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Scientists Determine Structure of Third Hydrogenase Enzyme; Insights Could Lead to Better Hydrogen Catalysts

Superimposed active-site structure of the three phylogenetically unrelated hydrogenases: [NiFe]-hydrogenase, [FeFe]-hydrogenase, and [Fe]-hydrogenase. Click to enlarge. Credit: Shima et al. (2008), Science

Some microbes use hydrogenases (enzymes) in their energy metabolism to catalyze H2/H+ interconversion reactions (H2 ⇋ 2H+ +2e–); these hydrogenases are more efficient catalysts than platinum, which is commonly used industrially to catalyze hydrogenation. There are three known and phylogenetically unrelated types of hydrogenases: [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenase.

The structures of the first two hydrogenases—which have a pair of metal atoms (either two iron atoms or an iron and a nickel atom) at their active sites—were known. Now, scientists in Germany have discovered the structure of the third type of hydrogenase—which has but the single iron atom at the active site—and shown that all three known hydrogenases have obvious structural similarities, including active sites that contain an iron atom linked to a CO group. Their work is reported in the 25 July issue of the journal Science.

The related iron ligation pattern of hydrogenases exemplifies convergent evolution and presumably plays an essential role in H2 activation. This finding may stimulate the ongoing synthesis of catalysts that could substitute for platinum in applications such as fuel cells.

—Shima et al. (2008)

The team, lead by led by Seigo Shima at the Max-Planck-Institut für Terrestrische Mikrobiologie and Ulrich Ermler at the Max-Planck-Institut für Biophysik, found several common structural features among the three different hydrogenases:

  • All three types contain a redox-inactive low-spin iron that is asymmetrically ligated by five or six ligands arranged as a distorted square pyramid or octahedron.

  • Three π-accepting ligands comprising CO, cyanide, or pyridinol (considered as a cyanide functional analog) are oriented perpendicular to each other in a geometrically related manner, and a thiolate sulfur always coordinates the iron trans to a diatomic molecule.

  • All three iron centers act together with a redox-active partner—methenyl-H4MPT+ in the case of [Fe]-hydrogenase, the distal iron in the case of [FeFe]-hydrogenase, and nickel in the case of [NiFe] hydrogenase—whose spatial position relative to the other ligands is also similar.

Apparently, these related iron centers, with unusual nonproteinaceous ligands thought to be synthesized by three different enzymatic machineries and embedded into three architecturally different hydrogenase structures, evolved independently. Remarkably, hydrogenases are the only metalloenzymes that use toxic CO and cyanide (or pyridinol) as metal ligands. Thus, hydrogenases are an impressive example of convergent evolutionary development as a consequence of specific biological and/or chemical restraints. However, the intrinsic physicochemical properties of the unique iron ligation pattern are not yet understood, nor are their implications for the technologically important H2 activation reaction.

—Shima et al. (2008)

The researchers also found that although there are structural similarities among the three, the [Fe]-hydrogenase uses a fundamentally different enzymatic mechanism from the other two because of the different nature of the redox-active partner and the accompanying electron delivery mode.

The [Fe]-hydrogenase reported by Shima et al. is different, because the hydride generated by splitting H2 is transferred directly to an electrophilic organic center in methenyl-tetrahydromethanopterin (methenyl-H4MPT), accomplishing a key stage in the reduction of CO2 to CH4...Only one metal is required for catalysis, which does not seem to require any formal change in oxidation state. In the classic [FeFe]- and [NiFe]-hydrogenases, the presumed role of the second metal is to orchestrate, in part or in full, the two one-electron transfers that subsequently convert H- to H+. The [Fe]-hydrogenase is thus very important for our understanding of H2 biocatalysis in general because it fulfills all the requirements for its activation and scission, the first stages of H2 oxidation by the classic hydrogenases.

...The remarkable convergent evolution that resulted in the presence of a common active-site Fe(CO)x(RS-) unit in all three classes of hydrogenases deserves a comment. The π-acceptor nature of CO (and hydrogen-bonded CN-) stabilizes low-spin, low-valence Fe with catalytic and hydride-binding properties that are normally found in second- and third-row transition metals, most notably platinum. Presumably, such metals were not available during evolution, and nature found a solution involving the much more common Fe ion and the abundant ligands CO and CN-.

—Armstrong and Fontecilla-Camps (2008)


  • Seigo Shima, Oliver Pilak, Sonja Vogt, Michael Schick, Marco S. Stagni, Wolfram Meyer-Klaucke, Eberhard Warkentin, Rudolf K. Thauer, Ulrich Ermler (2008) The Crystal Structure of [Fe]-Hydrogenase Reveals the Geometry of the Active Site. Science 25 July 2008: Vol. 321. no. 5888, pp. 572 - 575 doi: 10.1126/science.1158978

  • Fraser A. Armstrong and Juan C. Fontecilla-Camps (2008) A Natural Choice for Activating Hydrogen. Science 25 July 2008: Vol. 321. no. 5888, pp. 498 - 499 doi: 10.1126/science.1161326


Henry Gibson

Hydrogen is very expensive to make, transport and store, so it will never make a very good automobile fuel. It is cheaper and more efficient to store electricity in batteries in plug-in-hybrid-cars. Even lead batteries are more efficient than hydrogen. The ZEBRA battery or the Sodium sulphur battery may be the cheapest long distance batteries. Such batteries have a long life and when they have become too weak for running a car with high performance, they can be used at home to store energy for many more years. Individual failed cells can be replaced.

Fuel-cells are so much more expensive to build and operate than engines or batteries that they may never become cost competitive. Diesel engines are already more efficient than most production fuel cells on a well to wheels basis. Fuel cells also require a battery for regenerative braking and high power bursts as well as to operate the car while the fuel cell starts operating. Hydrogen burning very-high-compression engines are a much cheaper and efficient fuel cell replacement.

Plug-in-hybrids are not even a good use of the expensive fuel-cell because the goal is to mostly run on energy from the grid and the high expense of a fuel cell will be wasted. The engine of a car is wasted, to a degree, even now because the car is almost always parked.

A hydrogen fuel cell car or natural gas car might best leave the fuel cell or generator in the garage where the waste heat energy from the device can be used to heat water or cool the house while charging the car batteries for higher total efficiency. You can then buy expensive certified recycled carbon fuel for emergency use on the road in an ordinary engine.

Nuclear power plants are the lowest carbon producing sources of energy. Carlo Rubbia's energy amplifier allows for the full use of all uranium and thorium in the earth and the oceans, and makes use of all the uranium in the fuel not just a percent or so as now is done. All plutonium and other heavy metals are also used so none need be stored as nuclear wastes. Currently, spent fuel rods have at least 95% of their energy left, and it is known how to get all of it.

The real wastes, the split atoms, have such little volume that it is easy to store them cheaply in a way that reduces any danger to the public to far less than being killed as a pedestrian by a car on a cruise ship.

Nuclear waste transport will never result in the evacuation of a section of a town, such as has been caused by gasoline or chemical tankers or railcars... ..HG..


@ Henry Gibson

Hydrogen is not just a potential transportation fuel, it is an indispensable part of a wide range of industrial, and petrochemical processes. The current method of hydrogen production is very inefficient. Any new process that increases this efficiency is very welcome.

The ineffectiveness of the proponents of nuclear power is discouraging. Henry, I mean you, among many others.

What people want from nuclear power in order of priority is as follows:

1. Absolute safety in any conceivable situation.

2. No radiation no mater what.

3. No proliferation risk.

4. Little or no waste, no Yucca mountain, no waste transport.

5. High fuel utilization.

6. No fuel reprocessing.

7. Cheap constriction costs. $1000/kw or less.

8. Dirt cheap electricity costs, $.01/kwh or less.

9. Well tested in actual use over many years.

When you can justify these facts in your post, people might get interested. That sounds like a tough job. It is, but it’s possible.

Well, get on it.



Is that all?

How about cheaper than cheap negative or free (except on Sundays) nuclear electricity while you're at it.


You may be right. Very high efficiency nuclear power plants may be required to complement Sun and Wind power plants in many countries for many decades.

All electric personnal transportation vehicles is what we should be aiming at by 2020? Meanwhile, a mix of hybrids, PHEVs and first generation limited range BEVs (and a few die-hard ICE) will have to do for the next 10-15 years.

Fuel cells may evolve enough to meet the requirements for fixed applications, clean running ships, long haul trucks and buses and even clean running electric planes two or three decades from now.


After learning each step of Cellular Respiration and the final stage called Oxidative Phosphorylation, I asked myself, if single cells can easily cleave Hydrogen off of molecules, why cant we design something that can do the same? I am glad to see this progress, it may be the ultimate best way to produce hydrogen

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