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Ni-Fe Hydrogenase . Patrick McTernan BCMB 8010.

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ni fe hydrogenase

Ni-Fe Hydrogenase

Patrick McTernan

BCMB 8010

Image created by using Pymol and Microsoft Powerpoint. PDB code is 1h2r and the image is cited from Higuchi, Y.,  Ogata, H.,  Miki, K.,  Yasuoka, N.,  Yagi, T. (1999) Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des.7: 549-556

background
Background
  • Hydrogenases catalyze the reversible oxidation of molecular hydrogen.
  • H2 <-> 2 e- + 2 H+
  • Reaction can either be involved in hydrogen uptake or hydrogen evolution .
  • Three different types of hydrogenases.
  • Ni-Fe Hydrogenases are mostly found in the Bacteria and Archaea domains and the first three-dimensional structure was determined from the sulfate-reducing bacterium Desulfovibrio gigas.
  • First Ni containing hydrogenase was found to be in an alpha-beta heterodimer.
  • Desulfovibrio vulgaris Miyazaki F
alpha beta heterodimer
Alpha-Beta Heterodimer

. Movie created by using Pymol and Microsoft Powerpoint. PDB code is 1h2r and the image is cited from Higuchi, Y.,  Ogata, H.,  Miki, K.,  Yasuoka, N.,  Yagi, T. (1999) Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des.7: 549-556

Image created by using Pymol and Microsoft Powerpoint. PDB code is 1h2r and the image is cited from Higuchi, Y.,  Ogata, H.,  Miki, K.,  Yasuoka, N.,  Yagi, T. (1999) Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des.7: 549-556

ni fe active site
Ni-Fe Active Site
  • Ni-Fe active site is deeply buried in the alpha subunit.
  • Ni atom is bound by two thiolate bonds from two terminal cystienes.

- Cys 81 and Cys 546

  • The Ni and Fe are bound by two bridge cysteines.

- Cys 84 and Cys 549

  • Fe has three diatomic ligands.

-CO

-CN

-SO

Image created by using Pymol and Microsoft Powerpoint. PDB code is 1h2r and the image is cited from Higuchi, Y.,  Ogata, H.,  Miki, K.,  Yasuoka, N.,  Yagi, T. (1999) Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des.7: 549-556

active site

This picture was created by using Pymol and Microsoft Powerpoint. The PDB code for this picture is 1h2r and the image is cited from Higuchi, Y.,  Ogata, H.,  Miki, K.,  Yasuoka, N.,  Yagi, T. (1999) Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des.7: 549-556

Active Site
fe s clusters
Fe-S Clusters
  • The Fe-S clusters serve as a way of shuttling electrons from an electron donor to the buried Ni-Fe site.
  • There are three found in the small subunit.

- A proximal [4Fe-4S]

- A [3Fe-4S]

- A terminal [4Fe-4S]

Image created by using Pymol and Microsoft Powerpoint. PDB code is 1h2r and the image is cited from Higuchi, Y.,  Ogata, H.,  Miki, K.,  Yasuoka, N.,  Yagi, T. (1999) Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des.7: 549-556

fe s clusters within the beta subunit
Fe-S clusters within the beta subunit

. This picture was created by using Pymol and Microsoft Powerpoint. The PDB code for this picture is 1h2r and the image is cited from Higuchi, Y.,  Ogata, H.,  Miki, K.,  Yasuoka, N.,  Yagi, T. (1999) Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure Fold.Des.7: 549-556

mechanism of activation catalysis
Mechanism of Activation/Catalysis
  • The Ni atom has been found to be in different EPR states.

- Ni-A <-> Ni-SU (inactive unready state)

- Ni-B <-> Ni-SI (ready inactive state)

- Ni-C <-> Ni-R (catalytically active state)

conclusions
Conclusions
  • Ni-Fe Hydrogenases are used for the uptake of molecular hydrogen and hydrogen evolution.
  • The alpha subunit contains the buried active site and the beta subunit contains the three [Fe-S] clusters.
  • The Ni atom can exist in different redox states.
  • Upon removal of the bridging ligand, the enzyme is activated.
  • May have future applications in the production of molecular hydrogen.