4U9I

High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F

Summary for 4U9I

• Entry DOI: 10.2210/pdb4u9i/pdb
• Descriptor: Periplasmic [NiFe] hydrogenase small subunit, Periplasmic [NiFe] hydrogenase large subunit, IRON/SULFUR CLUSTER, ... (9 entities in total)
• Functional Keywords: metal-hydride, hydrogenase, oxidoreductase
• Biological source: Desulfovibrio vulgaris; More
• Cellular location: Periplasm: P21853 P21852
• Total number of polymer chains: 2
• Total formula weight: 89942.21

Authors

Ogata, H.,Nishikawa, K.,Lubitz, W. (deposition date: 2014-08-06, release date: 2015-01-21, Last modification date: 2024-11-20)

Primary citation

Ogata, H.,Nishikawa, K.,Lubitz, W.
Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.
Nature, 520:571-574, 2015

PubMed Abstract: The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. The location of the abundant hydrogens is of key importance for understanding structure and function of the protein. However, in protein X-ray crystallography the detection of hydrogen atoms is one of the major problems, since they display only weak contributions to diffraction and the quality of the single crystals is often insufficient to obtain sub-ångström resolution. Here we report the crystal structure of a standard [NiFe] hydrogenase (∼91.3 kDa molecular mass) at 0.89 Å resolution. The strictly anoxically isolated hydrogenase has been obtained in a specific spectroscopic state, the active reduced Ni-R (subform Ni-R1) state. The high resolution, proper refinement strategy and careful modelling allow the positioning of a large part of the hydrogen atoms in the structure. This has led to the direct detection of the products of the heterolytic splitting of dihydrogen into a hydride (H(-)) bridging the Ni and Fe and a proton (H(+)) attached to the sulphur of a cysteine ligand. The Ni-H(-) and Fe-H(-) bond lengths are 1.58 Å and 1.78Å, respectively. Furthermore, we can assign the Fe-CO and Fe-CN(-) ligands at the active site, and can obtain the hydrogen-bond networks and the preferred proton transfer pathway in the hydrogenase. Our results demonstrate the precise comprehensive information available from ultra-high-resolution structures of proteins as an alternative to neutron diffraction and other methods such as NMR structural analysis.

PubMed: 25624102
DOI: 10.1038/nature14110

Experimental method

X-RAY DIFFRACTION (1.06 Å)