title: Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.
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.
authors.affiliation: Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Ogata
authors.affiliation: Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
authors.forename: Koji
authors.initials: K
authors.lastname: Nishikawa
authors.affiliation: Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Lubitz
mesh_terms: D055162:Biocatalysis; D002248:Carbon Monoxide / Q000378:metabolism; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry / Q000378:metabolism; D016969:Desulfovibrio vulgaris / Q000201:enzymology*; D006859:Hydrogen / Q000032:analysis* / Q000737:chemistry*; D006860:Hydrogen Bonding; D006864:Hydrogenase / Q000737:chemistry* / Q000378:metabolism; D007501:Iron / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D008970:Molecular Weight; D009532:Nickel / Q000737:chemistry / Q000378:metabolism; D011522:Protons; D013455:Sulfur / Q000378:metabolism
chemical_list: D008024:Ligands; D011522:Protons; D013455:Sulfur; D009532:Nickel; D002248:Carbon Monoxide; D006859:Hydrogen; D007501:Iron; C043296:nickel-iron hydrogenase; D006864:Hydrogenase; D003545:Cysteine