1
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Pepelnjak M, Velten B, Näpflin N, von Rosen T, Palmiero UC, Ko JH, Maynard HD, Arosio P, Weber-Ban E, de Souza N, Huber W, Picotti P. In situ analysis of osmolyte mechanisms of proteome thermal stabilization. Nat Chem Biol 2024; 20:1053-1065. [PMID: 38424171 PMCID: PMC11288892 DOI: 10.1038/s41589-024-01568-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/03/2024] [Indexed: 03/02/2024]
Abstract
Organisms use organic molecules called osmolytes to adapt to environmental conditions. In vitro studies indicate that osmolytes thermally stabilize proteins, but mechanisms are controversial, and systematic studies within the cellular milieu are lacking. We analyzed Escherichia coli and human protein thermal stabilization by osmolytes in situ and across the proteome. Using structural proteomics, we probed osmolyte effects on protein thermal stability, structure and aggregation, revealing common mechanisms but also osmolyte- and protein-specific effects. All tested osmolytes (trimethylamine N-oxide, betaine, glycerol, proline, trehalose and glucose) stabilized many proteins, predominantly via a preferential exclusion mechanism, and caused an upward shift in temperatures at which most proteins aggregated. Thermal profiling of the human proteome provided evidence for intrinsic disorder in situ but also identified potential structure in predicted disordered regions. Our analysis provides mechanistic insight into osmolyte function within a complex biological matrix and sheds light on the in situ prevalence of intrinsically disordered regions.
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Affiliation(s)
- Monika Pepelnjak
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Britta Velten
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Centre for Organismal Studies (COS) & Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Nicolas Näpflin
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tatjana von Rosen
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Jeong Hoon Ko
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Heather D Maynard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute of Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Paola Picotti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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2
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Ferreira JC, Villanueva AJ, Fadl S, Al Adem K, Cinviz ZN, Nedyalkova L, Cardoso THS, Andrade ME, Saksena NK, Sensoy O, Rabeh WM. Residues in the fructose-binding pocket are required for ketohexokinase-A activity. J Biol Chem 2024; 300:107538. [PMID: 38971308 DOI: 10.1016/j.jbc.2024.107538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
Excessive fructose consumption is a primary contributor to the global surges in obesity, cancer, and metabolic syndrome. Fructolysis is not robustly regulated and is initiated by ketohexokinase (KHK). In this study, we determined the crystal structure of KHK-A, one of two human isozymes of KHK, in the apo-state at 1.85 Å resolution, and we investigated the roles of residues in the fructose-binding pocket by mutational analysis. Introducing alanine at D15, N42, or N45 inactivated KHK-A, whereas mutating R141 or K174 reduced activity and thermodynamic stability. Kinetic studies revealed that the R141A and K174A mutations reduced fructose affinity by 2- to 4-fold compared to WT KHK-A, without affecting ATP affinity. Molecular dynamics simulations provided mechanistic insights into the potential roles of the mutated residues in ligand coordination and the maintenance of an open state in one monomer and a closed state in the other. Protein-protein interactome analysis indicated distinct expression patterns and downregulation of partner proteins in different tumor tissues, warranting a reevaluation of KHK's role in cancer development and progression. The connections between different cancer genes and the KHK signaling pathway suggest that KHK is a potential target for preventing cancer metastasis. This study enhances our understanding of KHK-A's structure and function and offers valuable insights into potential targets for developing treatments for obesity, cancer, and metabolic syndrome.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kenana Al Adem
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Zeynep Nur Cinviz
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Lyudmila Nedyalkova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Mario Edson Andrade
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, USA
| | - Nitin K Saksena
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Ozge Sensoy
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey; Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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3
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Weeramange C, Menjivar C, O'Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. J Biol Chem 2024; 300:107352. [PMID: 38723750 PMCID: PMC11157272 DOI: 10.1016/j.jbc.2024.107352] [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: 01/23/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/21/2024] Open
Abstract
In Escherichia coli, the master transcription regulator catabolite repressor activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli's central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
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Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Pierce T O'Neil
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Kelly S Harrison
- The Department of Molecular Biosciences, The University of Kansas - Lawrence, Lawrence, Kansas, USA
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cole L Bird
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Aron W Fenton
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - P Scott Hefty
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Jeffrey L Bose
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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4
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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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5
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Shi Y, Pan X, Wu X, Xu J, Xiang W, Zheng Y, Dong F, Wang X. Uptake and Biotransformation of Guvermectin in Three Crops after In Vivo and In Vitro Exposure. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10842-10852. [PMID: 38708761 DOI: 10.1021/acs.jafc.4c01320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Guvermectin, as a novel nucleoside-like biopesticide, could increase the rice yield excellently, but the potential environmental behaviors remain unclear, which pose potential health risks. Therefore, the uptake and biotransformation of guvermectin in three types of crops (rice, lettuce, and carrot) were first evaluated with a hydroponic system. Guvermectin could be rapidly absorbed and reached equilibrium in roots (12-36 h) and shoots (24-60 h) in three plants, and guvermectin was also vulnerable to dissipation in roots (t1/2 1.02-3.65 h) and shoots (t1/2 9.30-17.91 h). In addition, 8 phase I and 2 phase II metabolites, transformed from guvermectin degradation in vivo and in vitro exposure, were identified, and one was confirmed as psicofuranine, which had antibacterial and antitumor properties; other metabolites were nucleoside-like chemicals. Molecular simulation and quantitative polymerase chain reaction further demonstrated that guvermectin was metabolized by the catabolism pathway of an endogenous nucleotide. Guvermectin had similar metabolites in three plants, but the biotransformation ability had a strong species dependence. In addition, all the metabolites exhibit neglectable toxicities (bioconcentration factor <2000 L/kg b.w., LC50,rat > 5000 mg/kg b.w.) by prediction. The study provided valuable evidence for the application of guvermectin and a better understanding of the biological behavior of nucleoside-like pesticides.
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Affiliation(s)
- Yuan Shi
- Key Laboratory of Microbiology, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinglu Pan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wensheng Xiang
- Key Laboratory of Microbiology, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangjing Wang
- Key Laboratory of Microbiology, Northeast Agricultural University, Harbin 150030, China
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6
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Weeramange C, Menjivar C, O’Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571569. [PMID: 38168282 PMCID: PMC10760178 DOI: 10.1101/2023.12.14.571569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In Escherichia coli, the master transcription regulator Catabolite Repressor Activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. The ΔfruK strain also alters biofilm formation. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
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Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, 3901 Rainbow Blvd, MSN 3029, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Pierce T. O’Neil
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Samir El Qaidi
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Kelly S. Harrison
- The Department of Molecular Biosciences, 2034 Haworth Hall, 1200 Sunnyside Avenue, The University of Kansas – Lawrence, Lawrence, Kansas, USA 66045
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Cole L. Bird
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Philip R. Hardwidge
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Aron W. Fenton
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - P. Scott Hefty
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Jeffrey L. Bose
- The Department of Microbiology, Molecular Genetics and Immunology, 3901 Rainbow Blvd, MSN 3029, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
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7
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Zayats EA, Fateev IV, Kostromina MA, Abramchik YA, Lykoshin DD, Yurovskaya DO, Timofeev VI, Berzina MY, Eletskaya BZ, Konstantinova ID, Esipov RS. Rational Mutagenesis in the Lid Domain of Ribokinase from E. coli Results in an Order of Magnitude Increase in Activity towards D-arabinose. Int J Mol Sci 2022; 23:ijms232012540. [PMID: 36293391 PMCID: PMC9604405 DOI: 10.3390/ijms232012540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/12/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Development of efficient approaches for the production of medically important nucleosides is a highly relevant challenge for biotechnology. In particular, cascade synthesis of arabinosides would allow relatively easy production of various cytostatic and antiviral drugs. However, the biocatalyst necessary for this approach, ribokinase from Escherichia coli (EcoRK), has a very low activity towards D-arabinose, making the synthesis using the state-of-art native enzyme technologically unfeasible. Here, we report the results of our enzyme design project, dedicated to engineering a mutant form of EcoRK with elevated activity towards arabinose. Analysis of the active site structure has allowed us to hypothesize the reasons behind the low EcoRK activity towards arabinose and select feasible mutations. Enzyme assay and kinetic studies have shown that the A98G mutation has caused a large 15-fold increase in kcat and 1.5-fold decrease in KM for arabinose phosphorylation. As a proof of concept, we have performed the cascade synthesis of 2-chloroadenine arabinoside utilizing the A98G mutant with 10-fold lower amount of enzyme compared to the wild type without any loss of synthesis efficiency. Our results are valuable both for the development of new technologies of synthesis of modified nucleosides and providing insight into the structural reasons behind EcoRK substrate specificity.
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8
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Kim SH, Kim M, Park D, Byun S, Rhee S. Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI. J Biol Chem 2022; 298:101869. [PMID: 35346685 PMCID: PMC9061257 DOI: 10.1016/j.jbc.2022.101869] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/24/2022] Open
Abstract
Pseudouridine, one major RNA modification, is catabolized into uracil and ribose-5′-phosphate by two sequential enzymatic reactions. In the first step, pseudouridine kinase (PUKI) phosphorylates pseudouridine to pseudouridine 5′-monophosphate. High-fidelity catalysis of pseudouridine by PUKI prevents possible disturbance of in vivo pyrimidine homeostasis. However, the molecular basis of how PUKI selectively phosphorylates pseudouridine over uridine with >100-fold greater efficiency despite minor differences in their Km values has not been elucidated. To investigate this selectivity, in this study we determined the structures of PUKI from Escherichia coli strain B (EcPUKI) in various ligation states. The structure of EcPUKI was determined to be similar to PUKI from Arabidopsis thaliana, including an α/β core domain and β-stranded small domain, with dimerization occurring via the β-stranded small domain. In a binary complex, we show that Ser30 in the substrate-binding loop of the small domain mediates interactions with the hallmark N1 atom of pseudouridine nucleobase, causing conformational changes in its quaternary structure. Kinetic and fluorescence spectroscopic analyses also showed that the Ser30-mediated interaction is a prerequisite for conformational changes and subsequent catalysis by EcPUKI. Furthermore, S30A mutation or EcPUKI complexed with other nucleosides homologous to pseudouridine but lacking the pseudouridine-specific N1 atom did not induce such conformational changes, demonstrating the catalytic significance of the proposed Ser30-mediated interaction. These analyses provide structural and functional evidence for a pseudouridine-dependent conformational change of EcPUKI and its functional linkage to catalysis.
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Affiliation(s)
- Sang-Hoon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Minjeong Kim
- Department of Molecular Science & Technology, Ajou University, Suwon, Korea
| | - Daechan Park
- Department of Molecular Science & Technology, Ajou University, Suwon, Korea; Department of Biological Sciences, Ajou University, Suwon, Korea
| | - Sujeong Byun
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
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9
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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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10
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Sharma M, Abayakoon P, Epa R, Jin Y, Lingford JP, Shimada T, Nakano M, Mui JWY, Ishihama A, Goddard-Borger ED, Davies GJ, Williams SJ. Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. ACS CENTRAL SCIENCE 2021; 7:476-487. [PMID: 33791429 PMCID: PMC8006165 DOI: 10.1021/acscentsci.0c01285] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 06/12/2023]
Abstract
The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on Earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolizes SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase, and sulfofructose-1-phosphate (SFP) aldolase. Our data show that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by three-dimensional structures of each enzyme, which reveal the presence of conserved sulfonate binding pockets. We show that SQ isomerase acts preferentially on the β-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a derepressor for the transcriptional repressor CsqR that regulates SQ-utilization. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex modulation by the metabolites SQ, SLA, AMP, ADP, ATP, F6P, FBP, PEP, DHAP, and citrate, and we show that SFP aldolase reversibly synthesizes SFP. This body of work provides fresh insights into the mechanism, specificity, and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.
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Affiliation(s)
- Mahima Sharma
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Palika Abayakoon
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ruwan Epa
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yi Jin
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - James P. Lingford
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tomohiro Shimada
- School
of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Masahiro Nakano
- Institute
for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Janice W.-Y. Mui
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
| | - Akira Ishihama
- Micro-Nano
Technology Research Center, Hosei University, Koganei, Tokyo, Japan
| | - Ethan D. Goddard-Borger
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
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11
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Kim SH, Witte CP, Rhee S. Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana. Nucleic Acids Res 2021; 49:491-503. [PMID: 33290549 PMCID: PMC7797080 DOI: 10.1093/nar/gkaa1144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022] Open
Abstract
RNA modifications can regulate the stability of RNAs, mRNA-protein interactions, and translation efficiency. Pseudouridine is a prevalent RNA modification, and its metabolic fate after RNA turnover was recently characterized in eukaryotes, in the plant Arabidopsis thaliana. Here, we present structural and biochemical analyses of PSEUDOURIDINE KINASE from Arabidopsis (AtPUKI), the enzyme catalyzing the first step in pseudouridine degradation. AtPUKI, a member of the PfkB family of carbohydrate kinases, is a homodimeric α/β protein with a protruding small β-strand domain, which serves simultaneously as dimerization interface and dynamic substrate specificity determinant. AtPUKI has a unique nucleoside binding site specifying the binding of pseudourine, in particular at the nucleobase, by multiple hydrophilic interactions, of which one is mediated by a loop from the small β-strand domain of the adjacent monomer. Conformational transition of the dimerized small β-strand domains containing active site residues is required for substrate specificity. These dynamic features explain the higher catalytic efficiency for pseudouridine over uridine. Both substrates bind well (similar Km), but only pseudouridine is turned over efficiently. Our studies provide an example for structural and functional divergence in the PfkB family and highlight how AtPUKI avoids futile uridine phosphorylation which in vivo would disturb pyrimidine homeostasis.
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Affiliation(s)
- Sang-Hoon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz University Hannover, Hannover, Germany
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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12
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Di Cera E. Mechanisms of ligand binding. BIOPHYSICS REVIEWS 2020; 1:011303. [PMID: 33313600 PMCID: PMC7714259 DOI: 10.1063/5.0020997] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022]
Abstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
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Affiliation(s)
- Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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13
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Smith A, Page BDG, Collier AC, Coughtrie MWH. Homology Modeling of Human Uridine-5'-diphosphate-glucuronosyltransferase 1A6 Reveals Insights into Factors Influencing Substrate and Cosubstrate Binding. ACS OMEGA 2020; 5:6872-6887. [PMID: 32258923 PMCID: PMC7114752 DOI: 10.1021/acsomega.0c00205] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/11/2020] [Indexed: 05/05/2023]
Abstract
The elimination of numerous endogenous compounds and xenobiotics via glucuronidation by uridine-5'-diphosphate glycosyltransferase enzymes (UGTs) is an essential process of the body's chemical defense system. UGTs have distinct but overlapping substrate preferences, but the molecular basis for their substrate specificity remains poorly understood. Three-dimensional protein structures can greatly enhance our understanding of the interactions between enzymes and their substrates, but because of the inherent difficulties in purifying and crystallizing integral endoplasmic reticulum membrane proteins, no complete mammalian UGT structure has yet been produced. To address this problem, we have created a homology model of UGT1A6 using I-TASSER to explore, in detail, the interactions of human UGT1A6 with its substrates. Ligands were docked into our model in the presence of the cosubstrate uridine-5'-diphosphate-glucuronic acid, interacting residues were examined, and poses were compared to those cocrystallized with various plant and bacterial glycosyltransferases (GTs). Our model structurally resembles other GTs, and docking experiments replicated many of the expected UGT-substrate interactions. Some bias toward the template structures' protein-substrate interactions and binding preferences was evident.
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14
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Khandokar Y, Srivastava P, Raidal S, Sarker S, Forwood JK. Structural basis for disulphide-CoA inhibition of a butyryl-CoA hexameric thioesterase. J Struct Biol 2020; 210:107477. [PMID: 32027968 DOI: 10.1016/j.jsb.2020.107477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 10/25/2022]
Abstract
Acyl-coenzyme A thioesterases (ACTs) catalyse the hydrolysis of thioester bonds between fatty-acyl chains and coenzyme A (CoA), producing a free fatty-acyl chain and CoA. These enzymes are expressed ubiquitously across prokaryotes and eukaryotes, and play important roles in lipid metabolism. There are 25 thioesterase families, subdivided based on their active site configuration, protein oligomerization, and substrate specificity. Understanding the mechanism of regulation within these families is important due to their roles in controlling the cell concentration of a range of fatty acids and CoA-bound compounds. Here we report a structural basis for a novel mode of inhibition of an ACT from Staphylococcus aureus. The enzyme displays a hotdog fold composed of five β-strands wrapping around a central α-helix, and an additional 30 residue α-helix located at its C-terminus. We show that the enzyme is a hexamer and has specificity towards butyryl-CoA. Structural analysis revealed putative catalytic residues, and we show through site directed mutagenesis that Asn28, Asp43, and Thr60 are critical for activity. Additionally, we show that the Asn28Ala destabilises the enzyme oligomeric state into two distinct populations. Co-crystallization of the enzyme with the substrate butyryl-CoA produced a crystal with three CoA ligands bound in the enzyme active sites: CoA, butyryl-CoA, and disulphide-CoA, the latter of which inhibits enzyme activity. Our study provides new insights into the structure and specificity of hexameric thioesterases, inhibitory feedback mechanisms, and possible biotechnological applications in short-chain fatty acid production such as biofuels, pharmaceuticals, and industrial compounds.
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Affiliation(s)
- Yogesh Khandokar
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3052 Australia; School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Parul Srivastava
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Shane Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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15
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Gatreddi S, Pillalamarri V, Vasudevan D, Addlagatta A, Qureshi IA. Unraveling structural insights of ribokinase from Leishmania donovani. Int J Biol Macromol 2019; 136:253-265. [PMID: 31170491 DOI: 10.1016/j.ijbiomac.2019.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/29/2019] [Accepted: 06/01/2019] [Indexed: 11/16/2022]
Abstract
Ribokinase (RK) is an ATP dependent sugar kinase that enables the entry of ribose in the metabolism. Leishmania accumulates ribose into the cytosol through hydrolysis of nucleosides and by transport from the extracellular environment. Activation by RK is critical to mobilize the ribose into the metabolism of Leishmania. To understand the catalytic role, the crystal structure of RK (LdRK) from L. donovani was determined in the apo and complex forms with several nucleotides (ATP, AMPPCP and ADP) in the presence of Na+ ion. The dual insertion of five amino acid stretches makes LdRK structurally unique from other reported structures of RKs. The structure of LdRK-ATP provided the basis for positioning of γ-phosphate of ATP by conserved -GAGD- motif. Liganded and unliganded structures of LdRK exists in similar conformation, which suggests binding of nucleotides does not make any significant conformational changes in nucleotide-bound structures. Substitution of a conserved asparagine with phenylalanine in ribose binding pocket differentiates the LdRK from other RKs. Glycerol molecule bound in the substrate binding pocket mimics the enzyme-substrate interactions but in turn, hampers the binding of ribose to LdRK. Comparative structural analysis revealed the flexibility of γ-phosphate, which adopts multiple conformations in the absence of divalent metal ion and ribose. Similar to other RKs, LdRK is also dependent on monovalent as well as divalent cations for its catalytic activity.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, Telangana, India
| | - Vijaykumar Pillalamarri
- CSIR-Indian Institute of Chemical Technology, Applied Biology, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | | | - Anthony Addlagatta
- CSIR-Indian Institute of Chemical Technology, Applied Biology, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, 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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16
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Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM. Enzyme promiscuity shapes adaptation to novel growth substrates. Mol Syst Biol 2019; 15:e8462. [PMID: 30962359 PMCID: PMC6452873 DOI: 10.15252/msb.20188462] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Evidence suggests that novel enzyme functions evolved from low‐level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems‐level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non‐native substrates in Escherichia coli K‐12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non‐native substrates—D‐lyxose, D‐2‐deoxyribose, D‐arabinose, m‐tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high‐efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome‐scale model simulations of metabolism with enzyme promiscuity.
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Affiliation(s)
- Gabriela I Guzmán
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ryan A LaCroix
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Henrietta Papp
- Virological Research Group, Szentágothai Research Centre University of Pécs, Pécs, Hungary
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Zachary A King
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Richard A Notebaart
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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17
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Kang PA, Oh J, Lee H, Witte CP, Rhee S. Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana. J Struct Biol 2019; 206:110-118. [PMID: 30822455 DOI: 10.1016/j.jsb.2019.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/07/2019] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
Abstract
Nitrogen remobilization is a key issue in plants. Recent studies in Arabidopsis thaliana have revealed that nucleoside catabolism supplies xanthine, a nitrogen-rich compound, to the purine ring catabolic pathway, which liberates ammonia from xanthine for reassimilation into amino acids. Similarly, pyrimidine nuclosides are degraded and the pyrimidine bases are fully catabolized. During nucleoside hydrolysis, ribose is released, and ATP-dependent ribokinase (RBSK) phosphorylates ribose to ribose-5'-phosphate to allow its entry into central metabolism recycling the sugar carbons from nucleosides. In this study, we report the crystal structure of RBSK from Arapidopsis thaliana (AtRBSK) in three different ligation states: an unliganded state, a ternary complex with ribose and ATP, and a binary complex with ATP in the presence of Mg2+. In the monomeric conformation, AtRBSK is highly homologous to bacterial RBSKs, including the binding sites for a monovalent cation, ribose, and ATP. Its dimeric conformation, however, does not exhibit the noticeable ligand-induced changes that were observed in bacterial orthologs. Only in the presence of Mg2+, ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg2+ in AtRBSK activity. The structural data combined with activity analyses of mutants allowed assignment of functional roles for the active site residues. Overall, this study provides the first structural characterization of plant RBSK, and experimentally validates a previous hypothetical model concerning the general reaction mechanism of RBSK.
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Affiliation(s)
- Pyeoung-Ann Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Juntaek Oh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Haehee Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Claus-Peter Witte
- Molecular Nutrition and Biochemistry of Plants, Leibniz University Hannover, Hannover, Germany
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
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18
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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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19
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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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20
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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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21
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McCluskey K, Carlos Penedo J. An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters. Phys Chem Chem Phys 2018; 19:6921-6932. [PMID: 28225108 DOI: 10.1039/c6cp08798a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Riboswitches are short RNA motifs that sensitively and selectively bind cognate ligands to modulate gene expression. Like protein receptor-ligand pairs, their binding dynamics are traditionally categorized as following one of two paradigmatic mechanisms: conformational selection and induced fit. In conformational selection, ligand binding stabilizes a particular state already present in the receptor's dynamic ensemble. In induced fit, ligand-receptor interactions enable the system to overcome the energetic barrier into a previously inaccessible state. In this article, we question whether a polarized division of RNA binding mechanisms truly meets the conceptual needs of the field. We will review the history behind this classification of RNA-ligand interactions, and the way induced fit in particular has been rehabilitated by single-molecule studies of RNA aptamers. We will highlight several recent results from single-molecule experimental studies of riboswitches that reveal gaps or even contradictions between common definitions of the two terms, and we will conclude by proposing a more robust framework that considers the range of RNA behaviors unveiled in recent years as a reality to be described, rather than an increasingly unwieldy set of exceptions to the traditional models.
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Affiliation(s)
- K McCluskey
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK.
| | - J Carlos Penedo
- Department of Physics and Astronomy, University of St. Andrews, St. Andrews, KY16 9SS, UK. and Biomolecular Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9SS, UK.
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22
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Gatreddi S, Are S, Qureshi IA. Ribokinase from Leishmania donovani: purification, characterization and X-ray crystallographic analysis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2018; 74:99-104. [PMID: 29400319 DOI: 10.1107/s2053230x18000109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/02/2018] [Indexed: 11/11/2022]
Abstract
Leishmania is an auxotrophic protozoan parasite which acquires D-ribose by transporting it from the host cell and also by the hydrolysis of nucleosides. The enzyme ribokinase (RK) catalyzes the first step of ribose metabolism by phosphorylating D-ribose using ATP to produce D-ribose-5-phosphate. To understand its structure and function, the gene encoding RK from L. donovani was cloned, expressed and purified using affinity and size-exclusion chromatography. Circular-dichroism spectroscopy of the purified protein showed comparatively more α-helix in the secondary-structure content, and thermal unfolding revealed the Tm to be 317.2 K. Kinetic parameters were obtained by functional characterization of L. donovani RK, and the Km values for ribose and ATP were found to be 296 ± 36 and 116 ± 9.0 µM, respectively. Crystals obtained by the hanging-drop vapour-diffusion method diffracted to 1.95 Å resolution and belonged to the hexagonal space group P61, with unit-cell parameters a = b = 100.25, c = 126.77 Å. Analysis of the crystal content indicated the presence of two protomers in the asymmetric unit, with a Matthews coefficient (VM) of 2.45 Å3 Da-1 and 49.8% solvent content. Further study revealed that human counterpart of this protein could be used as a template to determine the first three-dimensional structure of the RK from trypanosomatid parasites.
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Affiliation(s)
- Santhosh Gatreddi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Professor C. R. Rao Road, Hyderabad 500 046, India
| | - Sayanna Are
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Professor C. R. Rao Road, Hyderabad 500 046, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Professor C. R. Rao Road, Hyderabad 500 046, India
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23
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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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24
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Balogun EO, Inaoka DK, Shiba T, Tokuoka SM, Tokumasu F, Sakamoto K, Kido Y, Michels PAM, Watanabe YI, Harada S, Kita K. Glycerol kinase of African trypanosomes possesses an intrinsic phosphatase activity. Biochim Biophys Acta Gen Subj 2017; 1861:2830-2842. [PMID: 28778484 DOI: 10.1016/j.bbagen.2017.07.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/28/2017] [Accepted: 07/29/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND In general, glycerol kinases (GKs) are transferases that catalyze phospho group transfer from ATP to glycerol, and the mechanism was suggested to be random bi-bi. The reverse reaction i.e. phospho transfer from glycerol 3-phosphate (G3P) to ADP is only physiologically feasible by the African trypanosome GK. In contrast to other GKs the mechanism of Trypanosoma brucei gambiense glycerol kinase (TbgGK) was shown to be in an ordered fashion, and proceeding via autophosphorylation. From the unique reaction mechanism of TbgGK, we envisaged its potential to possess phosphatase activity in addition to being a kinase. METHODS Our hypothesis was tested by spectrophotometric and LC-MS/MS analyses using paranitrophenyl phosphate (pNPP) and TbgGK's natural substrate, G3P respectively. Furthermore, protein X-ray crystallography and site-directed mutagenesis were performed to examine pNPP binding, catalytic residues, and the possible reaction mechanism. RESULTS In addition to its widely known and expected phosphotransferase (class II) activity, TbgGK can efficiently facilitate the hydrolytic cleavage of phosphoric anhydride bonds (a class III property). This phosphatase activity followed the classical Michaelis-Menten pattern and was competitively inhibited by ADP and G3P, suggesting a common catalytic site for both activities (phosphatase and kinase). The structure of the TGK-pNPP complex, and structure-guided mutagenesis implicated T276 to be important for the catalysis. Remarkably, we captured a crystallographic molecular snapshot of the phosphorylated T276 reaction intermediate. CONCLUSION We conclude that TbgGK has both kinase and phosphatase activities. GENERAL SIGNIFICANCE This is the first report on a bifunctional kinase/phosphatase enzyme among members of the sugar kinase family.
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Affiliation(s)
- Emmanuel Oluwadare Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria 2222, Nigeria.
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; School of Tropical Medicine and Global Health, Nagasaki University 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Suzumi M Tokuoka
- Department of Lipidomics, Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan
| | - Fuyuki Tokumasu
- Department of Lipidomics, Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan
| | - Kimitoshi Sakamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Yasutoshi Kido
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; School of Tropical Medicine and Global Health, Nagasaki University 1-12-4, Sakamoto, Nagasaki 852-8523, Japan.
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25
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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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26
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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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27
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Crystal structure of apo and ligand bound vibrio cholerae ribokinase (Vc-RK): role of monovalent cation induced activation and structural flexibility in sugar phosphorylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 842:293-307. [PMID: 25408351 DOI: 10.1007/978-3-319-11280-0_19] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Rivas-Pardo JA, Alegre-Cebollada J, Ramírez-Sarmiento CA, Fernandez JM, Guixé V. Identifying sequential substrate binding at the single-molecule level by enzyme mechanical stabilization. ACS NANO 2015; 9:3996-4005. [PMID: 25840594 PMCID: PMC4467879 DOI: 10.1021/nn507480v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Enzyme-substrate binding is a dynamic process intimately coupled to protein structural changes, which in turn changes the unfolding energy landscape. By the use of single-molecule force spectroscopy (SMFS), we characterize the open-to-closed conformational transition experienced by the hyperthermophilic adenine diphosphate (ADP)-dependent glucokinase from Thermococcus litoralis triggered by the sequential binding of substrates. In the absence of substrates, the mechanical unfolding of TlGK shows an intermediate 1, which is stabilized in the presence of Mg·ADP(-), the first substrate to bind to the enzyme. However, in the presence of this substrate, an additional unfolding event is observed, intermediate 1*. Finally, in the presence of both substrates, the unfolding force of intermediates 1 and 1* increases as a consequence of the domain closure. These results show that SMFS can be used as a powerful experimental tool to investigate binding mechanisms of different enzymes with more than one ligand, expanding the repertoire of protocols traditionally used in enzymology.
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Affiliation(s)
- Jaime Andrés Rivas-Pardo
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Jorge Alegre-Cebollada
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
| | - César A. Ramírez-Sarmiento
- Laboratorio de Bioquímica y Biología Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Julio M. Fernandez
- Department of Biological Sciences, Columbia University, Northwest Corner Building, 550 West 120 Street, New York, New York 10027, USA
| | - Victoria Guixé
- 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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29
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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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30
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Vogt AD, Pozzi N, Chen Z, Di Cera E. Essential role of conformational selection in ligand binding. Biophys Chem 2013; 186:13-21. [PMID: 24113284 DOI: 10.1016/j.bpc.2013.09.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 11/26/2022]
Abstract
Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and only sufficient in a few cases. Therefore, the long assumed importance and preponderance of induced fit as a mechanism of ligand binding should be reconsidered.
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Affiliation(s)
- Austin D Vogt
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Zhiwei Chen
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States.
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31
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Vogt AD, Di Cera E. Conformational selection is a dominant mechanism of ligand binding. Biochemistry 2013; 52:5723-9. [PMID: 23947609 DOI: 10.1021/bi400929b] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular recognition in biological macromolecules is achieved by binding interactions coupled to conformational transitions that precede or follow the binding step, two limiting mechanisms known as conformational selection and induced fit, respectively. Sorting out the contribution of these mechanisms to any binding interaction remains a challenging task of general interest in biochemistry. Here we show that conformational selection is associated with a vast repertoire of kinetic behaviors, can never be disproved a priori as a mechanism of ligand binding, and is sufficient to explain the relaxation kinetics documented experimentally for a large number of systems. On the other hand, induced fit features a narrow spectrum of kinetic behaviors and can be disproved in many cases in which conformational selection offers the only possible explanation. This conclusion offers a paradigm shift in the analysis of relaxation kinetics, with conformational selection acquiring preeminence as a mechanism of ligand binding. The dominant role of conformational selection supports the emerging structural view of the macromolecule as a conformational ensemble from which the ligand selects the initial optimal fit to produce a biological response.
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Affiliation(s)
- Austin D Vogt
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Missouri 63104, United States
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32
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Rivas-Pardo JA, Herrera-Morande A, Castro-Fernandez V, Fernandez FJ, Vega MC, Guixé V. Crystal structure, SAXS and kinetic mechanism of hyperthermophilic ADP-dependent glucokinase from Thermococcus litoralis reveal a conserved mechanism for catalysis. PLoS One 2013; 8:e66687. [PMID: 23818958 PMCID: PMC3688580 DOI: 10.1371/journal.pone.0066687] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/10/2013] [Indexed: 11/18/2022] Open
Abstract
ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions associated with ligand binding and whether they are meaningful to the function of the enzyme. We used the ADP-dependent glucokinase from Thermococcus litoralis as a model to investigate the conformational changes observed in X-ray crystallographic structures upon substrate binding and to compare them with those determined in solution in order to understand their interplay with the glucokinase function. Initial velocity studies indicate that catalysis follows a sequential ordered mechanism that correlates with the structural transitions experienced by the enzyme in solution and in the crystal state. The combined data allowed us to resolve the open-closed conformational transition that accounts for the complete reaction cycle and to identify the corresponding clusters of aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across the ADP-dependent kinase family.
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Affiliation(s)
| | - Alejandra Herrera-Morande
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, España
| | | | | | | | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Kori LD, Hofmann A, Patel BKC. Expression, purification, crystallization and preliminary X-ray diffraction analysis of a ribokinase from the thermohalophile Halothermothrix orenii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:240-3. [PMID: 22298009 PMCID: PMC3274413 DOI: 10.1107/s1744309111041091] [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: 09/09/2011] [Accepted: 10/05/2011] [Indexed: 11/10/2022]
Abstract
A ribokinase gene (rbk) from the anaerobic halothermophilic bacterium Halothermothrix orenii was cloned and overexpressed in Escherichia coli. The recombinant protein (Ho-Rbk) was purified using immobilized metal-ion affinity chromatography and crystals were obtained using the sitting-drop method. Diffraction data were collected to a resolution of 3.1 Å using synchrotron radiation. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 45.6, b = 61.1, c = 220.2, and contained two molecules per asymmetric unit. A molecular-replacement solution has been found and attempts are currently under way to build a model of the ribokinase. Efforts to improve crystal quality so that higher resolution data can be obtained are also being considered.
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Affiliation(s)
- Lokesh D. Kori
- Microbial Gene Research and Resources Facility, School of Biomolecular and Physical Sciences, Griffith University, Brisbane, QLD 4111, Australia
| | - Andreas Hofmann
- Structural Chemistry, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Don Young Road, Brisbane Innovation Park, Nathan, Brisbane, QLD 4111, Australia
- Faculty of Veterinary Sciences, University of Melbourne, Werribee, VIC 3030, Australia
| | - Bharat K. C. Patel
- Microbial Gene Research and Resources Facility, School of Biomolecular and Physical Sciences, Griffith University, Brisbane, QLD 4111, Australia
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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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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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36
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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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37
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Guixé V, Merino F. The ADP-dependent sugar kinase family: kinetic and evolutionary aspects. IUBMB Life 2009; 61:753-61. [PMID: 19548321 DOI: 10.1002/iub.217] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Some archaea of the Euryarchaeota present a unique version of the Embden-Meyerhof pathway where glucose and fructose-6-phosphate are phoshporylated using ADP instead of ATP as the phosphoryl donor. These are the only ADP-dependent kinases known to date. Although initially they were believed to represent a new protein family, they can be classified as members of the ribokinase superfamily, which also include several ATP-dependent kinases. As they were first identified in members of the thermococcales it was proposed that the presence of these ADP-dependent kinases is an adaptation to high temperatures. Later, homologs of these enzymes were identified in the genomes of mesophilic and thermophilic methanogenic archaea and even in the genomes of higher eukaryotes, suggesting that the presence of these proteins is not related to the hyperthermophilic life. The ADP-dependent kinases are very restrictive to their ligands being unable to use triphosphorylated nucleotides such as ATP. However, it has been shown that they can bind ATP by competition kinetic experiments. The hyperthermophilic methanogenic archaeon Methanocaldococcus jannaschii has a homolog of these genes, which can phosphorylate glucose and fructose-6-phosphate. For this reason, it was proposed as an ancestral form for the family. However, recent studies have shown that the ancestral activity in the group is glucokinase, and a combination of gene duplication and lateral gene transfer could have originated the two paralogs in this member of the Euryarchaeota. Interestingly, based on structural comparisons made within the superfamily it has been suggested that the ADP-dependent kinases are the newest in the group. In several members of the superfamily, the presence of divalent metal cations has been shown to be crucial for catalysis, so its role in the ADP-dependent family was investigated through molecular dynamics. The simulation shows that, in fact, the metal coordinates the catalytic ensemble and interacts with crucial residues for catalysis.
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Affiliation(s)
- Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile.
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Trinh CH, Asipu A, Bonthron DT, Phillips SEV. Structures of alternatively spliced isoforms of human ketohexokinase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:201-11. [PMID: 19237742 PMCID: PMC2651755 DOI: 10.1107/s0907444908041115] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/05/2008] [Indexed: 11/10/2022]
Abstract
A molecular understanding of the unique aspects of dietary fructose metabolism may be the key to understanding and controlling the current epidemic of fructose-related obesity, diabetes and related adverse metabolic states in Western populations. Fructose catabolism is initiated by its phosphorylation to fructose 1-phosphate, which is performed by ketohexokinase (KHK). Here, the crystal structures of the two alternatively spliced isoforms of human ketohexokinase, hepatic KHK-C and the peripheral isoform KHK-A, and of the ternary complex of KHK-A with the substrate fructose and AMP-PNP are reported. The structure of the KHK-A ternary complex revealed an active site with both the substrate fructose and the ATP analogue in positions ready for phosphorylation following a reaction mechanism similar to that of the pfkB family of carbohydrate kinases. Hepatic KHK deficiency causes the benign disorder essential fructosuria. The effects of the disease-causing mutations (Gly40Arg and Ala43Thr) have been modelled in the context of the KHK structure.
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Affiliation(s)
- Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, England
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Ota H, Sakasegawa SI, Yasuda Y, Imamura S, Tamura T. A novel nucleoside kinase from Burkholderia thailandensis: a member of the phosphofructokinase B-type family of enzymes. FEBS J 2009; 275:5865-72. [PMID: 19021762 DOI: 10.1111/j.1742-4658.2008.06716.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genome of the mesophilic Gram-negative bacterium Burkholderia thailandensis contains an open reading frame (i.e. the Bth_I1158 gene) that has been annotated as a putative ribokinase and PFK-B family member. Notably, although the deduced amino acid sequence of the gene showed only 29% similarity to the recently identified nucleoside kinase from hyperthermophilic archaea Methanocaldococcus jannaschii, 15 of 17 residues reportedly involved in the catalytic activity of M. jannaschii nucleoside kinase were conserved. The gene was cloned and functionally overexpressed in Rhodococcus erythropolis, and the purified enzyme was characterized biochemically. The substrate specificity of the enzyme was unusually broad for a bacterial PFK-B protein, and the specificity extended not only to purine and purine-analog nucleosides but also to uridine. Inosine was the most effective phosphoryl acceptor, with the highest k(cat)/K(m) value (80 s(-1).mm(-1)) being achieved when ATP served as the phosphoryl donor. By contrast, this enzyme exhibited no activity toward ribose, indicating that the recombinant enzyme was a nucleoside kinase rather than a ribokinase. To our knowledge, this is the first detailed analysis of a bacterial nucleoside kinase in the PFK-B family.
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Affiliation(s)
- Hiroko Ota
- Asahi Kasei Pharma Corporation, Shizuoka, Japan
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Merino F, Guixé V. Specificity evolution of the ADP-dependent sugar kinase family -in silico studies of the glucokinase/phosphofructokinase bifunctional enzyme from Methanocaldococcus jannaschii. FEBS J 2008; 275:4033-44. [DOI: 10.1111/j.1742-4658.2008.06544.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Reddy MCM, Palaninathan SK, Shetty ND, Owen JL, Watson MD, Sacchettini JC. High resolution crystal structures of Mycobacterium tuberculosis adenosine kinase: insights into the mechanism and specificity of this novel prokaryotic enzyme. J Biol Chem 2007; 282:27334-27342. [PMID: 17597075 DOI: 10.1074/jbc.m703290200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adenosine kinase (ADK) catalyzes the phosphorylation of adenosine (Ado) to adenosine monophosphate (AMP). It is part of the purine salvage pathway that has been identified only in eukaryotes, with the single exception of Mycobacterium spp. Whereas it is not clear if Mycobacterium tuberculosis (Mtb) ADK is essential, it has been shown that the enzyme can selectively phosphorylate nucleoside analogs to produce products toxic to the cell. We have determined the crystal structure of Mtb ADK unliganded as well as ligand (Ado) bound at 1.5- and 1.9-A resolution, respectively. The structure of the binary complexes with the inhibitor 2-fluoroadenosine (F-Ado) bound and with the adenosine 5'-(beta,gamma-methylene)triphosphate (AMP-PCP) (non-hydrolyzable ATP analog) bound were also solved at 1.9-A resolution. These four structures indicate that Mtb ADK is a dimer formed by an extended beta sheet. The active site of the unliganded ADK is in an open conformation, and upon Ado binding a lid domain of the protein undergoes a large conformation change to close the active site. In the closed conformation, the lid forms direct interactions with the substrate and residues of the active site. Interestingly, AMP-PCP binding alone was not sufficient to produce the closed state of the enzyme. The binding mode of F-Ado was characterized to illustrate the role of additional non-bonding interactions in Mtb ADK compared with human ADK.
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Affiliation(s)
- Manchi C M Reddy
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843
| | | | - Nishant D Shetty
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843
| | - Joshua L Owen
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843
| | - Misty D Watson
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843
| | - James C Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843.
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Ogbunude POJ, Lamour N, Barrett MP. Molecular cloning, expression and characterization of ribokinase of Leishmania major. Acta Biochim Biophys Sin (Shanghai) 2007; 39:462-6. [PMID: 17558452 DOI: 10.1111/j.1745-7270.2007.00298.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Ribokinase (EC 2.1.7.15) from Leishmania major was cloned, sequenced and overexpressed in Escherichia coli. The gene expressed an active enzyme that had comparable activity to the same enzyme studied in E. coli. It specifically phosphorylated D-ribose. Under defined conditions, the K(m) for the substrates D-ribose and ATP were 0.3+/-0.04 mM and 0.2+/-0.02 mM, respectively. The turnover numbers of the enzyme for the substrates were 10.8 s(-1) and 10.2 s(-1), respectively. The enzyme product ribose 5-phosphate inhibited the phosphorylation of D-ribose with an apparent K(i) of 0.4 mM, which is close to the K(m) (0.3 mM) of D-ribose, suggesting that it might play a role in regulating flux through the enzyme.
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Affiliation(s)
- Patrick O J Ogbunude
- Department of Medical Biochemistry, University of Nigeria, Enugu 1000004, Nigeria.
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Muchmore SW, Smith RA, Stewart AO, Cowart MD, Gomtsyan A, Matulenko MA, Yu H, Severin JM, Bhagwat SS, Lee CH, Kowaluk EA, Jarvis MF, Jakob CL. Crystal Structures of Human Adenosine Kinase Inhibitor Complexes Reveal Two Distinct Binding Modes†. J Med Chem 2006; 49:6726-31. [PMID: 17154503 DOI: 10.1021/jm060189a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenosine kinase (AK) is an enzyme responsible for converting endogenous adenosine (ADO) to adenosine monophosphate (AMP) in an adenosine triphosphate- (ATP-) dependent manner. The structure of AK consists of two domains, the first a large alpha/beta Rossmann-like nucleotide binding domain that forms the ATP binding site, and a smaller mixed alpha/beta domain, which, in combination with the larger domain, forms the ADO binding site and the site of phosphoryl transfer. AK inhibitors have been under investigation as antinociceptive, antiinflammatory, and anticonvulsant as well as antiinfective agents. In this work, we report the structures of AK in complex with two classes of inhibitors: the first, ADO-like, and the second, a novel alkynylpyrimidine series. The two classes of structures, which contain structurally similar substituents, reveal distinct binding modes in which the AK structure accommodates the inhibitor classes by a 30 degrees rotation of the small domain relative to the large domain. This change in binding mode stabilizes an open and a closed intermediate structural state and provide structural insight into the transition required for catalysis. This results in a significant rearrangement of both the protein active site and the orientation of the alkynylpyrimidine ligand when compared to the observed orientation of nucleosidic inhibitors or substrates.
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Affiliation(s)
- Steven W Muchmore
- Structural Biology, R46Y, and Neuroscience Research, R4PM, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA.
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Newman JA, Das SK, Sedelnikova SE, Rice DW. The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parallel emergence of enzyme activity during evolution. J Mol Biol 2006; 363:520-30. [PMID: 16978644 DOI: 10.1016/j.jmb.2006.08.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2006] [Revised: 08/04/2006] [Accepted: 08/07/2006] [Indexed: 11/28/2022]
Abstract
Pyridoxal kinase catalyses the phosphorylation of pyridoxal, pyridoxine and pyridoxamine to their 5' phosphates and plays an important role in the pyridoxal 5' phosphate salvage pathway. The crystal structure of a dimeric pyridoxal kinase from Bacillus subtilis has been solved in complex with ADP to 2.8 A resolution. Analysis of the structure suggests that binding of the nucleotide induces the ordering of two loops, which operate independently to close a flap on the active site. Comparisons with other ribokinase superfamily members reveal that B. subtilis pyridoxal kinase is more closely related in both sequence and structure to the family of HMPP kinases than to other pyridoxal kinases, suggesting that this structure represents the first for a novel family of "HMPP kinase-like" pyridoxal kinases. Moreover this further suggests that this enzyme activity has evolved independently on multiple occasions from within the ribokinase superfamily.
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Affiliation(s)
- Joseph A Newman
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, UK
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45
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Tozzi MG, Camici M, Mascia L, Sgarrella F, Ipata PL. Pentose phosphates in nucleoside interconversion and catabolism. FEBS J 2006; 273:1089-101. [PMID: 16519676 DOI: 10.1111/j.1742-4658.2006.05155.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribose phosphates are either synthesized through the oxidative branch of the pentose phosphate pathway, or are supplied by nucleoside phosphorylases. The two main pentose phosphates, ribose-5-phosphate and ribose-1-phosphate, are readily interconverted by the action of phosphopentomutase. Ribose-5-phosphate is the direct precursor of 5-phosphoribosyl-1-pyrophosphate, for both de novo and 'salvage' synthesis of nucleotides. Phosphorolysis of deoxyribonucleosides is the main source of deoxyribose phosphates, which are interconvertible, through the action of phosphopentomutase. The pentose moiety of all nucleosides can serve as a carbon and energy source. During the past decade, extensive advances have been made in elucidating the pathways by which the pentose phosphates, arising from nucleoside phosphorolysis, are either recycled, without opening of their furanosidic ring, or catabolized as a carbon and energy source. We review herein the experimental knowledge on the molecular mechanisms by which (a) ribose-1-phosphate, produced by purine nucleoside phosphorylase acting catabolically, is either anabolized for pyrimidine salvage and 5-fluorouracil activation, with uridine phosphorylase acting anabolically, or recycled for nucleoside and base interconversion; (b) the nucleosides can be regarded, both in bacteria and in eukaryotic cells, as carriers of sugars, that are made available though the action of nucleoside phosphorylases. In bacteria, catabolism of nucleosides, when suitable carbon and energy sources are not available, is accomplished by a battery of nucleoside transporters and of inducible catabolic enzymes for purine and pyrimidine nucleosides and for pentose phosphates. In eukaryotic cells, the modulation of pentose phosphate production by nucleoside catabolism seems to be affected by developmental and physiological factors on enzyme levels.
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Affiliation(s)
- Maria G Tozzi
- Dipartimento di Biologia, Laboratorio di Biochimica, Pisa, Italy
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Datta R, Das I, Sen B, Chakraborty A, Adak S, Mandal C, Datta A. Mutational analysis of the active-site residues crucial for catalytic activity of adenosine kinase from Leishmania donovani. Biochem J 2006; 387:591-600. [PMID: 15606359 PMCID: PMC1134988 DOI: 10.1042/bj20041733] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Leishmania donovani adenosine kinase (LdAdK) plays a pivotal role in scavenging of purines from the host. Exploiting interspecies homology and structural co-ordinates of the enzyme from other sources, we generated a model of LdAdK that led us to target several amino acid residues (namely Gly-62, Arg-69, Arg-131 and Asp-299). Replacement of Gly-62 with aspartate caused a drastic reduction in catalytic activity, with decreased affinity for either substrate. Asp-299 was found to be catalytically indispensable. Mutation of either Arg-131 or Arg-69 caused a significant reduction in kcat. R69A (Arg-69-->Ala) and R131A mutants exhibited unaltered K(m) for either substrate, whereas ATP K(m) for R69K increased 6-fold. Importance of both of the arginine residues was reaffirmed by the R69K/R131A double mutant, which exhibited approx. 0.5% residual activity with a large increase in ATP K(m). Phenylglyoxal, which inhibits the wild-type enzyme, also inactivated the arginine mutants to different extents. Adenosine protected both of the Arg-69 mutants, but not the R131A variant, from inactivation. Binding experiments revealed that the AMP-binding property of R69K or R69A and D299A mutants remained largely unaltered, but R131A and R69K/R131A mutants lost their AMP binding ability significantly. The G62D mutant did not bind AMP at all. Free energy calculations indicated that Arg-69 and Arg-131 are functionally independent. Thus, apart from the mandatory requirement of flexibility around the diglycyl (Gly-61-Gly-62) motif, our results identified Asp-299 and Arg-131 as key catalytic residues, with the former functioning as the proton abstractor from the 5'-OH of adenosine, while the latter acts as a bidentate electrophile to stabilize the negative charge on the leaving group during the phosphate transfer. Moreover, the positive charge distribution of Arg-69 probably helps in maintaining the flexibility of the alpha-3 helix needed for proper domain movement. These findings provide the first comprehensive biochemical evidence implicating the mechanistic roles of the functionally important residues of this chemotherapeutically exploitable enzyme.
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Affiliation(s)
- Rupak Datta
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Ishita Das
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Banibrata Sen
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Anutosh Chakraborty
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Subrata Adak
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Chhabinath Mandal
- †Division of Drug Design, Development and Molecular Modelling, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
| | - Alok K. Datta
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, India
- To whom correspondence should be addressed (email )
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Datta R, Das I, Sen B, Chakraborty A, Adak S, Mandal C, Datta A. Homology-model-guided site-specific mutagenesis reveals the mechanisms of substrate binding and product-regulation of adenosine kinase from Leishmania donovani. Biochem J 2006; 394:35-42. [PMID: 16271040 PMCID: PMC1386000 DOI: 10.1042/bj20051513] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Despite designating catalytic roles of Asp299 and Arg131 during the transfer of gamma-phosphate from ATP to Ado (adenosine) [R. Datta, Das, Sen, Chakraborty, Adak, Mandal and A. K. Datta (2005) Biochem. J. 387, 591-600], the mechanisms that determine binding of substrate and cause product inhibition of adenosine kinase from Leishmania donovani remained unclear. In the present study, employing homology-model-guided site-specific protein mutagenesis, we show that Asp16 is indispensable, since its replacement with either valine or arginine resulted in a >200-fold increase in K(m) (Ado) with a 1000-fold decrease in k(cat)/K(m), implying its critical importance in Ado binding. Even glutamate replacement was not tolerated, indicating the essentiality of Asp16 in the maintenance of steric complementarity of the binding pocket. Use of 2'or 3'-deoxygenated Ado as substrates indicated that, although both the hydroxy groups play important roles in the formation of the enzyme-Ado complex, the binding energy (DeltaDeltaG(B)) contribution of the former was greater than the latter, suggesting possible formation of a bidentate hydrogen bond between Asp16 and the adenosyl ribose. Interestingly, AMP-inhibition and AMP-binding studies revealed that, unlike the R131A mutant, which showed abrogated AMP-binding and insensitivity towards AMP inhibition despite its unaltered K(m) (Ado), all the Asp16 mutants bound AMP efficiently and displayed AMP-sensitive catalytic activity, suggesting disparate mechanisms of binding of Ado and AMP. Molecular docking revealed that, although both Ado and AMP apparently occupied the same binding pocket, Ado binds in a manner that is subtly different from AMP binding, which relies heavily on hydrogen-bonding with Arg131 and thus creates an appropriate environment for competition with Ado. Hence, besides its role in catalysis, an additional novel function of the Arg131 residue as an effector of product-mediated enzyme regulation is proposed.
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Affiliation(s)
- Rupak Datta
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Ishita Das
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Banibrata Sen
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anutosh Chakraborty
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Subrata Adak
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Chhabinath Mandal
- †Division of Drug Design, Development and Molecular Modeling, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Alok K. Datta
- *Division of Infectious Diseases, Leishmania Group, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
- To whom correspondence should be addressed (email )
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Kunishima N, Asada Y, Sugahara M, Ishijima J, Nodake Y, Sugahara M, Miyano M, Kuramitsu S, Yokoyama S, Sugahara M. A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI. J Mol Biol 2005; 352:212-28. [PMID: 16061252 DOI: 10.1016/j.jmb.2005.07.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 06/29/2005] [Accepted: 07/03/2005] [Indexed: 10/25/2022]
Abstract
Hot dog fold proteins sharing the characteristic "hot dog" fold are known to involve certain coenzyme A binding enzymes with various oligomeric states. In order to elucidate the oligomerization-function relationship of the hot dog fold proteins, crystal structures of the phenylacetate degradation protein PaaI from Thermus thermophilus HB8 (TtPaaI), a tetrameric acyl-CoA thioesterase with the hot dog fold, have been determined and compared with those of other family members. In the liganded crystal forms with coenzyme A derivatives, only two of four intersubunit catalytic pockets of the TtPaaI tetramer are occupied by the ligands. A detailed structural comparison between several liganded and unliganded forms reveals that a subtle rigid-body rearrangement of subunits within 2 degrees upon binding of the first two ligand molecules can induce a strict negative cooperativity to prevent further binding at the remaining two pockets, indicating that the so-called "half-of-the-sites reactivity" of oligomeric enzymes is visualized for the first time. Considering kinetic and mutational analyses together, a possible reaction mechanism of TtPaaI is proposed; one tetramer binds only two acyl-CoA molecules with a novel asymmetric induced-fit mechanism and carries out the hydrolysis according to a base-catalyzed reaction through activation of a water molecule by Asp48. From a structural comparison with other family members, it is concluded that a subgroup of the hot dog fold protein family, referred to as "asymmetric hot dog thioesterases" including medium chain acyl-CoA thioesterase II from Escherichia coli and human thioesterase III, might share the same oligomerization mode and the asymmetric induced-fit mechanism as observed in TtPaaI.
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Affiliation(s)
- Naoki Kunishima
- Highthroughput Factory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Sayo-gun, Hyogo 679-5148, Japan.
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49
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McArthur F, Andersson CE, Loutet S, Mowbray SL, Valvano MA. Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis. J Bacteriol 2005; 187:5292-300. [PMID: 16030223 PMCID: PMC1196024 DOI: 10.1128/jb.187.15.5292-5300.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The core oligosaccharide component of the lipopolysaccharide can be subdivided into inner and outer core regions. In Escherichia coli, the inner core consists of two 3-deoxy-d-manno-octulosonic acid and three glycero-manno-heptose residues. The HldE protein participates in the biosynthesis of ADP-glycero-manno-heptose precursors used in the assembly of the inner core. HldE comprises two functional domains: an N-terminal region with homology to the ribokinase superfamily (HldE1 domain) and a C-terminal region with homology to the cytidylyltransferase superfamily (HldE2 domain). We have employed the structure of the E. coli ribokinase as a template to model the HldE1 domain and predict critical amino acids required for enzyme activity. Mutation of these residues renders the protein inactive as determined in vivo by functional complementation analysis. However, these mutations did not affect the secondary or tertiary structure of purified HldE1, as judged by fluorescence spectroscopy and circular dichroism. Furthermore, in vivo coexpression of wild-type, chromosomally encoded HldE and mutant HldE1 proteins with amino acid substitutions in the predicted ATP binding site caused a dominant negative phenotype as revealed by increased bacterial sensitivity to novobiocin. Copurification experiments demonstrated that HldE and HldE1 form a complex in vivo. Gel filtration chromatography resulted in the detection of a dimer as the predominant form of the native HldE1 protein. Altogether, our data support the notions that the HldE functional unit is a dimer and that structural components present in each HldE1 monomer are required for enzymatic activity.
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Affiliation(s)
- Fiona McArthur
- Department of Microbiology and Immunology, Siebens Drake Research Institute, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 5C1, Canada
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50
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Zhang Y, Dougherty M, Downs DM, Ealick SE. Crystal structure of an aminoimidazole riboside kinase from Salmonella enterica: implications for the evolution of the ribokinase superfamily. Structure 2005; 12:1809-21. [PMID: 15458630 DOI: 10.1016/j.str.2004.07.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 07/13/2004] [Accepted: 07/13/2004] [Indexed: 11/23/2022]
Abstract
The crystal structures of a Salmonella enterica aminoimidazole riboside (AIRs) kinase, its complex with the substrate AIRs, and its complex with AIRs and an ATP analog were determined at 2.6 angstroms, 2.9 angstroms, and 2.7 angstroms, respectively. The product of the Salmonella-specific gene stm4066, AIRs kinase, is a homodimer with one active site per monomer. The core structure, consisting of an eight-stranded beta sheet flanked by eight alpha helices, indicates that AIRs kinase is a member of the ribokinase superfamily. Unlike ribokinase and adenosine kinase in this superfamily, AIRs kinase does not show significant conformational changes upon substrate binding. The active site is covered by a lid formed by residues 16-28 and 86-100. A comparison of the structure of AIRs kinase with other ribokinase superfamily members suggests that the active site lid and conformational changes that occur upon substrate binding may be advanced features in the evolution of the ribokinase superfamily.
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Affiliation(s)
- Yan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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