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Successful Observation of Vibration States of the Enzymic Active Center in Hydrogenase (Press Release)

Release Date
29 Nov, 2012
  • BL09XU (Nuclear Resonant Scattering)
- A new possibility for research aiming at actualization of a sustainable-hydrogen society -

Japan Synchrotron Radiation Research Institute

Researchers at Japan Synchrotron Radiation Research Institute (JASRI) successfully used the high intensity X-ray available at SPring-8*1 to observe vibration states of the active center*2 of hydrogenase. The research was conducted in collaboration with the University of California (Davis), Max Planck Institutes, Lawrence Berkley National Laboratory, University of Illinois, Université d'Aix-Marseille, Centre national de la recherche scientifique, Philadelphia College of Osteopathic Medicine, University of Georgia, and Argonne National Laboratory

The establishment of highly effective methods for generating hydrogen - which may involve the development of an economic and efficient catalyst and the utilization of natural energy - is integral to help actualize a sustainable-hydrogen society, where clean hydrogen is used as a major energy source.

Hydrogenase is a native enzyme that exhibits catalytic action both in the generation and decomposition of hydrogen molecules. It is gaining special attention for its potentially economic structure: it exploits the capability of a naturally abundant element, such as Ni and Fe instead of costly precious metals such as Pt, in the core of its catalyst activity mechanism. The details of its activity mechanism, however, have been little known because of its highly complex molecular structure.

In this research, the first successful vibration state observation of hydrogenase’s active center - the catalyst site that governs generation/decomposition reactions of hydrogen molecules - was made by means of the nuclear resonance vibration spectroscopy (NRVS)*3. The results obtained are expected to accelerate research aimed at clarifying an overall picture of the activity mechanism inherent to hydrogenase, as well as to provide a novel approach for the development of a very efficient hydrogen generation technique required for the realization of a sustainable hydrogen society.

The results reported here were obtained through collaborative research carried out by Dr. Yoshitaka Yoda (principal researcher, JASRI) and an international research group whose members include Prof. Cramer (University of California) and Prof. Lubitz (Max Planck Institute).

The research results are scheduled for publication as a cover article in Angewandte Chemie International Edition (2nd issue, 2013), a German scientific journal with established worldwide influence in many areas of chemistry. They have already been published in the online version of the journal, on November 8, 2012.

"Observation of the Fe-CN and Fe-CO Vibrations in the Active Site of [NiFe] Hydrogenase by Nuclear Resonance Vibrational Spectroscopy"
S. Kamali, H. Wang, D. Mitra, H. Ogata, W. Lubitz, B.C. Manor, T.B. Rauchfuss, D. Byrne, V. Bonnefoy, F.E. Jenney Jr., M.W.W. Adams, Y. Yoda, E. Alp, J. Zhao, and S.P. Cramer
Angewandte Chemie international Edition


Fig.1 Molecular structure of hydrogenase
Fig.1 Molecular structure of hydrogenase

The site labeled as “Ni-Fe” indicates the active center that provides catalytic activities for creation and decomposition of hydrogen molecules.

Fig.2 The NRVS spectrum of hydrogenase and the estimated active center structure
Fig.2 The NRVS spectrum of hydrogenase and the estimated active center structure

The regions labeled as “Fe-S,” “Fe-CN,” and “Fe-CO” indicate the vibration modes assigned respectively to Fe-Sulphur, Fe-Carbon monoxide, and Fe-Cyano group bindings (red: oxidized state, blue: reduced state)

*1 SPring-8

A RIKEN facility located in Harima Science Garden City (Hyogo prefecture) is capable of producing the world's highest intensity synchronous radiation. The management and promotion of utilization of this facility are undertaken by JASRI. The name “SPring-8” comes from “Super Photon ring-8GeV.” An electron flying at nearly the speed of light, if deflected from its original trajectory through the effect exerted by a magnet, emits an electromagnetic wave in a direction tangential to its trajectory, which is called radiation light (or synchrotron radiation). At present, there are three “3rd Generation” large scale synchronous radiation facilities in the world: SPring-8 (Japan), APS (USA) and ESRF (France). The acceleration energy available at SPring-8 (8 billion electron volts) enables the provision of an extremely wide spectrum of radiation light: from far infrared to visible, vacuum ultraviolet, and soft X-ray up to hard X-ray. SPring-8 provides a theater for collaborative works involving researchers inside and outside Japan, and the research conducted at this facility cover such diverse areas as material science, geoscience, life science, environmental science, and various applications in industrial sectors.

*2 Active center
The site in an enzyme where catalytic reactions - highly selective binding reactions among substrates - take place. An active center that includes a metallic atom is called a metal-activated enzyme and plays an important role in a variety of scenes that support vital activities.

*3 Nuclear resonance vibration spectroscopy (NRVS)
A type of X-ray-based vibrational spectroscopic method: an X-ray, with an energy range near the resonance levels of the target atom, is irradiated to excite the atomic nucleus in the sample for the analysis of vibrational transitions, typically associated with phonon creation/annihilation. Taking advantage of the fact that each atomic species has its own characteristic energy levels with energy widths that are usually very narrow, the key feature of this method is its ability to focus on the vibration measurement of a specific atomic species. The method was first demonstrated in 1995 by Seto, et.al.

For more information, please contact:
  Dr. Yoshitaka Yoda (JASRI)
   E-mail : mail1

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