Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.
BACKGROUND
The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase.


RESULTS
The X-ray crystal structure of the reduced form of D. vulgaris Miyazaki F [NiFe] hydrogenase has been solved at 1.4 A resolution and refined to a crystallographic R factor of 21.8%. The overall structure is very similar to that of the oxidized form, with the exception that the third monatomic bridge observed at the Ni-Fe site in the oxidized enzyme is absent, leaving this site unoccupied in the reduced form.


CONCLUSIONS
The unusual ligand structure found in the oxidized form of D. vulgaris Miyazaki F [NiFe] hydrogenase was confirmed in the reduced form of the enzyme, with the exception that the electron density assigned to the monatomic sulfur bridge had almost disappeared. On the basis of this finding, as well as the observation that H2S is liberated from the oxidized enzyme under an atmosphere of H2 in the presence of its electron carrier, it was postulated that the monatomic sulfur bridge must be removed for the enzyme to be activated. A possible mechanism for the catalytic action of the hydrogenase is proposed.
Higuchi
Y
Y
Division of Chemistry, Graduate School of Science, Kyoto University, Japan. higuchi@kuchem.kyoto-u.ac.jp
Ogata
H
H
Miki
K
K
Yasuoka
N
N
Yagi
T
T
D001665:Binding Sites; D018360:Crystallography, X-Ray; D006859:Hydrogen / Q000737:chemistry*; D006864:Hydrogenase / Q000737:chemistry* / Q000378:metabolism; D007501:Iron / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D009532:Nickel / Q000378:metabolism*; D011487:Protein Conformation
D008024:Ligands; D009532:Nickel; D006859:Hydrogen; D007501:Iron; C043296:nickel-iron hydrogenase; D006864:Hydrogenase