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Djeghader A, Rossotti M, Abdulkarim S, Biaso F, Gerbaud G, Nitschke W, Schoepp-Cothenet B, Soulimane T, Grimaldi S. Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase. Chem Commun (Camb) 2020; 56:9850-9853. [DOI: 10.1039/d0cc03634j] [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]
Abstract
We provide structural and spectroscopic evidence for a molybdenum–phosphate adduct mimicking a proposed reaction intermediate in the active site of a prokaryotic sulfite oxidizing enzyme.
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Affiliation(s)
- Ahmed Djeghader
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
| | | | - Saleh Abdulkarim
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
| | | | | | | | | | - Tewfik Soulimane
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
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2
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Abstract
Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39–49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.
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Acid-facilitated product release from a Mo(IV) center: relevance to oxygen atom transfer reactivity of molybdenum oxotransferases. J Biol Inorg Chem 2017; 23:193-207. [PMID: 29177705 DOI: 10.1007/s00775-017-1518-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/10/2017] [Indexed: 01/27/2023]
Abstract
We report that pyridinium ions (HPyr+) accelerate the conversion of [Tp*MoIVOCl(OPMe3)] (1) to [Tp*MoIVOCl(NCCH3)] (2) by 103-fold, affording 2 in near-quantitative yield; Tp* = hydrotris(3,5-dimethyl-1-pyrazolyl)borate. This novel reactivity and the mechanism of this reaction were investigated in detail. The formation of 2 followed pseudo-first-order kinetics, with the observed pseudo-first-order rate constant (k obs) linearly correlated with [HPyr+]. An Eyring plot revealed that this HPyr+-facilitated reaction has a small positive value of ∆S ‡ indicative of a dissociative interchange (Id) mechanism, different from the slower associative interchange (Ia) mechanism in the absence of HPyr+ marked with a negative ∆S ‡. Interestingly, log(k obs) was found to be linearly correlated to the acidity of substituted pyridinium ions. This novel reactivity is further investigated using combined DFT and ab initio coupled cluster methods. Different reaction pathways, including Id, Ia, and possible alternative routes in the absence or presence of HPyr+, were considered, and enthalpy and free energies were calculated for each pathway. Our computational results further underscored that the Id route is energetically favored in the presence of HPyr+, in contrast with the preferred Ia-NNO pathway in the absence of HPyr+. Our computational results also revealed molecular-level details for the HPyr+-facilitated Id route. Specifically, HPyr+ initially becomes hydrogen-bonded to the oxygen atom of the Mo(IV)-OPMe3 moiety, which lowers the activation barrier for the Mo-OPMe3 bond cleavage in a rate-limiting step to dissociate the OPMe3 product. The implications of our results were discussed in the context of molybdoenzymes, particularly the reductive half-reaction of sulfite oxidase.
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Mirzaei S, Taherpour AA, Mohamadi S. Mechanistic study of allopurinol oxidation using aldehyde oxidase, xanthine oxidase and cytochrome P450 enzymes. RSC Adv 2016. [DOI: 10.1039/c6ra19197e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The oxidation reaction of allopurinol to its active metabolite (oxypurinol) is investigated using the AO and P450 enzymes. To the contrary of AO (and XO), the P450 enzyme can metabolize the allopurinol with a not self-inhibitory mechanism.
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Affiliation(s)
- Saber Mirzaei
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Avat Arman Taherpour
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
| | - Shahryar Mohamadi
- Department of Organic Chemistry
- Faculty of Chemistry
- Razi University
- Kermanshah
- Iran
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Heinze K. Bioinspired functional analogs of the active site of molybdenum enzymes: Intermediates and mechanisms. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.04.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Andrejić M, Mata RA. Local Hybrid QM/QM Calculations of Reaction Pathways in Metallobiosites. J Chem Theory Comput 2014; 10:5397-404. [DOI: 10.1021/ct5008313] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Milica Andrejić
- Institut
für Physikalische
Chemie, Georg-August-Universität Göttingen, Tammannstrasse
6, D-37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institut
für Physikalische
Chemie, Georg-August-Universität Göttingen, Tammannstrasse
6, D-37077 Göttingen, Germany
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Li J, Ryde U. Comparison of the Active-Site Design of Molybdenum Oxo-Transfer Enzymes by Quantum Mechanical Calculations. Inorg Chem 2014; 53:11913-24. [DOI: 10.1021/ic5010837] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jilai Li
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- State Key Laboratory of Theoretical and
Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical
Centre, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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A quantum-mechanical study of the reaction mechanism of sulfite oxidase. J Biol Inorg Chem 2014; 19:1165-79. [PMID: 24957901 DOI: 10.1007/s00775-014-1172-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 06/05/2014] [Indexed: 10/25/2022]
Abstract
The oxidation of sulfite to sulfate by two different models of the active site of sulfite oxidase has been studied. Both protonated and deprotonated substrates were tested. Geometries were optimized with density functional theory (TPSS/def2-SV(P)) and energies were calculated either with hybrid functionals and large basis sets (B3LYP/def2-TZVPD) including corrections for dispersion, solvation, and entropy, or with coupled-cluster theory (LCCSD(T0)) extrapolated toward a complete basis set. Three suggested reaction mechanisms have been compared and the results show that the lowest barriers are obtained for a mechanism where the substrate attacks a Mo-bound oxo ligand, directly forming a Mo-bound sulfate complex, which then dissociates into the products. Such a mechanism is more favorable than mechanisms involving a Mo-sulfite complex with the substrate coordinating either by the S or O atom. The activation energy is dominated by the Coulomb repulsion between the Mo complex and the substrate, which both have a negative charge of -1 or -2.
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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Liu P, Nicholas KM. Mechanism of Sulfite-Driven, MeReO3-Catalyzed Deoxydehydration of Glycols. Organometallics 2013. [DOI: 10.1021/om301251z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Liu
- Departments
of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California,
United States
| | - Kenneth M. Nicholas
- Departments of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
73019, United States
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Biaso F, Burlat B, Guigliarelli B. DFT Investigation of the Molybdenum Cofactor in Periplasmic Nitrate Reductases: Structure of the Mo(V) EPR-Active Species. Inorg Chem 2012; 51:3409-19. [DOI: 10.1021/ic201533p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frédéric Biaso
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bénédicte Burlat
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
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13
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Szaleniec M, Borowski T, Schühle K, Witko M, Heider J. Ab Inito Modeling of Ethylbenzene Dehydrogenase Reaction Mechanism. J Am Chem Soc 2010; 132:6014-24. [DOI: 10.1021/ja907208k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maciej Szaleniec
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Tomasz Borowski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Karola Schühle
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Malgorzata Witko
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
| | - Johann Heider
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland, and Laboratory of Microbial Biochemistry, Philipps-University of Marburg, Marburg, Germany
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Hadt RG, Nemykin VN, Olsen JG, Basu P. Comparative calculation of EPR spectral parameters in [Mo(V)OX4]-, [Mo(V)OX5]2-, and [Mo(V)OX4(H2O)]- complexes. Phys Chem Chem Phys 2009; 11:10377-84. [PMID: 19890522 PMCID: PMC2879133 DOI: 10.1039/b905554a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The EPR spectral parameters, i.e. g-tensors and molybdenum hyperfine couplings, for several d(1) systems of the general formula [Mo(V)EX(4)](n-), [Mo(V)OX(5)](2-), and [Mo(V)OX(4)(H(2)O)](-) (E = O, N; X = F, Cl, Br; n = 1 or 2) were calculated using Density Functional Theory. The influence of basis sets, their contraction scheme, the type of exchange-correlation functional, the amount of Hartree-Fock exchange, molecular geometry, and relativistic effects on the calculated EPR spectra parameters have been discussed. The g-tensors and molybdenum hyperfine coupling parameters were calculated using a relativistic Hamiltonian coupled with several LDA, GGA, and 'hybrid' exchange-correlation functionals and uncontracted full-electron DGauss DZVP basis sets. The calculated EPR parameters are found to be sensitive to the Mo=E distance and E=Mo-Cl angle, and thus the choice of starting molecular geometry should be considered as an important factor in predicting the g-tensors and hyperfine coupling constants in oxo-molybdenum compounds. In the present case, the GGA exchange-correlation functionals provide a better agreement between the theory and the experiment.
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Affiliation(s)
- Ryan G. Hadt
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Victor N. Nemykin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Joseph G. Olsen
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, USA.
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