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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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Quiroga-Roger D, Babul J, Guixé V. Role of monovalent and divalent metal cations in human ribokinase catalysis and regulation. Biometals 2015; 28:401-13. [DOI: 10.1007/s10534-015-9844-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 03/03/2015] [Indexed: 11/29/2022]
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Jissy AK, Datta A. Can Arsenates Replace Phosphates in Natural Biochemical Processes? A Computational Study. J Phys Chem B 2013; 117:8340-6. [PMID: 23789648 DOI: 10.1021/jp402917q] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- A. K. Jissy
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Thiruvananthapuram-695016, Kerala, India
| | - Ayan Datta
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram, CET Campus, Thiruvananthapuram-695016, Kerala, India
- Department of Spectroscopy, Indian Association for the Cultivation of Science,
Jadavpur-700032, West Bengal, India
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Méndez-Lucio O, Romo-Mancillas A, Medina-Franco JL, Castillo R. Computational study on the inhibition mechanism of cruzain by nitrile-containing molecules. J Mol Graph Model 2012; 35:28-35. [DOI: 10.1016/j.jmgm.2012.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/06/2012] [Accepted: 01/10/2012] [Indexed: 10/14/2022]
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Divalent metal cation requirements of phosphofructokinase-2 from E. coli. Evidence for a high affinity binding site for Mn2+. Arch Biochem Biophys 2011; 505:60-6. [DOI: 10.1016/j.abb.2010.09.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 08/31/2010] [Accepted: 09/23/2010] [Indexed: 11/23/2022]
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Jaffer M, Ebead A, Lee-Ruff E. Photochemical synthesis of nucleoside analogues from cyclobutanones: bicyclic and isonucleosides. Molecules 2010; 15:3816-28. [PMID: 20657410 PMCID: PMC6264288 DOI: 10.3390/molecules15063816] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 05/19/2010] [Accepted: 05/24/2010] [Indexed: 12/16/2022] Open
Abstract
The preparation of two nucleoside analogues are reported. Both syntheses involve a key photochemical ring-expansion of cyclobutanones to an oxacarbene and its subsequent scavenging by 6-chloropurine. The synthesis of a bicyclic (locked) purine starts from a oxabicycloheptanone with a hydroxymethyl pendant. The preparation of an isonucleoside uses a cyclobutanone with an α-substituted 6-chloropurine. Irradiation of the latter produces an isonucleoside and acyclic nucleoside analogues.
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Affiliation(s)
| | | | - Edward Lee-Ruff
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-416-736-5443; Fax: +1-416-736-5936
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van Bochove MA, Swart M, Bickelhaupt FM. Stepwise walden inversion in nucleophilic substitution at phosphorus. Phys Chem Chem Phys 2008; 11:259-67. [PMID: 19088981 DOI: 10.1039/b813152j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied the mechanism of S(N)2@P reactions in the model systems X(-) + PMe(2)Y and X(-) + POR(2)Y (with R=Me, OH, OMe; and X, Y=Cl, OH, MeO) using density functional theory at OLYP/TZ2P. Our main purpose is to analyze the nature of the Walden inversion in our model nucleophilic substitution reactions. Walden inversion is well-known to proceed, in general, as a concerted umbrella motion of the substituents at the central atom. Interestingly, we find here that, in certain model reactions, Walden inversion can also proceed in a stepwise fashion in which the individual substituents of the umbrella flip, consecutively, from the educt to the product conformation via separate barriers on the reaction profile. We also examine how variation in nucleophile and leaving group may tune the pentavalent transition structure between labile transition state (TS) and stable transition complex (TC). Furthermore, we explore the various competing multistep pathways in the symmetric (X=Y) and asymmetric (X not equal Y) substitution reactions in our model reaction systems.
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Affiliation(s)
- Marc A van Bochove
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, Netherlands
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Dyguda-Kazimierowicz E, Sokalski WA, Leszczyński J. Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions. J Mol Model 2007; 13:839-49. [PMID: 17384969 DOI: 10.1007/s00894-007-0192-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
The subject of this study was an analysis of the role of active site residues in the phosphoryl transfer reaction catalyzed by 4-methyl-5-beta-hydroxyethylthiazole kinase (ThiK). The ThiK-catalyzed reaction is of special interest due to the lack of a highly conserved aspartate residue serving as a catalytic base. ONIOM(B3LYP:PM3) models of stationary points along the reaction pathway consisted of reactants, two magnesium ions and several highly conserved ThiK active site residues. The results indicate that an S(N)2-like mechanism of ThiK, with gamma-phosphate acting as an alcohol-activating base is reasonable. Geometries of substrates, transition state and products were utilized in the non-empirical analysis of the physical nature of catalytic interactions taking place in the ThiK active site. The role of particular residues was investigated in terms of their ability to preferentially stabilize the transition state relative to substrates (differential transition state stabilization, DTSS) or products (differential product stabilization, DPS). It seems that Mg2, Glu126 and Cys198 play a major catalytic role, whereas Mg1 and the same Cys198 are responsible for product release. It is remarkable that no dominant role of an electrostatic term in the interactions involved in catalytic activity is observed for product release. Determination of catalytic fields expressing differential electrostatic potential of the transition state with respect to substrates revealed the optimal electrostatic features of an ideal catalyst for the studied reaction. The predicted catalytic environment is in agreement with experimental data showing increased catalytic activity of ThiK upon mutation of Cys198 to aspartate.
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Affiliation(s)
- Edyta Dyguda-Kazimierowicz
- Department of Chemistry, Wrocław University of Technology, Wyb.Wyspiańskiego 27, 50-370, Wrocław, Poland.
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Lott JS, Paget B, Johnston JM, Delbaere LTJ, Sigrell-Simon JA, Banfield MJ, Baker EN. The structure of an ancient conserved domain establishes a structural basis for stable histidine phosphorylation and identifies a new family of adenosine-specific kinases. J Biol Chem 2006; 281:22131-22141. [PMID: 16737961 DOI: 10.1074/jbc.m603062200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphorylation of both small molecules and proteins plays a central role in many biological processes. In proteins, phosphorylation most commonly targets the oxygen atoms of Ser, Thr, and Tyr. In contrast, stably phosphorylated His residues are rarely found, due to the lability of the N-P bond, and histidine phosphorylation features most often in transient processes. Here we present the crystal structure of a protein of previously unknown function, which proves to contain a stably phosphorylated histidine residue. The protein is the product of open reading frame PAE2307, from the hyperthermophilic archaeon Pyrobaculum aerophilum, and is representative of a highly conserved protein family found in archaea and bacteria. The crystal structure of PAE2307, solved at 1.45-A resolution (R = 0.208, R(free) = 0.227), forms a remarkably tightly associated hexamer. The phosphorylated histidine at the proposed active site, pHis85, occupies a cavity that is at the interface between two subunits and contains a number of fully conserved residues. Stable phosphorylation is attributed to favorable hydrogen bonding of the phosphoryl group and a salt bridge with pHis85 that provides electronic stabilization. In silico modeling suggested that the protein may function as an adenosine kinase, a conclusion that is supported by in vitro assays of adenosine binding, using fluorescence spectroscopy, and crystallographic visualization of an adenosine complex of PAE2307 at 2.25-A resolution.
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Affiliation(s)
- J Shaun Lott
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand
| | - Blake Paget
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand
| | - Jodie M Johnston
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand
| | - Louis T J Delbaere
- Department of Biochemistry, University of Saskatchewan, Saskatoon S7N 5E5, Canada
| | - Jill A Sigrell-Simon
- Department of Research and Development, GE Healthcare, Björkgatan 30, SE-751 84 Uppsala, Sweden
| | - Mark J Banfield
- Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Edward N Baker
- Laboratory of Structural Biology, Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds St., Private Bag 92-019, Auckland, New Zealand.
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Molecule dynamics and combined QM/MM study on one-carbon unit transfer reaction catalyzed by GAR transformylase. OPEN CHEM 2005. [DOI: 10.2478/bf02475196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AbstractBoth a molecule dynamic study and a combined quantum mechanics and molecule mechanics (QM/MM) study on Glycinamide ribonucleotide transformylase (GAR Tfase) catalytic mechanism are presented. The results indicate a direct one-carbon unit transfer process but not a stepwise mechanism in this reaction. The residues near the active center can fix the cofactor (N10-formyltetrahydrofolate) and GAR in proper relative positions by a H-bond network. The transition state and the minimum energy pathway are located on the potential energy surface. After all the residues (including H2O molecules) are removed from the system the activation energy has increased from 145.1 kJ/mol to 243.3 kJ/mol, and the formly transfer reaction is very hard to achieve. The interactions between coenzyme, GAR and residues near the reactive center are discussed as well.
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