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Literature summary for 2.8.4.1 extracted from
- Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation (2000), J. Mol. Biol., 303, 329-344.
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| ammonium sulfate precipitation, crystals of the inactive enzyme are obtained with PEG 550 monomethyl ether as precipitant. Diffraction data to 2.7 A resolution are collected from one crystal of methyl-coenzyme M reductase from Methanopyrus kandleri with a completeness of 63%. Due to the low completeness of the data, refinement of the structure is only possible constraining the 2-fold non-crystallographic symmetry of the methyl-coenzyme M reductase molecule. Comparison of crystal structures of methyl-coenzyme M reductase from Methanosarcina barkeri (growth temperature optimum, 37°C), Methanopyrus kandleri (growth temperature optimum, 98°C) and Methanobacterium thermoautotrophicum (growth temperature optimum, 65°C) | Methanopyrus kandleri |
| hanging drop method, comparison of crystal structures of methyl-coenzyme M reductase from Methanosarcina barkeri (growth temperature optimum, 37°C), Methanopyrus kandleri (growth temperature optimum, 98°C) and Methanobacterium thermoautotrophicum (growth temperature optimum, 65°C) | Methanosarcina barkeri |
| the crystal structures of methyl-coenzyme M reductase from Methanosarcina barkeri and Methanopyrus kandleri are determined and compared with the known structure of MCR from Methanobacterium thermoautotrophicum. The active sites of enzyme from Methanosarcina barkeri and Methanopyrus kandleri are almost identical to that of Methanobacterium thermoautotrophicum and predominantly occupied by coenzyme M and coenzyme B. Crystals of the inactive enzyme from Methanopyrus kandleri are obtained by hanging drop method with PEG 550 monomethylether as precipitant | Methanopyrus kandleri |
| the crystal structures of methyl-coenzyme M reductase from Methanosarcina barkeri and Methanopyrus kandleri are determined and compared with the known structure of MCR from Methanobacterium thermoautotrophicum. The active sites of enzyme from Methanosarcina barkeri and Methanopyrus kandleri are almost identical to that of Methanobacterium thermoautotrophicum and predominantly occupied by coenzyme M and coenzyme B. The electron density at 1.6 A resolution of the Methanosarcina barkeri enzyme reveals that four of the modified amino acid residues of enzyme from Methanopyrus thermoautotrophicum, namely a thiopeptide, an S-methylcysteine, a 1-N-methylhistidine and a 5-methylarginine are also present. Crystals of the enzyme from Methanosarcina barkeri are grown using a reservoir condition with PEG 5000 monomethylether as precipitant and glycerol as cryoprotectant | Methanosarcina barkeri |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Ni2+ | nickel enzyme | Methanopyrus kandleri |  |
| Ni2+ | nickel enzyme. The nickel center of F430 is coordinated by the coenzyme M sulfhydryl group from one side and by the oxygen atom of a glutamine side-chain from the other | Methanosarcina barkeri | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| methyl-CoM + CoB | Methanosarcina barkeri | - |
CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | Methanopyrus kandleri | - |
CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | Methanosarcina barkeri | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | Methanopyrus kandleri | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | Methanopyrus kandleri DSM 6324 | - |
CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | Methanopyrus kandleri DSM 6324 | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | Methanosarcina barkeri DSM 804 | - |
CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | Methanosarcina barkeri DSM 804 | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | CoM-S-S-CoB + methane | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Methanopyrus kandleri | Q49605 and Q49601 and Q49604 | Q49605: alpha subunit, Q49601: beta subunit, Q49604: gamma subunit | - |
| Methanopyrus kandleri | Q49605 and Q49601 and Q49604 | Q49605: alpha-subunit, Q49601: beta-subunit, Q49604: gamma-subunit | - |
| Methanopyrus kandleri DSM 6324 | Q49605 and Q49601 and Q49604 | Q49605: alpha subunit, Q49601: beta subunit, Q49604: gamma subunit | - |
| Methanosarcina barkeri | P07962 and P07955 and P07964 | P07962: alpha subunit, P07955: beta subunit, P07964: gamma subunit | - |
| Methanosarcina barkeri | P07962 and P07955 and P07964 | P07962: alpha-subunit, P07955: beta-subunit, P07964: gamma-subunit | - |
| Methanosarcina barkeri DSM 804 | P07962 and P07955 and P07964 | P07962: alpha subunit, P07955: beta subunit, P07964: gamma subunit | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
- |
Methanosarcina barkeri |
- |
Methanopyrus kandleri |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| methyl-CoM + CoB | - |
Methanosarcina barkeri | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | - |
Methanopyrus kandleri | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanosarcina barkeri | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanopyrus kandleri | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | - |
Methanopyrus kandleri DSM 6324 | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanopyrus kandleri DSM 6324 | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | - |
Methanosarcina barkeri DSM 804 | CoM-S-S-CoB + methane | - |
? | |
| methyl-CoM + CoB | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanosarcina barkeri DSM 804 | CoM-S-S-CoB + methane | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| MCR | - |
Methanosarcina barkeri |
| MCR | - |
Methanopyrus kandleri |
| methyl-coenzyme M reductase | - |
Methanosarcina barkeri |
| methyl-coenzyme M reductase | - |
Methanopyrus kandleri |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| F-430 | the enzyme molecule contains two mol of the nickel porphinoid factor 430 non-covalently bound. The nickel center of F430 is coordinated by the coenzyme M sulfhydryl group from one side and by the oxygen atom of a glutamine side-chain from the other | Methanosarcina barkeri | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| metabolism | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanosarcina barkeri |
| metabolism | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanopyrus kandleri |
| physiological function | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanosarcina barkeri |
| physiological function | the enzyme catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea | Methanopyrus kandleri |
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