NiFe hydrogenase

[1][2] The catalytic site on the enzyme provides simple hydrogen-metabolizing microorganisms a redox mechanism by which to store and utilize energy via the reaction This is particularly essential for the anaerobic, sulfate-reducing bacteria of the genus Desulfovibrio[3][4] as well as pathogenic organisms Escherichia coli and Helicobacter pylori.

[2] The mechanisms, maturation, and function of [NiFe] hydrogenases are actively being researched for applications to the hydrogen economy and as potential antibiotic targets.

The structure of [NiFe] hydrogenase was obtained from X-ray crystallography studies of five different sulfate-reducing bacteria: Desulfovibrio vulgaris Miyazaki F,[6] D. gigas,[7] D. frutosovorans,[8][9] D. desulfuricans,[10] and Desulfomicrobium baculatum.

At approximately 13 Å away from the [NiFe] moiety, this cation connects the active site to a hydrogen bonding network and serves as a proton (H+) transfer pathway.

[13] Studies, in which xenon was bound to the hydrogenase, suggest a hydrophobic gas channel through which H2, CO, and O2 gases could reach the deeply buried active site within the enzyme.

The electron paramagnetic resonance spectroscopic studies of the Ni-C state, which contained a Ni3+ with S = 1/2 and a hydride bridging the two metals, Ni and Fe, showed that the heterolytic cleavage of H2 takes place in the [NiFe] hydrogenase active site.

[2][16][17] The maturation of the active site is of special interest because of the synthesis of cyanide (CN) and carbon monoxide (CO) metal ligands which are usually toxic to living organism.

[17][18] Once the catalytic center is completed, the hydrogenase precursor undergoes a C-terminal cleavage that prompts rearrangement of its structure and association with the small subunit.

The soluble [NiFe] hydrogenase from Ralstonia eutropha H16 is a promising candidate enzyme for H2-based biofuel application as it favours H2 oxidation and is relatively oxygen-tolerant.

The structure of [NiFe] hydrogenase isolated from D. vulgaris Miyazaki F consists of two subunits: the large subunit ( blue ) and the small subunit ( magenta ). The Figure was prepared using Jmol [ 5 ] and the coordinates from PDB : 1H2A ​.
The active site of [NiFe] hydrogenase in the oxidized form. L refers to non-protein ligand (1 C≡O and 2 − C≡N). X can be an oxide , sulfur , hydroperoxide , or a hydroxide .
Illustration of [NiFe] hydrogenase enzyme with three Fe-S clusters in the small subunit and with Mg 2+ and Ni-Fe dimetal active site in the large subunit . Figure was prepared using Jmol [ 5 ] and the coordinates from PDB : 1H2A ​. Mg ion = neon green; Ni ion = dark green; Fe ion = orange; sulfur = yellow; oxygen = red; carbon = dark gray
Figure 5. Different redox states of [NiFe] hydrogenase's metal active site. The redox states in the red are the inactive redox states . The redox states in the green are the active redox states . (Adapted from [ 13 ] ).
Figure 6. Illustration of the [NiFe] hydrogenase active site inhibited by CO. Top-down view (left). Side view (center). Chemdraw depiction of the inhibited active site (right). The figure was prepared with Jmol [ 5 ] and coordinates from 1UBK.pdb. Ni ion = green; Fe ion = orange; sulfur = yellow; oxygen = red; carbon = dark gray; nitrogen = blue.