Hydrogenase

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 + Aox &rarr; 2H+ + Ared (1)
 * 2H+ + Dred &rarr; H2 + Dox (2)

Hydrogenases were first discovered in the 1930s, 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..

Biochemical classification
EC 1.2.1.2 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 ([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. 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.


 * The hydrogenases containing Fe-S clusters and no metal other than iron are called [FeFe]-hydrogenases ([FeFe]-H2ases). 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.


 * 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.