5D51

Krypton derivatization of an O2-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic gas tunnel network

Summary for 5D51

• Entry DOI: 10.2210/pdb5d51/pdb
• Descriptor: Uptake hydrogenase large subunit, Uptake hydrogenase small subunit, NI-FE OXIDIZED ACTIVE CENTER, ... (10 entities in total)
• Functional Keywords: oxidoreductase, [nife] hydrogenase, knallgasbacteria, proteobacteria, aerobic hydrogen bacteria, dehydrogenase, hydrogen, dihydrogen, hydrogen catalysis, metalloenzyme, metalloprotein catalytic center, nickel-iron cofactor, bimetallic, ni-fe active site, iron-sulfur cluster, t-cluster, [4fe-3s] cluster, [3fe-4s] cluster, [4fe-4s] cluster, oxidized state, oxygen-tolerant hydrogenase, membrane-bound, krypton, noble gas derivatization, hydrophobic tunnel, gas transport
• Biological source: Cupriavidus necator (Ralstonia eutropha); More
• Cellular location: Cell membrane; Peripheral membrane protein: P31891 P31892
• Total number of polymer chains: 2
• Total formula weight: 107496.68

Authors

Kalms, J.,Schmidt, A.,Frielingsdorf, S.,van der Linden, P.,von Stetten, D.,Lenz, O.,Carpentier, P.,Scheerer, P. (deposition date: 2015-08-10, release date: 2016-03-23, Last modification date: 2024-01-10)

Primary citation

Kalms, J.,Schmidt, A.,Frielingsdorf, S.,van der Linden, P.,von Stetten, D.,Lenz, O.,Carpentier, P.,Scheerer, P.
Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport.
Angew.Chem.Int.Ed.Engl., 55:5586-5590, 2016

PubMed Abstract: [NiFe] hydrogenases are metalloenzymes catalyzing the reversible heterolytic cleavage of hydrogen into protons and electrons. Gas tunnels make the deeply buried active site accessible to substrates and inhibitors. Understanding the architecture and function of the tunnels is pivotal to modulating the feature of O2 tolerance in a subgroup of these [NiFe] hydrogenases, as they are interesting for developments in renewable energy technologies. Here we describe the crystal structure of the O2 -tolerant membrane-bound [NiFe] hydrogenase of Ralstonia eutropha (ReMBH), using krypton-pressurized crystals. The positions of the krypton atoms allow a comprehensive description of the tunnel network within the enzyme. A detailed overview of tunnel sizes, lengths, and routes is presented from tunnel calculations. A comparison of the ReMBH tunnel characteristics with crystal structures of other O2 -tolerant and O2 -sensitive [NiFe] hydrogenases revealed considerable differences in tunnel size and quantity between the two groups, which might be related to the striking feature of O2 tolerance.

PubMed: 26913499
DOI: 10.1002/anie.201508976

Experimental method

X-RAY DIFFRACTION (1.47 Å)