A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F

J Biol Inorg Chem. 2006 Jan;11(1):41-51. doi: 10.1007/s00775-005-0048-7. Epub 2005 Nov 16.

Abstract

The catalytic center of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in the oxidized states was investigated by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy applied to single crystals of the enzyme. The experimental results were compared with density functional theory (DFT) calculations. For the Ni-B state, three hyperfine tensors could be determined. Two tensors have large isotropic hyperfine coupling constants and are assigned to the beta-CH2 protons of the Cys-549 that provides one of the bridging sulfur ligands between Ni and Fe in the active center. From a comparison of the orientation of the third hyperfine tensor with the tensor obtained from DFT calculations an OH- bridging ligand has been identified in the Ni-B state. For the Ni-A state broader signals were observed. The signals of the third proton, as observed for the "ready" state Ni-B, were not observed at the same spectral position for Ni-A, confirming a structural difference involving the bridging ligand in the "unready" state of the enzyme.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Crystallization
  • Cysteine / chemistry
  • Desulfovibrio vulgaris / enzymology*
  • Electron Spin Resonance Spectroscopy / methods
  • Hydrogenase / chemistry*
  • Hydrogenase / metabolism
  • Ligands
  • Oxidation-Reduction
  • Protein Conformation
  • Protons
  • Sulfur / chemistry

Substances

  • Ligands
  • Protons
  • Sulfur
  • nickel-iron hydrogenase
  • Hydrogenase
  • Cysteine