Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store
Updated BioCyc iOS App now
available in iTunes store

MetaCyc Enzyme: [NiFe]-hydrogenase (membrane bound)

Superclasses: a hydrogenasea [NiFe] hydrogenase

Species: Cupriavidus necator

Subunit composition of [NiFe]-hydrogenase (membrane bound) = [HoxZ][HoxK][HoxG]
         hydrogenase b-type cytochrome subunit = HoxZ (summary available)
         hydrogenase small subunit = HoxK (summary available)
         hydrogenase large subunit = HoxG (summary available)

General Background

Hydrogenases are responsible for the reversible oxidation of H2 to two protons (in the reverse direction, the enzyme catalyzes the reduction of protons resulting in molecular hydrogen production).

Most hydrogenases are metalloenzymes that contain iron-sulfur clusters. They have been subdivided into two main classes based on the composition of two metal atoms at their active center: [NiFe]-hydrogenases and [FeFe]-hydrogenases. These two classes are phylogenetically distinct. It should be noted that in some of the [NiFe]-hydrogenases one of the Ni-bound cysteine residues is replaced by selenocysteine. Those enzymes are known as [NiFeSe]-hydrogenases.

In addition, a third class of hydrogenases is found in some methanogenic archaea. These enzymes contain only a mononuclear Fe active site and no iron-sulfur clusters, and are known as [Fe]-hydrogenases.

The catalytic core of [NiFe]-hydrogenases is a heterodimeric protein, which is often associated with additional subunits. The catalytic core of [FeFe]-hydrogenases is a single domain of about 350 residues that accommodates the active site, known as the H cluster. Many [FeFe]-hydrogenases are monomeric but possess additional domains that contain redox centers, mostly Fe-S clusters.

About This Enzyme

Cupriavidus necator is capable of growth on hydrogen as the sole energy source. This organism is unique, since it contains three different kinds of NiFe-type hydrogenases, two of which produce energy, while the third one regulates the production of the other two [Kleihues00]. One of the energy-producing hydrogenases (this enzyme) is membrane-bound (MBH) and couples H2 oxidation to electron transport-dependent phosphorylation via an integral membrane-bound subunit, which is a b-type cytochrome. The other catalytic hydrogenase is cytoplasmic and transfers electrons directly to NAD, generating reducing equivalents (see [NiFe]-hydrogenase (soluble)).

The membrane-bound enzyme is a heterotrimer, composed of a catalytic heterodimer and a membrane-integral cytochrome b third unit, which is involved in both anchoring the complex to the membrane and the transfer of electrons from the complex to a quinone [Bernhard97]. The enzyme contains Ni2+ and iron-sulfur, the precise nature of which has not been determined [Schink79].

The MBH operon comprises 10 MBH-specific genes in addition to a set of accessory genes whose products are involved in the complex posttranslational maturation of the hydrogenases and the regulation of both catalytic hydrogenases [Bernhard96].

Locations: inner membrane

Gene-Reaction Schematic

Gene-Reaction Schematic

GO Terms:
Cellular Component:
GO:0005886 - plasma membrane []

Created 09-Aug-1999 by Pellegrini-Toole A, Marine Biological Laboratory
Revised 19-Oct-2006 by Caspi R, SRI International

Enzymatic reaction of: hydrogenase

Inferred from experiment

Synonyms: uptake hydrogenase, membrane-bound hydrogenase, MBH, hydrogenlyase, ferredoxin:H+ oxidoreductase, hydrogenase

EC Number:

an oxidized unknown electron acceptor + H2 ⇄ an reduced unknown electron acceptor

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

This reaction is reversible.

Alternative Substrates [ Comment 1]:

In Pathways: hydrogen oxidation I (aerobic)

Cofactors or Prosthetic Groups: an iron-sulfur cluster [Comment 2], Ni2+ [Friedrich93, Bernhard96, Vignais94]

Inhibitors (Unknown Mechanism): Cu2+ [Schink79], Ni2+ [Schink79], Hg2+ [Schink79], Mg2+ [Schink79], sodium citrate [Schink79], ferric chloride [Schink79], p-chloromercuribenzoate [Schink79]

Subunit of [NiFe]-hydrogenase (membrane bound): hydrogenase b-type cytochrome subunit

Synonyms: HoxZ

Gene: hoxZ Accession Number: G-9708 (MetaCyc)

Molecular Weight: 27.581 kD (from nucleotide sequence)

Unification Links: Protein Model Portal:P31898, UniProt:P31898

Relationship Links: InterPro:IN-FAMILY:IPR000516, InterPro:IN-FAMILY:IPR016174, Pfam:IN-FAMILY:PF00033, Prints:IN-FAMILY:PR00161, Prosite:IN-FAMILY:PS00882, Prosite:IN-FAMILY:PS00883

This subunit is a dual function b-type cytochrome. It works as a membrane anchor and as a redox center [Bernhard97].

Subunit of [NiFe]-hydrogenase (membrane bound): hydrogenase small subunit

Synonyms: HoxK, membrane-bound hydrogenase small subunit, MBH small subunit

Gene: hoxK Accession Number: G-310 (MetaCyc)

Locations: inner membrane

Molecular Weight: 39.472 kD (from nucleotide sequence)

GO Terms:
Cellular Component:
GO:0005886 - plasma membrane []

Unification Links: DIP:DIP-59145N, Protein Model Portal:P31892, UniProt:P31892

Relationship Links: InterPro:IN-FAMILY:IPR001821, InterPro:IN-FAMILY:IPR006137, InterPro:IN-FAMILY:IPR006311, InterPro:IN-FAMILY:IPR019546, InterPro:IN-FAMILY:IPR027394, Panther:IN-FAMILY:PTHR30013, PDB:Structure:3RGW, PDB:Structure:4IUB, PDB:Structure:4IUC, PDB:Structure:4IUD, PDB:Structure:4TTT, Pfam:IN-FAMILY:PF01058, Pfam:IN-FAMILY:PF14720, Prints:IN-FAMILY:PR00614, Prosite:IN-FAMILY:PS51318

An N-terminal signal peptide is removed by processing.

Subunit of [NiFe]-hydrogenase (membrane bound): hydrogenase large subunit

Synonyms: HoxG, membrane-bound hydrogenase large subunit, MBH large subunit

Gene: hoxG Accession Number: G-311 (MetaCyc)

Locations: inner membrane

Molecular Weight: 68.632 kD (from nucleotide sequence)

GO Terms:
Cellular Component:
GO:0005886 - plasma membrane []

Unification Links: DIP:DIP-59144N, Protein Model Portal:P31891, UniProt:P31891

Relationship Links: InterPro:IN-FAMILY:IPR001501, InterPro:IN-FAMILY:IPR018194, InterPro:IN-FAMILY:IPR029014, PDB:Structure:3RGW, PDB:Structure:4IUB, PDB:Structure:4IUC, PDB:Structure:4IUD, PDB:Structure:4TTT, Pfam:IN-FAMILY:PF00374, Prosite:IN-FAMILY:PS00507, Prosite:IN-FAMILY:PS00508

The hydrogenase large subunit contains the nickel-binding active site. [Bernhard96]


Bernhard96: Bernhard M, Schwartz E, Rietdorf J, Friedrich B (1996). "The Alcaligenes eutrophus membrane-bound hydrogenase gene locus encodes functions involved in maturation and electron transport coupling." J Bacteriol 1996;178(15);4522-9. PMID: 8755880

Bernhard97: Bernhard M, Benelli B, Hochkoeppler A, Zannoni D, Friedrich B (1997). "Functional and structural role of the cytochrome b subunit of the membrane-bound hydrogenase complex of Alcaligenes eutrophus H16." Eur J Biochem 1997;248(1);179-86. PMID: 9310376

Friedrich93: Friedrich B, Schwartz E (1993). "Molecular biology of hydrogen utilization in aerobic chemolithotrophs." Annu Rev Microbiol 1993;47;351-83. PMID: 8257102

Kleihues00: Kleihues L, Lenz O, Bernhard M, Buhrke T, Friedrich B (2000). "The H(2) sensor of Ralstonia eutropha is a member of the subclass of regulatory [NiFe] hydrogenases." J Bacteriol 182(10);2716-24. PMID: 10781538

Lorenz89: Lorenz B, Schneider K, Kratzin H, Schlegel HG (1989). "Immunological comparison of subunits isolated from various hydrogenases of aerobic hydrogen bacteria." Biochim Biophys Acta 1989;995(1);1-9. PMID: 2493816

Park06: Park YJ, Yoo CB, Choi SY, Lee HB (2006). "Purifications and characterizations of a ferredoxin and its related 2-oxoacid:ferredoxin oxidoreductase from the hyperthermophilic archaeon, Sulfolobus solfataricus P1." J Biochem Mol Biol 39(1);46-54. PMID: 16466637

Schink79: Schink B, Schlegel HG (1979). "The membrane-bound hydrogenase of Alcaligenes eutrophus. I. Solubilization, purification, and biochemical properties." Biochim Biophys Acta 1979;567(2);315-24. PMID: 36155

Sun10: Sun J, Hopkins RC, Jenney FE, McTernan PM, Adams MW (2010). "Heterologous expression and maturation of an NADP-dependent [NiFe]-hydrogenase: a key enzyme in biofuel production." PLoS One 5(5);e10526. PMID: 20463892

Vignais08: Vignais PM (2008). "Hydrogenases and H(+)-reduction in primary energy conservation." Results Probl Cell Differ 45;223-52. PMID: 18500479

Vignais94: Vignais PM, Toussaint B (1994). "Molecular biology of membrane-bound H2 uptake hydrogenases." Arch Microbiol 1994;161(1);1-10. PMID: 8304820

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by Pathway Tools version 19.5 (software by SRI International) on Sun Feb 7, 2016, biocyc13.