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Characterization of the active site of catalytically inactive forms of [NiFe] hydrogenases by density functional theory

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Abstract

The inactive forms, unready (Ni-A, Ni-SU) and ready (Ni-B), of NiFe hydrogenases are modeled by examining the possibility of hydroxo, oxo, hydroperoxo, peroxo, and sulfenate groups in active-site models and comparing predicted IR frequencies and g tensors with those of the enzyme. The best models for Ni-A and Ni-SU have hydroxo (μ-OH) bridges between Fe and Ni and a terminal sulfenate [Ni–S(=O)Cys] group, although a hydroperoxo model for Ni-A is also quite viable, whereas the best model for Ni-B has only a μ-OH bridge. In addition, a mechanism for the activation of unready hydrogenase is proposed on the basis of the relative stabilities of sulfenate models versus peroxide models.

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Acknowledgements

We thank the Laboratory for Molecular Simulation and the Supercomputing Facility at Texas A&M University for providing software and computer time for the theoretical calculations. Financial support of this research from The Welch Foundation (A-0648), The National Science Foundation (CHE 9800184, CHE 0518074, DMS 0216275) and The Spanish Ministry of Science and Technology (BQU2003–04221) is gratefully acknowledged.

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Authors and Affiliations

  1. Instituto de Catalisis, CSIC, c/ Marie Curie, 2, Campus Cantoblanco, 28049, Madrid, Spain

    Alejandro Pardo, Antonio L. De Lacey & Víctor M. Fernández

  2. Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX, 77843-3255, USA

    Yubo Fan & Michael B. Hall

Authors
  1. Alejandro Pardo
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  2. Antonio L. De Lacey
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  3. Víctor M. Fernández
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  4. Yubo Fan
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  5. Michael B. Hall
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Correspondence to Michael B. Hall.

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Pardo, A., De Lacey, A.L., Fernández, V.M. et al. Characterization of the active site of catalytically inactive forms of [NiFe] hydrogenases by density functional theory. J Biol Inorg Chem 12, 751–760 (2007). https://doi.org/10.1007/s00775-007-0227-9

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  • DOI: https://doi.org/10.1007/s00775-007-0227-9

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