8W6X
Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state
Replaces: 7YW6Summary for 8W6X
Entry DOI | 10.2210/pdb8w6x/pdb |
Descriptor | Periplasmic [NiFe] hydrogenase large subunit, Periplasmic [NiFe] hydrogenase small subunit, formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni), ... (10 entities in total) |
Functional Keywords | hydrogenase, nife complex, fes cluster, oxidized state, oxidoreductase |
Biological source | Desulfovibrio vulgaris str. 'Miyazaki F' More |
Total number of polymer chains | 2 |
Total formula weight | 90134.88 |
Authors | Hiromoto, T.,Tamada, T. (deposition date: 2023-08-30, release date: 2023-09-13, Last modification date: 2023-11-15) |
Primary citation | Hiromoto, T.,Nishikawa, K.,Inoue, S.,Ogata, H.,Hori, Y.,Kusaka, K.,Hirano, Y.,Kurihara, K.,Shigeta, Y.,Tamada, T.,Higuchi, Y. New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase. Chem Sci, 14:9306-9315, 2023 Cited by PubMed Abstract: [NiFe]-hydrogenase from Miyazaki F is an O-sensitive enzyme that is inactivated in the presence of O but the oxidized enzyme can recover its catalytic activity by reacting with H under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17 thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19 with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster. PubMed: 37712026DOI: 10.1039/d3sc02156d PDB entries with the same primary citation |
Experimental method | NEUTRON DIFFRACTION (2.2 Å) X-RAY DIFFRACTION (1.04 Å) |
Structure validation
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