N-O bond cleavage mechanism(s) in nitrous oxide reductase

Mehmed Z. Ertem, Chris Cramer, Fahmi Himo, Per E.M. Siegbahn

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

Quantum chemical calculations of active-site models of nitrous oxide reductase (N 2OR) have been undertaken to elucidate the mechanism of N-O bond cleavage mediated by the supported tetranuclear Cu 4S core (Cu Z) found in the enzymatic active site. Using either a minimal model previously employed by Gorelsky et al. (J. Am. Chem. Soc. 128:278-290, 2006) or a more extended model including key residue side chains in the active-site second shell, we found two distinct mechanisms. In the first model, N 2O binds to the fully reduced Cu Z in a bent μ-(1,3)-O,N bridging fashion between the Cu I and Cu IV centers and subsequently extrudes N 2 while generating the corresponding bridged μ-oxo species. In the second model, substrate N 2O binds loosely to one of the coppers of Cu Z in a terminal fashion, i.e., using only the oxygen atom; loss of N 2 generates the same μ-oxo copper core. The free energies of activation predicted for these two alternative pathways are sufficiently close to one another that theory does not provide decisive support for one over the other, posing an interesting problem with respect to experiments that might be designed to distinguish between the two. Effects of nearby residues and active-site water molecules are also explored.

Original languageEnglish (US)
Pages (from-to)687-698
Number of pages12
JournalJournal of Biological Inorganic Chemistry
Volume17
Issue number5
DOIs
StatePublished - Jun 2012

Bibliographical note

Funding Information:
Acknowledgments F.H. gratefully acknowledges financial support from the Swedish Research Council (grants 621-2009-4736 and 622-2009-371) and computer time from the PDC Center for High Performance Computing. C.J.C. and M.Z.E. thank the US National Science Foundation (CHE09-52054) for funding, and William B. Tolman for stimulating discussion.

Keywords

  • Density functional theory
  • Electronic structure
  • Molecular modeling
  • Transition state

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