1
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Zhang M, Li S, Yang H, Song G, Wu C, Li Z. Structure and Ultrafast X-ray Diffraction of the Hydrated Metaphosphate. J Phys Chem A 2024; 128:3086-3094. [PMID: 38605669 DOI: 10.1021/acs.jpca.4c00346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
We study the pathway of metaphosphate hydration when a metaphosphate anion is dissolved in liquid water with an explicit water model. For this purpose, we propose a sequential Monte Carlo algorithm incorporated with the ab initio quantum mechanics/molecular mechanics (QM/MM) method, which can reduce the amount of ab initio QM/MM sampling while retaining the accuracy of the simulation. We demonstrate the numerical calculation of the standard enthalpy change for the successive addition reaction PO3-·2H2O + H2O ⇌ PO3-·3H2O in the liquid phase, which helps to clarify the hydration pathway of the metaphosphate. With the obtained hydrated structure of the metaphosphate anion, we perform ab initio calculations for its relaxation dynamics upon vibrational excitation and characterize the energy transfer process in solution with simulated ultrafast X-ray diffraction signals, which can be experimentally implemented with X-ray free-electron lasers.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Sizhe Li
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hanwei Yang
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Gaoxing Song
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Chengyin Wu
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
| | - Zheng Li
- State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China
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2
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Márquez-Moñino MÁ, Ortega-García R, Whitfield H, Riley AM, Infantes L, Garrett SW, Shipton ML, Brearley CA, Potter BVL, González B. Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity. Nat Commun 2024; 15:1502. [PMID: 38374076 PMCID: PMC10876669 DOI: 10.1038/s41467-024-45917-5] [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: 08/19/2023] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
D-myo-inositol 1,4,5-trisphosphate (InsP3) is a fundamental second messenger in cellular Ca2+ mobilization. InsP3 3-kinase, a highly specific enzyme binding InsP3 in just one mode, phosphorylates InsP3 specifically at its secondary 3-hydroxyl group to generate a tetrakisphosphate. Using a chemical biology approach with both synthetised and established ligands, combining synthesis, crystallography, computational docking, HPLC and fluorescence polarization binding assays using fluorescently-tagged InsP3, we have surveyed the limits of InsP3 3-kinase ligand specificity and uncovered surprisingly unforeseen biosynthetic capacity. Structurally-modified ligands exploit active site plasticity generating a helix-tilt. These facilitated uncovering of unexpected substrates phosphorylated at a surrogate extended primary hydroxyl at the inositol pseudo 3-position, applicable even to carbohydrate-based substrates. Crystallization experiments designed to allow reactions to proceed in situ facilitated unequivocal characterization of the atypical tetrakisphosphate products. In summary, we define features of InsP3 3-kinase plasticity and substrate tolerance that may be more widely exploitable.
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Affiliation(s)
- María Ángeles Márquez-Moñino
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Raquel Ortega-García
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Hayley Whitfield
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew M Riley
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Lourdes Infantes
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Shane W Garrett
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Megan L Shipton
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Barry V L Potter
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Beatriz González
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain.
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3
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Yang J, Zhao Y, Yang B. Different binding modes of human centrin with peptides of Kar1p, Rad4 and Sfi1. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Malär AA, Wili N, Völker LA, Kozlova MI, Cadalbert R, Däpp A, Weber ME, Zehnder J, Jeschke G, Eckert H, Böckmann A, Klose D, Mulkidjanian AY, Meier BH, Wiegand T. Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase. Nat Commun 2021; 12:5293. [PMID: 34489448 PMCID: PMC8421360 DOI: 10.1038/s41467-021-25599-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.
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Affiliation(s)
| | - Nino Wili
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | | | - Maria I Kozlova
- Department of Physics, Osnabrück University, Osnabrück, Germany
| | | | | | | | | | | | - Hellmut Eckert
- Institut für Physikalische Chemie, WWU Münster, Münster, Germany
- Instituto de Física de Sao Carlos, Universidade de Sao Paulo, Sao Carlos, SP, Brazil
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Daniel Klose
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Armen Y Mulkidjanian
- Department of Physics, Osnabrück University, Osnabrück, Germany.
- School of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zürich, Zürich, Switzerland.
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany.
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen, Aachen, Germany.
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5
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Xu X, Zhang L, Chu JTS, Wang Y, Chin AWH, Chong TH, Dai Z, Poon LLM, Cheung PPH, Huang X. A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Nucleic Acids Res 2021; 49:8796-8810. [PMID: 34379778 PMCID: PMC8421151 DOI: 10.1093/nar/gkab660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.
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Affiliation(s)
- Xinzhou Xu
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julie Tung Sem Chu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuqing Wang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alex Wing Hong Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Tin Hang Chong
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Zixi Dai
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Leo Lit Man Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, Li Ka Shing Medical Sciences Building, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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6
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Wang G, Li J. Review, analysis, and optimization of the CRISPR Streptococcus pyogenes Cas9 system. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2021.100080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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7
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Recabarren R, Zinovjev K, Tuñón I, Alzate-Morales J. How a Second Mg 2+ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodrigo Recabarren
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Kirill Zinovjev
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, Valencia 46010, Spain
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
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8
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Chen CL, Paul LN, Mermoud JC, Steussy CN, Stauffacher CV. Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase. Nat Commun 2020; 11:3969. [PMID: 32769976 PMCID: PMC7414129 DOI: 10.1038/s41467-020-17733-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 06/30/2020] [Indexed: 01/04/2023] Open
Abstract
Mevalonate diphosphate decarboxylases (MDDs) catalyze the ATP-dependent-Mg2+-decarboxylation of mevalonate-5-diphosphate (MVAPP) to produce isopentenyl diphosphate (IPP), which is essential in both eukaryotes and prokaryotes for polyisoprenoid synthesis. The substrates, MVAPP and ATP, have been shown to bind sequentially to MDD. Here we report crystals in which the enzyme remains active, allowing the visualization of conformational changes in Enterococcus faecalis MDD that describe sequential steps in an induced fit enzymatic reaction. Initial binding of MVAPP modulates the ATP binding pocket with a large loop movement. Upon ATP binding, a phosphate binding loop bends over the active site to recognize ATP and bring the molecules to their catalytically favored configuration. Positioned substrates then can chelate two Mg2+ ions for the two steps of the reaction. Closure of the active site entrance brings a conserved lysine to trigger dissociative phosphoryl transfer of γ-phosphate from ATP to MVAPP, followed by the production of IPP.
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Affiliation(s)
- Chun-Liang Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Lake N Paul
- BioAnalysis, LLC, 1135 Dunton Street, Unit 2, Philadelphia, PA, 19123, USA
- Biophysical Analysis Laboratory, Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47906, USA
| | - James C Mermoud
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | | | - Cynthia V Stauffacher
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Purdue University Center for Cancer Research (PUCCR), Purdue University, West Lafayette, IN, 47907, USA.
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9
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Espinasse A, Wen X, Goodpaster JD, Carlson EE. Mechanistic Studies of Bioorthogonal ATP Analogues for Assessment of Histidine Kinase Autophosphorylation. ACS Chem Biol 2020; 15:1252-1260. [PMID: 32043868 DOI: 10.1021/acschembio.9b01024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Phosphorylation is an essential protein modification and is most commonly associated with hydroxyl-containing amino acids via an adenosine triphosphate (ATP) substrate. The last decades have brought greater appreciation to the roles that phosphorylation of myriad amino acids plays in biological signaling, metabolism, and gene transcription. Histidine phosphorylation occurs in both eukaryotes and prokaryotes but has been shown to dominate signaling networks in the latter due to its role in microbial two-component systems. Methods to investigate histidine phosphorylation have lagged behind those to study serine, threonine, and tyrosine modifications due to its inherent instability and the historical view that this protein modification was rare. An important strategy to overcome the reactivity of phosphohistidine is the development of substrate-based probes with altered chemical properties that improve modification longevity but that do not suffer from poor recognition or transfer by the protein. Here, we present combined experimental and computational studies to better understand the molecular requirements for efficient histidine phosphorylation by comparison of the native kinase substrate, ATP, and alkylated ATP derivatives. While recognition of the substrates by the histidine kinases is an important parameter for the formation of phosphohistidine derivatives, reaction sterics also affect the outcome. In addition, we found that stability of the resulting phosphohistidine moieties correlates with the stability of their hydrolysis products, specifically with their free energy in solution. Interestingly, alkylation dramatically affects the stability of the phosphohistidine derivatives at very acidic pH values. These results provide critical mechanistic insights into histidine phosphorylation and will facilitate the design of future probes to study enzymatic histidine phosphorylation.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Xuelan Wen
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jason D. Goodpaster
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
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10
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Bassenden AV, Park J, Rodionov D, Berghuis AM. Revisiting the Catalytic Cycle and Kinetic Mechanism of Aminoglycoside O-Nucleotidyltransferase(2″): A Structural and Kinetic Study. ACS Chem Biol 2020; 15:686-694. [PMID: 32100995 DOI: 10.1021/acschembio.9b00904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aminoglycoside antibiotics have lost much of their effectiveness due to widespread resistance, primarily via covalent modification. One of the most ubiquitous enzymes responsible for aminoglycoside resistance is aminoglycoside O-nucleotidyltransferase(2″), which catalyzes a nucleotidylation reaction. Due to its clinical importance, much research has focused on dissecting the mechanism of action, some of it dating back more than 30 years. Here, we present structural data for catalytically informative states of the enzyme, i.e., ANT(2″) in complex with adenosine monophosphate (AMP) and tobramycin (inactive-intermediate state) and in complex with adenylyl-2″-tobramycin, pyrophosphate, and Mn2+(product-bound state). These two structures in conjunction with our previously reported structure of ANT(2″)'s substrate-bound complex capture clinical states along ANT(2″)'s reaction coordinate. Additionally, isothermal titration calorimetry (ITC)-based studies are presented that assess the order of substrate binding and product release. Combined, these results outline a kinetic mechanism for ANT(2″) that contradicts what has been previously reported. Specifically, we show that the release of adenylated aminoglycoside precedes pyrophosphate. Furthermore, the ternary complex structures provide additional details on the catalytic mechanism, which reveals extensive similarities to the evolutionarily related DNA polymerase-β superfamily.
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Affiliation(s)
- Angelia V. Bassenden
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montréal, Québec Canada, H3G 1Y6
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life
Science Complex, 3649 Promenade Sir William Osler, Montréal, Québec Canada, H3G 0B1
| | - Jaeok Park
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montréal, Québec Canada, H3G 1Y6
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life
Science Complex, 3649 Promenade Sir William Osler, Montréal, Québec Canada, H3G 0B1
| | - Dmitry Rodionov
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montréal, Québec Canada, H3G 1Y6
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life
Science Complex, 3649 Promenade Sir William Osler, Montréal, Québec Canada, H3G 0B1
| | - Albert M. Berghuis
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montréal, Québec Canada, H3G 1Y6
- Department of Microbiology and Immunology, McGill University, Duff Medical Building, 3775 University Street, Montréal, Québec Canada, H3A 2B4
- Centre de Recherche en Biologie Structurale, McGill University, Bellini Life
Science Complex, 3649 Promenade Sir William Osler, Montréal, Québec Canada, H3G 0B1
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11
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Pettersson P, Barth A. Correlations between the structure and the vibrational spectrum of the phosphate group. Implications for the analysis of an important functional group in phosphoproteins. RSC Adv 2020; 10:4715-4724. [PMID: 35495230 PMCID: PMC9049017 DOI: 10.1039/c9ra10366j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 12/02/2022] Open
Abstract
Density functional theory calculations were used to establish correlations between the structure and the vibrational spectrum of the phosphate group in model compounds for phosphorylated amino acids. The model compounds were acetyl phosphate, methyl phosphate, and p-tolyl phosphate, which represented the phosphorylated amino acids aspartyl phosphate, serine or threonine phosphate, and tyrosine phosphate, respectively. The compounds were placed in different environments consisting of one or several HF or H2O molecules, which modeled interactions of phosphorylated amino acids in the protein environment. The calculations were performed with the B3LYP functional and the 6-311++G(3df, 3pd) basis set. In general, the wavenumbers (or frequencies) of the stretching vibrations of the terminal P–O bonds correlated better with bond lengths of the phosphate group than with its bond angles. The best correlations were obtained with the shortest and the mean terminal P–O bond lengths with standard deviations from the trend line of only 0.2 pm. Other useful correlations were observed with the bond length difference between the shortest and longest terminal P–O bond and with the bond length of the bridging P–O bond. Vibrational frequencies of phosphate are sensitive to bond length changes on the sub-picometer scale.![]()
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Affiliation(s)
- Pontus Pettersson
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- 10691 Stockholm
- Sweden
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12
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Recabarren R, Osorio EH, Caballero J, Tuñón I, Alzate-Morales JH. Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: A QM/MM study. PLoS One 2019; 14:e0215793. [PMID: 31483779 PMCID: PMC6726203 DOI: 10.1371/journal.pone.0215793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results suggest that the base-assisted mechanism is preferred over the substrate-assisted pathway when one Mg2+ is present in the active site, in agreement with a previous theoretical study. The base-assisted mechanism resulted to be dissociative, with a potential energy barrier of 14.3 kcal/mol, very close to the experimental derived value. An interesting feature of the mechanism is the proton transfer from Lys129 to the phosphoryl group at the second transition state, event that could be helping in neutralizing the charge on the phosphoryl group upon the absence of a second Mg2+ ion. Furthermore, important insights into the mechanisms in terms of bond order and charge analysis were provided. These descriptors helped to characterize the synchronicity of bond forming and breaking events, and to characterize charge transfer effects. Local interactions at the active site are key to modulate the charge distribution on the phosphoryl group and therefore alter its reactivity.
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Affiliation(s)
- Rodrigo Recabarren
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Edison H. Osorio
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Ibagué, Colombia
| | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de Valencia, Valencia, Spain
- * E-mail: (JAM); (IT)
| | - Jans H. Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
- * E-mail: (JAM); (IT)
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13
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McClory J, Lin JT, Timson DJ, Zhang J, Huang M. Catalytic mechanism of mevalonate kinase revisited, a QM/MM study. Org Biomol Chem 2019; 17:2423-2431. [PMID: 30735219 DOI: 10.1039/c8ob03197e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mevalonate Kinase (MVK) catalyses the ATP-Mg2+ mediated phosphate transfer of mevalonate to produce mevalonate 5-phosphate and is a key kinase in the mevalonate pathway in the biosynthesis of isopentenyl diphosphate, the precursor of isoprenoid-based biofuels. However, the crystal structure in complex with the native substrate mevalonate, ATP and Mg2+ has not been resolved, which has limited the understanding of its reaction mechanism and therefore its application in the production of isoprenoid-based biofuels. Here using molecular docking, molecular dynamics (MD) simulations and a hybrid QM/MM study, we revisited the location of Mg2+ resolved in the crystal structure of MVK and determined a catalytically competent MVK structure in complex with the native substrate mevalonate and ATP. We demonstrated that significant conformational change on a flexible loop connecting the α6 and α7 helix is induced by the substrate binding. Further, we found that Asp204 is coordinated to the Mg2+ ion. Arg241 plays a crucial role in organizing the triphosphoryl tail of ATP for in-line phosphate transfer and stabilizing the negative charge that accumulates at the β,γ-bridging oxygen of ATP upon bond cleavage. Remarkably, we revealed that the phosphorylation of mevalonate catalyzed by MVK occurs via a direct phosphorylation mechanism, instead of the conventionally postulated catalytic base mechanism. The catalytically competent complex structure of MVK as well as the mechanism of reaction will pave the way for the rational engineering of MVK to exploit its applications in the production of biofuels.
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Affiliation(s)
- James McClory
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, UK.
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Murillo-López J, Zinovjev K, Pereira H, Caniuguir A, Garratt R, Babul J, Recabarren R, Alzate-Morales J, Caballero J, Tuñón I, Cabrera R. Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations. Chem Sci 2019; 10:2882-2892. [PMID: 30996866 PMCID: PMC6429617 DOI: 10.1039/c9sc00094a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Phosphofructokinases catalyze the ATP-dependent phosphorylation of fructose-6-phosphate and they are highly regulated.
Phosphofructokinases (Pfks) catalyze the ATP-dependent phosphorylation of fructose-6-phosphate (F6P) and they are regulated in a wide variety of organisms. Although numerous aspects of the kinetics and regulation have been characterized for Pfks, the knowledge about the mechanism of the phosphoryl transfer reaction and the transition state lags behind. In this work, we describe the X-ray crystal structure of the homodimeric Pfk-2 from E. coli, which contains products in one site and reactants in the other, as well as an additional ATP molecule in the inhibitory allosteric site adjacent to the reactants. This complex was previously predicted when studying the kinetic mechanism of ATP inhibition. After removing the allosteric ATP, molecular dynamic (MD) simulations revealed conformational changes related to domain packing, as well as stable interactions of Lys27 and Asp256 with donor (ATP) and acceptor (fructose-6-) groups, and of Asp166 with Mg2+. The phosphoryl transfer reaction mechanism catalyzed by Pfk-2 was investigated through Quantum Mechanics/Molecular Mechanics (QM/MM) simulations using a combination of the string method and a path-collective variable for the exploration of its free energy surface. The calculated activation free energies showed that a dissociative mechanism, occurring with a metaphosphate intermediate formation followed by a proton transfer to Asp256, is more favorable than an associative one. The structural analysis reveals the role of Asp256 acting as a catalytic base and Lys27 stabilizing the transition state of the dissociative mechanism.
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Affiliation(s)
- Juliana Murillo-López
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Kirill Zinovjev
- Departament de Química Física , Universitat de València , 46100 Burjassot , Spain .
| | - Humberto Pereira
- Instituto de Física de São Carlos , Universidade de São Paulo , São Paulo , Brazil
| | - Andres Caniuguir
- Departamento de Biología , Facultad de Ciencias , Universidad de Chile , Santiago , Chile .
| | - Richard Garratt
- Instituto de Física de São Carlos , Universidade de São Paulo , São Paulo , Brazil
| | - Jorge Babul
- Departamento de Biología , Facultad de Ciencias , Universidad de Chile , Santiago , Chile .
| | - Rodrigo Recabarren
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Jans Alzate-Morales
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Iñaki Tuñón
- Departament de Química Física , Universitat de València , 46100 Burjassot , Spain .
| | - Ricardo Cabrera
- Departamento de Biología , Facultad de Ciencias , Universidad de Chile , Santiago , Chile .
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15
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Rodrigues JR, Cameselle JC, Cabezas A, Ribeiro JM. Closure of the Human TKFC Active Site: Comparison of the Apoenzyme and the Complexes Formed with Either Triokinase or FMN Cyclase Substrates. Int J Mol Sci 2019; 20:E1099. [PMID: 30836629 PMCID: PMC6429413 DOI: 10.3390/ijms20051099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 11/17/2022] Open
Abstract
Human triokinase/flavin mononucleotide (FMN) cyclase (hTKFC) catalyzes the adenosine triphosphate (ATP)-dependent phosphorylation of D-glyceraldehyde and dihydroxyacetone (DHA), and the cyclizing splitting of flavin adenine dinucleotide (FAD). hTKFC structural models are dimers of identical subunits, each with two domains, K and L, with an L2-K1-K2-L1 arrangement. Two active sites lie between L2-K1 and K2-L1, where triose binds K and ATP binds L, although the resulting ATP-to-triose distance is too large (≈14 Å) for phosphoryl transfer. A 75-ns trajectory of molecular dynamics shows considerable, but transient, ATP-to-DHA approximations in the L2-K1 site (4.83 Å or 4.16 Å). To confirm the trend towards site closure, and its relationship to kinase activity, apo-hTKFC, hTKFC:2DHA:2ATP and hTKFC:2FAD models were submitted to normal mode analysis. The trajectory of hTKFC:2DHA:2ATP was extended up to 160 ns, and 120-ns trajectories of apo-hTKFC and hTKFC:2FAD were simulated. The three systems were comparatively analyzed for equal lengths (120 ns) following the principles of essential dynamics, and by estimating site closure by distance measurements. The full trajectory of hTKFC:2DHA:2ATP was searched for in-line orientations and short distances of DHA hydroxymethyl oxygens to ATP γ-phosphorus. Full site closure was reached only in hTKFC:2DHA:2ATP, where conformations compatible with an associative phosphoryl transfer occurred in L2-K1 for significant trajectory time fractions.
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Affiliation(s)
- Joaquim Rui Rodrigues
- Laboratório Associado LSRE-LCM, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Leiria, P-2411-901 Leiria, Portugal.
| | - José Carlos Cameselle
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - Alicia Cabezas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain.
| | - João Meireles Ribeiro
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina, Universidad de Extremadura, E-06006 Badajoz, Spain.
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16
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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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17
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Ma Q, Gabelli SB, Raben DM. Diacylglycerol kinases: Relationship to other lipid kinases. Adv Biol Regul 2019; 71:104-110. [PMID: 30348515 PMCID: PMC6347529 DOI: 10.1016/j.jbior.2018.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 04/17/2023]
Abstract
Lipid kinases regulate a wide variety of cellular functions and have emerged as one the most promising targets for drug design. Diacylglycerol kinases (DGKs) are a family of enzymes that catalyze the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatidic acid (PtdOH). Despite the critical role in lipid biosynthesis, both DAG and PtdOH have been shown as bioactive lipids mediating a number of signaling pathways. Although there is increasing recognition of their role in signaling systems, our understanding of the key enzyme which regulate the balance of these two lipid messages remain limited. Solved structures provide a wealth of information for understanding the function and regulation of these enzymes. Solving the structures of mammalian DGKs by traditional NMR and X-ray crystallography approaches have been challenging and so far, there are still no three-dimensional structures of these DGKs. Despite this, some insights may be gained by examining the similarities and differences between prokaryotic DGKs and other mammalian lipid kinases. This review focuses on summarizing and comparing the structure of prokaryotic and mammalian DGKs as well as two other lipid kinases: sphingosine kinase and phosphatidylinositol-3-kinase. How these known lipid kinases structures relate to mammalian DGKs will also be discussed.
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Affiliation(s)
- Qianqian Ma
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sandra B Gabelli
- The Department of Biophysics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel M Raben
- The Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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18
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Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc Natl Acad Sci U S A 2018; 116:845-853. [PMID: 30591565 DOI: 10.1073/pnas.1817041116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterium Thermus thermophilus Argonaute (Ago; TtAgo) is a prokaryotic Ago (pAgo) that acts as the host defense against the uptake and propagation of foreign DNA by catalyzing the DNA cleavage reaction. The TtAgo active site consists of a plugged-in glutamate finger with two arginine residues (R545 and R486) located symmetrically around it. An interesting challenge is to understand how they can collaboratively facilitate enzymatic catalysis. In Kluyveromyces polysporus Ago, a eukaryotic Ago, the evolutionarily symmetrical residues are arginine and histidine, both of which function to stabilize the plugged-in catalytic tetrad conformation. Surprisingly, our simulation results indicated that, in TtAgo, only R545 is involved in the cleavage reaction by serving as a critical structural anchor to stabilize the catalytic tetrad Asp-Glu-Asp-Asp that is completed by the insertion of the glutamate finger, whereas R486 is not involved in target cleavage. The TtAgo-mediated target DNA cleavage occurs in a substrate-assisted mechanism, in which the pro-Rp (Rp, a tetrahedral phosphorus center with "R-type" chirality) oxygen of scissile phosphate acts as a general base to activate the nucleophilic water. Our unexpected theoretical findings on distinct roles played by R545 and R486 in TtAgo catalysis have been validated by single-point site-mutagenesis experiments, wherein the target cleavage is abolished for all mutants of R545. In sharp contrast, the cleavage activity is maintained for all mutants of R486. Our work provides mechanistic insights on the catalytic specificity of Ago proteins and could facilitate the design of new gene-editing tools in the long term.
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19
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Krachtus D, Smith JC, Imhof P. Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase. Molecules 2018; 23:E3342. [PMID: 30563005 PMCID: PMC6321591 DOI: 10.3390/molecules23123342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022] Open
Abstract
Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The proposed catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.
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Affiliation(s)
- Dieter Krachtus
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
| | - Jeremy C Smith
- Computational Molecular Biophysics Group, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, One Bethel Valley Road, P.O. Box 2008, Oak Ridge, TN 37831-6255, USA.
| | - Petra Imhof
- Freie Universität Berlin, Institute for Theoretical Physics, Arnimallee 14, 14195 Berlin, Germany.
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20
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Abstract
Enzymes are ubiquitous in living systems. Apart from traditional motor proteins, the function of enzymes was assumed to be confined to the promotion of biochemical reactions. Recent work shows that free swimming enzymes, when catalyzing reactions, generate enough mechanical force to cause their own movement, typically observed as substrate-concentration-dependent enhanced diffusion. Preliminary indication is that the impulsive force generated per turnover is comparable to the force produced by motor proteins and is within the range to activate biological adhesion molecules responsible for mechanosensation by cells, making force generation by enzymatic catalysis a novel mechanobiology-relevant event. Furthermore, when exposed to a gradient in substrate concentration, enzymes move up the gradient: an example of chemotaxis at the molecular level. The driving force for molecular chemotaxis appears to be the lowering of chemical potential due to thermodynamically favorable enzyme-substrate interactions and we suggest that chemotaxis promotes enzymatic catalysis by directing the motion of the catalyst and substrates toward each other. Enzymes that are part of a reaction cascade have been shown to assemble through sequential chemotaxis; each enzyme follows its own specific substrate gradient, which in turn is produced by the preceding enzymatic reaction. Thus, sequential chemotaxis in catalytic cascades allows time-dependent, self-assembly of specific catalyst particles. This is an example of how information can arise from chemical gradients, and it is tempting to suggest that similar mechanisms underlie the organization of living systems. On a practical level, chemotaxis can be used to separate out active catalysts from their less active or inactive counterparts in the presence of their respective substrates and should, therefore, find wide applicability. When attached to bigger particles, enzyme ensembles act as "engines", imparting motility to the particles and moving them directionally in a substrate gradient. The impulsive force generated by enzyme catalysis can also be transmitted to the surrounding fluid and molecular and colloidal tracers, resulting in convective fluid pumping and enhanced tracer diffusion. Enzyme-powered pumps that transport fluid directionally can be fabricated by anchoring enzymes onto a solid support and supplying the substrate. Thus, enzyme pumps constitute a novel platform that combines sensing and microfluidic pumping into a single self-powered microdevice. Taken in its entirety, force generation by active enzymes has potential applications ranging from nanomachinery, nanoscale assembly, cargo transport, drug delivery, micro- and nanofluidics, and chemical/biochemical sensing. We also hypothesize that, in vivo, enzymes may be responsible for the stochastic motion of the cytoplasm, the organization of metabolons and signaling complexes, and the convective transport of fluid in cells. A detailed understanding of how enzymes convert chemical energy to directional mechanical force can lead us to the basic principles of fabrication, development, and monitoring of biological and biomimetic molecular machines.
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Affiliation(s)
- Xi Zhao
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Kayla Gentile
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Farzad Mohajerani
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ayusman Sen
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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21
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Dissection of Protein Kinase Pathways in Live Cells Using Photoluminescent Probes: Surveillance or Interrogation? CHEMOSENSORS 2018. [DOI: 10.3390/chemosensors6020019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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McClory J, Lin JT, Timson DJ, Zhang J, Huang M. Water-mediated network in the resistance mechanism of fosfomycin. Phys Chem Chem Phys 2018; 20:21660-21667. [DOI: 10.1039/c8cp02860e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Resistance mechanism of fosfomycin mediated by a water network.
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Affiliation(s)
- James McClory
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- David Keir Building
- Belfast
- UK
| | - Jun-Tang Lin
- Stem Cells and Biotheraphy Engineering Research Centre of Henan
- College of Biomedical Engineering
- Xinxiang Medical University
- Xinxiang 453003
- China
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences
- The University of Brighton, Huxley Building
- Brighton
- UK
| | - Jian Zhang
- Shanghai Jiaotong University
- Shanghai 200025
- China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- David Keir Building
- Belfast
- UK
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23
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McClory J, Timson DJ, Singh W, Zhang J, Huang M. Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study. J Phys Chem B 2017; 121:11062-11071. [DOI: 10.1021/acs.jpcb.7b08770] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- James McClory
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG Northern Ireland, United Kingdom
| | - David J. Timson
- School
of Pharmacy and Biomolecular Sciences, The University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, United Kingdom
| | - Warispreet Singh
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG Northern Ireland, United Kingdom
- Almac Sciences, Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD Northern Ireland, United Kingdom
| | - Jian Zhang
- Shanghai Jiaotong University, 280 Chongqing Road, Shanghai 200025, China
| | - Meilan Huang
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG Northern Ireland, United Kingdom
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24
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Arif SM, Varshney U, Vijayan M. Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1. J Struct Biol 2017; 199:165-176. [PMID: 28705712 DOI: 10.1016/j.jsb.2017.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 10/19/2022]
Abstract
Diadenosine polyphosphates (ApnA, n=2-6), particularly Ap4A, are involved in several important physiological processes. The substantial sequence identity of the Nudix hydrolase domain (domain 1) of Mycobacterium smegmatis MutT1 (MsMutT1) with a known Ap4A hydrolase suggested that MsMutT1 could also hydrolyse diadenosine polyphosphates. Biochemical experiments yielded results in conformity with this suggestion, with Ap4A as the best among the substrates. ATP is a product in all experiments; small amounts of ADP were also observed in the experiments involving Ap4A and Ap6A. Hydrolysis was inhibited by fluoride ions in all cases. The mechanism of action and its inhibition in relation to ApnA were explored through the X-ray analysis of the crystals of the MsMutT1 complexes with Ap5A; Ap5A and MnCl2; Ap4A; ATP; and ATP.NaF.MgCl2. The aggregation pattern of molecules in the first four crystals is similar to that found in a majority of MsMutT1-NTP crystals. Substrate molecules occupy the primary binding site and ATP occupies a site at an intermolecular interface, in the first two. ATP occupies both the sites in the third and fourth crystal. The protein-ligand interactions observed in these crystal structures lead to an explanation of the molecular mechanism of hydrolysis of ApnA by MsMutT1. The fifth crystal exhibits a new packing arrangement. The structure of the complex provides an explanation for the fluoride inhibition of the activity of the enzyme. It would thus appear that MutT1 has a major role involving the hydrolysis of diadenosine polyphosphates, which could be elucidated at the molecular level.
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Affiliation(s)
- S M Arif
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - U Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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25
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes. Angew Chem Int Ed Engl 2017; 56:4110-4128. [PMID: 27862756 DOI: 10.1002/anie.201606474] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Indexed: 12/27/2022]
Abstract
The 1994 structure of a transition-state analogue with AlF4- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF4- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
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Affiliation(s)
- Yi Jin
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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26
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metallfluoride als Analoga für Studien an Phosphoryltransferenzymen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201606474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yi Jin
- Department of Chemistry; University of York; York YO10 5DD Großbritannien
| | - Nigel G. Richards
- School of Chemistry; Cardiff University; Cardiff CF10 3AT Großbritannien
| | | | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN Großbritannien
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27
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Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes. Top Curr Chem (Cham) 2017; 375:36. [PMID: 28299727 PMCID: PMC5480424 DOI: 10.1007/s41061-017-0130-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/01/2017] [Indexed: 10/31/2022]
Abstract
The phosphoryl group, PO3-, is the dynamic structural unit in the biological chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much more prevalent than nitrogen, carbon, or sulfur, is at the core of a great majority of enzyme-catalyzed reactions involving phosphate esters, anhydrides, amidates, and phosphorothioates. The serendipitous discovery that the phosphoryl group could be labeled by "nuclear mutation," by substitution of PO3- by MgF3- or AlF4-, has underpinned the application of metal fluoride (MF x ) complexes to mimic transition states for enzymatic phosphoryl transfer reactions, with sufficient stability for experimental analysis. Protein crystallography in the solid state and 19F NMR in solution have enabled direct observation of ternary and quaternary protein complexes embracing MF x transition state models with precision. These studies have underpinned a radically new mechanistic approach to enzyme catalysis for a huge range of phosphoryl transfer processes, as varied as kinases, phosphatases, phosphomutases, and phosphohydrolases. The results, without exception, have endorsed trigonal bipyramidal geometry (tbp) for concerted, "in-line" stereochemistry of phosphoryl transfer. QM computations have established the validity of tbp MF x complexes as reliable models for true transition states, delivering similar bond lengths, coordination to essential metal ions, and virtually identical hydrogen bond networks. The emergence of protein control of reactant orbital overlap between bond-forming species within enzyme transition states is a new challenging theme for wider exploration.
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28
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Trajtenberg F, Imelio JA, Machado MR, Larrieux N, Marti MA, Obal G, Mechaly AE, Buschiazzo A. Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action. eLife 2016; 5:e21422. [PMID: 27938660 PMCID: PMC5231405 DOI: 10.7554/elife.21422] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/09/2016] [Indexed: 01/19/2023] Open
Abstract
Two-component systems (TCS) are protein machineries that enable cells to respond to input signals. Histidine kinases (HK) are the sensory component, transferring information toward downstream response regulators (RR). HKs transfer phosphoryl groups to their specific RRs, but also dephosphorylate them, overall ensuring proper signaling. The mechanisms by which HKs discriminate between such disparate directions, are yet unknown. We now disclose crystal structures of the HK:RR complex DesK:DesR from Bacillus subtilis, comprising snapshots of the phosphotransfer and the dephosphorylation reactions. The HK dictates the reactional outcome through conformational rearrangements that include the reactive histidine. The phosphotransfer center is asymmetric, poised for dissociative nucleophilic substitution. The structural bases of HK phosphatase/phosphotransferase control are uncovered, and the unexpected discovery of a dissociative reactional center, sheds light on the evolution of TCS phosphotransfer reversibility. Our findings should be applicable to a broad range of signaling systems and instrumental in synthetic TCS rewiring.
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Affiliation(s)
- Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Juan A Imelio
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Matías R Machado
- Biomolecular Simulations, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Nicole Larrieux
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcelo A Marti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gonzalo Obal
- Protein Biophysics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Ariel E Mechaly
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Département de Microbiologie, Institut Pasteur, Paris, France
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29
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Li Q, Fan S, Li X, Jin Y, He W, Zhou J, Cen S, Yang Z. Insights into the Phosphoryl Transfer Mechanism of Human Ubiquitous Mitochondrial Creatine Kinase. Sci Rep 2016; 6:38088. [PMID: 27909311 PMCID: PMC5133464 DOI: 10.1038/srep38088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/03/2016] [Indexed: 12/31/2022] Open
Abstract
Human ubiquitous mitochondrial creatine kinase (uMtCK) is responsible for the regulation of cellular energy metabolism. To investigate the phosphoryl-transfer mechanism catalyzed by human uMtCK, in this work, molecular dynamic simulations of uMtCK∙ATP-Mg2+∙creatine complex and quantum mechanism calculations were performed to make clear the puzzle. The theoretical studies hereof revealed that human uMtCK utilizes a two-step dissociative mechanism, in which the E227 residue of uMtCK acts as the catalytic base to accept the creatine guanidinium proton. This catalytic role of E227 was further confirmed by our assay on the phosphatase activity. Moreover, the roles of active site residues in phosphoryl transfer reaction were also identified by site directed mutagenesis. This study reveals the structural basis of biochemical activity of uMtCK and gets insights into its phosphoryl transfer mechanism.
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Affiliation(s)
- Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shuai Fan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuanyuan Jin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Weiqing He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - ZhaoYong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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30
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Sunden F, AlSadhan I, Lyubimov AY, Ressl S, Wiersma-Koch H, Borland J, Brown CL, Johnson TA, Singh Z, Herschlag D. Mechanistic and Evolutionary Insights from Comparative Enzymology of Phosphomonoesterases and Phosphodiesterases across the Alkaline Phosphatase Superfamily. J Am Chem Soc 2016; 138:14273-14287. [PMID: 27670607 PMCID: PMC5096464 DOI: 10.1021/jacs.6b06186] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Naively one might have expected an early division between phosphate monoesterases and diesterases of the alkaline phosphatase (AP) superfamily. On the contrary, prior results and our structural and biochemical analyses of phosphate monoesterase PafA, from Chryseobacterium meningosepticum, indicate similarities to a superfamily phosphate diesterase [Xanthomonas citri nucleotide pyrophosphatase/phosphodiesterase (NPP)] and distinct differences from the three metal ion AP superfamily monoesterase, from Escherichia coli AP (EcAP). We carried out a series of experiments to map out and learn from the differences and similarities between these enzymes. First, we asked why there would be independent instances of monoesterases in the AP superfamily? PafA has a much weaker product inhibition and slightly higher activity relative to EcAP, suggesting that different metabolic evolutionary pressures favored distinct active-site architectures. Next, we addressed the preferential phosphate monoester and diester catalysis of PafA and NPP, respectively. We asked whether the >80% sequence differences throughout these scaffolds provide functional specialization for each enzyme's cognate reaction. In contrast to expectations from this model, PafA and NPP mutants with the common subset of active-site groups embedded in each native scaffold had the same monoesterase:diesterase specificities; thus, the >107-fold difference in native specificities appears to arise from distinct interactions at a single phosphoryl substituent. We also uncovered striking mechanistic similarities between the PafA and EcAP monoesterases, including evidence for ground-state destabilization and functional active-site networks that involve different active-site groups but may play analogous catalytic roles. Discovering common network functions may reveal active-site architectural connections that are critical for function, and identifying regions of functional modularity may facilitate the design of new enzymes from existing promiscuous templates. More generally, comparative enzymology and analysis of catalytic promiscuity can provide mechanistic and evolutionary insights.
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Affiliation(s)
- Fanny Sunden
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Ishraq AlSadhan
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Artem Y Lyubimov
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Science, Structural Biology, and Photon Science, Howard Hughes Medical Institute, Stanford University , Stanford, California 94305, United States
| | - Susanne Ressl
- Molecular and Cellular Biochemistry Department, Indiana University , Bloomington, Indiana 47405, United States
| | - Helen Wiersma-Koch
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States.,Department of Biology, Indian River State College , Fort Pierce, Florida 34981, United States
| | - Jamar Borland
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Clayton L Brown
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Tory A Johnson
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Zorawar Singh
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, Beckman Center, Stanford University , Stanford, California 94305, United States.,Departments of Chemical Engineering and Chemistry, and Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University , Stanford, California 94305, United States
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31
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Huang M, Wei K, Li X, McClory J, Hu G, Zou JW, Timson D. Phosphorylation Mechanism of Phosphomevalonate Kinase: Implications for Rational Engineering of Isoprenoid Biosynthetic Pathway Enzymes. J Phys Chem B 2016; 120:10714-10722. [DOI: 10.1021/acs.jpcb.6b08480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meilan Huang
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Kexin Wei
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Xiao Li
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - James McClory
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Guixiang Hu
- School
of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Jian-Wei Zou
- School
of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - David Timson
- School
of Pharmacy and Biomolecular Sciences, The University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, United Kingdom
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32
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Jiang Y, Tan H, Zheng J, Li X, Chen G, Jia Z. Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study. Phys Chem Chem Phys 2016; 17:25228-34. [PMID: 26352441 DOI: 10.1039/c5cp03342j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diacylglycerol kinase is an integral membrane protein which catalyzes phosphoryl transfer from ATP to diacylglycerol. As the smallest kinase known, it shares no sequence homology with conventional kinases and possesses a distinct trimer structure. Thus far, its catalytic mechanism remains elusive. Using molecular dynamics and quantum mechanics calculations, we investigated the co-factor and the substrate binding and phosphoryl transfer mechanism. Based on the analysis of density functional theory calculations, we reveal that the phosphorylation reaction of diacylglycerol kinase features the same phosphoryl transfer mechanism as other kinases, despite its unique structural properties. Our results further show that the active site is relatively open and able to accommodate ligands in multiple orientations, suggesting that the optimization of binding orientations and conformational changes would occur prior to actual phosphoryl transfer.
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Affiliation(s)
- Yafei Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
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33
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Jara GE, Martínez L. Anthrax Edema Factor: An Ion-Adaptive Mechanism of Catalysis with Increased Transition-State Conformational Flexibility. J Phys Chem B 2016; 120:6504-14. [DOI: 10.1021/acs.jpcb.6b02527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel E. Jara
- Institute of Chemistry, University of Campinas, Campinas, SP 13083-861, Brazil
| | - Leandro Martínez
- Institute of Chemistry, University of Campinas, Campinas, SP 13083-861, Brazil
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34
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Qin J, Tan H, Li X, Chen G, Zheng J, Wang Y, Ma J, Jia Z. Theoretical studies of the function switch and mechanism of AceK as a highly active ATPase. RSC Adv 2016. [DOI: 10.1039/c6ra11873a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
As a multi-function enzyme, AceK integrates kinase, phosphatase and ATPase activities in a single active site and these functions are delicately regulated..
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Affiliation(s)
- Jiajia Qin
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Hongwei Tan
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Xichen Li
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Guangju Chen
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Jimin Zheng
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Ye Wang
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Jianqiu Ma
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
| | - Zongchao Jia
- College of Chemistry
- Beijing Normal University
- 100875 Beijing
- China
- Department of Biomedical and Molecular Sciences
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35
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Marcos E, Crehuet R, Anglada JM. Inductive and External Electric Field Effects in Pentacoordinated Phosphorus Compounds. J Chem Theory Comput 2015; 4:49-63. [PMID: 26619979 DOI: 10.1021/ct700220z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pentacoordination at phosphorus is associated with a nucleophilic displacement reaction at tetracoordinated phosphorus compounds and shows a great variability in what respects their geometrical and energetic features. By means of a systematic theoretical study on a series of elementary model compounds, we have analyzed the bonding features. The pentacoordinated phosphorus compounds are held together by dative bonds, and the geometry and stability depends on the inductive effects originated by different substitutes at phosphorus. We show also that an external electric field can modify the geometrical features and the reactivity of the nucleophilic substitution reactions. This issue may have great interest in biological reactions involving pentacoordinated phosphorus where the electric field originated by the folded protein could influence the catalytic process. We report also additional calculations on the geometry and NMR spectra on three triphenyl phosphonium ylide derivatives, and our results compare well with the experimental data.
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Affiliation(s)
- Enrique Marcos
- Grup de Química Teòrica i Computacional, Departament de Química Orgànica Biològica, Institut d'Investigacions Químiques i Ambientals de Barcelona, IIQAB - CSIC, c/ Jordi Girona 18, E-08034 Barcelona, Spain
| | - Ramon Crehuet
- Grup de Química Teòrica i Computacional, Departament de Química Orgànica Biològica, Institut d'Investigacions Químiques i Ambientals de Barcelona, IIQAB - CSIC, c/ Jordi Girona 18, E-08034 Barcelona, Spain
| | - Josep M Anglada
- Grup de Química Teòrica i Computacional, Departament de Química Orgànica Biològica, Institut d'Investigacions Químiques i Ambientals de Barcelona, IIQAB - CSIC, c/ Jordi Girona 18, E-08034 Barcelona, Spain
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36
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Visualizing autophosphorylation in histidine kinases. Nat Commun 2015; 5:3258. [PMID: 24500224 DOI: 10.1038/ncomms4258] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/14/2014] [Indexed: 12/17/2022] Open
Abstract
Reversible protein phosphorylation is the most widespread regulatory mechanism in signal transduction. Autophosphorylation in a dimeric sensor histidine kinase is the first step in two-component signalling, the predominant signal-transduction device in bacteria. Despite being the most abundant sensor kinases in nature, the molecular bases of the histidine kinase autophosphorylation mechanism are still unknown. Furthermore, it has been demonstrated that autophosphorylation can occur in two directions, cis (intrasubunit) or trans (intersubunit) within the dimeric histidine kinase. Here, we present the crystal structure of the complete catalytic machinery of a chimeric histidine kinase. The structure shows an asymmetric histidine kinase dimer where one subunit is caught performing the autophosphorylation reaction. A structure-guided functional analysis on HK853 and EnvZ, two prototypical cis- and trans-phosphorylating histidine kinases, has allowed us to decipher the catalytic mechanism of histidine kinase autophosphorylation, which seems to be common independently of the reaction directionality.
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37
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Yang X, Zeng X, Moffat K, Yang X. Structure of the response regulator RPA3017 involved in red-light signaling in Rhodopseudomonas palustris. Acta Crystallogr F Struct Biol Commun 2015; 71:1215-22. [PMID: 26457509 PMCID: PMC4601582 DOI: 10.1107/s2053230x15014661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/04/2015] [Indexed: 11/10/2022] Open
Abstract
Two-component signal transduction is the major signaling mechanism that enables bacteria to survive and thrive in complex environmental conditions. The photosynthetic bacterium R. palustris employs two tandem bacteriophytochromes, RpBphP2 and RpBphP3, to perceive red-light signals that regulate the synthesis of light-harvesting complexes under low-light conditions. Both RpBphP2 and RpBphP3 are photosensory histidine kinases coupled to the same response regulator RPA3017. Together, they constitute a two-component system that converts a red-light signal into a biological signal. In this work, the crystal structure of RPA3017 in the unphosphorylated form at 1.9 Å resolution is presented. This structure reveals a tightly associated dimer arrangement that is conserved among phytochrome-related response regulators. The conserved active-site architecture provides structural insight into the phosphotransfer reaction between RpBphP2/RpBphP3 and RPA3017. Based on structural comparisons and homology modeling, how specific recognition between RpBphP2/RpBphP3 and RPA3017 is achieved at the molecular level is further explored.
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Affiliation(s)
- Xuefei Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, People’s Republic of China
| | - Xiaoli Zeng
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Keith Moffat
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
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38
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Ojeda-May P, Li Y, Ovchinnikov V, Nam K. Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase. J Am Chem Soc 2015; 137:12454-7. [PMID: 26374925 DOI: 10.1021/jacs.5b07996] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic and allosteric mechanisms of insulin receptor kinase (IRK) are investigated by a combination of ab initio and semiempirical quantum mechanical and molecular mechanical (QM/MM) methods and classical molecular dynamics (MD) simulations. The simulations reveal that the catalytic reaction proceeds in two steps, starting with the transfer of a proton from substrate Tyr to the catalytic Asp1132, followed by the phosphoryl transfer from ATP to substrate Tyr. The enhancement of the catalytic rate of IRK upon phosphorylations in the enzyme's activation loop is found to occur mainly via changes to the free energy landscape of the proton transfer step, favoring the proton transfer in the fully phosphorylated enzyme. In contrast, the effects of the phosphorylations on the phosphoryl transfer are smaller. Equilibrium MD simulations show that IRK phosphorylations affect the protein dynamics of the enzyme before the proton transfer to Asp1132 with only a minor effect after the proton transfer. This finding is consistent with the large change in the proton transfer free energy and the smaller change in the free energy barrier of phosphoryl transfer found by QM/MM simulations. Taken together, the present results provide details on how IRK phosphorylation exerts allosteric control of the catalytic activity via modifications of protein dynamics and free energy landscape of catalytic reaction. The results also highlight the importance of protein dynamics in connecting protein allostery and catalysis to control catalytic activity of enzymes.
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Affiliation(s)
- Pedro Ojeda-May
- Department of Chemistry and Computational Life Science Cluster (CLiC), Umeå University , 901 87 Umeå, Sweden
| | - Yaozong Li
- Department of Chemistry and Computational Life Science Cluster (CLiC), Umeå University , 901 87 Umeå, Sweden
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Kwangho Nam
- Department of Chemistry and Computational Life Science Cluster (CLiC), Umeå University , 901 87 Umeå, Sweden
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39
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Abstract
Protein kinases transfer a phosphoryl group from ATP onto target proteins and play a critical role in signal transduction and other cellular processes. Here, we review the kinase kinetic and chemical mechanisms and their application in understanding kinase structure and function. Aberrant kinase activity has been implicated in many human diseases, in particular cancer. We highlight applications of technologies and concepts derived from kinase mechanistic studies that have helped illuminate how kinases are regulated and contribute to pathophysiology.
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Affiliation(s)
- Zhihong Wang
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania, USA
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.
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40
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Martinez-Rodriguez L, Erdogan O, Jimenez-Rodriguez M, Gonzalez-Rivera K, Williams T, Li L, Weinreb V, Collier M, Chandrasekaran SN, Ambroggio X, Kuhlman B, Carter CW. Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene. J Biol Chem 2015; 290:19710-25. [PMID: 26088142 DOI: 10.1074/jbc.m115.642876] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Indexed: 01/11/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRS) catalyze both chemical steps that translate the universal genetic code. Rodin and Ohno offered an explanation for the existence of two aaRS classes, observing that codons for the most highly conserved Class I active-site residues are anticodons for corresponding Class II active-site residues. They proposed that the two classes arose simultaneously, by translation of opposite strands from the same gene. We have characterized wild-type 46-residue peptides containing ATP-binding sites of Class I and II synthetases and those coded by a gene designed by Rosetta to encode the corresponding peptides on opposite strands. Catalysis by WT and designed peptides is saturable, and the designed peptides are sensitive to active-site residue mutation. All have comparable apparent second-order rate constants 2.9-7.0E-3 M(-1) s(-1) or ∼750,000-1,300,000 times the uncatalyzed rate. The activities of the two complementary peptides demonstrate that the unique information in a gene can have two functional interpretations, one from each complementary strand. The peptides contain phylogenetic signatures of longer, more sophisticated catalysts we call Urzymes and are short enough to bridge the gap between them and simpler uncoded peptides. Thus, they directly substantiate the sense/antisense coding ancestry of Class I and II aaRS. Furthermore, designed 46-mers achieve similar catalytic proficiency to wild-type 46-mers by significant increases in both kcat and Km values, supporting suggestions that the earliest peptide catalysts activated ATP for biosynthetic purposes.
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Affiliation(s)
- Luis Martinez-Rodriguez
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Ozgün Erdogan
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Mariel Jimenez-Rodriguez
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Katiria Gonzalez-Rivera
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Tishan Williams
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Li Li
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Violetta Weinreb
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Martha Collier
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Srinivas Niranj Chandrasekaran
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Xavier Ambroggio
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Brian Kuhlman
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
| | - Charles W Carter
- From the Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260
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41
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Gerlits O, Tian J, Das A, Langan P, Heller WT, Kovalevsky A. Phosphoryl Transfer Reaction Snapshots in Crystals: INSIGHTS INTO THE MECHANISM OF PROTEIN KINASE A CATALYTIC SUBUNIT. J Biol Chem 2015; 290:15538-15548. [PMID: 25925954 DOI: 10.1074/jbc.m115.643213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 11/06/2022] Open
Abstract
To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the transition state. However, all previous crystal structures of the Michaelis complex mimics of the PKA catalytic subunit (PKAc) were obtained with either peptide inhibitors or ATP analogs. Here we utilized Ca(2+) ions and sulfur in place of the nucleophilic oxygen in a 20-residue pseudo-substrate peptide (CP20) and ATP to produce a close mimic of the Michaelis complex. In the ternary reactant complex, the thiol group of Cys-21 of the peptide is facing Asp-166 and the sulfur atom is positioned for an in-line phosphoryl transfer. Replacement of Ca(2+) cations with Mg(2+) ions resulted in a complex with trapped products of ATP hydrolysis: phosphate ion and ADP. The present structural results in combination with the previously reported structures of the transition state mimic and phosphorylated product complexes complete the snapshots of the phosphoryl transfer reaction by PKAc, providing us with the most thorough picture of the catalytic mechanism to date.
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Affiliation(s)
- Oksana Gerlits
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Jianhui Tian
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Amit Das
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Paul Langan
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - William T Heller
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831.
| | - Andrey Kovalevsky
- From the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831.
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42
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Roychowdhury A, Kundu A, Bose M, Gujar A, Mukherjee S, Das AK. Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism. FEBS J 2015; 282:1097-110. [DOI: 10.1111/febs.13205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/13/2015] [Accepted: 01/16/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Amlan Roychowdhury
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Anirban Kundu
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Madhuparna Bose
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Akanksha Gujar
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Somnath Mukherjee
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Amit Kumar Das
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
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43
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Kale S, Sode O, Weare J, Dinner AR. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol. J Chem Theory Comput 2014; 10:5467-5475. [PMID: 25516726 PMCID: PMC4263463 DOI: 10.1021/ct500852y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Indexed: 11/28/2022]
Abstract
Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled.
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Affiliation(s)
- Seyit Kale
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States
| | - Olaseni Sode
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jonathan Weare
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States
| | - Aaron R Dinner
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States
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44
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Zeringo NA, Bellizzi JJ. A PER2-derived mechanism-based bisubstrate analog for casein kinase 1ε. Chem Biol Drug Des 2014; 84:697-703. [PMID: 24985607 DOI: 10.1111/cbdd.12363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/20/2014] [Accepted: 05/28/2014] [Indexed: 11/30/2022]
Abstract
Casein kinase 1ε (CK1ε) plays an important regulatory role in various cellular processes including circadian rhythms. Mutations in CK1ε or the recognition site on its substrate PER2 result in modulation of the circadian period length. In particular, the tau mutation (R178C) in the catalytic domain of CK1ε was identified as the molecular basis for a dose-dependent heritable shortened circadian period in hamsters. However, the biochemical basis for the physiological effects of the tau mutant remains unclear. It has been reported that the tau mutation has reduced in vitro activity against some substrates but increased in vitro activity against other substrates. To better understand the effects of the CK1ε tau mutation, an ATP-phosphopeptide conjugate was synthesized to yield a transition-state bisubstrate analog. Kinase activity assays determined that the tau mutant has 80% reduced activity and a fourfold decrease in sensitivity to the bisubstrate analog compared to wild type. This confirms that Arg178 is important in the recognition of the preferred phosphosubstrates of CK1ε.
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Affiliation(s)
- Nicholas A Zeringo
- Department of Chemistry and Biochemistry, The University of Toledo, 2801 W. Bancroft St. MS 602, Toledo, OH, 43606, USA
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45
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IP6K structure and the molecular determinants of catalytic specificity in an inositol phosphate kinase family. Nat Commun 2014; 5:4178. [PMID: 24956979 DOI: 10.1038/ncomms5178] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/21/2014] [Indexed: 01/27/2023] Open
Abstract
Inositol trisphosphate kinases (IP3Ks) and inositol hexakisphosphate kinases (IP6Ks) each regulate specialized signalling activities by phosphorylating either InsP3 or InsP6 respectively. The molecular basis for these different kinase activities can be illuminated by a structural description of IP6K. Here we describe the crystal structure of an Entamoeba histolytica hybrid IP6K/IP3K, an enzymatic parallel to a 'living fossil'. Through molecular modelling and mutagenesis, we extrapolated our findings to human IP6K2, which retains vestigial IP3K activity. Two structural elements, an α-helical pair and a rare, two-turn 310 helix, together forge a substrate-binding pocket with an open clamshell geometry. InsP6 forms substantial contacts with both structural elements. Relative to InsP6, enzyme-bound InsP3 rotates 55° closer to the α-helices, which provide most of the protein's interactions with InsP3. These data reveal the molecular determinants of IP6K activity, and suggest an unusual evolutionary trajectory for a primordial kinase that could have favored efficient bifunctionality, before propagation of separate IP3Ks and IP6Ks.
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46
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Sirin GS, Zhang Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J Phys Chem A 2014; 118:9132-9. [PMID: 24786171 PMCID: PMC4183371 DOI: 10.1021/jp502712d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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Acetylcholinesterase (AChE) is a
crucial enzyme in the cholinergic
nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic
signals by reducing the effective concentration of ACh in the synaptic
clefts. Organophosphate compounds irreversibly inhibit AChEs, leading
to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella
sampling, a state-of-the-art approach to simulate enzyme reactions,
we have characterized the covalent inhibition mechanism between AChE
and the nerve toxin soman and determined its free energy profile for
the first time. Our results indicate that phosphonylation of the catalytic
serine by soman employs an addition–elimination mechanism,
which is highly associative and stepwise: in the initial addition
step, which is also rate-limiting, His440 acts as a general base to
facilitate the nucleophilic attack of Ser200 on the soman’s
phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate;
in the subsequent elimination step, Try121 of the catalytic gorge
stabilizes the leaving fluorine atom prior to its dissociation from
the active site. Together with our previous characterization of the
aging mechanism of soman inhibited AChE, our simulations have revealed
detailed molecular mechanistic insights into the damaging function
of the nerve agent soman.
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Affiliation(s)
- Gulseher Sarah Sirin
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine , New York, New York 10016, United States
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47
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Elsässer B, Fels G, Weare JH. QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer. J Am Chem Soc 2014; 136:927-36. [PMID: 24372083 DOI: 10.1021/ja406122c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.
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Affiliation(s)
- Brigitta Elsässer
- Department of Chemistry, University of Paderborn , Warburgerstr. 100, D-33098 Paderborn, Germany
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48
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Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling. Nucleic Acids Res 2013; 41:10542-55. [PMID: 23982515 PMCID: PMC3905902 DOI: 10.1093/nar/gkt756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 12/26/2022] Open
Abstract
Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure.
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Affiliation(s)
- Orsolya Barabás
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Veronika Németh
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - András Perczel
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Edina Rosta
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán Kele
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Imre Zagyva
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán Szabadka
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Vince I. Grolmusz
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Matthias Wilmanns
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Beáta G. Vértessy
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
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49
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Rudbeck ME, Blomberg MRA, Barth A. Hydrolysis of the E2P Phosphoenzyme of the Ca2+-ATPase: A Theoretical Study. J Phys Chem B 2013; 117:9224-32. [DOI: 10.1021/jp4049814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria E. Rudbeck
- Department of Biochemistry and
Biophysics, Arrhenius Laboratories, Stockholm University, 10691 Stockholm, Sweden
| | - Margareta R. A. Blomberg
- Department of Organic Chemistry,
Arrhenius Laboratories, Stockholm University, 10691 Stockholm, Sweden
| | - Andreas Barth
- Department of Biochemistry and
Biophysics, Arrhenius Laboratories, Stockholm University, 10691 Stockholm, Sweden
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50
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Huang M, Li X, Zou JW, Timson DJ. Role of Arg228 in the phosphorylation of galactokinase: the mechanism of GHMP kinases by quantum mechanics/molecular mechanics studies. Biochemistry 2013; 52:4858-68. [PMID: 23786354 DOI: 10.1021/bi400228e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
GHMP kinases are a group of structurally related small molecule kinases. They have been found in all kingdoms of life and are mostly responsible for catalyzing the ATP-dependent phosphorylation of intermediary metabolites. Although the GHMP kinases are of clinical, pharmaceutical, and biotechnological importance, the mechanism of GHMP kinases is controversial. A catalytic base mechanism was suggested for mevalonate kinase that has a structural feature of the γ-phosphate of ATP close to an aspartate residue; however, for one GHMP family member, homoserine kinase, where the residue acting as general base is absent, a direct phosphorylation mechanism was suggested. Furthermore, it was proposed by some authors that all the GHMP kinases function by a similar mechanism. This controversy in mechanism has limited our ability to exploit these enzymes as drug targets and in biotechnology. Here the phosphorylation reaction mechanism of the human galactokinase, a member of the GHMP kinase family, was investigated using molecular dynamics simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B3LYP-D/AMBER99). The reaction coordinates were localized by potential energy scan using an adiabatic mapping method. Our results indicate that a highly conserved Glu174 captures Arg105 in the proximity of the α-phosphate of ATP, forming a H-bond network; therefore, the mobility of ATP in the large oxyanion hole is restricted. Arg228 functions to stabilize the negative charge developed at the β,γ-bridging oxygen of the ATP during bond cleavage. The reaction occurs via a direct phosphorylation mechanism, and the Asp186 in the proximity of ATP does not directly participate in the reaction pathway. Because Arg228 is not conserved among GHMP kinases, reagents which form interactions with Arg228, and therefore can interrupt its function in phosphorylation, may be developed into potential selective inhibitors for galactokinase.
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Affiliation(s)
- Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University Belfast , David Keir Building, Stranmillis Road, Belfast BT9 5AG, U.K
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