Literature summary 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 .
Protein Variants
EC Number |
Protein Variants |
Comment |
Organism |
---|
2.8.4.1 |
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]
EC Number |
KM Value [mM] |
KM Value Maximum [mM] |
Substrate |
Comment |
Organism |
Structure |
---|
2.8.4.1 |
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
EC Number |
Metals/Ions |
Comment |
Organism |
Structure |
---|
2.8.4.1 |
Ni2+ |
contained in the coenzyme F430 |
Methanothermobacter marburgensis |
|
Natural Substrates/ Products (Substrates)
EC Number |
Natural Substrates |
Organism |
Comment (Nat. Sub.) |
Natural Products |
Comment (Nat. Pro.) |
Rev. |
Reac. |
---|
2.8.4.1 |
methyl-CoM + CoB |
Methanothermobacter marburgensis |
- |
CoM-S-S-CoB + methane |
- |
? |
|
Organism
EC Number |
Organism |
UniProt |
Comment |
Textmining |
---|
2.8.4.1 |
Methanothermobacter marburgensis |
P11558 and P11560 and P11562 |
subunits A, B, and G encoded by genes mcrA, mcrB, and mcrG |
- |
Reaction
EC Number |
Reaction |
Comment |
Organism |
Reaction ID |
---|
2.8.4.1 |
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 |
|
Substrates and Products (Substrate)
EC Number |
Substrates |
Comment Substrates |
Organism |
Products |
Comment (Products) |
Rev. |
Reac. |
---|
2.8.4.1 |
methyl-CoM + CoB |
- |
Methanothermobacter marburgensis |
CoM-S-S-CoB + methane |
- |
? |
|
2.8.4.1 |
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
EC Number |
Subunits |
Comment |
Organism |
---|
2.8.4.1 |
heterotrimer |
- |
Methanothermobacter marburgensis |
Synonyms
EC Number |
Synonyms |
Comment |
Organism |
---|
2.8.4.1 |
MCR |
- |
Methanothermobacter marburgensis |
2.8.4.1 |
mcrA |
subunit A |
Methanothermobacter marburgensis |
2.8.4.1 |
mcrB |
subunit B |
Methanothermobacter marburgensis |
2.8.4.1 |
McrC |
subunit C |
Methanothermobacter marburgensis |
2.8.4.1 |
methyl-coenzyme M reductase |
- |
Methanothermobacter marburgensis |
Temperature Optimum [°C]
EC Number |
Temperature Optimum [°C] |
Temperature Optimum Maximum [°C] |
Comment |
Organism |
---|
2.8.4.1 |
18 |
25 |
assay at |
Methanothermobacter marburgensis |
pH Optimum
EC Number |
pH Optimum Minimum |
pH Optimum Maximum |
Comment |
Organism |
---|
2.8.4.1 |
7.6 |
- |
assay at |
Methanothermobacter marburgensis |
Cofactor
EC Number |
Cofactor |
Comment |
Organism |
Structure |
---|
2.8.4.1 |
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
EC Number |
General Information |
Comment |
Organism |
---|
2.8.4.1 |
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 |
2.8.4.1 |
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 |