3MYR

Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state

Summary for 3MYR

• Entry DOI: 10.2210/pdb3myr/pdb
• Descriptor: Hydrogenase (NiFe) small subunit HydA, Nickel-dependent hydrogenase large subunit, IRON/SULFUR CLUSTER, ... (9 entities in total)
• Functional Keywords: [nife] hydrogenase, allochromatium vinosum, photosynthetic purple-sulfur bacterium, iron-sulfur cluster, ni-a state, oxidoreductase
• Biological source: Allochromatium vinosum (Chromatium vinosum); More
• Total number of polymer chains: 8
• Total formula weight: 369978.93

Authors

Ogata, H.,Kellers, P.,Lubitz, W. (deposition date: 2010-05-11, release date: 2010-08-04, Last modification date: 2024-11-06)

Primary citation

Ogata, H.,Kellers, P.,Lubitz, W.
The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state).
J.Mol.Biol., 402:428-444, 2010

PubMed Abstract: 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.

PubMed: 20673834
DOI: 10.1016/j.jmb.2010.07.041

Experimental method

X-RAY DIFFRACTION (2.1 Å)