Proton pathways in a [NiFe]-hydrogenase: A theoretical study

The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state)

The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 Å resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino acid sequence identity is ∼ 50%. The bimetallic [NiFe] active site is located in the large subunit of the heterodimer and possesses three diatomic non-protein ligands coordinated to the Fe (two CN(-) , one CO). Ni is bound to the protein backbone via four cysteine thiolates; two of them also bridge the two metals. One of the bridging cysteines (Cys64) exhibits a modified thiolate in part of the sample. A mono-oxo bridging ligand was assigned between the metal ions of the catalytic center. This is in contrast to a proposal for Desulfovibrio sp. hydrogenases that show a di-oxo species in this position for the Ni-A state. The additional metal site located in the large subunit appears to be a Mg(2+) ion. Three iron-sulfur clusters were found in the small subunit that forms the electron transfer chain connecting the catalytic site with the molecular surface. The calculated anomalous Fourier map indicates a distorted proximal iron-sulfur cluster in part of the crystals. This altered proximal cluster is supposed to be paramagnetic and is exchange coupled to the Ni(3+) ion and the medial [Fe(3)S(4)](+) cluster that are both EPR active (S=1/2 species). This finding of a modified proximal cluster in the [NiFe] hydrogenase might explain the observation of split EPR signals that are occasionally detected in the oxidized state of membrane-bound [NiFe] hydrogenases as from A. vinosum.

Intermediates in the catalytic cycle of [NiFe] hydrogenase: functional spectroscopy of the active site

The [NiFe] hydrogenase from the anaerobic sulphate reducing bacterium Desulfovibrio vulgaris Miyazaki F is an excellent model for constructing a mechanism for the function of the so-called 'oxygen-sensitive' hydrogenases. The present review focuses on spectroscopic investigations of the active site intermediates playing a role in the activation/deactivation and catalytic cycle of this enzyme as well as in the inhibition by carbon monoxide or molecular oxygen and the light-sensitivity of the hydrogenase. The methods employed include magnetic resonance and vibrational (FTIR) techniques combined with electrochemistry that deliver information about details of the geometrical and electronic structure of the intermediates and their redox behaviour. Based on these data a mechanistic scheme is developed.

Structure and Function of [NiFe]-Hydrogenases

[NiFe(Se)]-hydrogenases are hetero-dimeric enzymes present in many microorganisms where they catalyze the oxidation of molecular hydrogen or the reduction of protons. Like the other two types of hydrogen-metabolizing enzymes, the [FeFe]- and [Fe]-hydrogenases, [NiFe]-hydrogenases have a Fe(CO)x unit in their active sites that is most likely involved in hydride binding. Because of their complexity, hydrogenases require a maturation machinery that involves several gene products. They include nickel and iron transport, synthesis of CN− (and maybe CO), formation and insertion of a FeCO(CN−)2 unit in the apo form, insertion of nickel and proteolytic cleavage of a C-terminal stretch, a step that ends the maturation process. Because the active site is buried in the structure, electron and proton transfer are required between this site and the molecular surface. The former is mediated by either three or one Fe/S cluster(s) depending on the enzyme. When exposed to oxidizing conditions, such as the presence of O2, [NiFe]-hydrogenases are inactivated. Depending on the redox state of the enzyme, exposure to oxygen results in either a partially reduced oxo species probably a (hydro)peroxo ligand between nickel and iron or a more reduced OH– ligand instead. Under some conditions the thiolates that coordinate the NiFe center can be modified to sulfenates. Understanding this process is of biotechnological interest for H2 production by photosynthetic organisms.

Purification, crystallization and preliminary X-ray analysis of the membrane-bound [NiFe] hydrogenase from Allochromatium vinosum

The membrane-bound [NiFe] hydrogenase is a unique metalloprotein that is able to catalyze the reversible oxidation of hydrogen to protons and electrons during a complex reaction cycle. The [NiFe] hydrogenase was isolated from the photosynthetic purple sulfur bacterium Allochromatium vinosum and its crystallization and preliminary X-ray analysis are reported. It was crystallized by the hanging-drop vapour-diffusion method using sodium citrate and imidazole as crystallization agents. The crystals belong to space group P2(1)2(1)2, with unit-cell parameters a = 205.00, b = 217.42, c = 120.44 A. X-ray diffraction data have been collected to 2.5 A resolution.