Modeling the active sites in metalloenzymes 5. The heterolytic bond cleavage of H(2) in the [NiFe] hydrogenase of desulfovibrio gigas by a nucleophilic addition mechanism.
The H(2) activation catalyzed by an Fe(II)-Ni(III) model of the [NiFe] hydrogenase of Desulfovibrio gigas has been investigated by density functional theory (DFT/B3LYP) calculations on the neutral and anionic active site complexes, [(CO)(CN)(2)Fe(mu-SH)(2)Ni(SH)(SH(2))](0) and [(CO)(CN)(2)Fe(mu-SH)(2)Ni(SH)(2)](-). The results suggest that the reaction proceeds by a nucleophilic addition mechanism that cleaves the H-H bond heterolytically. The terminal cysteine residue Cys530 in the [NiFe] hydrogenase active site of the D. gigas enzyme plays a crucial role in the catalytic process by accepting the proton. The active site is constructed to provide access by this cysteine residue, and this role explains the change in activity observed when this cysteine is replaced by a selenocysteine. Furthermore, the optimized geometry of the transition state in the model bears a striking resemblance to the geometry of the active site as determined by X-ray crystallography.
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Contribution from HPCC Group, Environmental Molecular Science Laboratory, Battelle, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry; D003901:Desulfovibrio / Q000201:enzymology*; D006859:Hydrogen / Q000378:metabolism*; D006864:Hydrogenase / Q000737:chemistry / Q000378:metabolism; D007501:Iron / Q000737:chemistry; D008667:Metalloproteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D009532:Nickel / Q000737:chemistry; D010084:Oxidation-Reduction; D017279:Selenocysteine / Q000737:chemistry; D013055:Spectrophotometry, Infrared
D008667:Metalloproteins; D017279:Selenocysteine; D009532:Nickel; D006859:Hydrogen; D007501:Iron; C043296:nickel-iron hydrogenase; D006864:Hydrogenase; D003545:Cysteine