5MDK

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form (oxidized state - state 3)

Summary for 5MDK

• Entry DOI: 10.2210/pdb5mdk/pdb
• Descriptor: Uptake hydrogenase large subunit; HOXG, Uptake hydrogenase small subunit; HOXK, MAGNESIUM ION, ... (9 entities in total)
• Functional Keywords: [nife] hydrogenase, knallgasbacteria, proteobacteria, aerobic hydrogen bacteria, dehydrogenase, oxidoreductase, hydrogen catalysis, metalloenzyme, dihydrogen, bimetallic, metalloprotein catalytic center, ni-fe active site, t-cluster, fe-s cluster, [4fe-3s] cluster, [3fe-4s] cluster, [4fe-4s] cluster, as-isolated state, oxidized state, native, oxygen tolerant hydrogenase, membrane bound, membrane, hydrophobic tunnel, gas transport
• Biological source: Ralstonia eutropha H16; More
• Total number of polymer chains: 2
• Total formula weight: 104582.47

Authors

Schmidt, A.,Kalms, J.,Scheerer, P. (deposition date: 2016-11-11, release date: 2018-02-21, Last modification date: 2024-01-17)

Primary citation

Kalms, J.,Schmidt, A.,Frielingsdorf, S.,Utesch, T.,Gotthard, G.,von Stetten, D.,van der Linden, P.,Royant, A.,Mroginski, M.A.,Carpentier, P.,Lenz, O.,Scheerer, P.
Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.
Proc. Natl. Acad. Sci. U.S.A., 115:E2229-E2237, 2018

PubMed Abstract: [NiFe] hydrogenases catalyze the reversible splitting of H into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of , is able to overcome aerobic inactivation by catalytic reduction of O to water. This O tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O attack. Here, the O accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O concentrations used for MBH crystal derivatization. The examination of the O-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O tolerance of the enzyme.

PubMed: 29463722
DOI: 10.1073/pnas.1712267115

Experimental method

X-RAY DIFFRACTION (1.5 Å)