5XLE

Crystal structure of anaerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase

Summary for 5XLE

• Entry DOI: 10.2210/pdb5xle/pdb
• Descriptor: Periplasmic [NiFe] hydrogenase small subunit, Periplasmic [NiFe] hydrogenase large subunit, IRON/SULFUR CLUSTER, ... (9 entities in total)
• Functional Keywords: [nife]-hydrogenase d. vulgaris, oxidoreductase
• Biological source: Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637); More
• Total number of polymer chains: 2
• Total formula weight: 91566.01

Authors

Nishikawa, K.,Mochida, S.,Hiromoto, T.,Shibata, N.,Higuchi, Y. (deposition date: 2017-05-10, release date: 2018-06-06, Last modification date: 2024-03-27)

Primary citation

Nishikawa, K.,Mochida, S.,Hiromoto, T.,Shibata, N.,Higuchi, Y.
Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2.
J. Inorg. Biochem., 177:435-437, 2017

PubMed Abstract: Hydrogenase is a key enzyme for a coming hydrogen energy society, because it has strong catalytic activities on both uptake and production of dihydrogen. We, however, have to overcome the sensitivity against O of the enzyme, because hydrogenase is, generally, easily inactivated in the presence of O. In this study, we have revisited the crystal structures of [NiFe]‑hydrogenase from sulfate-reducing bacterium in the several oxidized and reduced conditions. Our results revealed that the Ni-Fe active site of the enzyme exposed into O showed two forms, Form-1 and Form-2. The Ni-Fe active site in Form-1 showed the typical Ni-B (inactive ready) structure, whereas those in Form-2 lost Ni with no relation to an exposure time to O, and two cysteinyl sulfur ligands made a disulfide bond. On the other hand, the formation of sulfenylation of the cysteinyl ligand to Ni, which is often observed in the oxidized form, did not correlate with the Ni-elimination, but with exposure time to O.

PubMed: 28967475
DOI: 10.1016/j.jinorgbio.2017.09.011

Experimental method

X-RAY DIFFRACTION (1.69 Å)