Density functional calculations for modeling the active site of nickel-iron hydrogenases. 2. Predictions for the unready and ready States and the corresponding activation processes.
ZORA relativistic DFT calculations are presented which aim to model the geometric and electronic structure of the active site of NiFe hydrogenases in its EPR-active oxidized states Ni-A (unready state) and Ni-B (ready state). Starting coordinates are taken from the X-ray structure of a mutant of Desulfovibrio fructosovorans hydrogenase refined at 1.81 A resolution. Nine possible candidates for Ni-A and Ni-B are analyzed in terms of their geometric and electronic structure. Comparison of calculated geometric and magnetic resonance parameters with available experimental data indicates that both oxidized states have a micro-hydroxo bridge between the two metal centers. The different electronic structures of both forms can be explained by a modification of a terminal cysteine in Ni-B, best modeled by protonation of the sulfur atom. A possible mechanism for the activation of both oxidized forms is presented.
Instituto de Catálisis, CSIC, Campus Universidad Autónoma, 28049 Madrid, Spain.
Christian
C
Stadler
Antonio L
AL
de Lacey
Yael
Y
Montet
Anne
A
Volbeda
Juan C
JC
Fontecilla-Camps
Jose C
JC
Conesa
Víctor M
VM
Fernández
D016880:Anisotropy; D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003901:Desulfovibrio / Q000201:enzymology*; D004578:Electron Spin Resonance Spectroscopy; D006864:Hydrogenase / Q000737:chemistry*; D007501:Iron / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D009532:Nickel / Q000737:chemistry; D010084:Oxidation-Reduction; D011487:Protein Conformation; D011522:Protons
D011522:Protons; D009532:Nickel; D007501:Iron; C043296:nickel-iron hydrogenase; D006864:Hydrogenase