6Z7R

Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Krypton gas - structure wtKr1

Summary for 6Z7R

• Entry DOI: 10.2210/pdb6z7r/pdb
• Descriptor: Periplasmic [NiFeSe] hydrogenase, small subunit, CHLORIDE ION, Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing, ... (11 entities in total)
• Functional Keywords: hydrogenase, selenium, gas channels, high-pressure derivatization, oxidoreductase
• Biological source: Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303); More
• Total number of polymer chains: 4
• Total formula weight: 174074.42

Authors

Zacarias, S.,Temporao, A.,Carpentier, P.,van der Linden, P.,Pereira, I.A.C.,Matias, P.M. (deposition date: 2020-06-01, release date: 2020-09-09, Last modification date: 2024-01-24)

Primary citation

Zacarias, S.,Temporao, A.,Carpentier, P.,van der Linden, P.,Pereira, I.A.C.,Matias, P.M.
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
J.Biol.Inorg.Chem., 25:863-874, 2020

PubMed Abstract: Hydrogenases are metalloenzymes that catalyse both H evolution and uptake. They are gas-processing enzymes with deeply buried active sites, so the gases diffuse through channels that connect the active site to the protein surface. The [NiFeSe] hydrogenases are a special class of hydrogenases containing a selenocysteine as a nickel ligand; they are more catalytically active and less O-sensitive than standard [NiFe] hydrogenases. Characterisation of the channel system of hydrogenases is important to understand how the inhibitor oxygen reaches the active site to cause oxidative damage. To this end, crystals of Desulfovibrio vulgaris Hildenborough [NiFeSe] hydrogenase were pressurized with krypton and oxygen, and a method for tracking labile O molecules was developed, for mapping a hydrophobic channel system similar to that of the [NiFe] enzymes as the major route for gas diffusion.

PubMed: 32865640
DOI: 10.1007/s00775-020-01814-y

Experimental method

X-RAY DIFFRACTION (1.77 Å)