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hydrogenase

 
American Heritage Dictionary:

hy·drog·e·nase

(hī-drŏj'ə-nās', -nāz') pronunciation
n.
An enzyme in certain microorganisms that catalyzes the hydrolysis or reduction of a substrate by molecular hydrogen.


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(hī-drŏj'ə-nās', -nāz')
n.

An enzyme in certain microorganisms that catalyzes the formation of hydrogen.


an enzyme that catalyses the production or consumption of dihydrogen. Hydrogen is produced by hydrogenases during the photosynthetic cleavage of water, and by fermentation processes in many anaerobic organisms. Hydrogen is also produced by nitrogenase as a by-product of the nitrogen-reducing reaction, but this enzyme not defined as a hydrogenase. Hydrogen is consumed by hydrogen-uptake hydrogenases in many bacteria, with the concomitant reduction of compounds such as oxygen, which is reduced to water, sulfate to sulfide, or carbon monoxide to methane. One of the most common hydrogen-consuming hydrogenases is hydrogen:quinone oxidoreductase, EC 1.12.7.2; in nitrogen-fixing bacteria, this enzyme recycles H2 produced by nitrogenase to increase the production of ATP and to protect nitrogenase against inhibition or damage by O2. In order to react with other electron carriers the hydrogenases employ various cosubstrates. Hydrogen dehydrogenase, EC 1.12.1.2, catalyses the reaction: H2 + NAD+ = H+ + NADH and contains FMN. This enzyme is structurally related to mitochondrial Complex I. EC 1.12.1.3 is similar, but reduces NADP+. Cytochrome-C3 hydrogenase, EC 1.12.2.1 is used by sulfate-reducing bacteria. Almost all hydrogenases are iron-sulfur proteins. The defining characteristic is an active site containing iron that has carbonyl and usually cyanide ligands. Two main nonhomologous classes are recognized: (1) hydrogenases containing an H cluster comprising a dimer of iron atoms linked to a [4Fe-4S] cluster,known as [Fe]- or [FeFe]-hydrogenases (see iron hydrogenase), and those containing nickel and iron (see nickel-iron-hydrogenase). In addition there is a third type, containing iron and no iron-sulfur clusters, of which the only example known so far is 5,10-methenyltetrahydromethanopterin hydrogenase (EC 1.12.98.2).

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An enzyme that catalyzes the reduction of various substances by combining them with molecular hydrogen.

Wikipedia on Answers.com:

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.[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 + Aox → 2H+ + Ared (1)
2H+ + Dred → H2 + Dox (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

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]

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

 
 
Related topics:
Coenzyme F420 hydrogenase
Ferredoxin hydrogenase
Cytochrome-c3 hydrogenase

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