8POX image
Entry Detail
PDB ID:
8POX
Keywords:
Title:
Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the H2-reduced state at 1.6 A Resolution.
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-07-05
Release Date:
2024-09-18
Method Details:
Experimental Method:
Resolution:
1.60 Å
R-Value Free:
0.15
R-Value Work:
0.12
R-Value Observed:
0.12
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Uptake hydrogenase large subunit
Chain IDs:A (auth: L)
Chain Length:603
Number of Molecules:1
Biological Source:Cupriavidus necator H16
Polymer Type:polypeptide(L)
Description:Uptake hydrogenase small subunit
Mutations:C19G
Chain IDs:B (auth: S)
Chain Length:328
Number of Molecules:1
Biological Source:Cupriavidus necator H16
Primary Citation
Stepwise conversion of the Cys 6 [4Fe-3S] to a Cys 4 [4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase.
Chem Sci 14 11105 11120 (2023)
PMID: 37860641 DOI: 10.1039/d3sc03739h

Abstact

The membrane-bound [NiFe]-hydrogenase of Cupriavidus necator is a rare example of a truly O2-tolerant hydrogenase. It catalyzes the oxidation of H2 into 2e- and 2H+ in the presence of high O2 concentrations. This characteristic trait is intimately linked to the unique Cys6[4Fe-3S] cluster located in the proximal position to the catalytic center and coordinated by six cysteine residues. Two of these cysteines play an essential role in redox-dependent cluster plasticity, which bestows the cofactor with the capacity to mediate two redox transitions at physiological potentials. Here, we investigated the individual roles of the two additional cysteines by replacing them individually as well as simultaneously with glycine. The crystal structures of the corresponding MBH variants revealed the presence of Cys5[4Fe-4S] or Cys4[4Fe-4S] clusters of different architecture. The protein X-ray crystallography results were correlated with accompanying biochemical, spectroscopic and electrochemical data. The exchanges resulted in a diminished O2 tolerance of all MBH variants, which was attributed to the fact that the modified proximal clusters mediated only one redox transition. The previously proposed O2 protection mechanism that detoxifies O2 to H2O using four protons and four electrons supplied by the cofactor infrastructure, is extended by our results, which suggest efficient shutdown of enzyme function by formation of a hydroxy ligand in the active site that protects the enzyme from O2 binding under electron-deficient conditions.

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