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The mechanism of formate oxidation by metal-dependent formate dehydrogenases

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Abstract

Metal-dependent formate dehydrogenases (Fdh) from prokaryotic organisms are members of the dimethyl sulfoxide reductase family of mononuclear molybdenum-containing and tungsten-containing enzymes. Fdhs catalyze the oxidation of the formate anion to carbon dioxide in a redox reaction that involves the transfer of two electrons from the substrate to the active site. The active site in the oxidized state comprises a hexacoordinated molybdenum or tungsten ion in a distorted trigonal prismatic geometry. Using this structural model, we calculated the catalytic mechanism of Fdh through density functional theory tools. The simulated mechanism was correlated with the experimental kinetic properties of three different Fdhs isolated from three different Desulfovibrio species. Our studies indicate that the C–H bond break is an event involved in the rate-limiting step of the catalytic cycle. The role in catalysis of conserved amino acid residues involved in metal coordination and near the metal active site is discussed on the basis of experimental and theoretical results.

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Abbreviations

DFT:

Density functional theory

ES:

Enzyme–substrate

Fdh:

Formate dehydrogenase

PDB:

Protein Data Bank

SeCys:

Selenocysteine

Si :

Inorganic sulfur atom

Tris–HCl:

Tris(hydroxymethyl)aminomethane hydrochloride

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Acknowledgments

C.S.M. thanks Fundação para a Ciência e a Tecnologia for funding (grant SFRH/BD/32478/2006). P.J.G. and N.M.F.S.A.C. thank Programa Ciência 2007 and 2008 of Fundação para a Ciência e a Tecnologia. This work was supported by projects PDCT/QUI/57701/2004 and PTDC/QUI/67052/2006 in Portugal and CAID-UNL, CONICET, and SEPCYT in Argentina. C.D.B. thanks to CONICET (Argentina).

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Authors and Affiliations

  1. REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal

    Cristiano S. Mota, Maria G. Rivas, Isabel Moura, José J. G. Moura & Pablo J. González

  2. Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, S3000ZAA, Santa Fe, Argentina

    Carlos D. Brondino

  3. REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal

    Nuno M. F. S. A. Cerqueira

Authors
  1. Cristiano S. Mota
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  2. Maria G. Rivas
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  3. Carlos D. Brondino
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  4. Isabel Moura
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  5. José J. G. Moura
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  6. Pablo J. González
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  7. Nuno M. F. S. A. Cerqueira
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Corresponding authors

Correspondence to José J. G. Moura, Pablo J. González or Nuno M. F. S. A. Cerqueira.

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Mota, C.S., Rivas, M.G., Brondino, C.D. et al. The mechanism of formate oxidation by metal-dependent formate dehydrogenases. J Biol Inorg Chem 16, 1255–1268 (2011). https://doi.org/10.1007/s00775-011-0813-8

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  • DOI: https://doi.org/10.1007/s00775-011-0813-8

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