Hydrogenase

A hydrogenase is an enzyme that catalyses the reversible oxidation of molecular hydrogen (H₂). Hydrogenases play a vital role in anaerobic metabolism.^[1][2]

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Hydrogen uptake (H₂ oxidation) (1) is coupled to the reduction of electron acceptors such as oxygen, nitrate, sulfate, carbon dioxide, and fumarate, whereas proton reduction (H₂ evolution) (2) is essential in pyruvate fermentation and in the disposal of excess electrons. Both low-molecular weight compounds and proteins such as ferredoxins, cytochrome c₃, and cytochrome c₆ can act as physiological electron donors (D) or acceptors (A) for hydrogenases:^[3]

H₂ + A_ox → 2H⁺ + A_red (1)

2H⁺ + D_red → H₂ + D_ox (2)

Hydrogenases were first discovered in the 1930s,^[4] and they have since attracted interest from many researchers including inorganic chemists who have synthesized a variety of hydrogenase mimics. Understanding the catalytic mechanism of hydrogenase might help scientists design clean biological energy sources, such as algae, that produce hydrogen..[1].^[5]

Biochemical classification

EC 1.12.1.2 hydrogen dehydrogenase (hydrogen:NAD⁺ oxidoreductase)

H₂ + NAD⁺ = H⁺ + NADH

EC 1.12.1.3 hydrogen dehydrogenase (NADP) (hydrogen:NADPH⁺ oxidoreductase)

H₂ + NADP⁺ = H⁺ + NADPH

EC 1.12.2.1 cytochrome-c₃ hydrogenase (hydrogen:ferricytochrome-c₃ oxidoreductase)

2H₂ + ferricytochrome c₃ = 4H⁺ + ferrocytochrome c₃

EC 1.12.7.2 ferredoxin hydrogenase (hydrogen:ferredoxin oxidoreductase)

H₂ + oxidized ferredoxin = 2H⁺ + reduced ferredoxin

EC 1.12.98.1 coenzyme F₄₂₀ hydrogenase (hydrogen:coenzyme F₄₂₀ oxidoreductase)

H₂ + coenzyme F₄₂₀ = reduced coenzyme F₄₂₀

EC 1.12.99.6 hydrogenase (acceptor) (hydrogen:acceptor oxidoreductase)

H₂ + A = AH₂

EC 1.12.5.1 hydrogen:quinone oxidoreductase

H₂ + menaquinone = menaquinol

EC 1.12.98.2 5,10-methenyltetrahydromethanopterin hydrogenase (hydrogen:5,10-methenyltetrahydromethanopterin oxidoreductase)

H₂ + 5,10-methenyltetrahydromethanopterin = H⁺ + 5,10-methylenetetrahydromethanopterin

EC 1.12.98.3 Methanosarcina-phenazine hydrogenase [hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase]

H₂ + 2-(2,3-dihydropentaprenyloxy)phenazine = 2-dihydropentaprenyloxyphenazine

Structural classification

Until 2004, hydrogenases were classified according to the metals thought to be at their active sites; three classes were recognized: iron-only (Fe-only), nickel-iron (NiFe), and "metal-free". In 2004, Thauer et al. showed that the metal-free hydrogenases in fact contain iron. Thus, those enzymes previously called "metal-free" are now named "FeS-free", since this protein contains no inorganic sulfide in contrast to the Fe-only enzymes. In some Ni-Fe hydrogenases, one of the Ni-bound cysteine residues is replaced by selenocysteine. On the basis of sequence similarity, however, the Ni-Fe and Ni-Fe-Se hydrogenases should be considered a single superfamily.

• The Ni-Fe hydrogenases are heterodimeric proteins consisting of small (S) and large (L) subunits. The small subunit contains three iron-sulfur clusters while the large subunit contains a nickel-iron centre. Periplasmic, cytoplasmic, and cytoplasmic membrane-bound hydrogenases have been found. The Ni-Fe hydrogenases, when isolated, are found to catalyse both H₂ evolution and uptake, with low-potential multihaem cytochromes such as cytochrome c₃ acting as either electron donors or acceptors, depending on their oxidation state.

• The hydrogenases containing Fe-S clusters and no other metal than iron are called Fe-hydrogenases ("Fe-Hases") or Fe-only hydrogenases.^[6] Three families of Fe-Hases are recognized:

• • (I) cytoplasmic, soluble, monomeric Fe-Hases, found in strict anaerobes such as Clostridium pasteurianum and Megasphaera elsdenii. They are extremely sensitive to inactivation by dioxygen (O₂) and catalyse both H₂ evolution and uptake.

• • (II) periplasmic, heterodimeric Fe-Hases from Desulfovibrio spp., which can be purified aerobically and catalyse mainly H₂ oxidation.

• • (III) soluble, monomeric Fe-Hases, found in chloroplasts of green alga Scenedesmus obliquus, catalyses H₂ evolution. The [Fe₂S₂] ferredoxin functions as natural electron donor linking the enzyme to the photosynthetic electron transport chain.

Ni-Fe and Fe-only hydrogenases have some common features in their structures: each enzyme has an active site and a few Fe-S clusters that are buried in protein. The active site, which is believed to be the place where catalysis takes place, is also a metallocluster, and each metal is coordinated by carbon monoxide (CO) and cyanide (CN^-) ligands.

• 5,10-methenyltetrahydromethanopterin hydrogenase (EC 1.12.98.2) found in methanogenic Archaea contains neither nickel nor iron-sulfur clusters but an iron-containing cofactor of yet unknown structure, presumably a pyridone GMP derivative.^[7]

References

1. ^ Adams, M.W.W. and Stiefel, E.I. (1998). "Biological hydrogen production: Not so elementary". Science 282: 1842–1843.
2. ^ Frey, M. (2002). "Hydrogenases: hydrogen-activating enzymes". ChemBioChem 3: 153–160.
3. ^ Vignais, P.M., Billoud, B. and Meyer, J. (2001). "Classification and phylogeny of hydrogenases". FEMS Microbiol. Rev. 25: 455–501.
4. ^ Thauer, R. K., "Biochemistry of methanogenesis: a tribute to Marjory Stephenson", Microbiology, 1998, 144, 2377-2406.
5. ^ Florin, L., Tsokoglou, A. and Happe, T. (2001). "A novel type of iron hydrogenase in the green alga Scenedesmus obliquus is linked to the photosynthetic electron transport chain". J. Biol. Chem. 276: 6125–6132.
6. ^ Nicolet, Y., Lemon, B.J., Fontecilla-Camps, J.C. and Peters, J.W. (2000). "A novel FeS cluster in Fe-only hydrogenases". Trends Biochem.Sci. 25: 138–143.
7. ^ Lyon, E.J., Shima, S., Boecher, R., Thauer, R.K., Grevels, F.-W., Bill, E., Roseboom, W. and Albracht, S.P.J. (2004). "Carbon monoxide as an intrinsic ligand to iron in the active site of the iron-sulfur-cluster-free hydrogenase H₂-forming methylenetetrahydromethanopterin dehydrogenase as revealed by infrared spectroscopy". J. Am. Chem. Soc. 126: 14239–14248.