- (1) H2 + Aox → 2H+ + Ared
- (2) 2H+ + Dred → H2 + Dox
Hydrogen uptake (1) is coupled to the reduction of electron acceptors such as oxygen, nitrate, sulfate, carbon dioxide, and fumarate. On the other hand, proton reduction (2) is coupled to the oxidation of electron donors such as ferredoxin (FNR), and serves to dispose excess electrons in cells (essential in pyruvate fermentation). Both low-molecular weight compounds and proteins such as FNRs, cytochrome c3, and cytochrome c6 can act as physiological electron donors or acceptors for hydrogenases.
Structural classification 
Hydrogenases are classified as one of the following three types based on metal atoms composing the active site: [NiFe], [FeFe], and [Fe]-only. Until 2004, the [Fe]-only hydrogenase was believed to be "metal-free". Then, Thauer et al. showed that the metal-free hydrogenases in fact contain iron atom in its active site. As a result, those enzymes previously classified as "metal-free" are now named [Fe]-only hydrogenases. This protein contains only a mononuclear Fe active site and no iron-sulfur clusters, in contrast to the [FeFe] hydrogenases. [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.
[NiFe] hydrogenase 
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. 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. To date, 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. Generally speaking, however, [NiFe] hydrogenases are more active in oxidizing H2.
Like [FeFe] hydrogenases, [NiFe] hydrogenases are known to be deactivated by molecular oxygen (O2). Recently, a novel hydrogenase from Ralstonia eutropha have been found to be oxygen-tolerant. This finding increased hope that hydrogenases can be used in photosynthetic production of molecular hydrogen via splitting water.
[FeFe] hydrogenase 
The hydrogenases containing Fe-S clusters and no metal other than iron are called [FeFe] hydrogenases. Three families of [FeFe] hydrogenases are recognized:
• cytoplasmic, soluble, monomeric hydrogenases, 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.
• periplasmic, heterodimeric hydrogenases from Desulfovibrio spp., which can be purified aerobically and catalyse mainly H2 oxidation.
• soluble, monomeric hydrogenases, 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.
In contrast to [NiFe] hydrogenases, [FeFe] hydrogenases are generally more active in production of molecular hydrogen. Turnover frequency (TOF) in the order of 10,000 s-1 have been reported in literature for [FeFe] hydrogenases from clostridium pasteurianum. This has led to intense research focusing on use of [FeFe] hydrogenase for sustainable production of H2.
[Fe]-only hydrogenase 
5,10-methenyltetrahydromethanopterin hydrogenase (EC 18.104.22.168) found in methanogenic Archaea contains neither nickel nor iron-sulfur clusters but an iron-containing cofactor that was recently characterized by X-ray diffraction.
Unlike the other two types, [Fe]-only hydrogenases are found only in some hydrogenotrophic methanogenic archaea. They also feature a fundamentally different enzymatic mechanism in terms of redox partners and how electrons are delivered to the active site. In [NiFe] and [FeFe] hydrogenases, electrons travel through a series of metallorganic clusters that comprise a long distance; the active site structures remain unchanged during the whole process. In [Fe]-only hydrogenases, however, electrons are directly delivered to the active site via a short distance. Methenyl-H4MPT+, a cofactor, directly accepts the hydride from H2 in the process. [Fe]-only hydrogenase is also known as H2-forming methylenetetrahydromethanopterin (methylene-H4MPT) dehydrogenase, because its function is the reversible reduction of methenyl-H4MPT+ to methylene-H4MPT. The hydrogenation of a methenyl-H4MPT+ occurs instead of H2 oxidation/production, which is the case for the other two types of hydrogenases. While the exact mechanism of the catalysis is still under study, recent finding suggests that molecular hydrogen is first heterolytically cleaved by Fe(II), followed by transfer of hydride to the carbocation of the acceptor.
The molecular mechanism by which protons are converted into hydrogen molecules within hydrogenases is still under extensive study. One popular approach employs mutagenesis to elucidate roles of amino acids and/or ligands in different steps of catalysis such as intramolecular transport of substrates. For instance, Cornish et al. conducted mutagenesis studies and found out that four amino acids located along the putative channel connecting the active site and protein surface are critical to enzymatic function of [FeFe] hydrogenase from clostridium pasteurianum (CpI).  On the other hand, one can also rely on computational analysis and simulations. Lill and Siegbahn have recently taken this approach in investigating the mechanism by which [NiFe] hydrogenases catalyze H2 cleavage. The two approaches are complementary and can benefit one another. In fact, Cao and Hall combined both approaches in developing the model that describes how hydrogen molecules are oxidized or produced within the active site of [FeFe] hydrogenases.  While more research and experimental data are required to complete our understanding of the mechanism, these findings have allowed scientists to apply the knowledge in, e.g., building artificial catalysts mimicking active sites of hydrogenases. 
Biological function 
Assuming that the Earth's atmosphere was initially rich in hydrogen, scientists hypothesize that hydrogenases were evolved to generate energy from/as molecular H2. Accordingly, hydrogenases can either help microorganisms to proliferate under such conditions, or to set up ecosystems empowered by H2.Microbian communities driven by molecular hydrogen have, in fact, been found in deep-sea settings where other sources of energy from photosynthesis are not available. Based on these grounds, the primary role of hydrogenases are believed to be energy generation, either for itself or others within the community.
Recent studies have revealed other biological functions of hydrogenases. To begin with, bidirectional hydrogenases can also act as "valves" to control excess reducing equivalents, especially in photosynthetic microorganisms. Such a role makes hydrogenases play a vital role in anaerobic metabolism. Moreover, hydrogenases may also be involved in membrane-linked energy conservation through the generation of a transmembrane protonmotive force.There is a possibility that hydrogenases have been responsible for bioremediation of chlorinated compounds. Hydrogenases proficient in H2 uptake can help heavy metal contaminants to be recovered in intoxicated forms. Interestingly, these uptake hydrogenases have been recently discovered in pathogenic bacteria and parasites and are believed to be involved in their virulence.
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.
Biological hydrogen production 
Various systems are capable of splitting water into O2 and H+ from incident sunlight. Likewise, numerous catalysts, either chemical or biological, can reduce the produced H+ into H2. Different catalysts require unequal overpotential for this reduction reaction to take place. Hydrogenases are attractive since they require a relatively low overpotential. In fact, its catalytic activity is more effective than platinum, which is the best known catalyst for H2 evolution reaction. Among three different types of hydrogenases, [FeFe] hydrogenases is considered as a strong candidate for an integral part of the solar H2 production system since they offer an additional advantage of high TOF (over 9000 s-1).
Low overpotential and high catalytic activity of [FeFe] hydrogenases are accompanied by high O2 sensitivity. It is necessary to engineer them O2-tolerant for use in solar H2 production since O2 is a by-product of water splitting reaction. Past research efforts by various groups around the world have focused on understanding the mechanisms involved in O2-inactivation of hydrogenases. For instance, Stripp et al. relied on protein film electrochemistry and discovered that O2 first converts into a reactive species at the active site of [FeFe] hydrogenases, and then damages its [4Fe-4S] domain. Cohen et al. investigated how oxygen can reach the active site that is buried inside the protein body by molecular dynamics simulation approach; their results indicate that O2 diffuses through mainly two pathways that are formed by enlargement of and interconnection between cavities during dynamic motion. These works, in combination with other reports, suggest that inactivation is governed by two phenomena: diffusion of O2 to the active site, and destructive modification of the active site.
Despite these findings, research is still under progress for engineering oxygen tolerance in hydrogenases. While researchers have found oxygen-tolerant [NiFe] hydrogenases, they are only efficient in hydrogen uptake and not production. Bingham et al.’s recent success in engineering [FeFe] hydrogenase from clostridium pasteurianum was also limited to retained activity (during exposure to oxygen) for H2 consumption, only.
Biochemical classification 
- H2 + NAD+ = H+ + NADH
EC 22.214.171.124 hydrogen dehydrogenase (NADP) (hydrogen:NADPH+ oxidoreductase)
- H2 + NADP+ = H+ + NADPH
- 2H2 + ferricytochrome c3 = 4H+ + ferrocytochrome c3
- H2 + oxidized ferredoxin = 2H+ + reduced ferredoxin
- H2 + coenzyme F420 = reduced coenzyme F420
EC 126.96.36.199 hydrogenase (acceptor) (hydrogen:acceptor oxidoreductase)
- H2 + A = AH2
EC 188.8.131.52 hydrogen:quinone oxidoreductase
- H2 + menaquinone = menaquinol
EC 184.108.40.206 5,10-methenyltetrahydromethanopterin hydrogenase (hydrogen:5,10-methenyltetrahydromethanopterin oxidoreductase)
- H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin
EC 220.127.116.11 Methanosarcina-phenazine hydrogenase [hydrogen:2-(2,3-dihydropentaprenyloxy)phenazine oxidoreductase]
- H2 + 2-(2,3-dihydropentaprenyloxy)phenazine = 2-dihydropentaprenyloxyphenazine
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- 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