55, MRS4380 (N)) and 5'-deoxy 38a (MRS4203 (S)) analogues, containing 7- and N(6)-NH phenyl groups in 7-deazaadenine, robustly inhibited AdK activity (IC50 ∼ 100 nM), while the 5'-hydroxy derivative 30 lacking the phenyl substituents was weak. Docking in the hAdK X-ray structure and MD simulation suggested a mode of binding similar to 5'-deoxy-5-iodotubercidin and other known inhibitors. Thus, a structure-based design approach for further potency enhancement is possible. The potent AdK inhibitors in this study are ready to be further tested in animal models of epilepsy.
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Affiliation(s)
- Kiran S Toti
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Danielle Osborne
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute , 1225 NE Second Avenue, Portland, Oregon 97232, United States
| | - Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
| | - Detlev Boison
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute , 1225 NE Second Avenue, Portland, Oregon 97232, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, United States
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28
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Abstract
Adenosine, as the brain’s endogenous anticonvulsant, is considered to be responsible for seizure arrest and postictal refractoriness. On the other hand, deficiencies within the adenosine-based neuromodulatory system may contribute to epileptogenesis. Based on these natural mechanisms and on findings that adenosine and its analogs can suppress pharmacoresistant seizures, a new field of adenosine-based therapies has emerged, including the use of adenosine receptor agonists and adenosine transport inhibitors, or the inhibition of adenosine kinase, which is thought to be the key enzyme for the regulation of intra- and extracellular adenosine levels. However, most of these pharmacological approaches are limited by strong systemic side effects ranging from a decrease of heart rate, blood pressure, and body temperature to sedation. Recently, new strategies have been developed aimed at the local reconstitution of the inhibitory adenosinergic tone by intracerebral implantation of cells engineered to release adenosine. Adenosine-releasing cells or devices implanted into or near a seizure focus offer new hopes for a side effect-free therapy for pharmacoresistant epilepsy.
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Affiliation(s)
- Detlev Boison
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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29
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Abarca-Lagunas MJ, Rivas-Pardo JA, Ramírez-Sarmiento CA, Guixé V. Dissecting the functional roles of the conserved NXXE and HXE motifs of the ADP-dependent glucokinase fromThermococcus litoralis. FEBS Lett 2015; 589:3271-6. [DOI: 10.1016/j.febslet.2015.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/11/2015] [Accepted: 09/20/2015] [Indexed: 11/28/2022]
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30
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Savi L, Brindisi M, Alfano G, Butini S, La Pietra V, Novellino E, Marinelli L, Lossani A, Focher F, Cavella C, Campiani G, Gemma S. Site-directed Mutagenesis of Key Residues Unveiled a Novel Allosteric Site on Human Adenosine Kinase for Pyrrolobenzoxa(thia)zepinone Non-Nucleoside Inhibitors. Chem Biol Drug Des 2015; 87:112-20. [PMID: 26242695 DOI: 10.1111/cbdd.12630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 12/21/2022]
Abstract
Most nucleoside kinases, besides the catalytic domain, feature an allosteric domain which modulates their activity. Generally, non-substrate analogs, interacting with allosteric sites, represent a major opportunity for developing more selective and safer therapeutics. We recently developed a series of non-nucleoside non-competitive inhibitors of human adenosine kinase (hAK), based on a pyrrolobenzoxa(thia)zepinone scaffold. Based on computational analysis, we hypothesized the existence of a novel allosteric site on hAK, topographically distinct from the catalytic site. In this study, we have adopted a multidisciplinary approach including molecular modeling, biochemical studies, and site-directed mutagenesis to validate our hypothesis. Based on a three-dimensional model of interaction between hAK and our molecules, we designed, cloned, and expressed specific, single and double point mutants of hAK (Q74A, Q78A, H107A, K341A, F338A, and Q74A-F338A). Kinetic characterization of recombinant enzymes indicated that these mutations did not affect enzyme functioning; conversely, mutated enzymes are endowed of reduced susceptibility to our non-nucleoside inhibitors, while maintaining comparable affinity for nucleoside inhibitors to the wild-type enzyme. This study represents the first characterization and validation of a novel allosteric site in hAK and may pave the way to the development of novel selective and potent non-nucleoside inhibitors of hAK endowed with therapeutic potential.
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Affiliation(s)
- Lida Savi
- Istituto di Genetica Molecolare, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Margherita Brindisi
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Gloria Alfano
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Stefania Butini
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Valeria La Pietra
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,Dipartimento di Farmacia, Università di Napoli Federico II, via D. Montesano 49, 80131, Napoli, Italy
| | - Ettore Novellino
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,Dipartimento di Farmacia, Università di Napoli Federico II, via D. Montesano 49, 80131, Napoli, Italy
| | - Luciana Marinelli
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,Dipartimento di Farmacia, Università di Napoli Federico II, via D. Montesano 49, 80131, Napoli, Italy
| | - Andrea Lossani
- Istituto di Genetica Molecolare, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Federico Focher
- Istituto di Genetica Molecolare, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Caterina Cavella
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Giuseppe Campiani
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Sandra Gemma
- Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy.,European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy
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31
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Horitani M, Byer AS, Shisler KA, Chandra T, Broderick JB, Hoffman BM. Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5'-dAdo• "Free Radical" Is Never Free. J Am Chem Soc 2015; 137:7111-21. [PMID: 25923449 PMCID: PMC4612528 DOI: 10.1021/jacs.5b00498] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysine 2,3-aminomutase (LAM) is a radical S-adenosyl-L-methionine (SAM) enzyme and, like other members of this superfamily, LAM utilizes radical-generating machinery comprising SAM anchored to the unique Fe of a [4Fe-4S] cluster via a classical five-membered N,O chelate ring. Catalysis is initiated by reductive cleavage of the SAM S-C5' bond, which creates the highly reactive 5'-deoxyadenosyl radical (5'-dAdo•), the same radical generated by homolytic Co-C bond cleavage in B12 radical enzymes. The SAM surrogate S-3',4'-anhydroadenosyl-L-methionine (anSAM) can replace SAM as a cofactor in the isomerization of L-α-lysine to L-β-lysine by LAM, via the stable allylic anhydroadenosyl radical (anAdo•). Here electron nuclear double resonance (ENDOR) spectroscopy of the anAdo• radical in the presence of (13)C, (2)H, and (15)N-labeled lysine completes the picture of how the active site of LAM from Clostridium subterminale SB4 "tames" the 5'-dAdo• radical, preventing it from carrying out harmful side reactions: this "free radical" in LAM is never free. The low steric demands of the radical-generating [4Fe-4S]/SAM construct allow the substrate target to bind adjacent to the S-C5' bond, thereby enabling the 5'-dAdo• radical created by cleavage of this bond to react with its partners by undergoing small motions, ∼0.6 Å toward the target and ∼1.5 Å overall, that are controlled by tight van der Waals contact with its partners. We suggest that the accessibility to substrate and ready control of the reactive C5' radical, with "van der Waals control" of small motions throughout the catalytic cycle, is common within the radical SAM enzyme superfamily and is a major reason why these enzymes are the preferred means of initiating radical reactions in nature.
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Affiliation(s)
- Masaki Horitani
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amanda S. Byer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Krista A. Shisler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Tilak Chandra
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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32
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Nagata R, Fujihashi M, Sato T, Atomi H, Miki K. Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation. Biochemistry 2015; 54:3494-503. [DOI: 10.1021/acs.biochem.5b00296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryuhei Nagata
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masahiro Fujihashi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takaaki Sato
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruyuki Atomi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kunio Miki
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- JST, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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33
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Snášel J, Nauš P, Dostál J, Hnízda A, Fanfrlík J, Brynda J, Bourderioux A, Dušek M, Dvořáková H, Stolaříková J, Zábranská H, Pohl R, Konečný P, Džubák P, Votruba I, Hajdúch M, Rezáčová P, Veverka V, Hocek M, Pichová I. Structural basis for inhibition of mycobacterial and human adenosine kinase by 7-substituted 7-(Het)aryl-7-deazaadenine ribonucleosides. J Med Chem 2014; 57:8268-79. [PMID: 25259627 DOI: 10.1021/jm500497v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenosine kinase (ADK) from Mycobacterium tuberculosis (Mtb) was selected as a target for design of antimycobacterial nucleosides. Screening of 7-(het)aryl-7-deazaadenine ribonucleosides with Mtb and human (h) ADKs and testing with wild-type and drug-resistant Mtb strains identified specific inhibitors of Mtb ADK with micromolar antimycobacterial activity and low cytotoxicity. X-ray structures of complexes of Mtb and hADKs with 7-ethynyl-7-deazaadenosine showed differences in inhibitor interactions in the adenosine binding sites. 1D (1)H STD NMR experiments revealed that these inhibitors are readily accommodated into the ATP and adenosine binding sites of Mtb ADK, whereas they bind preferentially into the adenosine site of hADK. Occupation of the Mtb ADK ATP site with inhibitors and formation of catalytically less competent semiopen conformation of MtbADK after inhibitor binding in the adenosine site explain the lack of phosphorylation of 7-substituted-7-deazaadenosines. Semiempirical quantum mechanical analysis confirmed different affinity of nucleosides for the Mtb ADK adenosine and ATP sites.
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Affiliation(s)
- Jan Snášel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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34
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Paul R, Dandopath Patra M, Banerjee R, Sen U. Crystallization and preliminary X-ray analysis of a ribokinase from Vibrio cholerae O395. Acta Crystallogr F Struct Biol Commun 2014; 70:1098-102. [PMID: 25084391 PMCID: PMC4118813 DOI: 10.1107/s2053230x14014411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Ribokinase (RK) is one of the principal enzymes in carbohydrate metabolism, catalyzing the reaction of D-ribose and adenosine triphosphate to produce ribose-5-phosphate and adenosine diphosphate (ADP). To provide further insight into the catalytic mechanism, the rbsK gene from Vibrio cholerae O395 encoding ribokinase was cloned and the protein was overexpressed in Escherichia coli BL21 (DE3) and purified using Ni(2+)-NTA affinity chromatography. Crystals of V. cholerae RK (Vc-RK) and of its complex with ribose and ADP were grown in the presence of polyethylene glycol 6000 and diffracted to 3.4 and 1.75 Å resolution, respectively. Analysis of the diffraction data showed that both crystals possess symmetry consistent with space group P1. In the Vc-RK crystals, 16 molecules in the asymmetric unit were arranged in a spiral fashion, leaving a large empty space inside the crystal, which is consistent with its high Matthews coefficient (3.9 Å(3) Da(-1)) and solvent content (68%). In the Vc-RK co-crystals four molecules were located in the asymmetric unit with a Matthews coefficient of 2.4 Å(3) Da(-1), corresponding to a solvent content of 50%.
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Affiliation(s)
- Rakhi Paul
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700 064, India
| | - Madhumita Dandopath Patra
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700 064, India
| | - Ramanuj Banerjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700 064, India
| | - Udayaditya Sen
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700 064, India
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35
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Timm J, González-Pacanowska D, Wilson KS. Structures of adenosine kinase from Trypanosoma brucei brucei. Acta Crystallogr F Struct Biol Commun 2014; 70:34-9. [PMID: 24419613 PMCID: PMC3943091 DOI: 10.1107/s2053230x13033621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/12/2013] [Indexed: 11/10/2022] Open
Abstract
Trypanosoma brucei is a single-cellular parasite of the genus Kinetoplastida and is the causative agent of African sleeping sickness in humans. Adenosine kinase is a key enzyme in the purine-salvage pathway, phosphorylating adenosine to AMP, and also activates cytotoxic analogues such as cordycepin and Ara-A by their phosphorylation. The structures of T. brucei brucei adenosine kinase (TbAK) in its unliganded open conformation and complexed with adenosine and ADP in the closed conformation are both reported to 2.6 Å resolution. The structures give insight into the binding mode of the substrates and the conformational change induced upon substrate binding. This information can be used to guide the improvement of cytotoxic substrate analogues as potential antitrypanosomal drugs.
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Affiliation(s)
- Jennifer Timm
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina ‘López-Neyra’, Consejo Superior de Investigaciones Científicas, 18100 Armilla, Granada, Spain
| | - Keith S. Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England
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Abstract
Adenosine kinase (ADK; EC 2.7.1.20) is an evolutionarily conserved phosphotransferase that converts the purine ribonucleoside adenosine into 5'-adenosine-monophosphate. This enzymatic reaction plays a fundamental role in determining the tone of adenosine, which fulfills essential functions as a homeostatic and metabolic regulator in all living systems. Adenosine not only activates specific signaling pathways by activation of four types of adenosine receptors but it is also a primordial metabolite and regulator of biochemical enzyme reactions that couple to bioenergetic and epigenetic functions. By regulating adenosine, ADK can thus be identified as an upstream regulator of complex homeostatic and metabolic networks. Not surprisingly, ADK dysfunction is involved in several pathologies, including diabetes, epilepsy, and cancer. Consequently, ADK emerges as a rational therapeutic target, and adenosine-regulating drugs have been tested extensively. In recent attempts to improve specificity of treatment, localized therapies have been developed to augment adenosine signaling at sites of injury or pathology; those approaches include transplantation of stem cells with deletions of ADK or the use of gene therapy vectors to downregulate ADK expression. More recently, the first human mutations in ADK have been described, and novel findings suggest an unexpected role of ADK in a wider range of pathologies. ADK-regulating strategies thus represent innovative therapeutic opportunities to reconstruct network homeostasis in a multitude of conditions. This review will provide a comprehensive overview of the genetics, biochemistry, and pharmacology of ADK and will then focus on pathologies and therapeutic interventions. Challenges to translate ADK-based therapies into clinical use will be discussed critically.
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Affiliation(s)
- Detlev Boison
- Legacy Research Institute, 1225 NE 16th Ave, Portland, OR 97202, USA.
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37
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Baranowski D, Golankiewicz B, Folkman W, Popenda M. 2-Methylwyosine, a nucleoside with restricted anti conformation in the east region enforced by nucleobase moiety modification: synthesis and conformational analysis by NMR and molecular dynamics. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 31:707-19. [PMID: 23067123 DOI: 10.1080/15257770.2012.724133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We synthesized a new 2-methyl derivative of wyosine using a multistep procedure starting from guanosine. We examined different synthetic paths and optimized the conditions for each step. Based on MD calculations and analysis of the (3) J (HH) and J (C1'H1') of the ribose moiety, we discovered that the sugar part adopted conformation specific for the East region rarely occurring in solution. This unusual conformational preference is probably due to steric repulsions between the methyl group at position 2 and the 5'-CH(2)OH group. We observed that N-glycosidic bond stability weakened 14-fold upon the introduction of the methyl group in position 2 compared with wyosine.
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Affiliation(s)
- Daniel Baranowski
- Laboratory of Nucleoside Chemistry, Institute of Bioorganic Chemistry PAS, Poznan, Poland.
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38
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Elkin SR, Kumar A, Price CW, Columbus L. A broad specificity nucleoside kinase from Thermoplasma acidophilum. Proteins 2013; 81:568-82. [PMID: 23161756 DOI: 10.1002/prot.24212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 10/18/2012] [Accepted: 11/01/2012] [Indexed: 11/07/2022]
Abstract
The crystal structure of Ta0880, determined at 1.91 Å resolution, from Thermoplasma acidophilum revealed a dimer with each monomer composed of an α/β/α sandwich domain and a smaller lid domain. The overall fold belongs to the PfkB family of carbohydrate kinases (a family member of the Ribokinase clan) which include ribokinases, 1-phosphofructokinases, 6-phosphofructo-2-kinase, inosine/guanosine kinases, fructokinases, adenosine kinases, and many more. Based on its general fold, Ta0880 had been annotated as a ribokinase-like protein. Using a coupled pyruvate kinase/lactate dehydrogenase assay, the activity of Ta0880 was assessed against a variety of ribokinase/pfkB-like family substrates; activity was not observed for ribose, fructose-1-phosphate, or fructose-6-phosphate. Based on structural similarity with nucleoside kinases (NK) from Methanocaldococcus jannaschii (MjNK, PDB 2C49, and 2C4E) and Burkholderia thailandensis (BtNK, PDB 3B1O), nucleoside kinase activity was investigated. Ta0880 (TaNK) was confirmed to have nucleoside kinase activity with an apparent KM for guanosine of 0.21 μM and catalytic efficiency of 345,000 M(-1) s(-1) . These three NKs have significantly different substrate, phosphate donor, and cation specificities and comparisons of specificity and structure identified residues likely responsible for the nucleoside substrate selectivity. Phylogenetic analysis identified three clusters within the PfkB family and indicates that TaNK is a member of a new sub-family with broad nucleoside specificities. Proteins 2013. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Sarah R Elkin
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904-4319, USA
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39
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Romanello L, Bachega JFR, Cassago A, Brandão-Neto J, DeMarco R, Garratt RC, Pereira HD. Adenosine kinase from Schistosoma mansoni: structural basis for the differential incorporation of nucleoside analogues. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 69:126-36. [PMID: 23275171 DOI: 10.1107/s0907444912044800] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/29/2012] [Indexed: 11/10/2022]
Abstract
In adult schistosomes, the enzyme adenosine kinase (AK) is responsible for the incorporation of some adenosine analogues, such as 2-fluoroadenosine and tubercidin, into the nucleotide pool, but not others. In the present study, the structures of four complexes of Schistosoma mansoni AK bound to adenosine and adenosine analogues are reported which shed light on this observation. Two differences in the adenosine-binding site in comparison with the human counterpart (I38Q and T36A) are responsible for their differential specificities towards adenosine analogues, in which the Schistosoma enzyme does not tolerate bulky substituents at the N7 base position. This aids in explaining experimental data which were reported in the literature more than two decades ago. Furthermore, there appears to be considerable plasticity within the substrate-binding sites that affects the side-chain conformation of Ile38 and causes a previously unobserved flexibility within the loop comprising residues 286-299. These results reveal that the latter can be sterically occluded in the absence of ATP. Overall, these results contribute to the body of knowledge concerning the enzymes of the purine salvage pathway in this important human parasite.
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Affiliation(s)
- Larissa Romanello
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Brazil
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Jones DC, Alphey MS, Wyllie S, Fairlamb AH. Chemical, genetic and structural assessment of pyridoxal kinase as a drug target in the African trypanosome. Mol Microbiol 2012; 86:51-64. [PMID: 22857512 PMCID: PMC3470933 DOI: 10.1111/j.1365-2958.2012.08189.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Pyridoxal-5′-phosphate (vitamin B6) is an essential cofactor for many important enzymatic reactions such as transamination and decarboxylation. African trypanosomes are unable to synthesise vitamin B6de novo and rely on uptake of B6 vitamers such as pyridoxal and pyridoxamine from their hosts, which are subsequently phosphorylated by pyridoxal kinase (PdxK). A conditional null mutant of PdxK was generated in Trypanosoma brucei bloodstream forms showing that this enzyme is essential for growth of the parasite in vitro and for infectivity in mice. Activity of recombinant T. brucei PdxK was comparable to previously published work having a specific activity of 327 ± 13 mU mg−1 and a Kmapp with respect to pyridoxal of 29.6 ± 3.9 µM. A coupled assay was developed demonstrating that the enzyme has equivalent catalytic efficiency with pyridoxal, pyridoxamine and pyridoxine, and that ginkgotoxin is an effective pseudo substrate. A high resolution structure of PdxK in complex with ATP revealed important structural differences with the human enzyme. These findings suggest that pyridoxal kinase is an essential and druggable target that could lead to much needed alternative treatments for this devastating disease.
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Affiliation(s)
- Deuan C Jones
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of Dundee, Dundee, UK
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Rodriguez JB, Szajnman SH. New antibacterials for the treatment of toxoplasmosis; a patent review. Expert Opin Ther Pat 2012; 22:311-33. [PMID: 22404108 DOI: 10.1517/13543776.2012.668886] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Toxoplasma gondii is an opportunistic protozoan parasite responsible for toxoplasmosis. T. gondii is able to infect a wide range of hosts, particularly humans and warm-blooded animals. Toxoplasmosis can be considered as one of the most prevalent parasitic diseases affecting close to one billion people worldwide, but its current chemotherapy is still deficient and is only effective in the acute phase of the disease. AREAS COVERED This review covers different approaches to toxoplasmosis chemotherapy focused on the metabolic differences between the host and the parasite. Selective action on different targets such as the isoprenoid pathway, dihydrofolate reductase, T. gondii adenosine kinase, different antibacterials, T. gondii histone deacetylase and calcium-dependent protein kinases is discussed. EXPERT OPINION A new and safe chemotherapy is needed, as T. gondii causes serious morbidity and mortality in pregnant women and immunodeficient patients undergoing chemotherapy. A particular drawback of the available treatments is the lack of efficacy against the tissue cyst of the parasite. During this review a broad scope of several attractive targets for drug design have been presented. In this context, the isoprenoid pathway, dihydrofolate reductase, T. gondii histone deacetylase are promising molecular targets.
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Affiliation(s)
- Juan Bautista Rodriguez
- Universidad de Buenos Aires, Química Orgánica & UMYMFOR (CONICET-FCEyN), Facultad de Ciencias Exactas y Naturales, Pab 2, Ciudad Universitaria, Buenos Aires, C1428EHA, Argentina.
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Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus. J Bacteriol 2011; 194:607-16. [PMID: 22101842 DOI: 10.1128/jb.06173-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Carbon catabolite repression (CCR) is a widespread phenomenon in many bacteria that is defined as the repression of catabolic enzyme activities for an unfavorable carbon source by the presence of a preferable carbon source. In Streptomyces, secondary metabolite production often is negatively affected by the carbon source, indicating the involvement of CCR in secondary metabolism. Although the CCR mechanism in Streptomyces still is unclear, glucokinase is presumably a central player in CCR. SgGlkA, a glucokinase from S. griseus, belongs to the ROK family glucokinases, which have two consensus sequence motifs (1 and 2). Here, we report the crystal structures of apo-SgGlkA, SgGlkA in complex with glucose, and SgGlkA in complex with glucose and adenylyl imidodiphosphate (AMPPNP), which are the first structures of an ROK family glucokinase. SgGlkA is divided into a small α/β domain and a large α+β domain, and it forms a dimer-of-dimer tetrameric configuration. SgGlkA binds a β-anomer of glucose between the two domains, and His157 in consensus sequence 1 plays an important role in the glucose-binding mechanism and anomer specificity of SgGlkA. In the structures of SgGlkA, His157 forms an HC3-type zinc finger motif with three cysteine residues in consensus sequence 2 to bind a zinc ion, and it forms two hydrogen bonds with the C1 and C2 hydroxyls of glucose. When the three structures are compared, the structure of SgGlkA is found to be modified by the binding of substrates. The substrate-dependent conformational changes of SgGlkA may be related to the CCR mechanism in Streptomyces.
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di Salvo ML, Contestabile R, Safo MK. Vitamin B6 salvage enzymes: Mechanism, structure and regulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1597-608. [DOI: 10.1016/j.bbapap.2010.12.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
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Yasutake Y, Ota H, Hino E, Sakasegawa SI, Tamura T. Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:945-56. [PMID: 22101821 DOI: 10.1107/s0907444911038777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 09/21/2011] [Indexed: 11/10/2022]
Abstract
The nucleoside kinase (NK) from the mesophilic Gram-negative bacterium Burkholderia thailandensis (BthNK) is a member of the phosphofructokinase B (Pfk-B) family and catalyzes the Mg(2+)- and ATP-dependent phosphorylation of a broad range of nucleosides such as inosine (INO), adenosine (ADO) and mizoribine (MZR). BthNK is currently used in clinical practice to measure serum MZR levels. Here, crystal structures of BthNK in a ligand-free form and in complexes with INO, INO-ADP, MZR-ADP and AMP-Mg(2+)-AMP are described. The typical homodimeric architecture of Pfk-B enzymes was detected in three distinct conformational states: an asymmetric dimer with one subunit in an open conformation and the other in a closed conformation (the ligand-free form), a closed conformation (the binary complex with INO) and a fully closed conformation (the other ternary and quaternary complexes). The previously unreported fully closed structures suggest the possibility that Mg(2+) might directly interact with the β- and γ-phosphates of ATP to maintain neutralization of the negative charge throughout the reaction. The nucleoside-complex structures also showed that the base moiety of the bound nucleoside is partly exposed to the solvent, thereby enabling the recognition of a wide range of nucleoside bases. Gly170 is responsible for the solvent accessibility of the base moiety and is assumed to be a key residue for the broad nucleoside recognition of BthNK. Remarkably, the G170Q mutation increases the specificity of BthNK for ADO. These findings provide insight into the conformational dynamics, catalytic mechanism and nucleoside selectivity of BthNK and related enzymes.
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Affiliation(s)
- Yoshiaki Yasutake
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Sapporo 062-8517, Japan
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Bjursell M, Blom H, Cayuela J, Engvall M, Lesko N, Balasubramaniam S, Brandberg G, Halldin M, Falkenberg M, Jakobs C, Smith D, Struys E, von Döbeln U, Gustafsson C, Lundeberg J, Wedell A. Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function. Am J Hum Genet 2011; 89:507-15. [PMID: 21963049 DOI: 10.1016/j.ajhg.2011.09.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/06/2011] [Accepted: 09/07/2011] [Indexed: 10/17/2022] Open
Abstract
Four inborn errors of metabolism (IEMs) are known to cause hypermethioninemia by directly interfering with the methionine cycle. Hypermethioninemia is occasionally discovered incidentally, but it is often disregarded as an unspecific finding, particularly if liver disease is involved. In many individuals the hypermethioninemia resolves without further deterioration, but it can also represent an early sign of a severe, progressive neurodevelopmental disorder. Further investigation of unclear hypermethioninemia is therefore important. We studied two siblings affected by severe developmental delay and liver dysfunction. Biochemical analysis revealed increased plasma levels of methionine, S-adenosylmethionine (AdoMet), and S-adenosylhomocysteine (AdoHcy) but normal or mildly elevated homocysteine (Hcy) levels, indicating a block in the methionine cycle. We excluded S-adenosylhomocysteine hydrolase (SAHH) deficiency, which causes a similar biochemical phenotype, by using genetic and biochemical techniques and hypothesized that there was a functional block in the SAHH enzyme as a result of a recessive mutation in a different gene. Using exome sequencing, we identified a homozygous c.902C>A (p.Ala301Glu) missense mutation in the adenosine kinase gene (ADK), the function of which fits perfectly with this hypothesis. Increased urinary adenosine excretion confirmed ADK deficiency in the siblings. Four additional individuals from two unrelated families with a similar presentation were identified and shown to have a homozygous c.653A>C (p.Asp218Ala) and c.38G>A (p.Gly13Glu) mutation, respectively, in the same gene. All three missense mutations were deleterious, as shown by activity measurements on recombinant enzymes. ADK deficiency is a previously undescribed, severe IEM shedding light on a functional link between the methionine cycle and adenosine metabolism.
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Merino F, Rivas-Pardo JA, Caniuguir A, García I, Guixé V. Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea. Biochimie 2011; 94:516-24. [PMID: 21906652 DOI: 10.1016/j.biochi.2011.08.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Accepted: 08/29/2011] [Indexed: 10/17/2022]
Abstract
In some archaea, glucose degradation proceeds through a modified version of the Embden-Meyerhof pathway where glucose and fructose-6-P phosphorylation is carried out by kinases that use ADP as the phosphoryl donor. Unlike their ATP-dependent counterparts these enzymes have been reported as non-regulated. Based on the three dimensional structure determination of several ADP-dependent kinases they can be classified as members of the ribokinase superfamily. In this work, we have studied the role of divalent metal cations on the catalysis and regulation of ADP-dependent glucokinases and phosphofructokinase from hyperthermophilic archaea by means of initial velocity assays as well as molecular dynamics simulations. The results show that a divalent cation is strictly necessary for the activity of these enzymes and they strongly suggest that the true substrate is the metal-nucleotide complex. Also, these enzymes are promiscuous in relation to their metal usage where the only considerations for metal assisted catalysis seem to be related to the ionic radii and coordination geometry of the cations. Molecular dynamics simulations strongly suggest that this metal is bound to the highly conserved NXXE motif, which constitutes one of the signatures of the ribokinase superfamily. Although free ADP cannot act as a phosphoryl donor it still can bind to these enzymes with a reduced affinity, stressing the importance of the metal in the proper binding of the nucleotide at the active site. Also, data show that the binding of a second metal to these enzymes produces a complex with a reduced catalytic constant. On the basis of these findings and considering evolutionary information for the ribokinase superfamily, we propose that the regulatory metal acts by modulating the energy difference between the protein-substrates complex and the reaction transition state, which could constitute a general mechanism for the metal regulation of the enzymes that belong this superfamily.
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Affiliation(s)
- Felipe Merino
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
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Physical and functional interaction between d-ribokinase and topoisomerase I has opposite effects on their respective activity in Mycobacterium smegmatis and Mycobacterium tuberculosis. Arch Biochem Biophys 2011; 512:135-42. [DOI: 10.1016/j.abb.2011.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 11/23/2022]
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Circadian rhythms and sleep--the metabolic connection. Pflugers Arch 2011; 463:23-30. [PMID: 21710201 DOI: 10.1007/s00424-011-0986-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 06/07/2011] [Accepted: 06/08/2011] [Indexed: 12/20/2022]
Abstract
The circadian system coordinates mammalian physiology and behavior with the environmental light-dark cycle. It allocates sleep to the inactivity phase using various mechanisms involving neurotransmitters, nuclear receptors, and protein kinases. These pathways are related to metabolism, indicating that the circadian system and sleep are connected via metabolic parameters. This suggests that organs other than the brain may "sleep." A hypothetic view on this aspect is presented providing a different perspective on sleep regulation.
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Kuettel S, Greenwald J, Kostrewa D, Ahmed S, Scapozza L, Perozzo R. Crystal structures of T. b. rhodesiense adenosine kinase complexed with inhibitor and activator: implications for catalysis and hyperactivation. PLoS Negl Trop Dis 2011; 5:e1164. [PMID: 21629723 PMCID: PMC3101181 DOI: 10.1371/journal.pntd.0001164] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 03/15/2011] [Indexed: 12/02/2022] Open
Abstract
Background The essential purine salvage pathway of Trypanosoma brucei bears interesting catalytic enzymes for chemotherapeutic intervention of Human African Trypanosomiasis. Unlike mammalian cells, trypanosomes lack de novo purine synthesis and completely rely on salvage from their hosts. One of the key enzymes is adenosine kinase which catalyzes the phosphorylation of ingested adenosine to form adenosine monophosphate (AMP) utilizing adenosine triphosphate (ATP) as the preferred phosphoryl donor. Methods and Findings Here, we present the first structures of Trypanosoma brucei rhodesiense adenosine kinase (TbrAK): the structure of TbrAK in complex with the bisubstrate inhibitor P1,P5-di(adenosine-5′)-pentaphosphate (AP5A) at 1.55 Å, and TbrAK complexed with the recently discovered activator 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine (compound 1) at 2.8 Å resolution. Conclusions The structural details and their comparison give new insights into substrate and activator binding to TbrAK at the molecular level. Further structure-activity relationship analyses of a series of derivatives of compound 1 support the observed binding mode of the activator and provide a possible mechanism of action with respect to their activating effect towards TbrAK. Recently, we discovered that 4-[5-(4-phenoxyphenyl)-2H-pyrazol-3-yl]morpholine (compound 1) and its derivatives exhibit specific antitrypanosomal activity toward T. b. rhodesiense, the causative agent of the acute form of HAT. We found that compound 1 would target the parasite adenosine kinase (TbrAK), an important enzyme of the purine salvage pathway, by acting via hyperactivation of the enzyme. This represents a novel and hitherto unexplored strategy for the development of trypanocides. These findings prompted us to investigate the mechanism of action at the molecular level. The present study reports the first three-dimensional crystal structures of TbrAK in complex with the bisubstrate inhibitor AP5A, and in complex with the activator (compound 1). The subsequent structural analysis sheds light on substrate and activator binding, and gives insight into the possible mechanism leading to hyperactivation. Further structure-activity relationships in terms of TbrAK activation properties support the observed binding mode of compound 1 in the crystal structure and may open the field for subsequent optimization of this compound series.
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Affiliation(s)
- Sabine Kuettel
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Lausanne, Switzerland
| | - Jason Greenwald
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dirk Kostrewa
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Shaheen Ahmed
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Lausanne, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Lausanne, Switzerland
- * E-mail: (LS); (RP)
| | - Remo Perozzo
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Lausanne, Switzerland
- * E-mail: (LS); (RP)
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Cui XA, Agarwal T, Singh B, Gupta RS. Molecular characterization of Chinese hamster cells mutants affected in adenosine kinase and showing novel genetic and biochemical characteristics. BMC BIOCHEMISTRY 2011; 12:22. [PMID: 21586167 PMCID: PMC3118340 DOI: 10.1186/1471-2091-12-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 05/17/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Two isoforms of the enzyme adenosine kinase (AdK), which differ at their N-terminal ends, are found in mammalian cells. However, there is no information available regarding the unique functional aspects or regulation of these isoforms. RESULTS We show that the two AdK isoforms differ only in their first exons and the promoter regions; hence they arise via differential splicing of their first exons with the other exons common to both isoforms. The expression of these isoforms also varied greatly in different rat tissues and cell lines with some tissues expressing both isoforms and others expressing only one of the isoforms. To gain insights into cellular functions of these isoforms, mutants resistant to toxic adenosine analogs formycin A and tubercidin were selected from Chinese hamster (CH) cell lines expressing either one or both isoforms. The AdK activity in most of these mutants was reduced to <5% of wild-type cells and they also showed large differences in the expression of the two isoforms. Thus, the genetic alterations in these mutants likely affected both regulatory and structural regions of AdK. We have characterized the molecular alterations in a number of these mutants. One of these mutants lacking AdK activity was affected in the conserved NxxE motif thereby providing evidence that this motif involved in the binding of Mg2+ and phosphate ions is essential for AdK function. Another mutant, FomR-4, exhibiting increased resistance to only C-adenosine analogs and whose resistance was expressed dominantly in cell-hybrids contained a single mutation leading to Ser191Phe alteration in AdK. We demonstrate that this mutation in AdK is sufficient to confer the novel genetic and biochemical characteristics of this mutant. The unusual genetic and biochemical characteristics of the FomR-4 mutant suggest that AdK in this mutant might be complexed with the enzyme AMP-kinase. Several other AdK mutants were altered in surface residues that likely affect its binding to the adenosine analogs and its interaction with other cellular proteins. CONCLUSIONS These AdK mutants provide important insights as well as novel tools for understanding the cellular functions of the two isoforms and their regulation in mammalian cells.
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Affiliation(s)
- Xianying A Cui
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Canada.
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