Formation of a Nickel−Methyl Species in Methyl-Coenzyme M Reductase, an Enzyme Catalyzing Methane Formation

Yang, Na; Reiher, Markus; Wang, Mi; Harmer, Jeffrey; Duin, Evert C.

doi:10.1021/ja0734501

Cited by 72 publications

(67 citation statements)

References 20 publications

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“…23 and g // = 2.01 which accounted for 65% of the nickel content ( Figure S4). 30 Figure S5). Finally, XAS analysis of 2 further supported the presence of a mononuclear nickel center coordinated to an apical chloride ligand (see XAS analyis below).…”

Section: IIImentioning

confidence: 99%

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

et al. 2016

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Abstract.Terminal high-valent metal-oxygen species are key reaction intermediates in the catalytic cycle of both enzymes (e.g., oxygenases) and synthetic oxidation catalysts. While tremendous efforts have been directed towards the characterization of the biologically relevant terminal manganese-oxygen and iron-oxygen species, the corresponding analogues based on late-transition metals such as cobalt, nickel or copper are relatively scarce. This is in part related to the "Oxo Wall" concept, which predicts that late transition elements cannot support a terminal oxido ligand in a tetragonal environment. Here, the nickel(II) complex (1) of the tetradentate macrocyclic ligand bearing a 2,6-pyridinedicarboxamidate unit is shown to be an effective catalyst in the chlorination and oxidation of C-H bonds with sodium hypochlorite as terminal oxidant in the presence of acetic acid (AcOH). Insight into the active species responsible for the observed reactivity was gained through the study of the reaction of 1 with ClO -at low temperature by UV/Vis absorption, resonance Raman, EPR, ESI-MS, and XAS analyses. DFT calculations aided the assignment of the trapped chromophoric species (3) as a nickel-hypochlorite species. Despite the fact that the formal oxidation state of the nickel in 3 is +4, experimental and computational analysis indicate that 3 is best formulated as a Ni III complex with one unpaired electron delocalized in the ligands surrounding the metal center. Most remarkably, 3 reacts rapidly with a range of substrates including those with strong aliphatic C-H bonds, indicating the direct involvement of 3 in the oxidation/chlorination reactions observed in the 1/ClO -

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Section: IIImentioning

confidence: 99%

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

et al. 2016

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“…Mechanism I involves attack of the Ni(I) nucleophile on the methyl group of methyl-SCoM to generate a methyl-Ni(III) intermediate (16,26). This proposed mechanism I is based on mechanistic work with F430 model complexes (27), on the location of substrates in the active site of inactive Ni(II) MCR structures (6), and on mechanistic and crystallographic studies of the active Ni(I) enzyme with 3-bromopropanesulfonate and methyl halide (10,11,13,28). Mechanism II starts with Ni(I) attack on the sulfur atom of methylSCoM, promoting the homolytic cleavage of the methyl-sulfur bond and generating a methyl radical ( ⅐ CH 3 ) and a Ni(II)⅐thiolate complex.…”

Section: Methyl-coenzyme M Reductase (Mcr)mentioning

confidence: 99%

“…Several experimental and theoretical studies have been performed in an effort to understand the catalytic mechanism of MCR and the geometric and electronic structures of the intermediates in the catalytic cycle (6,10,13,16,28,30,31,33,(41)(42)(43). The major distinction between the two competing mechanisms lies in the proposed intermediate generated in the first step of catalysis.…”

mentioning

confidence: 99%

“…This is followed by protonolysis to generate CH 4 and the heterodisulfide product. The putative methyl-Ni(III) intermediate has been generated independently by adding methyl halides to the active MCRNi(I) and is characterized by EPR spectroscopy (13,28) and x-ray crystal structure (10). The second mechanism involves a direct attack of the Ni(I) on the S of methyl-SCoM, resulting in a homolytic cleavage of the thioether bond and formation of a Ni(II)-thiolate species and a ⅐ CH 3 .…”

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confidence: 99%

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The Reaction Mechanism of Methyl-Coenzyme M Reductase

Wongnate

Ragsdale

2015

Journal of Biological Chemistry

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Background: Methyl-coenzyme M reductase (MCR) catalyzes the final step in methanogenesis. Results: MCR forms binary complexes with both substrates, but stabilizes only the productive binary and ternary complexes. Conclusion: Substrate-induced conformational changes promote correct binding order and chemistry. Significance: This first rapid kinetics study of MCR with natural substrates describes how an enzyme can enforce a strictly ordered ternary complex reaction mechanism.

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“…in the active site [14][15][16][17], with Br -/I -as the leaving group. Additional evidence is provided by the reaction of free Ni(I)F 430 derivatives with electrophilic methyl donors such as methyl-dialkylsulfonium ions and methyl halides [16,17].…”

Section: -Ni(iii)f 430mentioning

confidence: 99%

Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase

et al. 2008

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Methane formation in methanogenic Archaea is catalyzed by methyl-coenzyme M reductase (MCR) and takes place via the reduction of methyl-coenzyme M (CH 3 -S-CoM) with coenzyme B (HS-CoB) to methane and the heterodisulfide CoM-S-S-CoB. MCR harbors the nickel porphyrinoid coenzyme F 430 as a prosthetic group, which has to be in the Ni(I) oxidation state for the enzyme to be active. To date no intermediates in the catalytic cycle of MCR red1 (red for reduced Ni) have been identified. Here, we report a detailed characterization of MCR red1m (''m'' for methyl-coenzyme M), which is the complex of MCR red1a (''a'' for absence of substrate) with CH 3 -S-CoM. Using continuous-wave and pulse electron paramagnetic resonance spectroscopy in combination with selective isotope labeling ( 13 C and 2 H) of CH 3 -S-CoM, it is shown that CH 3 -S-CoM binds in the active site of MCR such that its thioether sulfur is weakly coordinated to the Ni(I) of F 430 . The complex is stable until the addition of the second substrate, HS-CoB. Results from EPR spectroscopy, along with quantum mechanical calculations, are used to characterize the electronic and geometric structure of this complex, which can be regarded as the first intermediate in the catalytic mechanism.

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Formation of a Nickel−Methyl Species in Methyl-Coenzyme M Reductase, an Enzyme Catalyzing Methane Formation

Cited by 72 publications

References 20 publications

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

The Reaction Mechanism of Methyl-Coenzyme M Reductase

Coordination and binding geometry of methyl-coenzyme M in the red1m state of methyl-coenzyme M reductase

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