Is there a Ni-methyl intermediate in the mechanism of methyl-coenzyme M reductase?
The formation of methyl-Ni(F(430)) species in methyl-coenzyme M reductase (MCR) has been investigated using the B3LYP hybrid density functional method and an active-site model built on the basis of X-ray crystal structure. CH(3)-I, CH(3)-Br, CH(3)-Cl, and CH(3)-S-CH(3) were chosen as the substrates, the last one regarded as a model of the native substrate (methyl-coenzyme M, CH(3)-SCoM). The calculations indicate that the formation of CH(3)-Ni(F(430)) in MCR is dependent on the acidity of the substrate leaving group. A CH(3)-Ni(F(430)) species has been observed with methyl halides as substrates, while the formation of CH(3)-Ni(F(430)) from the native substrate is demonstrated to be inaccessible energetically. These results agree well with the current experiments.
Chen
Shi-lu
SL
Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden. shlchen@physto.se
Pelmenschikov
Vladimir
V
Blomberg
Margareta R A
MR
Siegbahn
Per E M
PE
D020134:Catalytic Domain; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008956:Models, Chemical; D008958:Models, Molecular; D009532:Nickel / Q000737:chemistry / Q000378:metabolism*; D010088:Oxidoreductases / Q000737:chemistry / Q000378:metabolism*
D009532:Nickel; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase