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Tcherkez G. Modelling the reaction mechanism of ribulose-1,5-bisphosphate carboxylase/oxygenase and consequences for kinetic parameters. PLANT, CELL & ENVIRONMENT 2013; 36:1586-96. [PMID: 23305122 DOI: 10.1111/pce.12066] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/12/2012] [Accepted: 12/26/2012] [Indexed: 05/20/2023]
Abstract
Although ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was discovered nearly 60 years ago, the associated chemical mechanism of the reaction is still incompletely understood. The catalytic cycle consists of four major steps: ribulose-1,5-bisphosphate binding, enolization, CO₂ or O₂ addition and hydration, and cleavage of the intermediate. The use of individual rate constants for these elemental steps yields mathematical expressions for usual kinetic constants (k(cat), K(m)), CO₂ versus O₂ specificity (S(c/o)) as well as other chemical parameters such as the ¹²C/¹³C isotope effect. That said, most of them are not simple and thus the interpretation of experimental and observed values of kcat , Km and Sc/o may be more complicated than expected. That is, Rubisco effective catalysis depends on several kinetic parameters that are influenced by both the biological origin and the cellular medium (which, in turn, can vary with environmental conditions). In this brief review, we present the basic model of Rubisco kinetics and describe how subtle biochemical changes (which may have occurred along Evolution) can easily modify Rubisco catalysis.
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Affiliation(s)
- Guillaume Tcherkez
- Institut de Biologie des Plantes, CNRS UMR 8618, Université Paris-Sud, 91405 Orsay Cedex, France.
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Götze JP, Saalfrank P. Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO. J Mol Model 2011; 18:1877-83. [PMID: 21866315 DOI: 10.1007/s00894-011-1207-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 07/31/2011] [Indexed: 10/17/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO(2) carbon atom. This kinetic isotope effect α = k(12)/k(13) for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of (12)CO(2) compared to (13)CO(2). The latter is the dominant mode for the product formation at the transition state.
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Affiliation(s)
- Jan Philipp Götze
- Theoretische Chemie, Institut für Chemie, Universität Potsdam, Potsdam-Golm, Germany.
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Structural framework for catalysis and regulation in ribulose-1,5-bisphosphate carboxylase/oxygenase. Arch Biochem Biophys 2003; 414:130-40. [PMID: 12781764 DOI: 10.1016/s0003-9861(03)00164-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the enzyme assimilating CO2 in biology. Despite serious efforts, using many different methods, a detailed understanding of activity and regulation in Rubisco still eludes us. New results in X-ray crystallography may provide a structural framework on which to base experimental approaches for more detailed analyses of the function of Rubisco at the molecular level. This article gives a critical review of the field and summarizes recent results from structural studies of Rubisco.
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Mauser H, King WA, Gready JE, Andrews TJ. CO(2) fixation by Rubisco: computational dissection of the key steps of carboxylation, hydration, and C-C bond cleavage. J Am Chem Soc 2001; 123:10821-9. [PMID: 11686683 DOI: 10.1021/ja011362p] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite intensive experimental and computational studies, some important features of the mechanism of the photosynthetic CO(2)-fixing enzyme, Rubisco, are still not understood. To complement our previous investigation of the first catalytic step, the enolization of D-ribulose-1,5-bisphosphate (King et al., Biochemistry 1998, 44, 15414-15422), we present the first complete computational dissection of subsequent steps of the carboxylation reaction that includes the roles of the central magnesium ion and modeled residues of the active site. We investigated carboxylation, hydration, and C-C bond cleavage using the density functional method and the B3LYP/6-31G(d) level to perform geometry optimizations. The energies were determined by B3LYP/6-311+G(2d,p) single-point calculations. We modeled a fragment of the active site and substrate, taking into account experimental findings that the residues coordinated to the Mg ion, especially the carbamylated Lys-201, play critical roles in this reaction sequence. The carbamate appears to act as a general base, not only for enolization but also for hydration of the beta ketoacid formed by addition of CO(2) and, as well, cleavage of the C2-C3 bond of the hydrate. We show that CO(2) is added directly, without assistance of a Michaelis complex, and that hydration of the resultant beta ketoacid occurs in a separate subsequent step with a discrete transition state. We suggest that two conformations of the hydrate (gem-diol), with different metal coordination, are possible. The step with the highest activation energy during the carboxylation cycle is the C-C bond cleavage. Depending on the conformations of the gem-diol, different pathways are possible for this step. In either case, special arrangements of the metal coordination result in bond breaking occurring at remarkably low activation energies (between 28 and 37 kcal mol(-1)) which might be reduced further in the enzyme environment.
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Affiliation(s)
- H Mauser
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, Canberra ACT 0200, Australia
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Oliva M, Safont VS, Andrés J, Tapia O. Transition State Structures and Intermediates Modeling Carboxylation Reactions Catalyzed by Rubisco. A Quantum Chemical Study of the Role of Magnesium and Its Coordination Sphere. J Phys Chem A 2001. [DOI: 10.1021/jp0113533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mónica Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - Vicent S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - Juan Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532, S-75121 Uppsala, Sweden
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Oliva M, Safont VS, Andrés J, Tapia O. Electronic mechanistic pattern for C–C bond-breaking from transition structures in Rubisco's chemistry. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)00242-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Oliva M, Safont VS, Andrés J, Tapia O. Transition Structures for d-Ribulose-1,5-bisphosphate Carboxylase/Oxygenase-Catalyzed Oxygenation Chemistry: Role of Carbamylated Lysine in a Model Magnesium Coordination Sphere. J Phys Chem A 2001. [DOI: 10.1021/jp004287y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mónica Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - Vicent S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - Juan Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532, S-75121 Uppsala, Sweden
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Tapia O, Oliva M, Safont VS, Andrés J. A quantum-chemical study of transition structures for enolization and oxygenation steps catalyzed by rubisco: on the role of magnesium and carbamylated Lys-201 in opening oxygen capture channel. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00500-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Safont V, Oliva M, Andrés J, Tapia O. Alternative pathways for the C2–C3 bond cleavage and C2 configuration inversion processes for the Rubisco-catalyzed carboxylation sequence. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00050-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Castillo R, Andrés J, Moliner V. Catalytic Mechanism of Dihydrofolate Reductase Enzyme. A Combined Quantum-Mechanical/Molecular-Mechanical Characterization of Transition State Structure for the Hydride Transfer Step. J Am Chem Soc 1999. [DOI: 10.1021/ja9843019] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Castillo
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - J. Andrés
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
| | - V. Moliner
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Castelló, Spain
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Oliva M, Safont VS, Andrés J, Tapia O. A Theoretical Study of the Molecular Mechanism for the Carboxylation Chemistry in Rubisco. J Phys Chem A 1999. [DOI: 10.1021/jp992052k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - V. S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - J. Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532,S-75121 Uppsala, Sweden
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Oliva M, Safont VS, Andrés J, Tapia O. Theoretical Study of the Molecular Mechanism for the Oxygenation Chemistry in Rubisco. J Phys Chem A 1999. [DOI: 10.1021/jp9907342] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - V. S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - J. Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - O. Tapia
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
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Rotinov A, Chuchani G, Andrés J, Domingo LR, Safont V. A combined experimental and theoretical study of the unimolecular elimination kinetics of 2-alkoxypropionic acids in the gas phase. Chem Phys 1999. [DOI: 10.1016/s0301-0104(99)00137-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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King WA, Gready JE, Andrews TJ. Quantum chemical analysis of the enolization of ribulose bisphosphate: the first hurdle in the fixation of CO2 by Rubisco. Biochemistry 1998; 37:15414-22. [PMID: 9799503 DOI: 10.1021/bi981598e] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A study, using ab initio quantum chemical methods, of the first step in the reaction mechanism of Rubisco, the enolization of the substrate, ribulose bisphosphate, is reported. This is the first such study that takes into account the likely roles of critical features within the active site. On the basis of molecular dynamics relaxation of the complex between activated enzyme and substrate using X-ray crystallographic structures as starting coordinates, a 29-atom fragment that mimicked the active site was constructed. States along a proposed reaction pathway were calculated using density functional theory and Moller-Plesset second-order perturbation theory. The results are consistent with the postulate that the base that abstracts the C3 proton of ribulose bisphosphate is the metal-stabilized carbamate of Lys-201 formed during the activation process. The calculations suggest that the active-site residue, Lys-175, is charged before enolization commences and they indicate a possible means by which the enzyme directs the incoming CO2 to attack the C2 carbon atom of the enediol, rather than the chemically very similar C3 atom.
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Affiliation(s)
- W A King
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, Canberra
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