Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

Hideaki Ogata, Tobias Kraemer, Hongxin Wang, Maurice van Gastel, Frank Neese, Thomas B. Rauchfuss, David Schilter, Vladimir Pelmenschikov, Leland B. Gee, Aubrey D. Scott, Yoshitaka Yoda, Yoshihito Tanaka, Wolfgang Lubitz, Stephen P. Cramer

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Abstract

The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the Fe-57-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique 'wagging' mode involving H- motion perpendicular to the Ni(mu-H)Fe-57 plane was studied using Fe-57-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(mu-D)Fe-57 deuteride substitution, this wagging causes a characteristic perturbation of Fe-CO/CN bands. Spectra have been interpreted by comparison with Ni(mu-H/D)Fe-57 enzyme mimics [(dppe)Ni(mu-pdt)(mu-H/D)Fe-57(CO) 3](+) and DFT calculations, which collectively indicate a low-spin Ni(II)(mu-H)Fe(II) core for Ni-R, with H- binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe-H moieties in other important natural and synthetic catalysts.

Original languageEnglish
Article number7890
Number of pages8
JournalNature Communications
Volume6
DOIs
Publication statusPublished - 10 Aug 2015

Keywords

  • DENSITY-FUNCTIONAL CALCULATIONS
  • NICKEL-IRON HYDROGENASE
  • NI-FE HYDROGENASES
  • ACTIVE-SITE
  • RAMAN-SPECTROSCOPY
  • DESULFOVIBRIO-GIGAS
  • ENZYMATIC MECHANISM
  • AQUIFEX-AEOLICUS
  • CATALYTIC CYCLE
  • 4FE-4S CLUSTER

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