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]

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]

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

Biochemical classification

EC 1.2.1.2 [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 ([FeFe]), 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 [Fe]-hydrogenases, since this protein contains only a mononuclear Fe active site and no iron-sulfur clusters, in contrast to the [FeFe]-enzymes. In some [NiFe]-hydrogenases, one of the Ni-bound cysteine residues is replaced by selenocysteine. On the basis of sequence similarity, however, the [NiFe]- and [NiFeSe]-hydrogenases should be considered a single superfamily.

• The [NiFe]-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 the active site, a nickel-iron centre which is connected to the solvent by a molecular tunnel.^[6] Periplasmic, cytoplasmic, and cytoplasmic membrane-bound hydrogenases have been found. The [NiFe]-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 novel [NiFe] hydrogenases of Ralstonia eutropha are unlike typical [NiFe] hydrogenases because they are tolerant to oxygen and carbon monoxide.^[7]

• The hydrogenases containing Fe-S clusters and no metal other than iron are called [FeFe]-hydrogenases ([FeFe]-H₂ases).^[8] Three families of [FeFe]-H₂ases are recognized:

• • (I) cytoplasmic, soluble, monomeric [FeFe]-H₂ases, 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 [FeFe]-H₂ases from Desulfovibrio spp., which can be purified aerobically and catalyse mainly H₂ oxidation.

• • (III) soluble, monomeric [FeFe]-H₂ases, 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.

[NiFe]- and [FeFe]-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.^[9]

• 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 that was recently characterized by X-ray diffraction.^[10]

References

1. ^ Adams, M.W.W. and Stiefel, E.I. (1998). "Biological hydrogen production: Not so elementary". Science 282 (5395): 1842–1843. doi:10.1126/science.282.5395.1842. PMID 9874636. 
2. ^ Frey, M. (2002). "Hydrogenases: hydrogen-activating enzymes". ChemBioChem 3 (2-3): 153–160. doi:10.1002/1439-7633(20020301)3:2/3<153::AID-CBIC153>3.0.CO;2-B. PMID 11921392. 
3. ^ Vignais, P.M., Billoud, B. and Meyer, J. (2001). "Classification and phylogeny of hydrogenases". FEMS Microbiol. Rev. 25 (4): 455–501. PMID 11524134. 
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 (9): 6125–6132. doi:10.1074/jbc.M008470200. PMID 11096090. 
6. ^ Liebgott PP, Leroux F, Burlat B, Dementin S, Baffert C, Lautier T, Fourmond V, Ceccaldi P, Cavazza C, Meynial-Salles I, Soucaille P, Fontecilla-Camps JC, Guigliarelli B, Bertrand P, Rousset M, Léger C. (2010). "Relating diffusion along the substrate tunnel and oxygen sensitivity in hydrogenase.". Nat Chem Biol 6 (1): 63–70. doi:10.1038/nchembio.276. PMID 19966788. 
7. ^ Burgdorf, T., Buhrke, T., van der Linden, E., Jones, A., Albracht, S. and Friedrich, B. (2005). "[NiFe]-Hydrogenases of Ralstonia eutropha H16: Modular Enzymes for Oxygen-Tolerant Biological Hydrogen Oxidation". J Mol Microbiol Biotechnol 10: 181–196. doi:10.1159/000091564. PMID 16645314. 
8. ^ 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 (3): 138–143. doi:10.1016/S0968-0004(99)01536-4. PMID 10694885. 
9. ^ Fontecilla-Camps, J.C., Volbeda, A., Cavazza, C., Nicolet Y. (2007). "Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases". Chem Rev 107 (10): 4273–4303. doi:10.1021/cr050195z. PMID 17850165. 
10. ^ Shima, S., Pilak, O., Vogt, S., Schick, M., Stagni, M.S., Meyer-Klaucke, W., Warkentin, E., Thauer, R.K., Ermler, U. (2008). "The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site.". Science 321 (5888): 572–575. doi:10.1126/science.1158978. PMID 18653896. 

External links

• 2B0J - PDB Structure of the Apoenzyme of the Iron-sulphur cluster-free hydrogenase from Methanothermococcus jannaschii
• 1HFE - PDB structure of [FeFe]-hydrogenase from Desulfovibrio desulfuricans
• 1C4A - PDB structure of [FeFe]-hydrogenase from Clostridium pasteurianum
• 1UBR - PDB structure of [NiFe]-hydrogenase from Desulfovibrio vulgaris
• 1CC1 - PDB structure of [NiFeSe]-hydrogenase from Desulfomicrobium baculatum
• Animation - Mechanism of [NiFe]-hydrogenase