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Literature summary for 2.8.4.1 extracted from

  • Wongnate, T.; Sliwa, D.; Ginovska, B.; Smith, D.; Wolf, M.W.; Lehnert, N.; Raugei, S.; Ragsdale, S.W.
    The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase (2016), Science, 352, 953-958 .
    View publication on PubMed
Search for more literature for 2.8.4.1

Protein Variants

Protein Variants Comment Organism
additional information identifying the key intermediate in methanogenesis provides fundamental insights to develop better catalysts for producing and activating an important fuel and potent greenhouse gas Methanothermobacter marburgensis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
 additional information transient kinetic, spectroscopic [ultraviolet-visible (UV-Vis), EPR, and MCD], and computational studies of the first step in the MCR catalytic mechanism are performed to trap and identify the key intermediates that differ between proposed mechanisms I and II, detailed overview. Rapid kinetic studies rule out methyl-Ni(III) and trap the MCRox1-silent intermediate Methanothermobacter marburgensis

Metals/Ions

Metals/Ions Comment Organism Structure
Ni2+ contained in the coenzyme F430 Methanothermobacter marburgensis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
methyl-CoM + CoB Methanothermobacter marburgensis
-
 CoM-S-S-CoB + methane
-
 ?

Organism

Organism UniProt Comment Textmining
Methanothermobacter marburgensis P11558 and P11560 and P11562 subunits A, B, and G encoded by genes mcrA, mcrB, and mcrG
-

Reaction

Reaction Comment Organism Reaction ID
methyl-CoM + CoB = CoM-S-S-CoB + methane radical mechanism of biological methane synthesis by methyl-coenzyme M reductase, overview. Transient kinetic, spectroscopic [ultraviolet-visible (UV-Vis), EPR, and MCD], and computational studies of the first step in the MCR catalytic mechanism are performed to trap and identify the key intermediates that differ between proposed mechanisms I and II Methanothermobacter marburgensis
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
methyl-CoM + CoB
-
 Methanothermobacter marburgensis CoM-S-S-CoB + methane
-
 ?
additional information the substrates bind inside a deep substrate channel with CoBSH nearer to the surface, stretching toward methyl-SCoM, which is close to F430 Methanothermobacter marburgensis ?
-
-

Subunits

Subunits Comment Organism
heterotrimer
-
 Methanothermobacter marburgensis

Synonyms

Synonyms Comment Organism
MCR
-
 Methanothermobacter marburgensis
mcrA subunit A Methanothermobacter marburgensis
mcrB subunit B Methanothermobacter marburgensis
McrC subunit C Methanothermobacter marburgensis
methyl-coenzyme M reductase
-
 Methanothermobacter marburgensis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
18 25 assay at Methanothermobacter marburgensis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.6
-
 assay at Methanothermobacter marburgensis

Cofactor

Cofactor Comment Organism Structure
F-430 coenzyme F430, rapid kinetic studies rule out methyl-Ni(III) and trap the MCRox1-silent intermediate. Identification of an MCRox1-like state, specifically a F430-Ni(III)-SCoM/CoBS- intermediate, from direct DFT calculations Methanothermobacter marburgensis

General Information

General Information Comment Organism
additional information initial steps in three proposed mechanisms of MCR catalysis: (i) mechanism I involves nucleophilic attack of Ni(I)-MCRred1 on the methyl group of methyl-SCoM to generate a methyl-Ni(III) intermediate. This mechanism is similar to that of B12-dependent methyltransferases, which generate a methyl-cob(III) alamin intermediate. (ii) In mechanism II, Ni(I) attack on the sulfur atom of methyl-SCoM promotes the homolytic cleavage of the methyl-sulfur bond to produce a methyl radical and a Ni(II)-thiolate. (iii) Mechanism III involves nucleophilic attack of Ni(I) on the sulfur of methyl-SCoM to form a highly reactive methyl anion and Ni(III)-SCoM (MCRox1) Methanothermobacter marburgensis
physiological function the enzyme that catalyzes the chemical step of methane synthesis or oxidation is methyl-coenzyme M reductase (MCR), which contains a nickel hydrocorphinate F430 at its active site. This reaction involves conversion of the methyl donor, methylcoenzyme M (methyl-SCoM), and the electron donor, coenzyme B (CoBSH, N-7-mercaptoheptanoylthreonine phosphate), to methane and the mixed disulfide CoBS-SCoM Methanothermobacter marburgensis