Hydrogenase

General information

In 1887, Hoppe-Seyler discovers that Bactérie S can break up the Formiate into H₂ and CO₂. The name “hydrogenase” is given by Stevenson and Stickland in 1931 after having observed the production of hydrogen by bacteria of the colonist and its use to reduce Substrat S. the hydrogenases now indicate a class of enzyme which can catalyze in a reversible way conversion of the protons into hydrogen:

They catalyze this reaction to a potential very close to the thermodynamic potential (E°app= - 413 mV in water, with 25 °C, under 0,1 bar of H₂ and pH 7). In these organizations, hydrogen can have two functions.

The first function is energy: a surplus of reduction can be eliminated in the form of hydrogen.

The second metabolic function uses hydrogen as reducing substrate: reduction of the CO₂ in Methane at Methanobacterium , in Ethanoic acid at Acetobacterium , Hydrogenation of the Fumarate at Vibrio succinogenes , production of NAD (P) H in the hydrogenases Diaphorases as at Ralstonia eutropha …

If the hydrogenases are known since more than one century, the determination of their structures and more particularly that of their active sites followed a long advance:

In 1956, the presence of iron not Hémique is confirmed. During years 1970, experiments of RPE showed that the hydrogenases contained clusters iron-sulfur of the type Ferredoxine HiPIP (“high potential iron-sulfur protein”). In 1980, Thauer detected the presence of nickel in certain hydrogenases giving place to many speculations on the nature of the active site. It is now established that there exist two principal classes of hydrogenases, the hydrogenases and the hydrogenases with iron, as well as a related class called hydrogenases without Cluster iron-sulfur or Hmd. One knows a hundred hydrogenases distributed at forty organizations.

Classes of hydrogenases

The two principal classes of hydrogenases are characterized by their activities like by their very original active sites. Indeed, the presence of organometallic sites having of the ligands Cyanide and Carbonyle are a single fact in biology. That is all the more remarkable as these molecules Prosthétique S are generally regarded as poisons for the organizations living.

Hydrogenases with iron

They are present only at the Eubactérie S and the Eucaryote S (can be even in the mammals). Structures of these enzymes were solved almost simultaneously at two organizations: D. desulfuricans and C. pasteurianum . The structures of these enzymes are rather different but they have both of the clusters able to drain electrons between surface and the active site deeply hidden in protein. The active site called cluster-H is composed of a cluster dependant via a cystein bridging on a cluster dinucléaire with iron (cf fig. 2). The iron atoms of this cluster dinucléaire have ligands cyanides and carbonyls and are connected by a prosthetic ligand bridging of type. The analysis of the hydrogen bonds between this ligand and the cavity as well as the intuition of the Cristallographe can let think that the central atom would be a nitrogen atom. The bridging ligand would be then the Dithiométhylamine.

Hydrogenases and

The hydrogenases are most numerous of the hydrogenases. They are present at many micro-organisms like the eubacteries Méthanogène S, Acétogène S, fixing of nitrogen, Sulfato - reducing of the Cyanobactéries (blue algas) but also at archées. There exists on the other hand little of hydrogenases. One can classify these two types of hydrogenases in four great groups according to their cellular functions. The comparison of alignments of sequences and more particularly of two areas preserved (around cysteins of the active site and close to zones N and C-final) makes it possible to find these four classes. Group 1 is composed of the hydrogenases associated with the membranes and which make use of hydrogen like energy source. The second group is composed of hydrogenases Cytoplasmique S Hétérodimérique S and absent at are archées. The third group is composed of hydrogenases Cytoplasmique S Hétéromultimérique S which can bind a Cofacteur (F420, NAD or NADP) and function in a reversible way. The fourth and last group gather the hydrogenases associated with the membranes which produce hydrogen. They are between 50 and 100 times less active than the hydrogenases with iron in production and oxidation of hydrogen (up to 1000 catalytic cycles a second).

The hydrogenases are characterized by an active site heterobimetallic containing an iron atom and a nickel atom. Structures Cristallographique S of these enzymes are known for five organizations and are of two types: hydrogenases and hydrogenases with ligands carbonyls. The hydrogenases are present in the sulfato-reducing bacteria and can be perished or cytoplasmic.

Hydrogenases

These are the first hydrogenases of which the crystallographic structures were known. It also is studied. The hydrogenase of Desulvibrio (D.) gigas , is a protein Périplasmique Hétérodimère, made up of two sub-units of 60 and 28 kDa. It has three clusters: a cluster ^1+/0 and two clusters ^2+/1+. They set out again in an almost linear way in the small sub-unit over a length of 12 Å. the cluster nearest to the active site are located at 13 Å of the active site and are called cluster Proximal or cluster-p. The cluster furthest away from the active site (cluster Distal or cluster-d) is located almost at the surface of protein. These clusters thus forms a “way” for the electrons, between a donor extraproteic and the active site. The hydrogenases would have a magnesium atom in the C-terminal field. In addition, a channel Hydrophobe allows the hydrogen circulation of outside until the active site and more precisely close to a vacant final site of nickel. The active site includes/understands a coordinate nickel atom by four Cystéinates forming a Tétraèdre strongly distorted (cf fig. 4 and fig. 6). Two of these cystéinates coordinent also an atom of iron. This iron atom also has two ligands cyanides and a ligand carbonyl. The ligands cyanides are in hydrogen interaction with the side chains of residues of the cavity. A site of coordination on iron is thus vacant and to supplement the sphere of coordination of iron, another ligand can be present. Recent crystallographic results suggest the presence of a ligand oxygenated Hydroxyde or Hydropéroxyde, bridging between nickel and iron when the protein is oxidized. Other crystallographic and electrochemical results suggest that this ligand could also be a sulfide.

Hydrogenases

The hydrogenases form a subclass of the hydrogenases. They contain a selenium atom by protein. The periplasmic hydrogenase of D.baculatum was crystallized. It is about a hétérodimère including/understanding two pennies units of 26 and 49 kDa. Three clusters are located in the small one under unit, whereas the gross under unit does not contain " que" the active site. It resembles that of the hydrogenases much. The principal originality of this enzyme is the replacement of a final cystein by a Sélénocystéine ligand of the active site. The Sélénocystéinate S could protoner more easily than the cystéinates. That would explain the differences in reactivity. In the active site of the crystallized hydrogenase, the distance between nickel and iron are of 2,5 Ǻ. the hydrogenases would have a magnesium atom in the C-terminal field. For the hydrogenases, this atom would be replaced by an iron atom.

Hydrogenases without cluster iron sulfur

It is not with propoment speaking about the hydrogenases because they do not use protons to produce hydrogen. However, the many similarities with the hydrogenases confer this denomination to him. Called a long time hydrogenases without metal (metal free hydrogenases), they were re-elected in 2000 hydrogenases without cluster following the discovery of a reason with iron within the cofactor of this enzyme. This iron is non-hemic and would have two ligands carbonyls. The cofactor inactive with the light by losing the reason iron carbonyl which would be dependant for him. The structure holo of these hydrogenases is still unknown contrary to the form apo.

They are also known under the name of Hmd for H-₂-forming methylentetrahydromethanopterin dehydrogenase. Only some archées méthanogénes have some. These hydrogenases different largely from both others because they do not contain a clusters and do not have the same reactivity. Indeed, they reversibly catalyze the reaction of reduction of the '' NR '' ₅, '' NR '' ₁₀-méthényltétrahydrométhanopterine in '' NR '' ₅, '' NR '' ₁₀-méthénylénetétrahydrométhanopterine in the presence of hydrogen. That corresponds to a transfer of hydride on the substrate and to the release of a proton in solution. These hydrogenases are not able to catalyze the reduction of the Méthylviologène by H₂, nor to catalyze the exchange of the protons of H₂ with deuterium of heavy water. Therefore they are not hydrogenases strictly speaking. However, their capacity to use hydrogen their are worth name " hydrogénase".

The activity of these enzymes strongly depends on the pH. A basic pH supports the formation of methenyl-H₄MPT+, whereas an acid pH and the presence of hydrogen support the formation of methylene-H₄MPT. For example the reaction of dehydrogenation can be done with a maximum speed of 2700 protein μmol/min/mg for Methanopyrus kandleri with pH lower than 4,5 with more 90°C.

Refer

External bonds

2B0J - PDB Structure of the apoenzyme hydrogenase without cluster iron sulfur of Methanothermococcus jannaschii
1HFE - PDB Structure of the hydrogenase with iron alone of Desulfovibrio desulfuricans
1C4A - Structure PDB of the hydrogenase with iron alone of Clostridium pasteurianum
1UBR - Structure PDB of the hydrogenase of Desulfovibrio vulgaris
1CC1 - Structure PDB of the hydrogenase of Desulfomicrobium baculatum
Animation (in) Proposal of catalytic mechanism for the hydrogenases * - Thesis of which part of the introduction describes in detail the hydrogenases

Random links: