Hydrogenase

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

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:

H₂ + A_ox → 2H⁺ + A_red (1)

2H⁺ + D_red → H₂ + D_ox (2)

Hydrogenases were first discovered in the 1930s, and they have attracted interest from many researchers. The mechanism of the catalysis of hydrogenase might help scientists design clean biological energy sources, such as algae, that produce hydrogen molecules.[1].

Contents 1 Biochemical classification 2 Structural classification 3 References 4 External links

[edit] 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

[edit] 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. 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 Achaea contains neither nickel nor iron-sulfur clusters but an iron-containing cofactor of yet unknown structure, presumably a pyridone GMP derivative

[edit] References

• Adams, M.W.W. and Stiefel, E.I. (1998). "Biological hydrogen production: Not so elementary". Science 282: 1842–1843. 
• 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. 
• Frey, M. (2002). "Hydrogenases: hydrogen-activating enzymes". ChemBioChem 3: 153–160. 
• 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. 
• Nicolet, Y., Piras, C., Legrand, P., Hatchikian, E.C. and Fontecilla-Camps, J.C. (1999). "Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center". Structure Fold. Des. 7: 13–23. 
• 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. 
• Peters, J.W., Lanzilotta, W.N., Lemon, B.J. and Seefeldt, L.C. (1998). "X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 Å resolution". Science 282: 1853–1858. 
• Vignais, P.M., Billoud, B. and Meyer, J. (2001). "Classification and phylogeny of hydrogenases". FEMS Microbiol. Rev. 25: 455–501. 
• Volbeda, A., Charon, M.-H., Piras, C., Hatchikian, E.C., Frey, M. and Fontecilla-Camps, J.C. (1995). "Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas". Nature 373: 580–587. 

[edit] External links

• 2B0J - PDB Structure of the Apoenzyme of the Iron-sulphur cluster-free hydrogenase from Methanothermococcus jannaschii
• 1HFE - PDB structure of Fe-only hydrogenase from Desulfovibrio desulfuricans
• 1C4A - PDB structure of Fe-only hydrogenase from Clostridium pasteurianum
• 1UBR - PDB structure of Ni-Fe hydrogenase from Desulfovibrio vulgaris
• 1CC1 - PDB structure of Ni-Fe-Se hydrogenase from Desulfomicrobium baculatum
• Animation - Mechanism of nickel-iron hydrogenase