Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy
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 57Fe-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)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(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. Lastly, the present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts.
- Authors:
-
- Max Planck Inst. for Chemical Energy Conversion, Mulheim, (Germany)
- Univ. of California, Davis, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Univ. of Illinois, Urbana, IL (United States)
- Technical Univ. Berlin (Germany)
- Univ. of California, Davis, CA (United States)
- SPring-8/JASRI, Hyogo (Japan)
- RIKEN SPring-8, Hyogo (Japan)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1256036
- Grant/Contract Number:
- FG02-90ER14146
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Citation Formats
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, and Cramer, Stephen P.. Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy. United States: N. p., 2015.
Web. doi:10.1038/ncomms8890.
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.. Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy. United States. https://doi.org/10.1038/ncomms8890
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, and Cramer, Stephen P.. Mon .
"Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy". United States. https://doi.org/10.1038/ncomms8890. https://www.osti.gov/servlets/purl/1256036.
@article{osti_1256036,
title = {Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy},
author = {Ogata, Hideaki and Krämer, Tobias and Wang, Hongxin and Schilter, David and Pelmenschikov, Vladimir and van Gastel, Maurice and Neese, Frank and Rauchfuss, Thomas B. and Gee, Leland B. and Scott, Aubrey D. and Yoda, Yoshitaka and Tanaka, Yoshihito and Lubitz, Wolfgang and Cramer, Stephen P.},
abstractNote = {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 57Fe-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)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(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. Lastly, the present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts.},
doi = {10.1038/ncomms8890},
journal = {Nature Communications},
number = ,
volume = 6,
place = {United States},
year = {Mon Aug 10 00:00:00 EDT 2015},
month = {Mon Aug 10 00:00:00 EDT 2015}
}
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High level ab initio and DFT calculations of models of the catalytically active Ni–Fe hydrogenases
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Nuclear resonance vibrational spectroscopic and computational study of high-valent diiron complexes relevant to enzyme intermediates
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Nuclear resonant spectroscopy
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- Sturhahn, Wolfgang
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Vibrational dynamics (IR, Raman, NRVS) and a DFT study of a new antitumor tetranuclearstannoxane cluster, Sn( iv )-oxo-{di-o-vanillin} dimethyl dichloride
journal, January 2016
- Arjmand, F.; Sharma, S.; Usman, M.
- Physical Chemistry Chemical Physics, Vol. 18, Issue 27
Comprehensive reaction mechanisms at and near the Ni–Fe active sites of [NiFe] hydrogenases
journal, January 2018
- Tai, Hulin; Higuchi, Yoshiki; Hirota, Shun
- Dalton Transactions, Vol. 47, Issue 13
Coumarin centered copper( ii ) complex with appended-imidazole as cancer chemotherapeutic agents against lung cancer: molecular insight via DFT-based vibrational analysis
journal, January 2017
- Usman, Mohammad; Zaki, Mehvash; Khan, Rais Ahmad
- RSC Advances, Vol. 7, Issue 57
Edwardsiella tarda Sip2: A Serum-Induced Protein That Is Essential to Serum Survival, Acid Resistance, Intracellular Replication, and Host Infection
journal, May 2018
- Li, Mo-fei; Sun, Li
- Frontiers in Microbiology, Vol. 9
Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes
journal, October 2016
- Serrano, Pauline N.; Wang, Hongxin; Crack, Jason C.
- Angewandte Chemie, Vol. 128, Issue 47
High-Frequency Fe-H Vibrations in a Bridging Hydride Complex Characterized by NRVS and DFT
journal, June 2018
- Pelmenschikov, Vladimir; Gee, Leland B.; Wang, Hongxin
- Angewandte Chemie International Edition, Vol. 57, Issue 30
Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes
journal, October 2016
- Serrano, Pauline N.; Wang, Hongxin; Crack, Jason C.
- Angewandte Chemie, Vol. 128, Issue 47
What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes
journal, September 2017
- Scheidt, W. Robert; Li, Jianfeng; Sage, J. Timothy
- Chemical Reviews, Vol. 117, Issue 19
QM/MM Investigation of the Role of a Second Coordination Shell Arginine in [NiFe]-Hydrogenases
journal, May 2018
- Escorcia, Andrés M.; Stein, Matthias
- Frontiers in Chemistry, Vol. 6
Edwardsiella tarda Sip2: A Serum-Induced Protein That Is Essential to Serum Survival, Acid Resistance, Intracellular Replication, and Host Infection
journal, May 2018
- Li, Mo-fei; Sun, Li
- Frontiers in Microbiology, Vol. 9