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.
Ogata
Hideaki
H
Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany. ogata@mpi-muelheim.mpg.de
Kellers
Petra
P
Lubitz
Wolfgang
W
D020134:Catalytic Domain; D002841:Chromatiaceae / Q000201:enzymology*; D018360:Crystallography, X-Ray; D003901:Desulfovibrio / Q000201:enzymology; D004578:Electron Spin Resonance Spectroscopy; D006864:Hydrogenase / Q000737:chemistry*; D008958:Models, Molecular; D009532:Nickel / Q000378:metabolism; D010084:Oxidation-Reduction; D011485:Protein Binding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D021122:Protein Subunits; D017550:Spectroscopy, Fourier Transform Infrared
D021122:Protein Subunits; D009532:Nickel; C043296:nickel-iron hydrogenase; D006864:Hydrogenase