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

• Published in: Nature communications Vol. 6; no. 1; p. 7890
• Main Authors: Ogata, Hideaki, Krämer, Tobias, Wang, Hongxin, Schilter, David, Pelmenschikov, Vladimir, van Gastel, Maurice, Neese, Frank, Rauchfuss, Thomas B., Gee, Leland B., Scott, Aubrey D., Yoda, Yoshitaka, Tanaka, Yoshihito, Lubitz, Wolfgang, Cramer, Stephen P.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.08.2015; Nature Publishing Group
• Subjects: 119/118; 639/638/11; 639/638/45/535; 639/638/45/56; 639/638/92/607; Desulfovibrio vulgaris - enzymology; Electrons; Enzymes; Fourier transforms; Humanities and Social Sciences; Hydrogenase - chemistry; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Magnetic Resonance Spectroscopy; multidisciplinary; Science; Science (multidisciplinary); California; United States > US; Illinois; Japan; Germany
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms8890

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 57 Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging’ mode involving H − motion perpendicular to the Ni( μ -H) 57 Fe plane was studied using 57 Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni( μ -D) 57 Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni( μ -H/D) 57 Fe enzyme mimics [(dppe)Ni( μ -pdt)( μ -H/D) 57 Fe(CO) 3 ] + and DFT calculations, which collectively indicate a low-spin Ni( II )( μ -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. Understanding the catalytic mechanism of redox-active hydrogenases is a key to efficient hydrogen production and consumption. Here, the authors use nuclear resonance vibrational spectroscopy to study [NiFe]-hydrogenase, and observe a bridging hydride structure in an EPR silent intermediate.