Hydrogenase

A hydrogenase is an enzyme that catalyses the reversible oxidation of molecular hydrogen (H₂). Hydrogenases play a vital role in anaerobic metabolism. [cite journal | author=Adams, M.W.W. and Stiefel, E.I. | title=Biological hydrogen production: Not so elementary | journal=Science | year=1998 | volume=282 | pages=1842–1843 | doi=10.1126/science.282.5395.1842 | pmid=9874636] [cite journal | author=Frey, M. | title=Hydrogenases: hydrogen-activating enzymes | journal=ChemBioChem | year=2002 | volume=3 | pages=153–160 | doi=10.1002/1439-7633(20020301)3:2/3<153::AID-CBIC153>3.0.CO;2-B]

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 "c"₃, and cytochrome "c"₆ can act as physiological electron donors (D) or acceptors (A) for hydrogenases: [ cite journal | author=Vignais, P.M., Billoud, B. and Meyer, J. | title=Classification and phylogeny of hydrogenases | journal=FEMS Microbiol. Rev. | year=2001 | volume=25 | pages=455–501] : H₂ + A_ox &rarr; 2H⁺ + A_red (1): 2H⁺ + D_red &rarr; H₂ + D_ox (2)

Hydrogenases were first discovered in the 1930s, [Thauer, R. K., "Biochemistry of methanogenesis: a tribute to Marjory Stephenson", Microbiology, 1998, 144, 2377-2406.] 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.. [http://www.wired.com/news/technology/0,70273-0.html?tw=rss.index] . [cite journal | author=Florin, L., Tsokoglou, A. and Happe, T. | title=A novel type of iron hydrogenase in the green alga "Scenedesmus obliquus" is linked to the photosynthetic electron transport chain | journal=J. Biol. Chem. | year=2001 | volume=276 | pages=6125–6132 | doi=10.1074/jbc.M008470200 | pmid=11096090]

Biochemical classification

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.1.2 1.12.1.2] hydrogen dehydrogenase (hydrogen:NAD⁺ oxidoreductase): H₂ + NAD⁺ = H⁺ + NADH

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.1.3 1.12.1.3] hydrogen dehydrogenase (NADP) (hydrogen:NADPH⁺ oxidoreductase): H₂ + NADP⁺ = H⁺ + NADPH

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.2.1 1.12.2.1] cytochrome-"c"₃ hydrogenase (hydrogen:ferricytochrome-"c"₃ oxidoreductase): 2H₂ + ferricytochrome "c"₃ = 4H⁺ + ferrocytochrome "c"₃

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.7.2 1.12.7.2] ferredoxin hydrogenase (hydrogen:ferredoxin oxidoreductase): H₂ + oxidized ferredoxin = 2H⁺ + reduced ferredoxin

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.98.1 1.12.98.1] coenzyme F₄₂₀ hydrogenase (hydrogen:coenzyme F₄₂₀ oxidoreductase): H₂ + coenzyme F₄₂₀ = reduced coenzyme F₄₂₀

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.99.6 1.12.99.6] hydrogenase (acceptor) (hydrogen:acceptor oxidoreductase): H₂ + A = AH₂

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.5.1 1.12.5.1] hydrogen:quinone oxidoreductase: H₂ + menaquinone = menaquinol

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.98.2 1.12.98.2] 5,10-methenyltetrahydromethanopterin hydrogenase (hydrogen:5,10-methenyltetrahydromethanopterin oxidoreductase): H₂ + 5,10-methenyltetrahydromethanopterin = H⁺ + 5,10-methylenetetrahydromethanopterin

EC [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.98.3 1.12.98.3] "Methanosarcina"-phenazine hydrogenase [hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase] : H₂ + 2-(2,3-dihydropentaprenyloxy)phenazine = 2-dihydropentaprenyloxyphenazine

tructural 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 "c"₃ 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. [cite journal | author=Nicolet, Y., Lemon, B.J., Fontecilla-Camps, J.C. and Peters, J.W. | title=A novel FeS cluster in Fe-only hydrogenases | journal=Trends Biochem.Sci. | year=2000 | volume=25 | pages=138–143 | doi=10.1016/S0968-0004(99)01536-4] 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 [http://www.expasy.org/cgi-bin/get-enzyme-entry?1.12.98.2 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. [cite journal | author=Lyon, E.J., Shima, S., Boecher, R., Thauer, R.K., Grevels, F.-W., Bill, E., Roseboom, W. and Albracht, S.P.J. | title=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 | journal=J. Am. Chem. Soc. | year=2004 | volume=126 | pages=14239–14248 | doi=10.1021/ja046818s]

References

External links

* [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=2B0J 2B0J] - PDB Structure of the Apoenzyme of the Iron-sulphur cluster-free hydrogenase from "Methanothermococcus jannaschii"
* [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1HFE 1HFE] - PDB structure of Fe-only hydrogenase from "Desulfovibrio desulfuricans"
* [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1C4A 1C4A] - PDB structure of Fe-only hydrogenase from "Clostridium pasteurianum"
* [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1UBR 1UBR] - PDB structure of Ni-Fe hydrogenase from "Desulfovibrio vulgaris"
* [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1CC1 1CC1] - PDB structure of Ni-Fe-Se hydrogenase from "Desulfomicrobium baculatum"
* [http://www.kcl.ac.uk/ip/richardcammack/H2/animation/movie1.html Animation] - Mechanism of nickel-iron hydrogenase