title: A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations.
abstract: We propose a new DFT-based mechanism for methane production using the full F430 cofactor of MCR (methyl-coenzyme M reductase) along with a coordinated O=CH2CH2C(H)NH2C(H)O (surrogate for glutamine) as a model of the active site for conversion of CH3SCoM(-) (CH3SCH2CH2SO3(-)) + HSCoB to methane plus the corresponding heterodisulfide. The cycle begins with the protonation of F430, either on Ni or on the C-ring nitrogen of the tetrapyrrole ring, both of which are nearly equally favorable. The C-ring protonated form is predicted to oxidatively add CH3SCoM(-) to give a 4-coordinate Ni center where the Ni moves out of the plane of the four ring nitrogens. The movement of Ni (and the attached CH3 and SCH2CH2SO3(2-) ligands) toward the SCoB(-) (deprotonated HSCoB) cofactor allows a 2c-3e interaction to form between the two sulfur atoms. The release of the heterodisulfide yields a Ni(III) center with a methyl group attached. The concerted elimination of methane, where the methyl group coordinated to Ni abstracts the proton from the C-ring nitrogen, has a very small calculated activation barrier (5.4 kcal/mol). The NPA charge on Ni for the various reaction steps indicates that the oxidation state changes occur largely on the attached ligands.
authors.affiliation: Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
authors.forename: Evert C
authors.initials: EC
authors.lastname: Duin
authors.forename: Michael L
authors.initials: ML
authors.lastname: McKee
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008024:Ligands; D008665:Metalloporphyrins / Q000378:metabolism; D008697:Methane / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D009532:Nickel / Q000378:metabolism; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000737:chemistry / Q000378:metabolism*; D011789:Quantum Theory
chemical_list: D008024:Ligands; D008665:Metalloporphyrins; C023540:factor F430; D009532:Nickel; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase; D008697:Methane