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A quantum-mechanical study of the reaction mechanism of sulfite oxidase

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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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Acknowledgments

This investigation has been supported by grants from the Swedish research council (project 2010-5025), from the Swedish Institute, the Crafoord Foundation, the National Basic Research Program of China (973 Program, 2012CB932800), the National Natural Science Foundation of China (NSFC 21103064), and from COST through Action CM1003. It has also been supported by computer resources of Lunarc at Lund University. The collaboration between the Universities of Lund and Göttingen has been carried out within the framework of the International Research Training Group “Metal Sites in Biomolecules—Structures, Regulation, Mechanisms” and M. A. is supported through a Ph.D. scholarship in this International Research Training Group.

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Authors and Affiliations

  1. Theoretical Chemistry, Department of Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden

    Marie-Céline van Severen, Jilai Li & Ulf Ryde

  2. Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, 37077, Göttingen, Germany

    Milica Andrejić & Ricardo A. Mata

  3. State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People’s Republic of China

    Jilai Li

  4. Chemical Physics, Department of Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden

    Kerstin Starke & Ebbe Nordlander

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  1. Marie-Céline van Severen
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Correspondence to Ulf Ryde.

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van Severen, MC., Andrejić, M., Li, J. et al. A quantum-mechanical study of the reaction mechanism of sulfite oxidase. J Biol Inorg Chem 19, 1165–1179 (2014). https://doi.org/10.1007/s00775-014-1172-z

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