Hydrogenase

Hydrogenase

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Encyclopedia
A hydrogenase is an enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

 that catalyses
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....

 the reversible oxidation
Redox
Redox reactions describe all chemical reactions in which atoms have their oxidation state changed....

 of molecular hydrogen
Hydrogen
Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. With an average atomic weight of , hydrogen is the lightest and most abundant chemical element, constituting roughly 75% of the Universe's chemical elemental mass. Stars in the main sequence are mainly...

 (H2). Hydrogenases play a vital role in anaerobic metabolism
Glycolysis
Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+...

.

Hydrogen uptake (H2 oxidation) (1) is coupled to the reduction of electron acceptors such as oxygen
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...

, nitrate
Nitrate
The nitrate ion is a polyatomic ion with the molecular formula NO and a molecular mass of 62.0049 g/mol. It is the conjugate base of nitric acid, consisting of one central nitrogen atom surrounded by three identically-bonded oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a...

, sulfate
Sulfate
In inorganic chemistry, a sulfate is a salt of sulfuric acid.-Chemical properties:...

, carbon dioxide
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...

, 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 ferredoxin
Ferredoxin
Ferredoxins are iron-sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co...

s, cytochrome
Cytochrome
Cytochromes are, in general, membrane-bound hemoproteins that contain heme groups and carry out electron transport.They are found either as monomeric proteins or as subunits of bigger enzymatic complexes that catalyze redox reactions....

 c3, and cytochrome c6 can act as physiological electron donors (D) or acceptors (A) for hydrogenases:
H2 + Aox → 2H+ + Ared (1)
2H+ + Dred → H2 + Dox (2)


Hydrogenases were first discovered in the 1930s, and they have since attracted interest from many researchers including inorganic chemists
Inorganic chemistry
Inorganic chemistry is the branch of chemistry concerned with the properties and behavior of inorganic compounds. This field covers all chemical compounds except the myriad organic compounds , which are the subjects of organic chemistry...

 who have synthesized a variety of hydrogenase mimic
Hydrogenase mimic
-Overview:The fields of molecular biology and inorganic chemistry overlap in the study of metalloenzymes in the form of enzyme mimics among other. The advantage of indirect modeling or enzyme mimicry is high-resolution crystal structures and well-defined spectral data from which comparisons can be...

s. 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.

Biochemical classification


EC
EC number
The Enzyme Commission number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze....

 1.2.1.2 http://enzyme.expasy.org/EC/1.2.1.2 hydrogen dehydrogenase
Hydrogen dehydrogenase
In enzymology, a hydrogen dehydrogenase is an enzyme that catalyzes the chemical reactionThus, the two substrates of this enzyme are H2 and NAD+, whereas its two products are H+ and NADH....

 (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
Cytochrome-c3 hydrogenase
In enzymology, a cytochrome-c3 hydrogenase is an enzyme that catalyzes the chemical reactionThus, the two substrates of this enzyme are H2 and ferricytochrome c3, whereas its two products are H+ and ferrocytochrome c3....

 (hydrogen:ferricytochrome-c3 oxidoreductase)
2H2 + ferricytochrome c3 = 4H+ + ferrocytochrome c3


EC 1.12.7.2
ferredoxin hydrogenase
Ferredoxin hydrogenase
In enzymology, a ferredoxin hydrogenase is an enzyme that catalyzes the chemical reactionThus, the two substrates of this enzyme are H2 and oxidized ferredoxin, whereas its two products are reduced ferredoxin and H+....

 (hydrogen:ferredoxin oxidoreductase)
H2 + oxidized ferredoxin = 2H+ + reduced ferredoxin


EC 1.12.98.1
coenzyme F420 hydrogenase
Coenzyme F420 hydrogenase
In enzymology, a coenzyme F420 hydrogenase is an enzyme that catalyzes the chemical reactionThus, the two substrates of this enzyme are H2 and coenzyme F420, whereas its product is reduced coenzyme F420....

 (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
Selenocysteine
Selenocysteine is an amino acid that is present in several enzymes .-Nomenclature:...

. 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 cluster
    Iron-sulfur cluster
    For biological Fe-S clusters, see iron-sulfur proteins.Iron-sulfur clusters are ensembles of iron and sulfide centres. Fe-S clusters are most often discussed in the context of the biological role for iron-sulfur proteins. Many Fe-S clusters are known in the area of organometallic chemistry and as...

    s 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
      Ralstonia eutropha
      Ralstonia eutropha is a gram-negative soil bacterium of the betaproteobacteria class.-Taxonomy:R. eutropha has gone through a series of name changes. In the first half of the 20th century many microorganisms were isolated for their ability to utilize hydrogen. Hydrogen metabolizing...

      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
Carbon monoxide
Carbon monoxide , also called carbonous oxide, is a colorless, odorless, and tasteless gas that is slightly lighter than air. It is highly toxic to humans and animals in higher quantities, although it is also produced in normal animal metabolism in low quantities, and is thought to have some normal...

 (CO) and cyanide
Cyanide
A cyanide is a chemical compound that contains the cyano group, -C≡N, which consists of a carbon atom triple-bonded to a nitrogen atom. Cyanides most commonly refer to salts of the anion CN−. Most cyanides are highly toxic....

 (CN-) ligands.
  • 5,10-methenyltetrahydromethanopterin hydrogenase
    5,10-methenyltetrahydromethanopterin hydrogenase
    The 5,10-methenyltetrahydromethanopterin hydrogenase , the so-called iron-sulfur cluster-free hydrogenase, is an enzyme found in methanogenic archea such as Methanothermacter marburgensis. It was discovered and first characterized by the Thauer group at the Max Planck Institute in Marburg...

     (EC 1.12.98.2) found in methanogen
    Methanogen
    Methanogens are microorganisms that produce methane as a metabolic byproduct in anoxic conditions. They are classified as archaea, a group quite distinct from bacteria...

    ic Archaea
    Archaea
    The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

     contains neither nickel nor iron-sulfur clusters but an iron-containing cofactor that was recently characterized by X-ray diffraction.

External links

  • 2B0J - PDB
    Protein Data Bank
    The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....

     Structure of the Apoenzyme of the Iron-sulphur cluster-free hydrogenase from Methanothermococcus jannaschii
  • 1HFE - PDB
    Protein Data Bank
    The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....

    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